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Zhiyong S, Yaxuan G, Yuanyuan W, Xiang Y, Xu G, Zhenhong L, Jingping N, Jianping L, Zhenyu L. Nitrogen-fixing bacteria promote growth and bioactive components accumulation of Astragalus mongholicus by regulating plant metabolism and rhizosphere microbiota. BMC Microbiol 2024; 24:261. [PMID: 39004720 PMCID: PMC11247893 DOI: 10.1186/s12866-024-03409-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2024] [Accepted: 07/02/2024] [Indexed: 07/16/2024] Open
Abstract
BACKGROUND The excessive application of chemical fertilizers in the cultivation of Astragalus mongholicus Bunge results in a reduction in the quality of the medicinal plant and compromises the sustainable productivity of the soil. PGPB inoculant is a hot topic in ecological agriculture research. In the cultivation of Astragalus mongholicus, the screened nitrogen-fixing bacteria can promote plant growth, however, whether it can promote the accumulation of main bioactive components remains unknown. In this study, mixed inoculants containing 5 strains of growth promoting bacteria (Rhizobium T16 , Sinorhizobium T21 , Bacillus J1 , Bacillus G4 and Arthrobacter J2) were used in the field experiment. The metabolic substances in the root tissues of Astragalus mongholicus were identified during the harvest period by non-targeted metabolomics method, and the differential metabolites between groups were identified by statistical analysis. Meanwhile, high-throughput sequencing was performed to analyze the changes of rhizosphere soil and endophytic microbial community structure after mixed microbial treatment. RESULTS The results of non-targeted metabolism indicated a significant increase in the levels of 26 metabolites after treatment including 13 flavonoids, 3 saponins and 10 other components. The contents of three plant hormones (abscisic acid, salicylic acid and spermidine) also increased after treatment, which presumed to play an important role in regulating plant growth and metabolism. Studies on endosphere and rhizosphere bacterial communities showed that Rhzobiaceae, Micromonosporaceae, and Hypomicrobiaceae in endophytic, and Oxalobactereae in rhizosphere were significantly increased after treatment. These findings suggest their potential importance in plant growth promotion and secondary metabolism regulation. CONCLUSIONS This finding provides a basis for developing nitrogen-fixing bacteria fertilizer and improving the ecological planting efficiency of Astragalus mongholicus.
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Affiliation(s)
- Shi Zhiyong
- College Of Life Sciences, Shanxi Agricultural University, Jinzhong, 030801, China
| | - Guo Yaxuan
- Modern Research Center for Traditional Chinese Medicine, Shanxi University, Taiyuan, 030006, China
| | - Wang Yuanyuan
- College Of Life Sciences, Shanxi Agricultural University, Jinzhong, 030801, China
| | - Yan Xiang
- College Of Life Sciences, Shanxi Agricultural University, Jinzhong, 030801, China
| | - Guo Xu
- College Of Life Sciences, Shanxi Agricultural University, Jinzhong, 030801, China
| | - Lei Zhenhong
- Shanxi Zhendong Pharmaceutical (China), Changzhi, 047000, China
| | - Niu Jingping
- College Of Life Sciences, Shanxi Agricultural University, Jinzhong, 030801, China
| | - Liang Jianping
- College Of Life Sciences, Shanxi Agricultural University, Jinzhong, 030801, China.
- Shanxi Key Laboratory of Chinese Veterinary Medicine Modernization, Shanxi Agricultural University, Jinzhong, 030801, China.
| | - Li Zhenyu
- Modern Research Center for Traditional Chinese Medicine, Shanxi University, Taiyuan, 030006, China.
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Hussain M, Xuan P, Xin Y, Ma H, Zhou Y, Wen S, Hamid MI, Wan T, Hu J, Li Y, Kang S, Liu X, Xiang M. Redundancy in microbiota-mediated suppression of the soybean cyst nematode. MICROBIOME 2024; 12:125. [PMID: 39004755 PMCID: PMC11247744 DOI: 10.1186/s40168-024-01840-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Accepted: 05/19/2024] [Indexed: 07/16/2024]
Abstract
BACKGROUND Soybean cyst nematodes (SCN) as animal parasites of plants are not usually interested in killing the host but are rather focused on completing their life cycle to increase population, resulting in substantial yield losses. Remarkably, some agricultural soils after long-term crop monoculture show a significant decline in SCN densities and suppress disease in a sustainable and viable manner. However, relatively little is known about the microbes and mechanisms operating against SCN in such disease-suppressive soils. RESULTS Greenhouse experiments showed that suppressive soils (S) collected from two provinces of China and transplantation soils (CS, created by mixing 10% S with 90% conducive soils) suppressed SCN. However, SCN suppressiveness was partially lost or completely abolished when S soils were treated with heat (80 °C) and formalin. Bacterial community analysis revealed that the specific suppression in S and CS was mainly associated with the bacterial phylum Bacteroidetes, specifically due to the enrichment of Chitinophaga spp. and Dyadobacter sp., in the cysts. SCN cysts colonized by Chitinophaga spp. showed dramatically reduced egg hatching, with unrecognizable internal body organization of juveniles inside the eggshell due to chitinase activity. Whereas, Dyadobacter sp. cells attached to the surface coat of J2s increased soybean resistance against SCN by triggering the expression of defence-associated genes. The disease-suppressive potential of these bacteria was validated by inoculating them into conducive soil. The Dyadobacter strain alone or in combination with Chitinophaga strains significantly decreased egg densities after one growing cycle of soybeans. In contrast, Chitinophaga strains alone required more than one growing cycle to significantly reduce SCN egg hatching and population density. CONCLUSION This study revealed how soybean monoculture for decades induced microbiota homeostasis, leading to the formation of SCN-suppressive soil. The high relative abundance of antagonistic bacteria in the cyst suppressed the SCN population both directly and indirectly. Because uncontrolled proliferation will likely lead to quick demise due to host population collapse, obligate parasites like SCN may have evolved to modulate virulence/proliferation to balance these conflicting needs. Video Abstract.
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Affiliation(s)
- Muzammil Hussain
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Peixue Xuan
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yi Xin
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Haikun Ma
- Department of Microbiology, State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Frontiers Science Center for Cell Responses, College of Life Science, Nankai University, Tianjin, 300071, China
| | - Yahan Zhou
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Shihui Wen
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - M Imran Hamid
- Department of Botany and Plant Science, University of California, Riverside, CA, 92507, USA
| | - Tianyu Wan
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Jianyang Hu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yuezhong Li
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Seogchan Kang
- Department of Plant Pathology & Environmental Microbiology, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Xingzhong Liu
- Department of Microbiology, State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Frontiers Science Center for Cell Responses, College of Life Science, Nankai University, Tianjin, 300071, China.
| | - Meichun Xiang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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Rana ML, Hoque MN, Rahman MS, Pramanik PK, Islam MS, Punom SA, Ramasamy S, Schreinemachers P, Oliva R, Rahman MT. Soil bacteriome diversity and composition of rooftop and surface gardens in urban and peri-urban areas of Bangladesh. ENVIRONMENTAL MONITORING AND ASSESSMENT 2024; 196:729. [PMID: 39001908 DOI: 10.1007/s10661-024-12850-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2024] [Accepted: 06/22/2024] [Indexed: 07/15/2024]
Abstract
Soil microbiome science, rapidly evolving, predominantly focuses on field crop soils. However, understanding garden soil microbiomes is essential for enhancing food production sustainability in garden environments. This study aimed to unveil the bacteriome diversity and composition in rooftop garden soils (RGS) and surface garden soils (SGS) across urban (Dhaka North and Dhaka South City Corporations) and peri-urban (Gazipur City Corporation) areas of Dhaka Division, Bangladesh. We analyzed 11 samples, including six RGS and five SGS samples from 11 individual gardens using 16S rRNA (V3-V4 region) gene-based amplicon sequencing. A total of 977 operational taxonomic units (OTUs), including 270 and 707 in RGS and SGS samples, respectively, were identified. The observed OTUs were represented by 21 phyla, 45 classes, 84 orders, 173 families, and 293 genera of bacteria. Alpha diversity indices revealed significantly higher bacterial diversity in SGS samples (p = 0.01), while beta diversity analyses indicated distinct bacteriome compositions between RGS and SGS samples (p = 0.028, PERMANOVA). Despite substantial taxonomic variability between sample categories, there was also a considerable presence of shared bacterial taxa. At the phylum level, Bacilliota (61.14%), Pseudomonadota (23.42%), Actinobacteria (6.33%), and Bacteroidota (3.32%) were the predominant bacterial phyla (comprising > 94.0% of the total abundances) in both types of garden soil samples. Of the identified genera, Bacillus (69.73%) and Brevibacillus (18.81%) in RGS and Bacillus (19.22%), Methylophaga (19.21%), Acinetobacter (6.27%), Corynebacterium (5.06%), Burkholderia (4.78%), Paracoccus (3.98%) and Lysobacter (2.07%) in SGS were the major bacterial genera. Importantly, we detected that 52.90% of genera were shared between RGS and SGS soil samples. Our data reveal unique and shared bacteriomes with probiotic potential in soil samples from both rooftop and surface gardens. Further studies should explore the functional roles of shared bacterial taxa in garden soils and how urban environmental factors affect microbiome composition to optimize soil health and sustainable food production.
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Affiliation(s)
- Md Liton Rana
- Department of Microbiology and Hygiene, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh, 2202, Bangladesh
| | - M Nazmul Hoque
- Molecular Biology and Bioinformatics Laboratory, Department of Gynecology, Obstetrics and Reproductive Health, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, 1706, Bangladesh
| | - M Shaminur Rahman
- Department of Microbiology, Jashore University of Science and Technology, Jashore, 7408, Bangladesh
| | - Pritom Kumar Pramanik
- Department of Microbiology and Hygiene, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh, 2202, Bangladesh
| | - Md Saiful Islam
- Department of Microbiology and Hygiene, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh, 2202, Bangladesh
- Department of Animal Sciences, University of California - Davis, Davis, 95616, USA
| | - Sadia Afrin Punom
- Department of Microbiology and Hygiene, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh, 2202, Bangladesh
| | | | | | | | - Md Tanvir Rahman
- Department of Microbiology and Hygiene, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh, 2202, Bangladesh.
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Martins BR, Radl V, Treder K, Michałowska D, Pritsch K, Schloter M. The rhizosphere microbiome of 51 potato cultivars with diverse plant growth characteristics. FEMS Microbiol Ecol 2024; 100:fiae088. [PMID: 38839598 PMCID: PMC11242454 DOI: 10.1093/femsec/fiae088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 04/22/2024] [Accepted: 06/04/2024] [Indexed: 06/07/2024] Open
Abstract
Rhizosphere microbial communities play a substantial role in plant productivity. We studied the rhizosphere bacteria and fungi of 51 distinct potato cultivars grown under similar greenhouse conditions using a metabarcoding approach. As expected, individual cultivars were the most important determining factor of the rhizosphere microbial composition; however, differences were also obtained when grouping cultivars according to their growth characteristics. We showed that plant growth characteristics were related to deterministic and stochastic assembly processes of bacterial and fungal communities, respectively. The bacterial genera Arthrobacter and Massilia (known to produce indole acetic acid and siderophores) exhibited greater relative abundance in high- and medium-performing cultivars. Bacterial co-occurrence networks were larger in the rhizosphere of these cultivars and were characterized by a distinctive combination of plant beneficial Proteobacteria and Actinobacteria along with a module of diazotrophs namely Azospira, Azoarcus, and Azohydromonas. Conversely, the network within low-performing cultivars revealed the lowest nodes, hub taxa, edges density, robustness, and the highest average path length resulting in reduced microbial associations, which may potentially limit their effectiveness in promoting plant growth. Our findings established a clear pattern between plant productivity and the rhizosphere microbiome composition and structure for the investigated potato cultivars, offering insights for future management practices.
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Affiliation(s)
- Benoit Renaud Martins
- Research Unit for Comparative Microbiome Analysis (COMI), Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Ingolstädter Landstraße 1, 85764 Neuherberg, Germany
| | - Viviane Radl
- Research Unit for Comparative Microbiome Analysis (COMI), Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Ingolstädter Landstraße 1, 85764 Neuherberg, Germany
| | - Krzysztof Treder
- Plant Breeding and Acclimatization Institute – National Research Institute in Radzików, Bonin Division, Department of Potato Protection and Seed Science at Bonin, Bonin Str 3, 76-009 Bonin, Poland
| | - Dorota Michałowska
- Plant Breeding and Acclimatization Institute – National Research Institute in Radzików, Bonin Division, Department of Potato Protection and Seed Science at Bonin, Bonin Str 3, 76-009 Bonin, Poland
| | - Karin Pritsch
- Research Unit for Environmental Simulation (EUS), Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Ingolstädter Landstraße 1, 85764 Neuherberg, Germany
| | - Michael Schloter
- Research Unit for Comparative Microbiome Analysis (COMI), Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Ingolstädter Landstraße 1, 85764 Neuherberg, Germany
- Chair for Environmental Microbiology, Department of Life Science Systems, School of Life Sciences, Technical University of Munich, Alte Akademie 8, 85354 Freising, Germany
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Che J, Wu Y, Yang H, Chang Y, Wu W, Lyu L, Wang X, Cao F, Li W. Metabolites of blueberry roots at different developmental stages strongly shape microbial community structure and intra-kingdom interactions at the root-soil interface. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 947:174333. [PMID: 38945231 DOI: 10.1016/j.scitotenv.2024.174333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Revised: 06/24/2024] [Accepted: 06/25/2024] [Indexed: 07/02/2024]
Abstract
The rhizosphere microorganisms of blueberry plants have long coexisted with their hosts under distinctively acidic soil conditions, exerting a profound influence on host performance through mutualistic symbiotic interactions. Meanwhile, plants can regulate rhizosphere microorganisms by exerting host effects to meet the functional requirements of plant growth and development. However, it remains unknown how the developmental stages of blueberry plants affect the structure, function, and interactions of the rhizosphere microbial communities. Here, we examined bacterial communities and root metabolites at three developmental stages (flower and leaf bud development stage, fruit growth and development stage, and fruit maturation stage) of blueberry plants. The results revealed that the Shannon and Chao 1 indices as well as community composition varied significantly across all three developmental stages. The relative abundance of Actinobacteria significantly increased by 10 % (p < 0.05) from stage 1 to stage 2, whereas that of Proteobacteria decreased significantly. The co-occurrence network analysis revealed a relatively complex network with 1179 edges and 365 nodes in the stage 2. Niche breadth was highest at stage 2, while niche overlap tended to increase as the plant developed. Furthermore, the untargeted metabolome analysis revealed that the number of differential metabolites of vitamins, nucleic acids, steroids, and lipids increased between stage 1 to stage2 and stage 2 to stage 3, while those for differential metabolites of carbohydrates and peptides decreased. Significant changes in expression levels of levan, L-glutamic acid, indoleacrylic acid, oleoside 11-methyl ester, threo-syringoylglycerol, gingerglycolipid B, and bovinic acid were highly correlated with the bacterial community structure. Collectively, our study reveals that significant alterations in dominant bacterial taxa are strongly correlated with the dynamics of root metabolites. These findings lay the groundwork for developing prebiotic products to enhance the beneficial effects of root microorganisms and boosting blueberry productivity via a sustainable approach.
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Affiliation(s)
- Jilu Che
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry and Grassland, Nanjing Forestry University, Nanjing 210037, China; Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Nanjing 210014, China; Department of Biological Sciences, Faculty of Science, National University of Singapore, 117543, Singapore.
| | - Yaqiong Wu
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Nanjing 210014, China.
| | - Hao Yang
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry and Grassland, Nanjing Forestry University, Nanjing 210037, China; Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Nanjing 210014, China
| | - Ying Chang
- Department of Biological Sciences, Faculty of Science, National University of Singapore, 117543, Singapore; Science Division, Yale-NUS College, 138527, Singapore.
| | - Wenlong Wu
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Nanjing 210014, China
| | - Lianfei Lyu
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Nanjing 210014, China
| | - Xiaomin Wang
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Nanjing 210014, China
| | - Fuliang Cao
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry and Grassland, Nanjing Forestry University, Nanjing 210037, China
| | - Weilin Li
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry and Grassland, Nanjing Forestry University, Nanjing 210037, China.
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Chen P, Huang P, Yu H, Yu H, Xie W, Wang Y, Zhou Y, Chen L, Zhang M, Yao R. Strigolactones shape the assembly of root-associated microbiota in response to phosphorus availability. mSystems 2024; 9:e0112423. [PMID: 38780241 PMCID: PMC11237589 DOI: 10.1128/msystems.01124-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 04/22/2024] [Indexed: 05/25/2024] Open
Abstract
Plants rely on strigolactones (SLs) to regulate their development and form symbiotic relationships with microbes as part of the adaptive phosphorus (P) efficiency strategies. However, the impact of SLs on root-associated microbial communities in response to P availability remains unknown. Here, root microbiota of SL biosynthesis (max3-11) and perception (d14-1) were compared to wild-type Col-0 plants under different P concentrations. Using high-throughput sequencing, the relationship between SLs, P concentrations, and the root-associated microbiota was investigated to reveal the variation in microbial diversity, composition, and interaction. Plant genotypes and P availability played important but different roles in shaping the root-associated microbial community. Importantly, SLs were found to attract Acinetobacter in low P conditions, which included an isolated CP-2 (Acinetobacter soli) that could promote plant growth in cocultivation experiments. Moreover, SLs could change the topologic structure within co-occurrence networks and increase the number of keystone taxa (e.g., Rhizobiaceae and Acidobacteriaceae) to enhance microbial community stability. This study reveals the key role of SLs in mediating root-associated microbiota interactions.IMPORTANCEStrigolactones (SLs) play a crucial role in plant development and their symbiotic relationships with microbes, particularly in adapting to phosphorus levels. Using high-throughput sequencing, we compared the root microbiota of plants with SL biosynthesis and perception mutants to wild-type plants under different phosphorus concentrations. These results found that SLs can attract beneficial microbes in low phosphorus conditions to enhance plant growth. Additionally, SLs affect microbial network structures, increasing the stability of microbial communities. This study highlights the key role of SLs in shaping root-associated microbial interactions, especially in response to phosphorus availability.
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Affiliation(s)
- Pubo Chen
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha, China
- Hunan Provincial Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha, China
- College of Biology, Hunan University, Changsha, China
- Yuelushan Lab, Changsha, China
| | - Pingliang Huang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha, China
- Hunan Provincial Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha, China
- College of Biology, Hunan University, Changsha, China
- Yuelushan Lab, Changsha, China
| | - Haiyang Yu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha, China
- Hunan Provincial Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha, China
- College of Biology, Hunan University, Changsha, China
- Yuelushan Lab, Changsha, China
| | - Huang Yu
- School of Resource and Environment and Safety Engineering, University of South China, Hengyang, China
| | - Weicheng Xie
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha, China
- Hunan Provincial Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha, China
- College of Biology, Hunan University, Changsha, China
- Yuelushan Lab, Changsha, China
| | - Yuehua Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha, China
- Hunan Provincial Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha, China
- College of Biology, Hunan University, Changsha, China
- Yuelushan Lab, Changsha, China
| | - Yu Zhou
- Hunan Institute of Microbiology, Changsha, China
| | - Li Chen
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha, China
- Hunan Provincial Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha, China
- College of Biology, Hunan University, Changsha, China
- Yuelushan Lab, Changsha, China
- Greater Bay Area Institute for Innovation, Hunan University, Guangzhou, China
| | - Meng Zhang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha, China
- Hunan Provincial Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha, China
- College of Biology, Hunan University, Changsha, China
- Yuelushan Lab, Changsha, China
- Greater Bay Area Institute for Innovation, Hunan University, Guangzhou, China
| | - Ruifeng Yao
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha, China
- Hunan Provincial Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha, China
- College of Biology, Hunan University, Changsha, China
- Yuelushan Lab, Changsha, China
- Greater Bay Area Institute for Innovation, Hunan University, Guangzhou, China
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Jones KR, Belden LK, Hughey MC. Priority effects alter microbiome composition and increase abundance of probiotic taxa in treefrog tadpoles. Appl Environ Microbiol 2024; 90:e0061924. [PMID: 38757977 PMCID: PMC11218634 DOI: 10.1128/aem.00619-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Accepted: 04/21/2024] [Indexed: 05/18/2024] Open
Abstract
Host-associated microbial communities, like other ecological communities, may be impacted by the colonization order of taxa through priority effects. Developing embryos and their associated microbiomes are subject to stochasticity during colonization by bacteria. For amphibian embryos, often developing externally in bacteria-rich environments, this stochasticity may be particularly impactful. For example, the amphibian microbiome can mitigate lethal outcomes from disease for their hosts; however, this may depend on microbiome composition. Here, we examined the assembly of the bacterial community in spring peeper (Pseudacris crucifer) embryos and tadpoles. First, we reared embryos from identified mating pairs in either lab or field environments to examine the relative impact of environment and parentage on embryo and tadpole bacterial communities. Second, we experimentally inoculated embryos to determine if priority effects (i) could be used to increase the relative abundance of Janthinobacterium lividum, an amphibian-associated bacteria capable of preventing fungal infection, and (ii) would lead to observed differences in the relative abundances of two closely related bacteria from the genus Pseudomonas. Using 16S rRNA gene amplicon sequencing, we observed differences in community composition based on rearing location and parentage in embryos and tadpoles. In the inoculation experiment, we found that priority inoculation could increase the relative abundance of J. lividum, but did not find that either Pseudomonas isolate was able to prevent colonization by the other when given priority. These results highlight the importance of environmental source pools and parentage in determining microbiome composition, while also providing novel methods for the administration of a known amphibian probiotic. IMPORTANCE Harnessing the functions of host-associated bacteria is a promising mechanism for managing disease outcomes across different host species. In the case of amphibians, certain frog-associated bacteria can mitigate lethal outcomes of infection by the fungal pathogen Batrachochytrium dendrobatidis. Successful probiotic applications require knowledge of community assembly and an understanding of the ecological mechanisms that structure these symbiotic bacterial communities. In our study, we show the importance of environment and parentage in determining bacterial community composition and that community composition can be influenced by priority effects. Further, we provide support for the use of bacterial priority effects as a mechanism to increase the relative abundance of target probiotic taxa in a developing host. While our results show that priority effects are not universally effective across all host-associated bacteria, our ability to increase the relative abundance of specific probiotic taxa may enhance conservation strategies that rely on captive rearing of endangered vertebrates.
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Affiliation(s)
- Korin Rex Jones
- Department of Biological Sciences, Virginia Tech, Blacksburg, Virginia, USA
| | - Lisa K. Belden
- Department of Biological Sciences, Virginia Tech, Blacksburg, Virginia, USA
| | - Myra C. Hughey
- Department of Biology, Vassar College, Poughkeepsie, New York, USA
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Berrios L, Bogar GD, Bogar LM, Venturini AM, Willing CE, Del Rio A, Ansell TB, Zemaitis K, Velickovic M, Velickovic D, Pellitier PT, Yeam J, Hutchinson C, Bloodsworth K, Lipton MS, Peay KG. Ectomycorrhizal fungi alter soil food webs and the functional potential of bacterial communities. mSystems 2024; 9:e0036924. [PMID: 38717159 PMCID: PMC11237468 DOI: 10.1128/msystems.00369-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Accepted: 04/11/2024] [Indexed: 06/19/2024] Open
Abstract
Most of Earth's trees rely on critical soil nutrients that ectomycorrhizal fungi (EcMF) liberate and provide, and all of Earth's land plants associate with bacteria that help them survive in nature. Yet, our understanding of how the presence of EcMF modifies soil bacterial communities, soil food webs, and root chemistry requires direct experimental evidence to comprehend the effects that EcMF may generate in the belowground plant microbiome. To this end, we grew Pinus muricata plants in soils that were either inoculated with EcMF and native forest bacterial communities or only native bacterial communities. We then profiled the soil bacterial communities, applied metabolomics and lipidomics, and linked omics data sets to understand how the presence of EcMF modifies belowground biogeochemistry, bacterial community structure, and their functional potential. We found that the presence of EcMF (i) enriches soil bacteria linked to enhanced plant growth in nature, (ii) alters the quantity and composition of lipid and non-lipid soil metabolites, and (iii) modifies plant root chemistry toward pathogen suppression, enzymatic conservation, and reactive oxygen species scavenging. Using this multi-omic approach, we therefore show that this widespread fungal symbiosis may be a common factor for structuring soil food webs.IMPORTANCEUnderstanding how soil microbes interact with one another and their host plant will help us combat the negative effects that climate change has on terrestrial ecosystems. Unfortunately, we lack a clear understanding of how the presence of ectomycorrhizal fungi (EcMF)-one of the most dominant soil microbial groups on Earth-shapes belowground organic resources and the composition of bacterial communities. To address this knowledge gap, we profiled lipid and non-lipid metabolites in soils and plant roots, characterized soil bacterial communities, and compared soils amended either with or without EcMF. Our results show that the presence of EcMF changes soil organic resource availability, impacts the proliferation of different bacterial communities (in terms of both type and potential function), and primes plant root chemistry for pathogen suppression and energy conservation. Our findings therefore provide much-needed insight into how two of the most dominant soil microbial groups interact with one another and with their host plant.
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Affiliation(s)
- Louis Berrios
- Department of Biology, Stanford University, Stanford, California, USA
| | - Glade D. Bogar
- Kellogg Biological Station, Michigan State University, Hickory Corners, Michigan, USA
| | - Laura M. Bogar
- Department of Plant Biology, University of California, Davis, Davis, California, USA
| | | | - Claire E. Willing
- Department of Biology, Stanford University, Stanford, California, USA
- School of Environmental and Forest Sciences, University of Washington, Seattle, Washington, USA
| | - Anastacia Del Rio
- Department of Biology, Stanford University, Stanford, California, USA
| | - T. Bertie Ansell
- Department of Biology, Stanford University, Stanford, California, USA
- Division of CryoEM and Bioimaging, SSRL, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - Kevin Zemaitis
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Marija Velickovic
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Dusan Velickovic
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA
| | | | - Jay Yeam
- Department of Biology, Stanford University, Stanford, California, USA
| | - Chelsea Hutchinson
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Kent Bloodsworth
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Mary S. Lipton
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Kabir G. Peay
- Department of Biology, Stanford University, Stanford, California, USA
- Department of Earth System Science, Stanford University, Stanford, California, USA
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9
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Wang X, Wang S, Huang M, He Y, Guo S, Yang K, Wang N, Sun T, Yang H, Yang T, Xu Y, Shen Q, Friman VP, Wei Z. Phages enhance both phytopathogen density control and rhizosphere microbiome suppressiveness. mBio 2024; 15:e0301623. [PMID: 38780276 PMCID: PMC11237578 DOI: 10.1128/mbio.03016-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 03/21/2024] [Indexed: 05/25/2024] Open
Abstract
Bacteriophages, viruses that specifically target plant pathogenic bacteria, have emerged as a promising alternative to traditional agrochemicals. However, it remains unclear how phages should be applied to achieve efficient pathogen biocontrol and to what extent their efficacy is shaped by indirect interactions with the resident microbiota. Here, we tested if the phage biocontrol efficacy of Ralstonia solanacearum phytopathogenic bacterium can be improved by increasing the phage cocktail application frequency and if the phage efficacy is affected by pathogen-suppressing bacteria already present in the rhizosphere. We find that increasing phage application frequency improves R. solanacearum density control, leading to a clear reduction in bacterial wilt disease in both greenhouse and field experiments with tomato. The high phage application frequency also increased the diversity of resident rhizosphere microbiota and enriched several bacterial taxa that were associated with the reduction in pathogen densities. Interestingly, these taxa often belonged to Actinobacteria known for antibiotics production and soil suppressiveness. To test if they could have had secondary effects on R. solanacearum biocontrol, we isolated Actinobacteria from Nocardia and Streptomyces genera and tested their suppressiveness to the pathogen in vitro and in planta. We found that these taxa could clearly inhibit R. solanacearum growth and constrain bacterial wilt disease, especially when combined with the phage cocktail. Together, our findings unravel an undiscovered benefit of phage therapy, where phages trigger a second line of defense by the pathogen-suppressing bacteria that already exist in resident microbial communities. IMPORTANCE Ralstonia solanacearum is a highly destructive plant-pathogenic bacterium with the ability to cause bacterial wilt in several crucial crop plants. Given the limitations of conventional chemical control methods, the use of bacterial viruses (phages) has been explored as an alternative biological control strategy. In this study, we show that increasing the phage application frequency can improve the density control of R. solanacearum, leading to a significant reduction in bacterial wilt disease. Furthermore, we found that repeated phage application increased the diversity of rhizosphere microbiota and specifically enriched Actinobacterial taxa that showed synergistic pathogen suppression when combined with phages due to resource and interference competition. Together, our study unravels an undiscovered benefit of phages, where phages trigger a second line of defense by the pathogen-suppressing bacteria present in resident microbial communities. Phage therapies could, hence, potentially be tailored according to host microbiota composition to unlock the pre-existing benefits provided by resident microbiota.
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Affiliation(s)
- Xiaofang Wang
- Jiangsu provincial key lab for solid organic waste utilization, Key lab of organic-based fertilizers of China,Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing, China
| | - Shuo Wang
- Jiangsu provincial key lab for solid organic waste utilization, Key lab of organic-based fertilizers of China,Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing, China
| | - Mingcong Huang
- Jiangsu provincial key lab for solid organic waste utilization, Key lab of organic-based fertilizers of China,Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing, China
| | - Yilin He
- Jiangsu provincial key lab for solid organic waste utilization, Key lab of organic-based fertilizers of China,Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing, China
| | - Saisai Guo
- Jiangsu provincial key lab for solid organic waste utilization, Key lab of organic-based fertilizers of China,Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing, China
| | - Keming Yang
- Jiangsu provincial key lab for solid organic waste utilization, Key lab of organic-based fertilizers of China,Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing, China
- College of Agro-grassland Science, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Ningqi Wang
- Jiangsu provincial key lab for solid organic waste utilization, Key lab of organic-based fertilizers of China,Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing, China
| | - Tianyu Sun
- Jiangsu provincial key lab for solid organic waste utilization, Key lab of organic-based fertilizers of China,Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing, China
| | - Hongwu Yang
- China National Tobacco Corporation Hunan Company, Changsha, Hunan, China
| | - Tianjie Yang
- Jiangsu provincial key lab for solid organic waste utilization, Key lab of organic-based fertilizers of China,Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing, China
| | - Yangchun Xu
- Jiangsu provincial key lab for solid organic waste utilization, Key lab of organic-based fertilizers of China,Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing, China
| | - Qirong Shen
- Jiangsu provincial key lab for solid organic waste utilization, Key lab of organic-based fertilizers of China,Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing, China
| | - Ville-Petri Friman
- Jiangsu provincial key lab for solid organic waste utilization, Key lab of organic-based fertilizers of China,Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing, China
- Department of Microbiology, University of Helsinki, Helsinki, Finland
| | - Zhong Wei
- Jiangsu provincial key lab for solid organic waste utilization, Key lab of organic-based fertilizers of China,Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing, China
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10
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Reddy BD, Kumar B, Sahni S, Yashaswini G, Karthik S, Reddy MSS, Kumar R, Mukherjee U, Krishna KS. Harnessing the power of native biocontrol agents against wilt disease of Pigeonpea incited by Fusarium udum. Sci Rep 2024; 14:12500. [PMID: 38822009 PMCID: PMC11143286 DOI: 10.1038/s41598-024-60039-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Accepted: 04/18/2024] [Indexed: 06/02/2024] Open
Abstract
Fusarium wilt, caused by (Fusarium udum Butler), is a significant threat to pigeonpea crops worldwide, leading to substantial yield losses. Traditional approaches like fungicides and resistant cultivars are not practical due to the persistent and evolving nature of the pathogen. Therefore, native biocontrol agents are considered to be more sustainable solution, as they adapt well to local soil and climatic conditions. In this study, five isolates of F. udum infecting pigeonpea were isolated from various cultivars and characterized morphologically and molecularly. The isolate from the ICP 8858 cultivar displayed the highest virulence of 90%. Besides, 100 endophytic bacteria, 100 rhizosphere bacteria and three Trichoderma spp. were isolated and tested against F. udum isolated from ICP 8858 under in vitro conditions. Out of the 200 bacteria tested, nine showed highest inhibition, including Rb-4 (Bacillus sp.), Rb-11 (B. subtilis), Rb-14 (B. megaterium), Rb-18 (B. subtilis), Rb-19 (B. velezensis), Eb-8 (Bacillus sp.), Eb-11 (B. subtilis), Eb-13 (P. aeruginosa), and Eb-21 (P. aeruginosa). Similarly, Trichoderma spp. were identified as T. harzianum, T. asperellum and Trichoderma sp. Notably, Rb-18 (B. subtilis) and Eb-21 (P. aeruginosa) exhibited promising characteristics such as the production of hydrogen cyanide (HCN), cellulase, siderophores, ammonia and nutrient solubilization. Furthermore, treating pigeonpea seedlings with these beneficial microorganisms led to increased levels of key enzymes (POD, PPO, and PAL) associated with resistance to Fusarium wilt, compared to untreated controls. In field trials conducted for four seasons, the application of these potential biocontrol agents as seed treatments on the susceptible ICP2376 cultivar led to the lowest disease incidence. Specifically, treatments T2 (33.33) (P. aeruginosa) and T3 (35.41) (T. harzianium) exhibited the lowest disease incidence, followed by T6 (36.5) (Carbendizim), T1 (36.66) (B. subtilis), T4 (52.91) (T. asperellum) and T5 (53.33) (Trichoderma sp.). Results of this study revealed that, P. aeruginosa (Eb-21), B. subtilis (Rb-18) and T. harzianum can be used for plant growth promotion and management of Fusarium wilt of pigeonpea.
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Affiliation(s)
- B Deepak Reddy
- Department of Plant Pathology, Dr. Rajendra Prasad Central Agricultural University, Pusa, Bihar, India.
| | - Birendra Kumar
- Department of Plant Pathology, Dr. Rajendra Prasad Central Agricultural University, Pusa, Bihar, India
| | - Sangita Sahni
- Department of Plant Pathology, Dr. Rajendra Prasad Central Agricultural University, Pusa, Bihar, India
| | - G Yashaswini
- Department of Entomology, Dr. Rajendra Prasad Central Agricultural University, Pusa, Bihar, India
| | - Somala Karthik
- Department of Entomology, Dr. Rajendra Prasad Central Agricultural University, Pusa, Bihar, India
| | - M S Sai Reddy
- Department of Entomology, Dr. Rajendra Prasad Central Agricultural University, Pusa, Bihar, India
| | - Rajeev Kumar
- Department of Agricultural Biotechnology and Molecular Biology, Dr. Rajendra Prasad, Central Agricultural University, Pusa, Bihar, India
| | - U Mukherjee
- Department of Entomology, Dr. Rajendra Prasad Central Agricultural University, Pusa, Bihar, India
| | - K Sai Krishna
- Department of Basic Sciences and Languages, Dr. Rajendra Prasad Central Agricultural University, Pusa, Bihar, India
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11
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Mukherjee A, Singh BN, Kaur S, Sharma M, Ferreira de Araújo AS, Pereira APDA, Morya R, Puopolo G, Melo VMM, Verma JP. Unearthing the power of microbes as plant microbiome for sustainable agriculture. Microbiol Res 2024; 286:127780. [PMID: 38970905 DOI: 10.1016/j.micres.2024.127780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2024] [Revised: 05/20/2024] [Accepted: 05/21/2024] [Indexed: 07/08/2024]
Abstract
In recent years, research into the complex interactions and crosstalk between plants and their associated microbiota, collectively known as the plant microbiome has revealed the pivotal role of microbial communities for promoting plant growth and health. Plants have evolved intricate relationships with a diverse array of microorganisms inhabiting their roots, leaves, and other plant tissues. This microbiota mainly includes bacteria, archaea, fungi, protozoans, and viruses, forming a dynamic and interconnected network within and around the plant. Through mutualistic or cooperative interactions, these microbes contribute to various aspects of plant health and development. The direct mechanisms of the plant microbiome include the enhancement of plant growth and development through nutrient acquisition. Microbes have the ability to solubilize essential minerals, fix atmospheric nitrogen, and convert organic matter into accessible forms, thereby augmenting the nutrient pool available to the plant. Additionally, the microbiome helps plants to withstand biotic and abiotic stresses, such as pathogen attacks and adverse environmental conditions, by priming the plant's immune responses, antagonizing phytopathogens, and improving stress tolerance. Furthermore, the plant microbiome plays a vital role in phytohormone regulation, facilitating hormonal balance within the plant. This regulation influences various growth processes, including root development, flowering, and fruiting. Microbial communities can also produce secondary metabolites, which directly or indirectly promote plant growth, development, and health. Understanding the functional potential of the plant microbiome has led to innovative agricultural practices, such as microbiome-based biofertilizers and biopesticides, which harness the power of beneficial microorganisms to enhance crop yields while reducing the dependency on chemical inputs. In the present review, we discuss and highlight research gaps regarding the plant microbiome and how the plant microbiome can be used as a source of single and synthetic bioinoculants for plant growth and health.
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Affiliation(s)
- Arpan Mukherjee
- Plant-Microbe Interaction Lab, Institute of Environment and Sustainable Development, Banaras Hindu University, Varanasi, Uttar Pradesh 221005, India
| | - Bansh Narayan Singh
- Plant-Microbe Interaction Lab, Institute of Environment and Sustainable Development, Banaras Hindu University, Varanasi, Uttar Pradesh 221005, India
| | - Simranjit Kaur
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, NSW 2753, Australia; Crop Research Centre, Oak Park, Carlow, Ireland
| | - Minaxi Sharma
- CARAH ASBL, Rue Pal Pastur 11, Ath 7800, Belgium; China Beacons of Excellence Research and Innovation Institute (CBI), University of Nottingham Ningbo China, Ningbo 315000, China
| | | | | | - Raj Morya
- Department of Civil and Environmental engineering, Yonsei University, Seodaemun-gu, Seoul 03722, Republic of Korea
| | - Gerardo Puopolo
- Center Agriculture Food Environment (C3A), University of Trento, Via Mach 1, San Michele all'Adige 38098, Italy; Research and Innovation center, Fondazione Edmund Mach, Via E. Mach 1, San Michelle all'Adige 38098, Italy
| | - Vânia Maria Maciel Melo
- Department of Biological Sciences, Faculty of Science, Federal University of Ceará, Pici, Fortaleza, Ceará 60020-181, Brazil
| | - Jay Prakash Verma
- Plant-Microbe Interaction Lab, Institute of Environment and Sustainable Development, Banaras Hindu University, Varanasi, Uttar Pradesh 221005, India.
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12
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Geng H, Wang F, Wu H, Qin Q, Ma S, Chen H, Zhou B, Yuan R, Luo S, Sun K. Biochar and nano-hydroxyapatite combined remediation of soil surrounding tailings area: Multi-metal(loid)s fixation and soybean rhizosphere soil microbial improvement. JOURNAL OF HAZARDOUS MATERIALS 2024; 469:133817. [PMID: 38422730 DOI: 10.1016/j.jhazmat.2024.133817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2023] [Revised: 02/11/2024] [Accepted: 02/15/2024] [Indexed: 03/02/2024]
Abstract
The soil near tailings areas is relatively barren and contaminated by multi-metal(loid)s, seriously threatening the safety of crop production. Here, biochar and nano-hydroxyapatite (nHAP) were combined to improve the sterilized and unsterilized polymetallic contaminated soil, and soil incubation and soybean pot experiments were designed. Results showed that biochar and nHAP not only increased soil C, N, and P but also effectively reduced multi-metal bioavailability, wherein the combined application of the two amendments had the best effect on metal immobilization. The synergistic effect of the two amendments decreased the acid-soluble contents of Co, Cu, Fe, and Pb in rhizosphere soils up to 86.75%, 80.69%, 89.09%, and 96.70%, respectively. The ameliorant reduced the accumulation of metal(loid)s in soybean plants, and rhizosphere microorganisms inhibited the migration of soil metals to plants. Additionally, biochar and nHAP regulated the rhizosphere soil microbial community. The rhizosphere soil of the sterilization group tended to prioritize the restoration of the original dominant bacteria. As, Pb, Fe, Urease, OM, TN, and TP were the critical environmental variables affecting rhizosphere soil bacterial communities. Therefore, combining biochar and nHAP is an environmentally friendly strategy to reduce polymetallic mobility in tailings soil and crops and improve soil microbial community structure.
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Affiliation(s)
- Huanhuan Geng
- School of Environment, Beijing Normal University, No.19, Xinjiekouwai St, Haidian District, Beijing 100875, PR China; School of Energy & Environmental Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing 100083, PR China
| | - Fei Wang
- School of Environment, Beijing Normal University, No.19, Xinjiekouwai St, Haidian District, Beijing 100875, PR China.
| | - Haoming Wu
- School of Environment, Beijing Normal University, No.19, Xinjiekouwai St, Haidian District, Beijing 100875, PR China
| | - Qizheng Qin
- School of Chemical & Environmental Engineering, China University of Mining & Technology (Beijing), D11 Xueyuan Road, Haidian District, Beijing 100083, PR China
| | - Shuai Ma
- School of Environment, Beijing Normal University, No.19, Xinjiekouwai St, Haidian District, Beijing 100875, PR China
| | - Huilun Chen
- School of Energy & Environmental Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing 100083, PR China
| | - Beihai Zhou
- School of Energy & Environmental Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing 100083, PR China
| | - Rongfang Yuan
- School of Energy & Environmental Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing 100083, PR China
| | - Shuai Luo
- School of Energy & Environmental Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing 100083, PR China
| | - Ke Sun
- School of Environment, Beijing Normal University, No.19, Xinjiekouwai St, Haidian District, Beijing 100875, PR China
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13
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Meng XJ, Wang LQ, Ma BG, Wei XH, Zhou Y, Sun ZX, Li YY. Screening, identification and evaluation of an acidophilic strain of Bacillus velezensis B4-7 for the biocontrol of tobacco bacterial wilt. FRONTIERS IN PLANT SCIENCE 2024; 15:1360173. [PMID: 38751839 PMCID: PMC11094357 DOI: 10.3389/fpls.2024.1360173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 04/15/2024] [Indexed: 05/18/2024]
Abstract
Tobacco (Nicotiana tabacum L.) bacterial wilt, caused by Ralstonia solanacearum, is indeed a highly destructive plant disease, leading to substantial damage in tobacco production. While biological control is considered an effective measure for managing bacterial wilt, related research in this area has been relatively limited compared to other control methods. In order to discover new potential antagonistic bacteria with high biocontrol efficacy against tobacco bacterial wilt, we conducted an analysis of the microbial composition differences between disease-suppressive and disease-conducive soils using Illumina sequencing. As a result, we successfully isolated six strains from the disease-suppressive soil that exhibited antibacterial activity against Ralstonia solanacearum. Among these strains, B4-7 showed the strongest antibacterial activity, even at acidic conditions with a pH of 4.0. Based on genome analysis using Average Nucleotide Identity (ANI), B4-7 was identified as Bacillus velezensis. In greenhouse and field trials, strain B4-7 significantly reduced the disease index of tobacco bacterial wilt, with control efficiencies reaching 74.03% and 46.88% respectively. Additionally, B4-7 exhibited plant-promoting abilities that led to a 35.27% increase in tobacco production in field conditions. Quantitative real-time (qPCR) analysis demonstrated that strain B4-7 effectively reduced the abundance of R. solanacearum in the rhizosphere. Genome sequencing and Liquid Chromatography-Mass Spectrometry (LC-MS) analysis revealed that strain B4-7 potentially produces various lipopeptide metabolites, such as microlactin, bacillaene, difficidin, bacilysin, and surfactin. Furthermore, B4-7 influenced the structure of the rhizosphere soil microbial community, increasing bacterial abundance and fungal diversity, while also promoting the growth of different beneficial microorganisms. In addition, B4-7 enhanced tobacco's resistance to R. solanacearum by increasing the activities of defense enzymes, including superoxide dismutase (SOD), phenylalanine ammonia-lyase (PAL), peroxidase (POD), catalase (CAT), and polyphenol oxidase (PPO). Collectively, these findings suggest that B. velezensis B4-7 holds significant biocontrol potential and can be considered a promising candidate strain for eco-friendly management of tobacco bacterial wilt.
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Affiliation(s)
- Xiang-jia Meng
- College of Agriculture, Yangtze University, Jingzhou, Hubei, China
| | - Lan-qin Wang
- College of Agriculture, Yangtze University, Jingzhou, Hubei, China
| | - Bai-ge Ma
- College of Agriculture, Yangtze University, Jingzhou, Hubei, China
| | - Xi-hong Wei
- College of Agriculture, Yangtze University, Jingzhou, Hubei, China
| | - Yi Zhou
- College of Agriculture, Yangtze University, Jingzhou, Hubei, China
- Early Detection and Management of Agricultural and Forestry Pests, Jingzhou, Hubei, China
| | - Zheng-xiang Sun
- College of Agriculture, Yangtze University, Jingzhou, Hubei, China
- Early Detection and Management of Agricultural and Forestry Pests, Jingzhou, Hubei, China
| | - Yan-yan Li
- Tobacco Research Institute of Hubei Province, Wuhan, Hubei, China
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14
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Qiao H, Wu L, Li C, Yuan T, Gao J. Microbial perspective on restoration of degraded urban soil using ornamental plants. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2024; 359:120920. [PMID: 38688130 DOI: 10.1016/j.jenvman.2024.120920] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 04/11/2024] [Accepted: 04/13/2024] [Indexed: 05/02/2024]
Abstract
The urban soil where abandoned buildings are demolished is barren and structurally poor, and this degraded soil requires restoration. Ornamental plants enhance the urban environment, increase biodiversity, and affect soil physicochemical properties, microbial diversity; however, their effects remain unclear. Thus, in this study, a mixed-planting meadow consisting of 14 perennial ornamental flower species, including Iris tectorum, Iris lacteal, and Patrinia scabiosaefolia, etc. Was planted at a demolition site with sewage-contaminated soil in Beijing. Simultaneously, a single-planting lawn of I. tectorum was established in a nearby park. We aimed to examine soil physicochemical properties, sequence soil bacterial 16S rRNA and fungal ITS amplicons, and analyze soil microbial diversity and community structure at both sites at five time points in the year after planting, To explore the effect of herbaceous ornamental plants on degraded urban soil, we used FAPROTAX and FUNGuild to predict bacterial and fungal functions, the bin-based null model to evaluate the soil microbial community, and random matrix theory to construct soil microbial molecular networks. The mixed-planting meadow produced a visually appealing landscape and dynamic seasonal enrichment, significantly increasing soil total nitrogen (TN) and organic matter (SOM) contents by 1.99 and 1.21 times, respectively. TN had a positive correlation with soil microbial α diversity and community structure. Dominant phyla at both sites included Proteobacteria, Actinobacteria, and Ascomycota. Although soil microorganisms were primarily influenced by stochastic processes, stochasticity was notably higher in the mixed-planting meadow than in the single-planting lawn. The mixed-planting meadow significantly increased the relative abundance of beneficial microorganisms, improving nitrification and aerobic ammonium oxidation of soil bacteria, as well as symbiotroph of fungi. No significant changes were observed in the single-planting lawn. The mixed-planting meadow established a complex soil microbial molecular network, enhancing the correlation between bacteria and fungi and increasing the number of key microorganisms. Our findings suggest the potential of mixed-planting meadow in restoring degraded urban soils by influencing the soil microbial community and enhancing the ecological service function. Our study provides theoretical support for applying mixed-planting meadow communities to improve the soil environment of urban green spaces.
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Affiliation(s)
- Hongyong Qiao
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, Beijing, PR China; National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Beijing, PR China; Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, Beijing, PR China; School of Landscape Architecture, Beijing Forestry University, Beijing, PR China
| | - Luyao Wu
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, Beijing, PR China; National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Beijing, PR China; Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, Beijing, PR China; School of Landscape Architecture, Beijing Forestry University, Beijing, PR China; Zhejiang Provincial Institute of Cultural Relice and Archaeology, Zhejiang Province, PR China
| | - Chaonan Li
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, Beijing, PR China; National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Beijing, PR China; Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, Beijing, PR China; School of Landscape Architecture, Beijing Forestry University, Beijing, PR China
| | - Tao Yuan
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, Beijing, PR China; National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Beijing, PR China; Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, Beijing, PR China; School of Landscape Architecture, Beijing Forestry University, Beijing, PR China.
| | - Jianzhou Gao
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, Beijing, PR China; National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Beijing, PR China; Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, Beijing, PR China; School of Landscape Architecture, Beijing Forestry University, Beijing, PR China
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15
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Liu S, Liu R, Zhang S, Shen Q, Chen J, Ma H, Ge C, Hao L, Zhang J, Shi S, Pang C. The Contributions of Sub-Communities to the Assembly Process and Ecological Mechanisms of Bacterial Communities along the Cotton Soil-Root Continuum Niche Gradient. Microorganisms 2024; 12:869. [PMID: 38792699 PMCID: PMC11123189 DOI: 10.3390/microorganisms12050869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 04/12/2024] [Accepted: 04/16/2024] [Indexed: 05/26/2024] Open
Abstract
Soil microbes are crucial in shaping the root-associated microbial communities. In this study, we analyzed the effect of the soil-root niche gradient on the diversity, composition, and assembly of the bacterial community and co-occurrence network of two cotton varieties. The results revealed that the bacterial communities in cotton soil-root compartment niches exhibited a skewed species abundance distribution, dominated by abundant taxa showing a strong spatial specificity. The assembly processes of the rhizosphere bacterial communities were mainly driven by stochastic processes, dominated by the enrichment pattern and supplemented by the depletion pattern to recruit bacteria from the bulk soil, resulting in a more stable bacterial community. The assembly processes of the endosphere bacterial communities were determined by processes dominated by the depletion pattern and supplemented by the enrichment pattern to recruit species from the rhizosphere, resulting in a decrease in the stability and complexity of the community co-occurrence network. The compartment niche shaped the diversity of the bacterial communities, and the cotton variety genotype was an important source of diversity in bacterial communities within the compartment niche. We suggest that the moderate taxa contribute to significantly more changes in the diversity of the bacterial community than the rare and abundant taxa during the succession of bacterial communities in the cotton root-soil continuum.
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Affiliation(s)
- Shaodong Liu
- Engineering Research Centre of Cotton, Ministry of Education/College of Agriculture, Xinjiang Agricultural University, Urumqi 830052, China
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Zhengzhou University, Zhengzhou 450001, China
| | - Ruihua Liu
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Zhengzhou University, Zhengzhou 450001, China
| | - Siping Zhang
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Zhengzhou University, Zhengzhou 450001, China
| | - Qian Shen
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Zhengzhou University, Zhengzhou 450001, China
| | - Jing Chen
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Zhengzhou University, Zhengzhou 450001, China
| | - Huijuan Ma
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Zhengzhou University, Zhengzhou 450001, China
| | - Changwei Ge
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Zhengzhou University, Zhengzhou 450001, China
| | - Lidong Hao
- Postdoctoral Mobile Station, Lanzhou University, Lanzhou 730000, China
| | - Jinshan Zhang
- Engineering Research Centre of Cotton, Ministry of Education/College of Agriculture, Xinjiang Agricultural University, Urumqi 830052, China
| | - Shubing Shi
- Engineering Research Centre of Cotton, Ministry of Education/College of Agriculture, Xinjiang Agricultural University, Urumqi 830052, China
| | - Chaoyou Pang
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Zhengzhou University, Zhengzhou 450001, China
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16
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Fujita H, Yoshida S, Suzuki K, Toju H. Soil prokaryotic and fungal biome structures associated with crop disease status across the Japan Archipelago. mSphere 2024; 9:e0080323. [PMID: 38567970 PMCID: PMC11036807 DOI: 10.1128/msphere.00803-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Accepted: 02/29/2024] [Indexed: 04/24/2024] Open
Abstract
Archaea, bacteria, and fungi in the soil are increasingly recognized as determinants of agricultural productivity and sustainability. A crucial step for exploring soil microbiomes with important ecosystem functions is to perform statistical analyses on the potential relationship between microbiome structure and functions based on comparisons of hundreds or thousands of environmental samples collected across broad geographic ranges. In this study, we integrated agricultural field metadata with microbial community analyses by targeting 2,903 bulk soil samples collected along a latitudinal gradient from cool-temperate to subtropical regions in Japan (26.1-42.8 °N). The data involving 632 archaeal, 26,868 bacterial, and 4,889 fungal operational taxonomic units detected across the fields of 19 crop plant species allowed us to conduct statistical analyses (permutational analyses of variance, generalized linear mixed models, randomization analyses, and network analyses) on the relationship among edaphic factors, microbiome compositions, and crop disease prevalence. We then examined whether the diverse microbes form species sets varying in potential ecological impacts on crop plants. A network analysis suggested that the observed prokaryotes and fungi were classified into several species sets (network modules), which differed substantially in association with crop disease prevalence. Within the network of microbe-to-microbe coexistence, ecologically diverse microbes, such as an ammonium-oxidizing archaeon, an antibiotics-producing bacterium, and a potentially mycoparasitic fungus, were inferred to play key roles in shifts between crop-disease-promotive and crop-disease-suppressive states of soil microbiomes. The bird's-eye view of soil microbiome structure will provide a basis for designing and managing agroecosystems with high disease-suppressive functions.IMPORTANCEUnderstanding how microbiome structure and functions are organized in soil ecosystems is one of the major challenges in both basic ecology and applied microbiology. Given the ongoing worldwide degradation of agroecosystems, building frameworks for exploring structural diversity and functional profiles of soil microbiomes is an essential task. Our study provides an overview of cropland microbiome states in light of potential crop-disease-suppressive functions. The large data set allowed us to explore highly functional species sets that may be stably managed in agroecosystems. Furthermore, an analysis of network architecture highlighted species that are potentially used to cause shifts from disease-prevalent states of agroecosystems to disease-suppressive states. By extending the approach of comparative analyses toward broader geographic ranges and diverse agricultural practices, agroecosystem with maximized biological functions will be further explored.
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Affiliation(s)
- Hiroaki Fujita
- Center for Ecological Research, Kyoto University, Otsu, Shiga, Japan
| | - Shigenobu Yoshida
- Institute for Plant Protection, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, Japan
| | - Kenta Suzuki
- Integrated Bioresource Information Division, BioResource Research Center, Tsukuba, Ibaraki, Japan
| | - Hirokazu Toju
- Center for Ecological Research, Kyoto University, Otsu, Shiga, Japan
- Center for Living Systems Information Science (CeLiSIS), Graduate School of Biostudies, Kyoto University, Kyoto, Japan
- Laboratory of Ecosystems and Coevolution, Graduate School of Biostudies, Kyoto University, Kyoto, Japan
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17
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Zhao C, Onyino J, Gao X. Current Advances in the Functional Diversity and Mechanisms Underlying Endophyte-Plant Interactions. Microorganisms 2024; 12:779. [PMID: 38674723 PMCID: PMC11052469 DOI: 10.3390/microorganisms12040779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2024] [Revised: 04/06/2024] [Accepted: 04/08/2024] [Indexed: 04/28/2024] Open
Abstract
Plant phenotype is a complex entity largely controlled by the genotype and various environmental factors. Importantly, co-evolution has allowed plants to coexist with the biotic factors in their surroundings. Recently, plant endophytes as an external plant phenotype, forming part of the complex plethora of the plant microbial assemblage, have gained immense attention from plant scientists. Functionally, endophytes impact the plant in many ways, including increasing nutrient availability, enhancing the ability of plants to cope with both abiotic and biotic stress, and enhancing the accumulation of important plant secondary metabolites. The current state of research has been devoted to evaluating the phenotypic impacts of endophytes on host plants, including their direct influence on plant metabolite accumulation and stress response. However, there is a knowledge gap in how genetic factors influence the interaction of endophytes with host plants, pathogens, and other plant microbial communities, eventually controlling the extended microbial plant phenotype. This review will summarize how host genetic factors can impact the abundance and functional diversity of the endophytic microbial community, how endophytes influence host gene expression, and the host-endophyte-pathogen disease triangle. This information will provide novel insights into how breeders could specifically target the plant-endophyte extended phenotype for crop improvement.
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Affiliation(s)
- Caihong Zhao
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China; (C.Z.); (J.O.)
- Collaborative Innovation Center for Modern Crop Production Co-Sponsored by Province and Ministry, Nanjing 210095, China
- College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Johnmark Onyino
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China; (C.Z.); (J.O.)
- Collaborative Innovation Center for Modern Crop Production Co-Sponsored by Province and Ministry, Nanjing 210095, China
- College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiquan Gao
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China; (C.Z.); (J.O.)
- Collaborative Innovation Center for Modern Crop Production Co-Sponsored by Province and Ministry, Nanjing 210095, China
- College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
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18
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Wang Z, Xu L, Lu X, Wang R, Han J, Yan A. The endophytic microbiome response patterns of Juglans regia to two pathogenic fungi. Front Microbiol 2024; 15:1378273. [PMID: 38666257 PMCID: PMC11043491 DOI: 10.3389/fmicb.2024.1378273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Accepted: 03/20/2024] [Indexed: 04/28/2024] Open
Abstract
The endophytic microbial community reassembles to participate in plant immune balance when the host plants are stressed by pathogens. However, it remains unclear whether this assembly is pathogen-specific and how regulatory pathways are coordinated in multi-pathogens. In order to investigate the effects of infection with Colletotrichum gloeosporioides (Cg treatment) and Fusarium proliferatum (Fp treatment) on walnut leaf endophytic microbiome in their assembly, co-occurrence pattern, and on comprehensive chemical function of the internal environment of leaf, an interaction system of the walnut-pathogenic fungi was constructed using seed embryo tissue culture technology. The study showed differences in the assembly of endophytic microbial communities in walnut trees across three groups (control group, Ck; Cg; Fp) after Cg and Fp treatments. Despite changes in relative abundances, the dominant communities in phyla and genera remained comparable during the infection of the two pathogens. Endophyte fungi were more sensitive to the pathogen challenge than endophyte bacteria. Both promoted the enrichment of beneficial bacteria such as Bacillus and Pseudomonas, changed the modularity of the community, and reduced the stability and complexity of the endophyte community. Pathogenic fungi infection mainly affects the metabolism of porphyrin and chlorophyll, purine metabolism, phenylpropane metabolism, and amino acid metabolism. However, there was no significant difference in the secondary metabolites for the different susceptible plants. By screening endogenous antagonistic bacteria, we further verified that Pseudomonas psychrotolerans and Bacillus subtilis had inhibitory effects on the two pathogenic fungi and participated in the interaction between the leaves and pathogenic fungi. The antibacterial substances may be 1-methylnaphthalene, 1,3-butadiene, 2,3-butanediol, and toluene aldehyde.
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Affiliation(s)
- Ziye Wang
- Key Laboratory of Forest Protection of National Forestry and Grassland Administration, Chinese Academy of Forestry, Ecology and Nature Conservation Institute, Beijing, China
- College of Forestry, Hebei Agricultural University, Baoding, Hebei, China
| | - Lu Xu
- College of Forestry, Hebei Agricultural University, Baoding, Hebei, China
- Hebei Province Key Laboratory of Forest Trees Germplasm Resources and Forest Protection, Baoding, Hebei, China
| | - Xiaoyue Lu
- College of Forestry, Hebei Agricultural University, Baoding, Hebei, China
- Hebei Province Key Laboratory of Forest Trees Germplasm Resources and Forest Protection, Baoding, Hebei, China
| | - Ruidong Wang
- College of Forestry, Hebei Agricultural University, Baoding, Hebei, China
- Hebei Province Key Laboratory of Forest Trees Germplasm Resources and Forest Protection, Baoding, Hebei, China
| | - Jie Han
- College of Forestry, Hebei Agricultural University, Baoding, Hebei, China
- Hebei Province Key Laboratory of Forest Trees Germplasm Resources and Forest Protection, Baoding, Hebei, China
| | - Aihua Yan
- College of Forestry, Hebei Agricultural University, Baoding, Hebei, China
- Hebei Urban Forest Health Technology Innovation Center, Baoding, Hebei, China
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19
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Wang X, Tang Y, Yue X, Wang S, Yang K, Xu Y, Shen Q, Friman VP, Wei Z. The role of rhizosphere phages in soil health. FEMS Microbiol Ecol 2024; 100:fiae052. [PMID: 38678007 PMCID: PMC11065364 DOI: 10.1093/femsec/fiae052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Revised: 03/22/2024] [Accepted: 04/25/2024] [Indexed: 04/29/2024] Open
Abstract
While the One Health framework has emphasized the importance of soil microbiomes for plant and human health, one of the most diverse and abundant groups-bacterial viruses, i.e. phages-has been mostly neglected. This perspective reviews the significance of phages for plant health in rhizosphere and explores their ecological and evolutionary impacts on soil ecosystems. We first summarize our current understanding of the diversity and ecological roles of phages in soil microbiomes in terms of nutrient cycling, top-down density regulation, and pathogen suppression. We then consider how phages drive bacterial evolution in soils by promoting horizontal gene transfer, encoding auxiliary metabolic genes that increase host bacterial fitness, and selecting for phage-resistant mutants with altered ecology due to trade-offs with pathogen competitiveness and virulence. Finally, we consider challenges and avenues for phage research in soil ecosystems and how to elucidate the significance of phages for microbial ecology and evolution and soil ecosystem functioning in the future. We conclude that similar to bacteria, phages likely play important roles in connecting different One Health compartments, affecting microbiome diversity and functions in soils. From the applied perspective, phages could offer novel approaches to modulate and optimize microbial and microbe-plant interactions to enhance soil health.
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Affiliation(s)
- Xiaofang Wang
- Jiangsu provincial key lab for solid organic waste utilization, Key lab of organic-based fertilizers of China,Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing 210095, China
| | - Yike Tang
- Jiangsu provincial key lab for solid organic waste utilization, Key lab of organic-based fertilizers of China,Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiufeng Yue
- Jiangsu provincial key lab for solid organic waste utilization, Key lab of organic-based fertilizers of China,Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing 210095, China
| | - Shuo Wang
- Jiangsu provincial key lab for solid organic waste utilization, Key lab of organic-based fertilizers of China,Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing 210095, China
| | - Keming Yang
- Jiangsu provincial key lab for solid organic waste utilization, Key lab of organic-based fertilizers of China,Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing 210095, China
| | - Yangchun Xu
- Jiangsu provincial key lab for solid organic waste utilization, Key lab of organic-based fertilizers of China,Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing 210095, China
| | - Qirong Shen
- Jiangsu provincial key lab for solid organic waste utilization, Key lab of organic-based fertilizers of China,Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing 210095, China
| | - Ville-Petri Friman
- Jiangsu provincial key lab for solid organic waste utilization, Key lab of organic-based fertilizers of China,Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing 210095, China
- Department of Microbiology, University of Helsinki, 00014 Helsinki, Finland
| | - Zhong Wei
- Jiangsu provincial key lab for solid organic waste utilization, Key lab of organic-based fertilizers of China,Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing 210095, China
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20
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Jiang L, Ke D, Sun B, Zhang J, Lyu S, Yu H, Chen P, Mao X, Liu Q, Chen W, Fan Z, Huang L, Yin S, Deng Y, Li C. Root microbiota analysis of Oryza rufipogon and Oryza sativa reveals an orientation selection during the domestication process. Microbiol Spectr 2024; 12:e0333023. [PMID: 38470483 PMCID: PMC10986595 DOI: 10.1128/spectrum.03330-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Accepted: 02/15/2024] [Indexed: 03/13/2024] Open
Abstract
The root-associated microbiota has a close relation to the life activities of plants, and its composition is affected by the rhizospheric environment and plant genotypes. Rice (Oryza sativa) was domesticated from the ancestor species Oryza rufipogon. Many important agricultural traits and adversity resistance of rice have changed during a long time of natural domestication and artificial selection. However, the influence of rice genotypes on root microbiota in important agricultural traits remains to be explained. In this study, we performed 16S rRNA and internal transcribed spacer (ITS) gene amplicon sequencing to generate bacterial and fungal community profiles of O. rufipogon and O. sativa, both of which were planted in a farm in Guangzhou and had reached the reproductive stage. We compared their root microbiota in detail by alpha diversity, beta diversity, different species, core microbiota, and correlation analyses. We found that the relative abundance of bacteria was significantly higher in the cultivated rice than in the common wild rice, while the relative abundance of fungi was the opposite. Significant differences in agricultural traits between O. rufipogon and O. sativa showed a high correlation with core microorganisms in the two Oryza species, which only existed in either or had obviously different abundance in both two species, indicating that rice genotype/phenotype had a strong influence on recruiting specific microorganisms. Our study provides a theoretical basis for the in-depth understanding of rice root microbiota and the improvement of rice breeding from the perspective of the interaction between root microorganisms and plants.IMPORTANCEPlant root microorganisms play a vital role not only in plant growth and development but also in responding the biotic and abiotic stresses. Oryza sativa is domesticated from Oryza rufipogon which has many excellent agricultural traits especially containing resistance to biotic and abiotic stresses. To improve the yield and resistance of cultivated rice, it is particularly important to deeply research on differences between O. sativa and O. rufipogon and find beneficial microorganisms to remodel the root microbiome of O. sativa.
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Affiliation(s)
- Liqun Jiang
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Guangzhou, China
| | - Da Ke
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Guangzhou, China
| | - Bingrui Sun
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Guangzhou, China
| | - Jing Zhang
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Guangzhou, China
| | - Shuwei Lyu
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Guangzhou, China
| | - Hang Yu
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Guangzhou, China
| | - Pingli Chen
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Guangzhou, China
| | - Xingxue Mao
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Guangzhou, China
| | - Qing Liu
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Guangzhou, China
| | - Wenfeng Chen
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Guangzhou, China
| | - Zhilan Fan
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Guangzhou, China
| | - Li Huang
- Healthtimegene Institute, Shenzhen, China
| | - Sanjun Yin
- Healthtimegene Institute, Shenzhen, China
| | - Yizhen Deng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, China
| | - Chen Li
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Guangzhou, China
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21
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Darriaut R, Marzari T, Lailheugue V, Tran J, Martins G, Marguerit E, Masneuf-Pomarède I, Lauvergeat V. Microbial dysbiosis in roots and rhizosphere of grapevines experiencing decline is associated with active metabolic functions. FRONTIERS IN PLANT SCIENCE 2024; 15:1358213. [PMID: 38628369 PMCID: PMC11018932 DOI: 10.3389/fpls.2024.1358213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 03/11/2024] [Indexed: 04/19/2024]
Abstract
When grapevine decline, characterized by a premature decrease in vigor and yield and sometimes plant death, cannot be explained by pathological or physiological diseases, one may inquire whether the microbiological status of the soil is responsible. Previous studies have shown that the composition and structure of bacterial and fungal microbial communities in inter-row soil are affected in areas displaying vine decline, compared to areas with non-declining vines within the same plot. A more comprehensive analysis was conducted in one such plot. Although soil chemical parameters could not directly explain these differences, the declining vines presented lower vigor, yield, berry quality, and petiole mineral content than those in non-declining vines. The bacterial and fungal microbiome of the root endosphere, rhizosphere, and different horizons of the bulk soil were explored through enzymatic, metabolic diversity, and metabarcoding analysis in both areas. Despite the lower microbial diversity and richness in symptomatic roots and soil, higher microbial activity and enrichment of potentially both beneficial bacteria and pathogenic fungi were found in the declining area. Path modeling analysis linked the root microbial activity to berry quality, suggesting a determinant role of root microbiome in the berry mineral content. Furthermore, certain fungal and bacterial taxa were correlated with predicted metabolic pathways and metabolic processes assessed with Eco-Plates. These results unexpectedly revealed active microbial profiles in the belowground compartments associated with stressed vines, highlighting the interest of exploring the functional microbiota of plants, and more specifically roots and rhizosphere, under stressed conditions.
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Affiliation(s)
- Romain Darriaut
- EGFV, Univ. Bordeaux, Bordeaux Sciences Agro, INRAE, ISVV, Villenave d’Ornon, France
| | - Tania Marzari
- EGFV, Univ. Bordeaux, Bordeaux Sciences Agro, INRAE, ISVV, Villenave d’Ornon, France
| | - Vincent Lailheugue
- EGFV, Univ. Bordeaux, Bordeaux Sciences Agro, INRAE, ISVV, Villenave d’Ornon, France
| | - Joseph Tran
- EGFV, Univ. Bordeaux, Bordeaux Sciences Agro, INRAE, ISVV, Villenave d’Ornon, France
| | - Guilherme Martins
- Université de Bordeaux, INRAE, Bordeaux INP, Bordeaux Sciences Agro, UMR Œnologie 1366, ISVV, Villenave d’Ornon, France
- Bordeaux Sciences Agro, 1 cours du Général de Gaulle, Gradignan, France
| | - Elisa Marguerit
- EGFV, Univ. Bordeaux, Bordeaux Sciences Agro, INRAE, ISVV, Villenave d’Ornon, France
| | - Isabelle Masneuf-Pomarède
- Université de Bordeaux, INRAE, Bordeaux INP, Bordeaux Sciences Agro, UMR Œnologie 1366, ISVV, Villenave d’Ornon, France
- Bordeaux Sciences Agro, 1 cours du Général de Gaulle, Gradignan, France
| | - Virginie Lauvergeat
- EGFV, Univ. Bordeaux, Bordeaux Sciences Agro, INRAE, ISVV, Villenave d’Ornon, France
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22
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Pacheco-Moreno A, Bollmann-Giolai A, Chandra G, Brett P, Davies J, Thornton O, Poole P, Ramachandran V, Brown JKM, Nicholson P, Ridout C, DeVos S, Malone JG. The genotype of barley cultivars influences multiple aspects of their associated microbiota via differential root exudate secretion. PLoS Biol 2024; 22:e3002232. [PMID: 38662644 PMCID: PMC11045101 DOI: 10.1371/journal.pbio.3002232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 03/19/2024] [Indexed: 04/28/2024] Open
Abstract
Plant-associated microbes play vital roles in promoting plant growth and health, with plants secreting root exudates into the rhizosphere to attract beneficial microbes. Exudate composition defines the nature of microbial recruitment, with different plant species attracting distinct microbiota to enable optimal adaptation to the soil environment. To more closely examine the relationship between plant genotype and microbial recruitment, we analysed the rhizosphere microbiomes of landrace (Chevallier) and modern (NFC Tipple) barley (Hordeum vulgare) cultivars. Distinct differences were observed between the plant-associated microbiomes of the 2 cultivars, with the plant-growth promoting rhizobacterial genus Pseudomonas substantially more abundant in the Tipple rhizosphere. Striking differences were also observed between the phenotypes of recruited Pseudomonas populations, alongside distinct genotypic clustering by cultivar. Cultivar-driven Pseudomonas selection was driven by root exudate composition, with the greater abundance of hexose sugars secreted from Tipple roots attracting microbes better adapted to growth on these metabolites and vice versa. Cultivar-driven selection also operates at the molecular level, with both gene expression and the abundance of ecologically relevant loci differing between Tipple and Chevallier Pseudomonas isolates. Finally, cultivar-driven selection is important for plant health, with both cultivars showing a distinct preference for microbes selected by their genetic siblings in rhizosphere transplantation assays.
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Affiliation(s)
- Alba Pacheco-Moreno
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, United Kingdom
| | | | - Govind Chandra
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, United Kingdom
| | - Paul Brett
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, United Kingdom
| | - Jack Davies
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, United Kingdom
| | - Owen Thornton
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, United Kingdom
| | - Philip Poole
- Department of Biology, University of Oxford, South Parks Road, Oxford, United Kingdom
| | - Vinoy Ramachandran
- Department of Biology, University of Oxford, South Parks Road, Oxford, United Kingdom
| | - James K. M. Brown
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, United Kingdom
| | - Paul Nicholson
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, United Kingdom
| | - Chris Ridout
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, United Kingdom
- New Heritage Barley, Norwich Research Park, Norwich, United Kingdom
| | - Sarah DeVos
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, United Kingdom
- New Heritage Barley, Norwich Research Park, Norwich, United Kingdom
| | - Jacob G. Malone
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, United Kingdom
- School of Biological Sciences, University of East Anglia, Norwich, United Kingdom
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23
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Calderon RB, Dangi SR. Arbuscular Mycorrhizal Fungi and Rhizobium Improve Nutrient Uptake and Microbial Diversity Relative to Dryland Site-Specific Soil Conditions. Microorganisms 2024; 12:667. [PMID: 38674611 PMCID: PMC11052256 DOI: 10.3390/microorganisms12040667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Revised: 03/21/2024] [Accepted: 03/25/2024] [Indexed: 04/28/2024] Open
Abstract
Arbuscular mycorrhizal fungi (AMF) and rhizobium play a significant role in plant symbiosis. However, their influence on the rhizosphere soil microbiome associated with nutrient acquisition and soil health is not well defined in the drylands of Montana (MT), USA. This study investigated the effect of microbial inoculants as seed treatment on pea yield, nutrient uptake, potential microbial functions, and rhizosphere soil microbial communities using high-throughput sequencing of 16S and ITS rRNA genes. The experiment was conducted under two contrasting dryland conditions with four treatments: control, single inoculation with AMF or Rhizobium, and dual inoculations of AMF and Rhizobium (AMF+Rhizobium). Our findings revealed that microbial inoculation efficacy was site-specific. AMF+Rhizobium synergistically increased grain yield at Sidney dryland field site (DFS) 2, while at Froid site, DFS 1, AMF improved plant resilience to acidic soil but contributed a marginal yield under non-nutrient limiting conditions. Across dryland sites, the plants' microbial dependency on AMF+Rhizobium (12%) was higher than single inoculations of AMF (8%) or Rhizobium (4%) alone. Variations in microbial community structure and composition indicate a site-specific response to AMF and AMF+Rhizobium inoculants. Overall, site-specific factors significantly influenced plant nutrient uptake, microbial community dynamics, and functional potential. It underscores the need for tailored management strategies that consider site-specific characteristics to optimize benefits from microbial inoculation.
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Affiliation(s)
- Rosalie B. Calderon
- Agricultural Research Service, Northern Plains Agricultural Research Laboratory, USDA, 1500 N Central Avenue, Sidney, MT 59270, USA
| | - Sadikshya R. Dangi
- Correspondence: (R.B.C.); (S.R.D.); Tel.: +1-(406)-433-9479 (R.B.C.); +1-(406)-433-9490 (S.R.D.); Fax: +1-(406)-433-5038 (R.B.C. & S.R.D.)
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24
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Argiroff WA, Carrell AA, Klingeman DM, Dove NC, Muchero W, Veach AM, Wahl T, Lebreux SJ, Webb AB, Peyton K, Schadt CW, Cregger MA. Seasonality and longer-term development generate temporal dynamics in the Populus microbiome. mSystems 2024; 9:e0088623. [PMID: 38421171 PMCID: PMC10949431 DOI: 10.1128/msystems.00886-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 02/08/2024] [Indexed: 03/02/2024] Open
Abstract
Temporal variation in community composition is central to our understanding of the assembly and functioning of microbial communities, yet the controls over temporal dynamics for microbiomes of long-lived plants, such as trees, remain unclear. Temporal variation in tree microbiomes could arise primarily from seasonal (i.e., intra-annual) fluctuations in community composition or from longer-term changes across years as host plants age. To test these alternatives, we experimentally isolated temporal variation in plant microbiome composition using a common garden and clonally propagated plants, and we used amplicon sequencing to characterize bacterial/archaeal and fungal communities in the leaf endosphere, root endosphere, and rhizosphere of two Populus spp. over four seasons across two consecutive years. Microbial community composition differed among seasons and years (which accounted for up to 21% of the variation in microbial community composition) and was correlated with seasonal dissimilarity in climatic conditions. However, microbial community dissimilarity was also positively correlated with time, reflecting longer-term compositional shifts as host trees aged. Together, our findings demonstrate that temporal patterns in tree microbiomes arise from both seasonal fluctuations and longer-term changes, which interact to generate unique seasonal patterns each year. In addition to shedding light on two important controls over the assembly of plant microbiomes, our results also suggest future studies of tree microbiomes should account for background temporal dynamics when testing the drivers of spatial patterns in microbial community composition and temporal responses of plant microbiomes to environmental change.IMPORTANCEMicrobiomes are integral to the health of host plants, but we have a limited understanding of the factors that control how the composition of plant microbiomes changes over time. Especially little is known about the microbiome of long-lived trees, relative to annual and non-woody plants. We tested how tree microbiomes changed between seasons and years in poplar (genus Populus), which are widespread and ecologically important tree species that also serve as important biofuel feedstocks. We found the composition of bacterial, archaeal, and fungal communities differed among seasons, but these seasonal differences depended on year. This dependence was driven by longer-term changes in microbial composition as host trees developed across consecutive years. Our findings suggest that temporal variation in tree microbiomes is driven by both seasonal fluctuations and longer-term (i.e., multiyear) development.
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Affiliation(s)
- William A. Argiroff
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Alyssa A. Carrell
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Dawn M. Klingeman
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Nicholas C. Dove
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Wellington Muchero
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Allison M. Veach
- Department of Integrative Biology, The University of Texas, San Antonio, Texas, USA
| | - Toni Wahl
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Steven J. Lebreux
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Amber B. Webb
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Kellie Peyton
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Christopher W. Schadt
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, USA
| | - Melissa A. Cregger
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
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25
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Raza W, Jiang G, Eisenhauer N, Huang Y, Wei Z, Shen Q, Kowalchuk GA, Jousset A. Microbe-induced phenotypic variation leads to overyielding in clonal plant populations. Nat Ecol Evol 2024; 8:392-399. [PMID: 38195997 DOI: 10.1038/s41559-023-02297-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 12/06/2023] [Indexed: 01/11/2024]
Abstract
Overyielding, the high productivity of multispecies plant communities, is commonly seen as the result of plant genetic diversity. Here we demonstrate that biodiversity-ecosystem functioning relationships can emerge in clonal plant populations through interaction with microorganisms. Using a model clonal plant species, we found that exposure to volatiles of certain microorganisms led to divergent plant phenotypes. Assembling communities out of plants associated with different microorganisms led to transgressive overyielding in both biomass and seed yield. Our results highlight the importance of belowground microbial diversity in plant biodiversity research and open new avenues for precision ecosystem management.
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Affiliation(s)
- Waseem Raza
- College of Resources and Environmental Science, Key Lab of Organic-Based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, China
- Institute for Environmental Biology, Ecology and Biodiversity, Utrecht University, Utrecht, the Netherlands
| | - Gaofei Jiang
- College of Resources and Environmental Science, Key Lab of Organic-Based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, China
| | - Nico Eisenhauer
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
- Institute of Biology, Leipzig University, Leipzig, Germany
| | - Yishuo Huang
- College of Resources and Environmental Science, Key Lab of Organic-Based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, China
| | - Zhong Wei
- College of Resources and Environmental Science, Key Lab of Organic-Based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, China.
| | - Qirong Shen
- College of Resources and Environmental Science, Key Lab of Organic-Based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, China
| | - George A Kowalchuk
- Institute for Environmental Biology, Ecology and Biodiversity, Utrecht University, Utrecht, the Netherlands
| | - Alexandre Jousset
- College of Resources and Environmental Science, Key Lab of Organic-Based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, China.
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26
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Gfeller V, Thoenen L, Erb M. Root-exuded benzoxazinoids can alleviate negative plant-soil feedbacks. THE NEW PHYTOLOGIST 2024; 241:2575-2588. [PMID: 38087806 DOI: 10.1111/nph.19401] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2023] [Accepted: 10/23/2023] [Indexed: 02/03/2024]
Abstract
Plants can suppress the growth of other plants by modifying soil properties. These negative plant-soil feedbacks are often species-specific, suggesting that some plants possess resistance strategies. However, the underlying mechanisms remain largely unknown. Here, we investigated whether benzoxazinoids, a class of dominant secondary metabolites that are exuded into the soil by maize and other cereals, allow maize plants to cope with plant-soil feedbacks. We find that three out of five tested crop species reduce maize (Zea mays L.) performance via negative plant-soil feedbacks relative to the mean across species. This effect is partially alleviated by the capacity of maize plants to produce benzoxazinoids. Soil complementation with purified benzoxazinoids restores the protective effect for benzoxazinoid-deficient mutants. Sterilization and reinoculation experiments suggest that benzoxazinoid-mediated protection acts via changes in soil biota. Substantial variation of the protective effect between experiments and soil types illustrates context dependency. In conclusion, exuded plant secondary metabolites allow plants to cope with plant-soil feedbacks. These findings expand the functional repertoire of plant secondary metabolites and reveal a mechanism by which plants can resist negative effects of soil feedbacks. The uncovered phenomenon may represent a promising avenue to stabilize plant performance in crop rotations.
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Affiliation(s)
- Valentin Gfeller
- Institute of Plant Sciences, University of Bern, 3013, Bern, Switzerland
- Department of Crop Sciences, Research Institute of Organic Agriculture (FiBL), 5070, Frick, Switzerland
| | - Lisa Thoenen
- Institute of Plant Sciences, University of Bern, 3013, Bern, Switzerland
| | - Matthias Erb
- Institute of Plant Sciences, University of Bern, 3013, Bern, Switzerland
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27
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Kimotho RN, Maina S. Unraveling plant-microbe interactions: can integrated omics approaches offer concrete answers? JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:1289-1313. [PMID: 37950741 PMCID: PMC10901211 DOI: 10.1093/jxb/erad448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 11/08/2023] [Indexed: 11/13/2023]
Abstract
Advances in high throughput omics techniques provide avenues to decipher plant microbiomes. However, there is limited information on how integrated informatics can help provide deeper insights into plant-microbe interactions in a concerted way. Integrating multi-omics datasets can transform our understanding of the plant microbiome from unspecified genetic influences on interacting species to specific gene-by-gene interactions. Here, we highlight recent progress and emerging strategies in crop microbiome omics research and review key aspects of how the integration of host and microbial omics-based datasets can be used to provide a comprehensive outline of complex crop-microbe interactions. We describe how these technological advances have helped unravel crucial plant and microbial genes and pathways that control beneficial, pathogenic, and commensal plant-microbe interactions. We identify crucial knowledge gaps and synthesize current limitations in our understanding of crop microbiome omics approaches. We highlight recent studies in which multi-omics-based approaches have led to improved models of crop microbial community structure and function. Finally, we recommend holistic approaches in integrating host and microbial omics datasets to achieve precision and efficiency in data analysis, which is crucial for biotic and abiotic stress control and in understanding the contribution of the microbiota in shaping plant fitness.
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Affiliation(s)
- Roy Njoroge Kimotho
- Hebei Key Laboratory of Soil Ecology, Key Laboratory of Agricultural Water Resources, Centre for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang 050021, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Solomon Maina
- Elizabeth Macarthur Agricultural Institute, NSW Department of Primary Industries, Menangle, New South Wales 2568, Australia
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28
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Kang H, Chai A, Lin Z, Shi Y, Xie X, Li L, Fan T, Xiang S, Xie J, Li B. Deciphering Differences in Microbial Community Diversity between Clubroot-Diseased and Healthy Soils. Microorganisms 2024; 12:251. [PMID: 38399655 PMCID: PMC10893227 DOI: 10.3390/microorganisms12020251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Revised: 01/16/2024] [Accepted: 01/24/2024] [Indexed: 02/25/2024] Open
Abstract
Clubroot (Plasmodiophora brassicae) is an important soilborne disease that causes severe damage to cruciferous crops in China. This study aims to compare the differences in chemical properties and microbiomes between healthy and clubroot-diseased soils. To reveal the difference, we measured soil chemical properties and microbial communities by sequencing 18S and 16S rRNA amplicons. The available potassium in the diseased soils was higher than in the healthy soils. The fungal diversity in the healthy soils was significantly higher than in the diseased soils. Ascomycota and Proteobacteria were the most dominant fungal phylum and bacteria phylum in all soil samples, respectively. Plant-beneficial microorganisms, such as Chaetomium and Sphingomonas, were more abundant in the healthy soils than in the diseased soils. Co-occurrence network analysis found that the healthy soil networks were more complex and stable than the diseased soils. The link number, network density, and clustering coefficient of the healthy soil networks were higher than those of the diseased soil networks. Our results indicate that the microbial community diversity and network structure of the clubroot-diseased soils were different from those of the healthy soils. This study is of great significance in exploring the biological control strategies of clubroot disease.
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Affiliation(s)
- Huajun Kang
- College of Horticulture, Gansu Agricultural University, Lanzhou 730070, China;
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (A.C.); (Z.L.); (Y.S.); (X.X.); (L.L.); (T.F.); (S.X.)
| | - Ali Chai
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (A.C.); (Z.L.); (Y.S.); (X.X.); (L.L.); (T.F.); (S.X.)
| | - Zihan Lin
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (A.C.); (Z.L.); (Y.S.); (X.X.); (L.L.); (T.F.); (S.X.)
| | - Yanxia Shi
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (A.C.); (Z.L.); (Y.S.); (X.X.); (L.L.); (T.F.); (S.X.)
| | - Xuewen Xie
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (A.C.); (Z.L.); (Y.S.); (X.X.); (L.L.); (T.F.); (S.X.)
| | - Lei Li
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (A.C.); (Z.L.); (Y.S.); (X.X.); (L.L.); (T.F.); (S.X.)
| | - Tengfei Fan
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (A.C.); (Z.L.); (Y.S.); (X.X.); (L.L.); (T.F.); (S.X.)
| | - Sheng Xiang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (A.C.); (Z.L.); (Y.S.); (X.X.); (L.L.); (T.F.); (S.X.)
| | - Jianming Xie
- College of Horticulture, Gansu Agricultural University, Lanzhou 730070, China;
| | - Baoju Li
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (A.C.); (Z.L.); (Y.S.); (X.X.); (L.L.); (T.F.); (S.X.)
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29
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Meng L, Chen Y, Tang L, Sun X, Huo H, He Y, Huang Y, Shao Q, Pan S, Li Z. Effects of temperature-related changes on charred bone in soil: From P release to microbial community. CURRENT RESEARCH IN MICROBIAL SCIENCES 2024; 6:100221. [PMID: 38292865 PMCID: PMC10825478 DOI: 10.1016/j.crmicr.2024.100221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2024] Open
Abstract
Phosphorus (P) is one of the most common limited nutrients in terrestrial ecosystems. Animal bones, with abundant bioapatite, are considerable P sources in terrestrial ecosystems. Heating significantly promotes P release from bone bioapatite, which may alleviate P limitation in soil. This study aimed to explore P release from charred bone (CB) under heating at various temperatures (based on common natural heating). It showed that heating at ∼300 °C significantly increased the P release (up to ∼30 mg/kg) from CB compared with other heating temperatures. Then, the subsequent changes of available P and pH induced evident alternation of soil microbial community composition. For instance, CB heated at ∼300 °C caused elevation of phosphate-solubilizing fungi (PSF) abundance. This further stimulated P mobility in the soil. Meanwhile, the fungal community assembly process was shifted from stochastic to deterministic, whereas the bacterial community was relatively stable. This indicated that the bacterial community showed fewer sensitive responses to the CB addition. This study hence elucidated the significant contribution of heated bone materials on P supply. Moreover, functional fungi might assist CB treated by natural heating (e.g., fire) to construct P "Hot Spots".
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Affiliation(s)
- Lingzi Meng
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
- State Key Laboratory of Lake Science and Environment, Nanjing 210008, China
| | - Yunhui Chen
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
- State Key Laboratory of Lake Science and Environment, Nanjing 210008, China
| | - Lingyi Tang
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Xiaoqin Sun
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, Jiangsu 210014, China
| | - Hongxun Huo
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Yuxin He
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Yinan Huang
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Qi Shao
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Shang Pan
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Zhen Li
- State Key Laboratory of Lake Science and Environment, Nanjing 210008, China
- State Key Laboratory of Biogeology and Environmental Geology, Wuhan 430074, China
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Nanjing Agricultural University, Nanjing 210095, China
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30
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Lyng M, Jørgensen JPB, Schostag MD, Jarmusch SA, Aguilar DKC, Lozano-Andrade CN, Kovács ÁT. Competition for iron shapes metabolic antagonism between Bacillus subtilis and Pseudomonas marginalis. THE ISME JOURNAL 2024; 18:wrad001. [PMID: 38365234 PMCID: PMC10811728 DOI: 10.1093/ismejo/wrad001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 11/03/2023] [Indexed: 02/18/2024]
Abstract
Siderophores have long been implicated in sociomicrobiology as determinants of bacterial interrelations. For plant-associated genera, like Bacillus and Pseudomonas, siderophores are well known for their biocontrol functions. Here, we explored the functional role of the Bacillus subtilis siderophore bacillibactin (BB) in an antagonistic interaction with Pseudomonas marginalis. The presence of BB strongly influenced the outcome of the interaction in an iron-dependent manner. The BB producer B. subtilis restricts colony spreading of P. marginalis by repressing the transcription of histidine kinase-encoding gene gacS, thereby abolishing production of secondary metabolites such as pyoverdine and viscosin. By contrast, lack of BB restricted B. subtilis colony growth. To explore the specificity of the antagonism, we cocultured B. subtilis with a collection of fluorescent Pseudomonas spp. and found that the Bacillus-Pseudomonas interaction is conserved, expanding our understanding of the interplay between two of the most well-studied genera of soil bacteria.
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Affiliation(s)
- Mark Lyng
- Bacterial Interactions and Evolution Group, DTU Bioengineering, Technical University of Denmark, Kgs Lyngby 2800, Denmark
| | - Johan P B Jørgensen
- Bacterial Interactions and Evolution Group, DTU Bioengineering, Technical University of Denmark, Kgs Lyngby 2800, Denmark
| | - Morten D Schostag
- Bacterial Ecophysiology & Biotechnology, DTU Bioengineering, Technical University of Denmark, Kgs Lyngby 2800, Denmark
| | - Scott A Jarmusch
- Natural Product Discovery, DTU Bioengineering, Technical University of Denmark, Kgs Lyngby 2800, Denmark
| | - Diana K C Aguilar
- Bacterial Interactions and Evolution Group, DTU Bioengineering, Technical University of Denmark, Kgs Lyngby 2800, Denmark
| | - Carlos N Lozano-Andrade
- Bacterial Interactions and Evolution Group, DTU Bioengineering, Technical University of Denmark, Kgs Lyngby 2800, Denmark
| | - Ákos T Kovács
- Bacterial Interactions and Evolution Group, DTU Bioengineering, Technical University of Denmark, Kgs Lyngby 2800, Denmark
- Institute of Biology Leiden, Leiden University, Leiden 2333 BE, The Netherlands
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31
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Luo X, Sun K, Li HR, Zhang XY, Pan YT, Luo DL, Wu YB, Jiang HJ, Wu XH, Ma CY, Dai CC, Zhang W. Depletion of protective microbiota promotes the incidence of fruit disease. THE ISME JOURNAL 2024; 18:wrae071. [PMID: 38691444 DOI: 10.1093/ismejo/wrae071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 03/11/2024] [Accepted: 04/24/2024] [Indexed: 05/03/2024]
Abstract
Plant-associated microbiomes play important roles in plant health and productivity. However, despite fruits being directly linked to plant productivity, little is known about the microbiomes of fruits and their potential association with fruit health. Here, by integrating 16S rRNA gene, ITS high-throughput sequencing data, and microbiological culturable approaches, we reported that roots and fruits (pods) of peanut, a typical plant that bears fruits underground, recruit different bacterial and fungal communities independently of cropping conditions and that the incidence of pod disease under monocropping conditions is attributed to the depletion of Bacillus genus and enrichment of Aspergillus genus in geocarposphere. On this basis, we constructed a synthetic community (SynCom) consisting of three Bacillus strains from geocarposphere soil under rotation conditions with high culturable abundance. Comparative transcriptome, microbiome profiling, and plant phytohormone signaling analysis reveal that the SynCom exhibited more effective Aspergillus growth inhibition and pod disease control than individual strain, which was underpinned by a combination of molecular mechanisms related to fungal cell proliferation interference, mycotoxins biosynthesis impairment, and jasmonic acid-mediated plant immunity activation. Overall, our results reveal the filter effect of plant organs on the microbiome and that depletion of key protective microbial community promotes the fruit disease incidence.
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Affiliation(s)
- Xue Luo
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Jiangsu Province, 210023, China
| | - Kai Sun
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Jiangsu Province, 210023, China
| | - Hao-Ran Li
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Jiangsu Province, 210023, China
| | - Xiang-Yu Zhang
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Jiangsu Province, 210023, China
| | - Yi-Tong Pan
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Jiangsu Province, 210023, China
| | - De-Lin Luo
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Jiangsu Province, 210023, China
| | - Yi-Bo Wu
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Jiangsu Province, 210023, China
| | - Hui-Jun Jiang
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Jiangsu Province, 210023, China
| | - Xiao-Han Wu
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Jiangsu Province, 210023, China
| | - Chen-Yu Ma
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Jiangsu Province, 210023, China
| | - Chuan-Chao Dai
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Jiangsu Province, 210023, China
| | - Wei Zhang
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Jiangsu Province, 210023, China
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Han Z, Leng Y, Sun Z, Li Z, Xu P, Wu S, Liu S, Li S, Wang J, Zou J. Substitution of organic and bio-organic fertilizers for mineral fertilizers to suppress nitrous oxide emissions from intensive vegetable fields. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2024; 349:119390. [PMID: 37897895 DOI: 10.1016/j.jenvman.2023.119390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 10/09/2023] [Accepted: 10/11/2023] [Indexed: 10/30/2023]
Abstract
To gain insight into the microbial mechanisms associated with the replacement of chemical fertilizers with organic or bio-organic fertilizers to mitigate soil nitrous oxide (N2O) emissions, we measured N2O emissions from greenhouse vegetable soils through field observations and pot experiments. Results showed that organic substitution suppressed N2O emissions by reducing soil mineral N content and stimulating the abundance of the nosZII gene. The trade-off effect of bio-organic substitution on N2O emissions may be due to the stimulated activity of the AOA-amoA gene, resulting in unfavorable conditions for N2O production and thus reduced N2O loss. We also linked the inhibitory effect of organic and bio-organic substitution on N2O emissions to the increased abundance of key species in bacterial co-occurrence networks represented by Patescibacteria as they were significantly and negatively correlated with N2O emissions. However, the mitigation effect of bio-organic substitution on N2O emissions was conteracted by an increase in Bacillus abundance due to the direct negative effect of Bacillus on the nosZII gene abundance. These findings suggest that conventional or bio-organic substitution is a promising strategy for alleviating the environmental costs of crop production.
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Affiliation(s)
- Zhaoqiang Han
- Key Laboratory of Green and Low-carbon Agriculture in Southeastern China, Ministry of Agriculture and Rural Affairs, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China; Jiangsu Key Laboratory of Low Carbon Agriculture and GHGs Mitigation, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing, 210095, China
| | - Yi Leng
- Key Laboratory of Green and Low-carbon Agriculture in Southeastern China, Ministry of Agriculture and Rural Affairs, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Zhirong Sun
- Key Laboratory of Green and Low-carbon Agriculture in Southeastern China, Ministry of Agriculture and Rural Affairs, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Zhutao Li
- Key Laboratory of Green and Low-carbon Agriculture in Southeastern China, Ministry of Agriculture and Rural Affairs, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Pinshang Xu
- Key Laboratory of Green and Low-carbon Agriculture in Southeastern China, Ministry of Agriculture and Rural Affairs, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Shuang Wu
- Key Laboratory of Green and Low-carbon Agriculture in Southeastern China, Ministry of Agriculture and Rural Affairs, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China; Jiangsu Key Laboratory of Low Carbon Agriculture and GHGs Mitigation, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing, 210095, China
| | - Shuwei Liu
- Key Laboratory of Green and Low-carbon Agriculture in Southeastern China, Ministry of Agriculture and Rural Affairs, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China; Jiangsu Key Laboratory of Low Carbon Agriculture and GHGs Mitigation, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing, 210095, China
| | - Shuqing Li
- Key Laboratory of Green and Low-carbon Agriculture in Southeastern China, Ministry of Agriculture and Rural Affairs, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China; Jiangsu Key Laboratory of Low Carbon Agriculture and GHGs Mitigation, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing, 210095, China
| | - Jinyang Wang
- Key Laboratory of Green and Low-carbon Agriculture in Southeastern China, Ministry of Agriculture and Rural Affairs, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China; Jiangsu Key Laboratory of Low Carbon Agriculture and GHGs Mitigation, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing, 210095, China.
| | - Jianwen Zou
- Key Laboratory of Green and Low-carbon Agriculture in Southeastern China, Ministry of Agriculture and Rural Affairs, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China; Jiangsu Key Laboratory of Low Carbon Agriculture and GHGs Mitigation, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing, 210095, China
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Hrovat K, Dutilh BE, Medema MH, Melkonian C. Taxonomic resolution of different 16S rRNA variable regions varies strongly across plant-associated bacteria. ISME COMMUNICATIONS 2024; 4:ycae034. [PMID: 38559569 PMCID: PMC10980831 DOI: 10.1093/ismeco/ycae034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 02/26/2024] [Accepted: 03/05/2024] [Indexed: 04/04/2024]
Abstract
Plant-microbiome research plays a pivotal role in understanding the relationships between plants and their associated microbial communities, with implications for agriculture and ecosystem dynamics. Metabarcoding analysis on variable regions of the 16S ribosomal RNA (rRNA) gene remains the dominant technology to study microbiome diversity in this field. However, the choice of the targeted variable region might affect the outcome of the microbiome studies. In our in silico analysis, we have evaluated whether the targeted variable region has an impact on taxonomic resolution in 16 plant-related microbial genera. Through a comparison of 16S rRNA gene variable regions with whole-genome data, our findings suggest that the V1-V3 region is generally a more suitable option than the widely used V3-V4 region for targeting microbiome analysis in plant-related genera. However, sole reliance on one region could introduce detection biases for specific genera. Thus, we are suggesting that while transitioning to full-length 16S rRNA gene and whole-genome sequencing for plant-microbiome analysis, the usage of genus-specific variable regions can achieve more precise taxonomic assignments. More broadly, our approach provides a blueprint to identify the most discriminating variable regions of the 16S rRNA gene for genera of interest.
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Affiliation(s)
- Katarina Hrovat
- Bioinformatics Group, Wageningen University and Research, 6708 PB Wageningen, The Netherlands
| | - Bas E Dutilh
- Theoretical Biology and Bioinformatics, Department of Biology, Faculty of Science, Utrecht University, 3584 CH Utrecht, The Netherlands
- Institute of Biodiversity, Faculty of Biological Sciences, Friedrich Schiller University Jena, 07743 Jena, Germany
- Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, 07745 Jena, Germany
| | - Marnix H Medema
- Bioinformatics Group, Wageningen University and Research, 6708 PB Wageningen, The Netherlands
| | - Chrats Melkonian
- Bioinformatics Group, Wageningen University and Research, 6708 PB Wageningen, The Netherlands
- Theoretical Biology and Bioinformatics, Department of Biology, Faculty of Science, Utrecht University, 3584 CH Utrecht, The Netherlands
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Sun X, Xie J, Zheng D, Xia R, Wang W, Xun W, Huang Q, Zhang R, Kovács ÁT, Xu Z, Shen Q. Metabolic interactions affect the biomass of synthetic bacterial biofilm communities. mSystems 2023; 8:e0104523. [PMID: 37971263 PMCID: PMC10734490 DOI: 10.1128/msystems.01045-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Accepted: 10/05/2023] [Indexed: 11/19/2023] Open
Abstract
IMPORTANCE Co-occurrence network analysis is an effective tool for predicting complex networks of microbial interactions in the natural environment. Using isolates from a rhizosphere, we constructed multi-species biofilm communities and investigated co-occurrence patterns between microbial species in genome-scale metabolic models and in vitro experiments. According to our results, metabolic exchanges and resource competition may partially explain the co-occurrence network analysis results found in synthetic bacterial biofilm communities.
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Affiliation(s)
- Xinli Sun
- Key lab of organic-based fertilizers of China and Jiangsu provincial key lab for solid organic waste utilization, Nanjing Agricultural University, Nanjing, Jiangsu, China
- Bacterial Interactions and Evolution Group, DTU Bioengineering, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Jiyu Xie
- Key lab of organic-based fertilizers of China and Jiangsu provincial key lab for solid organic waste utilization, Nanjing Agricultural University, Nanjing, Jiangsu, China
- Bacterial Interactions and Evolution Group, DTU Bioengineering, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Daoyue Zheng
- Key lab of organic-based fertilizers of China and Jiangsu provincial key lab for solid organic waste utilization, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Riyan Xia
- Key lab of organic-based fertilizers of China and Jiangsu provincial key lab for solid organic waste utilization, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Wei Wang
- Key lab of organic-based fertilizers of China and Jiangsu provincial key lab for solid organic waste utilization, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Weibing Xun
- Key lab of organic-based fertilizers of China and Jiangsu provincial key lab for solid organic waste utilization, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Qiwei Huang
- Key lab of organic-based fertilizers of China and Jiangsu provincial key lab for solid organic waste utilization, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Ruifu Zhang
- Key lab of organic-based fertilizers of China and Jiangsu provincial key lab for solid organic waste utilization, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Ákos T. Kovács
- Bacterial Interactions and Evolution Group, DTU Bioengineering, Technical University of Denmark, Kongens Lyngby, Denmark
- Institute of Biology Leiden, Leiden University, Leiden, the Netherlands
| | - Zhihui Xu
- Key lab of organic-based fertilizers of China and Jiangsu provincial key lab for solid organic waste utilization, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Qirong Shen
- Key lab of organic-based fertilizers of China and Jiangsu provincial key lab for solid organic waste utilization, Nanjing Agricultural University, Nanjing, Jiangsu, China
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Zhao W, Wen M, Zhao C, Zhang S, Dou R, Liang X, Zhang X, Liu Z, Jiang Z. Warm Temperature Increments Strengthen the Crosstalk between Roots and Soil in the Rhizosphere of Soybean Seedlings. PLANTS (BASEL, SWITZERLAND) 2023; 12:4135. [PMID: 38140462 PMCID: PMC10747358 DOI: 10.3390/plants12244135] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 11/18/2023] [Accepted: 12/08/2023] [Indexed: 12/24/2023]
Abstract
The plant rhizosphere underlies the crosstalk between plant and soil and has a crucial role in plant growth and development under various environments. We examined the effect of temperature rise on the rhizosphere environment of soybean roots to clarify the rhizosphere crosstalk between roots and soil in response to warm temperature rises in a global warming background. The in situ results of root enzyme activity revealed that soybean roots secrete β-glucosidase, and enzyme spectrum imaging demonstrated different enzymatic activities under different temperature environments. The soil enzyme kinetics results showed that soil enzymatic activity increased with increasing temperature, and soybean rhizosphere soil enzymatic activity was higher than that of non-rhizosphere soil. Rhizosphere soil and non-rhizosphere soil showed that the dominant bacterial phylum in soybean rhizosphere soil was Acidobacteria, and the dominant bacterial genus was JG30-KF-AS9. Compared with non-rhizosphere soil, rhizosphere soil was more nutrient-rich, and root secretions provided abundant carbon sources and other nutrients for soil microorganisms in the rhizosphere. Rhizosphere microorganisms affect plant growth by influencing the decomposition of soil organic carbon. The organic carbon content of rhizosphere soil was higher than that of non-rhizosphere soil under high temperatures.
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Affiliation(s)
- Wanying Zhao
- Key Laboratory of Soybean Biology in Chinese Ministry of Education, Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry, College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (W.Z.); (M.W.); (C.Z.); (S.Z.); (R.D.); (X.L.)
| | - Mingxing Wen
- Key Laboratory of Soybean Biology in Chinese Ministry of Education, Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry, College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (W.Z.); (M.W.); (C.Z.); (S.Z.); (R.D.); (X.L.)
| | - Caitong Zhao
- Key Laboratory of Soybean Biology in Chinese Ministry of Education, Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry, College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (W.Z.); (M.W.); (C.Z.); (S.Z.); (R.D.); (X.L.)
| | - Shurui Zhang
- Key Laboratory of Soybean Biology in Chinese Ministry of Education, Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry, College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (W.Z.); (M.W.); (C.Z.); (S.Z.); (R.D.); (X.L.)
| | - Runa Dou
- Key Laboratory of Soybean Biology in Chinese Ministry of Education, Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry, College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (W.Z.); (M.W.); (C.Z.); (S.Z.); (R.D.); (X.L.)
| | - Xuefeng Liang
- Key Laboratory of Soybean Biology in Chinese Ministry of Education, Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry, College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (W.Z.); (M.W.); (C.Z.); (S.Z.); (R.D.); (X.L.)
| | - Xianfeng Zhang
- The Training Center of the Undergraduate, Northeast Agricultural University, Harbin 150030, China;
| | - Zhihua Liu
- College of Resources and Environment, Northeast Agricultural University, Harbin 150030, China
| | - Zhenfeng Jiang
- Key Laboratory of Soybean Biology in Chinese Ministry of Education, Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry, College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (W.Z.); (M.W.); (C.Z.); (S.Z.); (R.D.); (X.L.)
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Liu Y, Li H, Li X, Zhang H, Zhu J, Peng Y, Sun G, Xu J. Effect of soil bioremediation on soil microbial community structure aimed at controlling tobacco bacterial wilt. Appl Microbiol Biotechnol 2023; 107:7543-7555. [PMID: 37755511 PMCID: PMC10656326 DOI: 10.1007/s00253-023-12753-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 07/21/2023] [Accepted: 08/24/2023] [Indexed: 09/28/2023]
Abstract
Rebuilding soil healthy microbiota is very important for preventing bacterial wilt. A 3-year-long field trial was conducted in China as follows: T1 (conventional fertilization), T2 (T1 + liming), T3 (T1 + bioorganic fertilizer), and T4 (T2 + bioorganic fertilizer). Fluorescence quantitative PCR and high-throughput sequencing were employed to study the dynamics of Ralstonia solanacearum population, microbial community, and network organizations between bacteria and quality-related variables. After 3 years of bioremediation, the control efficacy of tobacco bacterial wilt reached 61.30% and the occurrence delayed by approximately 40 days in T4, which had the highest tobacco yield and output value. The pathogen population of T4 remained below 106 copies/g soil during the entire growth period. Role-shifts prevailed among the network members. Microbes were unipathically associated with variables in T1 but multiplex in T4. In conclusion, soil bioremediation rebuilds a healthy soil microbiota and forms a more interactive and relevant micro-system, thus effectively controlling tobacco bacterial wilt. KEY POINTS: • This is the first time to effectively bio-control tobacco bacterial wilt in practical production in China, as well as to high-efficiently use the organic waste, thus promoting the organic cycling of the environment. • Soil bioremediation can effectively control soil-borne disease by rebuilding soil healthy microbiota and reducing abundance of pathogenic bacteria, thereby to prevent the soil borne disease occurrence. • After the soil remediated, microbes associated with soil and tobacco characteristics changed from unipathical to multiplex, and the keystone species play different roles compared with the original soil, thus signifying the complexity of multi-species interactions and achieving a closely relevant micro-system, which was ecologically meaningful to the environment.
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Affiliation(s)
- Yanxia Liu
- Guizhou Academy of Tobacco Science (Guizhou Provincial Academician Workstation of Microbiology and Health), Guiyang, 550000, China
| | - Han Li
- Guizhou Academy of Tobacco Science (Guizhou Provincial Academician Workstation of Microbiology and Health), Guiyang, 550000, China
| | - Xiang Li
- Guizhou Tobacco Corporation of CNTC, Guiyang, 550000, China.
| | - Heng Zhang
- Guizhou Academy of Tobacco Science (Guizhou Provincial Academician Workstation of Microbiology and Health), Guiyang, 550000, China.
| | - Jingwei Zhu
- Guizhou Academy of Tobacco Science (Guizhou Provincial Academician Workstation of Microbiology and Health), Guiyang, 550000, China
| | - Yu Peng
- Guizhou Tobacco Corporation of CNTC, Guiyang, 550000, China
| | - Guangjun Sun
- Guizhou Tobacco Corporation of CNTC, Guiyang, 550000, China
| | - Jian Xu
- Guizhou Tobacco Corporation of CNTC, Guiyang, 550000, China
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Ma CY, Zhang W, Luo DL, Jiang HJ, Wu XH, Sun K, Dai CC. Fungal endophyte promotes plant growth and disease resistance of Arachis hypogaea L. by reshaping the core root microbiome under monocropping conditions. Microbiol Res 2023; 277:127491. [PMID: 37769598 DOI: 10.1016/j.micres.2023.127491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 09/03/2023] [Accepted: 09/12/2023] [Indexed: 10/03/2023]
Abstract
Fungal endophytes play critical roles in helping plants adapt to adverse environmental conditions. The root endophyte Phomopsis liquidambaris can promote the growth and disease control of peanut plants grown under monocropping systems; however, how such beneficial traits are produced is largely unknown. Since the plant endophytic microbiome is directly linked to plant growth and health, and the composition of which has been found to be potentially influenced by microbial inoculants, this study aims to clarify the roles of root endophytic bacterial communities in P. liquidambaris-mediated plant fitness enhancement under monocropping conditions. Here, we found that P. liquidambaris inoculation induced significant changes in the root bacterial community: enriching some beneficial bacteria such as Bradyrhizobium sp. and Streptomyces sp. in the roots, and improving the core microbial-based interaction network. Next, we assembled and simplified a synthetic community (SynII) based on P. liquidambaris-derived key taxa, including Bacillus sp. HB1, Bacillus sp. HB9, Burkholderia sp. MB7, Pseudomonas sp. MB2, Streptomyces sp. MB6, and Bradyrhizobium sp. MB15. Furthermore, the application of the simplified synthetic community suppressed root rot caused by Fusarium oxysporum, promoted plant growth, and increased peanut yields under continuous monocropping conditions. The resistance of synII to F. oxysporum is related to the increased activity of defense enzymes. In addition, synII application significantly increased shoot and root biomass, and yield by 35.56%, 81.19%, and 34.31%, respectively. Collectively, our results suggest that the reshaping of root core microbiota plays an important role in the probiotic-mediated adaptability of plants under adverse environments.
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Affiliation(s)
- Chen-Yu Ma
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology and Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu, China
| | - Wei Zhang
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology and Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu, China
| | - De-Lin Luo
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology and Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu, China
| | - Hui-Jun Jiang
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology and Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu, China
| | - Xiao-Han Wu
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology and Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu, China
| | - Kai Sun
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology and Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu, China
| | - Chuan-Chao Dai
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology and Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu, China.
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Pino V, Fajardo M, McBratney A, Minasny B, Wilson N, Baldock C. Australian soil microbiome: A first sightseeing regional prediction driven by cycles of soil temperature and pedogenic variations. Mol Ecol 2023; 32:6243-6259. [PMID: 36862079 DOI: 10.1111/mec.16911] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Revised: 02/05/2023] [Accepted: 02/27/2023] [Indexed: 03/03/2023]
Abstract
Declines in soil multifunctionality (e.gsoil capacity to provide food and energy) are closely related to changes in the soil microbiome (e.g., diversity) Determining ecological drivers promoting such microbiome changes is critical knowledge for protecting soil functions. However, soil-microbe interactions are highly variable within environmental gradients and may not be consistent across studies. Here we propose that analysis of community dissimilarity (β-diversity) is a valuable tool for overviewing soil microbiome spatiotemporal changes. Indeed, β-diversity studies at larger scales (modelling and mapping) simplify complex multivariate interactions and refine our understanding of ecological drivers by also giving the possibility of expanding the environmental scenarios. This study represents the first spatial investigation of β-diversity in the soil microbiome of New South Wales (800,642 km2 ), Australia. We used metabarcoding soil data (16S rRNA and ITS genes) as exact sequence variants (ASVs) and UMAP (Uniform Manifold Approximation and Projection) as the distance metric. β-Diversity maps (1000-m resolution)-concordance correlations of 0.91-0.96 and 0.91-0.95 for bacteria and fungi, respectively-showed soil biome dissimilarities driven primarily by soil chemistry-pH and effective cation exchange capacity (ECEC)-and cycles of soil temperature-land surface temperature (LST-phase and LST-amplitude). Regionally, the spatial patterns of microbes parallel the distribution of soil classes (e.g., Vertosols) beyond spatial distances and rainfall, for example. Soil classes can be valuable discriminants for monitoring approaches, for example pedogenons and pedophenons. Ultimately, cultivated soils exhibited lower richness due to declines in rare microbes which might compromise soil functions over time.
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Affiliation(s)
- Vanessa Pino
- School of Life and Environmental Sciences & Sydney Institute of Agriculture, Faculty of Science, The University of Sydney, Sydney, New South Wales, Australia
| | - Mario Fajardo
- School of Life and Environmental Sciences & Sydney Institute of Agriculture, Faculty of Science, The University of Sydney, Sydney, New South Wales, Australia
| | - Alex McBratney
- School of Life and Environmental Sciences & Sydney Institute of Agriculture, Faculty of Science, The University of Sydney, Sydney, New South Wales, Australia
| | - Budiman Minasny
- School of Life and Environmental Sciences & Sydney Institute of Agriculture, Faculty of Science, The University of Sydney, Sydney, New South Wales, Australia
| | - Neil Wilson
- Metagenomic Laboratory, Metagen Pty, Ltd., Gatton, Queensland, Australia
| | - Chris Baldock
- Metagenomic Laboratory, Metagen Pty, Ltd., Gatton, Queensland, Australia
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Xu X, Nielsen LJD, Song L, Maróti G, Strube ML, Kovács ÁT. Enhanced specificity of Bacillus metataxonomics using a tuf-targeted amplicon sequencing approach. ISME COMMUNICATIONS 2023; 3:126. [PMID: 38012258 PMCID: PMC10682494 DOI: 10.1038/s43705-023-00330-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2023] [Revised: 11/01/2023] [Accepted: 11/08/2023] [Indexed: 11/29/2023]
Abstract
Bacillus species are ubiquitous in nature and have tremendous application potential in agriculture, medicine, and industry. However, the individual species of this genus vary widely in both ecological niches and functional phenotypes, which, hence, requires accurate classification of these bacteria when selecting them for specific purposes. Although analysis of the 16S rRNA gene has been widely used to disseminate the taxonomy of most bacterial species, this gene fails proper classification of Bacillus species. To circumvent this restriction, we designed novel primers and optimized them to allow exact species resolution of Bacillus species in both synthetic and natural communities using high-throughput amplicon sequencing. The primers designed for the tuf gene were not only specific for the Bacillus genus but also sufficiently discriminated species both in silico and in vitro in a mixture of 11 distinct Bacillus species. Investigating the primers using a natural soil sample, 13 dominant species were detected including Bacillus badius, Bacillus velezensis, and Bacillus mycoides as primary members, neither of which could be distinguished with 16S rRNA sequencing. In conclusion, a set of high-throughput primers were developed which allows unprecedented species-level identification of Bacillus species and aids the description of the ecological distribution of Bacilli in various natural environment.
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Affiliation(s)
- Xinming Xu
- Bacterial Interactions and Evolution Group, DTU Bioengineering, Technical University of Denmark, 2800, Lyngby, Denmark
- Institute of Biology Leiden, Leiden University, 2333 BE, Leiden, The Netherlands
| | - Lasse Johan Dyrbye Nielsen
- Bacterial Interactions and Evolution Group, DTU Bioengineering, Technical University of Denmark, 2800, Lyngby, Denmark
| | - Lijie Song
- Bacterial Interactions and Evolution Group, DTU Bioengineering, Technical University of Denmark, 2800, Lyngby, Denmark
- BGI-Tianjin, BGI-Shenzhen, 300308, Tianjin, China
| | - Gergely Maróti
- Institute of Plant Biology, Biological Research Center, ELKH, 6726, Szeged, Hungary
| | - Mikael Lenz Strube
- Bacterial Ecophysiology and Biotechnology Group, DTU Bioengineering, Technical University of Denmark, 2800, Lyngby, Denmark
| | - Ákos T Kovács
- Bacterial Interactions and Evolution Group, DTU Bioengineering, Technical University of Denmark, 2800, Lyngby, Denmark.
- Institute of Biology Leiden, Leiden University, 2333 BE, Leiden, The Netherlands.
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Guo Y, Zhang D, Qi W. Bacterial diversity of herbal rhizospheric soils in Ordos desert steppes under different degradation gradients. PeerJ 2023; 11:e16289. [PMID: 37927778 PMCID: PMC10625353 DOI: 10.7717/peerj.16289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 09/22/2023] [Indexed: 11/07/2023] Open
Abstract
Objectives This study explored the effects of different degradation gradients on bacterial diversity in the rhizospheric soils of herb plants. Methods The alpha diversity, species composition and correlations of bacterial communities in the rhizospheric soils of herb plants were studied using metagenomics 16SrDNA gene high-throughput sequencing. Results The diversity of bacterial communities in the rhizospheric soils of herb plants differed during the degradation of desert steppes. An analysis of bacterial community alpha diversity indices showed the bacterial diversity and species evenness of rhizospheric soils were best in moderately degraded desert steppes. Among all samples, a total of 43 phyla, 133 classes, 261 orders, 421 families, 802 genera and 1,129 species were detected. At the phylum level, the predominant bacterial phyla were: Actinobacteria, Proteobacteria, Acidobacteria, Gemmatimonadetes, Chloroflexi, Planctomycetes and Bacteroidetes. At the genus level, the predominant bacterial genera were: RB41, Sphingomonas, WD2101_soil_group_unclassified, Pseudomonas and Actinomyces. The relative abundance of unknown genera was very large, which deserves further research. At the phylum and genus levels, the species abundance levels under slight and moderate degradation were significantly higher than those under extreme degradation. Correlation network diagrams showed there were many nodes in both slightly deteriorated and moderately deteriorated soils, and the node proportions were large and mostly positively correlated. These results indicate the bacterial communities in rhizospheric soils under slight or moderate deterioration are relatively stable. The rhizospheric soil microbes of desert steppes can form a stable network structure, allowing them to adequately respond to environmental conditions. Conclusions The bacterial communities in the rhizospheric soils of herb plants differ between different degradation gradients. The species number, abundance and diversity of bacterial communities in rhizospheric soils are not directly correlated with degree of degradation. The abundance, species diversity and species abundance of bacterial communities in the rhizospheric soils of moderately degraded desert steppes are the highest and most stable. The soil bacterial diversity is lowest in severely degraded desert steppes.
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Affiliation(s)
- Yuefeng Guo
- College of Desert Control Science and Engineering, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, Asia, China
| | - Dan Zhang
- College of Desert Control Science and Engineering, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, Asia, China
| | - Wei Qi
- Inner Mongolia Autonomous Region Water Conservancy Development Center, Hohot, Inner Mongolia, Asia, China
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41
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Fazal A, Wen Z, Yang M, Wang C, Hao C, Lai X, Jie W, Yang L, He Z, Yang H, Cai J, Qi J, Lu G, Niu K, Sun S, Yang Y. Triple-transgenic soybean in conjunction with glyphosate drive patterns in the rhizosphere microbial community assembly. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 335:122337. [PMID: 37562532 DOI: 10.1016/j.envpol.2023.122337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 07/23/2023] [Accepted: 08/06/2023] [Indexed: 08/12/2023]
Abstract
Plant roots continuously influence the rhizosphere, which also serves as a recruitment site for microorganisms with desirable functions. The development of genetically engineered (GE) crop varieties has offered unparalleled yield advantages. However, in-depth research on the effects of GE crops on the rhizosphere microbiome is currently insufficient. We used a triple-transgenic soybean cultivar (JD606) that is resistant to insects, glyphosate, and drought, along with its control, ZP661, and JD606 treated with glyphosate (JD606G). Using 16S and ITS rDNA sequencing, their effects on the taxonomy and function of the bacterial and fungal communities in the rhizosphere, surrounding, and bulk soil compartment niches were determined. Alpha diversity demonstrated a strong influence of JD606 and JD606G on bacterial Shannon diversity. Both treatments significantly altered the soil's pH and nitrogen content. Beta diversity identified the soil compartment niche as a key factor with a significant probability of influencing the bacterial and fungal communities associated with soybeans. Further analysis showed that the rhizosphere effect had a considerable impact on bacterial communities in JD606 and JD606G soils but not on fungal communities. Microbacterium, Bradyrhizobium, and Chryseobacterium were found as key rhizobacterial nodes. In addition, the LEfSe analysis identified biomarker taxa with plant-beneficial attributes, demonstrating rhizosphere-driven microbial recruitment. FUNGuild, Bugbase, and FAPROTAX functional predictions showed that ZP661 soils had more plant pathogen-associated microbes, while JD606 and JD606G soils had more stress-tolerance, nitrogen, and carbon cycle-related microbes. Bacterial rhizosphere networks had more intricate topologies than fungal networks. Furthermore, correlation analysis revealed that the bacteria and fungi with higher abundances exhibited varying degrees of positive and negative correlations. Our findings shed new light on the niche partitioning of bacterial and fungal communities in soil. It also indicates that following triple-transgenic soybean cultivation and glyphosate application, plant roots recruit microbes with beneficial taxonomic and functional traits in the rhizosphere.
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Affiliation(s)
- Aliya Fazal
- Institute for Plant Molecular Biology, State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China; Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
| | - Zhongling Wen
- Institute for Plant Molecular Biology, State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China; Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
| | - Minkai Yang
- Institute for Plant Molecular Biology, State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China; Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
| | - Changyi Wang
- Institute for Plant Molecular Biology, State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China; Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
| | - Chenyu Hao
- Institute for Plant Molecular Biology, State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Xiaohui Lai
- Institute for Plant Molecular Biology, State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Wencai Jie
- Institute for Plant Molecular Biology, State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Liu Yang
- Institute for Plant Molecular Biology, State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Zhuoyu He
- Institute for Plant Molecular Biology, State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Huan Yang
- Institute for Plant Molecular Biology, State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Jinfeng Cai
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
| | - Jinliang Qi
- Institute for Plant Molecular Biology, State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Guihua Lu
- Institute for Plant Molecular Biology, State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China; Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China; School of Life Sciences, Huaiyin Normal University, Huaian, 223300, China
| | - Kechang Niu
- Institute for Plant Molecular Biology, State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Shucun Sun
- Institute for Plant Molecular Biology, State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Yonghua Yang
- Institute for Plant Molecular Biology, State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China; Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China.
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Qin Z, Zhao Z, Xia L, Yu G, Miao A, Yang Z. Vertical and seasonal dynamics of bacterial pathogenic communities at an aged organic contaminated site: Insights into microbial diversity, composition, interactions, and assembly processes. JOURNAL OF HAZARDOUS MATERIALS 2023; 460:132255. [PMID: 37703736 DOI: 10.1016/j.jhazmat.2023.132255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2023] [Revised: 07/26/2023] [Accepted: 08/07/2023] [Indexed: 09/15/2023]
Abstract
Under the background of the Coronavirus Disease 2019 (COVID-19) pandemic, research on pathogens deserves greater attention in the natural environment, especially in the widely distributed contaminated sites with complicated and severe organic pollution. In this study, the community composition and assembly of soil pathogens identified by the newly-developed 16S-based pipeline of multiple bacterial pathogen detection (MBPD) have been investigated on spatiotemporal scales in the selected organic polluted site. We demonstrated that the richness and diversity of the pathogenic communities were primarily controlled by soil depth, while the structure and composition of pathogenic communities varied pronouncedly with seasonal changes, which were driven by the alterations in both physiochemical parameters and organic contaminants over time. Network analysis revealed that the overwhelmingly positive interactions, identified multiple keystone species, and a well-organized modular structure maintained the stability and functionality of the pathogenic communities under environmental pressures. Additionally, the null-model analysis showed that deterministic processes dominated the pathogenic community assembly across soil profiles. In three seasons, stochasticity-dominated processes in spring and summer changed into determinism-dominated processes in winter. These findings extend our knowledge of the response of the bacterial pathogenic community to environmental disruptions brought on by organic contaminated sites.
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Affiliation(s)
- Zhirui Qin
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lake of Ministry of Education, College of Environment, Hohai University, Nanjing 210098, China
| | - Zhenhua Zhao
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lake of Ministry of Education, College of Environment, Hohai University, Nanjing 210098, China.
| | - Liling Xia
- Nanjing Vocational University of Industry Technology, Nanjing 210016, China
| | - Guangwen Yu
- China National Chemical Civil Engineering Co., Ltd, Nanjing 210031, China
| | - Aihua Miao
- China National Chemical Civil Engineering Co., Ltd, Nanjing 210031, China
| | - Zijun Yang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lake of Ministry of Education, College of Environment, Hohai University, Nanjing 210098, China
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Świątczak J, Kalwasińska A, Szabó A, Brzezinska MS. The effect of seed bacterization with Bacillus paralicheniformis 2R5 on bacterial and fungal communities in the canola rhizosphere. Microbiol Res 2023; 275:127448. [PMID: 37453237 DOI: 10.1016/j.micres.2023.127448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 05/29/2023] [Accepted: 07/03/2023] [Indexed: 07/18/2023]
Abstract
Bacillus sp. is one of the best-studied plant growth-promoting rhizobacteria (PGPR). However, more detailed studies targeting its effect on the rhizosphere microbial community are required for improving management practices regarding its commercial application in the field. Our earlier study showed that PGPR Bacillus paralicheniformis 2R5 stimulated canola growth. Hence, this study aimed to assess the time-course impact of B. paralicheniformis 2R5 on bacterial and fungal community structure and diversity. The results showed that inoculation with B. paralicheniformis 2R5 initially significantly decreased the observed bacterial richness compared to the control, while after 44 days of treatment this alpha diversity metrics increased. A linear discriminant analysis effect size showed that B. paralicheniformis 2R5 altered the soil bacterial and fungal community structure by increasing the abundance of plants' beneficial microorganisms such as Nitrospira, Ramlibacter, Sphingomonas, Massilia, Terrimonas as well as Solicoccozyma, Schizothecium, Cyphellophora, Fusicolla, Humicola. B. paralicheniformis 2R5 seems to be a promising alternative to chemical pesticides and can be considered for practical application in the field. Its ability to alter the rhizosphere microbiome by increasing the diversity and composition of bacterial communities and increasing plants' beneficial groups of fungi, appears to be important in terms of improving canola development. However, further studies on these increased microbial taxa are necessary to confirm their function in promoting canola growth.
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Affiliation(s)
- Joanna Świątczak
- Department of Environmental Microbiology and Biotechnology, Nicolaus Copernicus University in Toruń, Lwowska 1, 87-100 Toruń, Poland.
| | - Agnieszka Kalwasińska
- Department of Environmental Microbiology and Biotechnology, Nicolaus Copernicus University in Toruń, Lwowska 1, 87-100 Toruń, Poland
| | - Attila Szabó
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, Lennart Hjelms väg 9, SE-75007 Uppsala, Sweden
| | - Maria Swiontek Brzezinska
- Department of Environmental Microbiology and Biotechnology, Nicolaus Copernicus University in Toruń, Lwowska 1, 87-100 Toruń, Poland
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44
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Gu Y, Li Z, Lei P, Wang R, Xu H, Friman VP. Phylogenetic distance-decay patterns are not explained by local community assembly processes in freshwater lake microbial communities. Environ Microbiol 2023; 25:1940-1954. [PMID: 37254577 DOI: 10.1111/1462-2920.16437] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 05/23/2023] [Indexed: 06/01/2023]
Abstract
While water and sediment microbial communities exhibit pronounced spatio-temporal patterns in freshwater lakes, the underlying drivers are yet poorly understood. Here, we evaluated the importance of spatial and temporal variation in abiotic environmental factors for bacterial and microeukaryotic community assembly and distance-decay relationships in water and sediment niches in Hongze Lake. By sampling across the whole lake during both Autumn and Spring sampling time points, we show that only bacterial sediment communities were governed by deterministic community assembly processes due to abiotic environmental drivers. Nevertheless, consistent distance-decay relationships were found with both bacterial and microeukaryotic communities, which were relatively stable with both sampling time points. Our results suggest that spatio-temporal variation in environmental factors was important in explaining mainly bacterial community assembly in the sediment, possibly due lesser disturbance. However, clear distance-decay patterns emerged also when the community assembly was stochastic. Together, these results suggest that abiotic environmental factors do not clearly drive the spatial structuring of lake microbial communities, highlighting the need to understand the role of other potential drivers, such as spatial heterogeneity and biotic species interactions.
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Affiliation(s)
- Yian Gu
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing, China
- Jiangsu Key Laboratory for Eco-Agricultural Biotechnology around Hongze Lake, Huaiyin Normal University, China
| | - Zhidan Li
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China
| | - Peng Lei
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing, China
| | - Rui Wang
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing, China
| | - Hong Xu
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing, China
| | - Ville-Petri Friman
- Department of Microbiology, University of Helsinki, Helsinki, Finland
- Department of Biology, University of York, York, UK
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45
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Li Z, Sun L, Liu S, Lei P, Wang R, Li S, Gu Y. Interkingdom network analyses reveal microalgae and protostomes as keystone taxa involved in nutrient cycling in large freshwater lake sediment. FEMS Microbiol Ecol 2023; 99:fiad111. [PMID: 37715306 DOI: 10.1093/femsec/fiad111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 07/26/2023] [Accepted: 09/14/2023] [Indexed: 09/17/2023] Open
Abstract
Few studies have explored the role of interkingdom interactions between bacteria and microeukaryotes in nutrient cycling in lake ecosystems. We conducted sediment sampling from 40 locations covering Hongze Lake and analyzed their chemical properties. Intra- and interkingdom networks were constructed using 16S and 18S rRNA gene amplicon sequencing. Microeukaryotic intranetworks were more complex in spring than in autumn, while no clear variation in the complexity of bacterial intranetworks was found between autumn and spring. Larger and more complex bacterial-microeukaryotic bipartite networks emerged in spring than in autumn, correlated with lower carbon, nitrogen, and phosphorus levels in spring, likely resulting in intense microbial competition. Bacteria and microeukaryotes played different topological roles in interkingdom networks, with microeukaryotes contributing to the networks' greater complexity. Seven keystone modules were identified in spring and autumn nutrient cycling. Importantly, keystone taxa in these modules belonged to photoautotrophic microalgae or predatory protostomes, indicating that these organisms are key drivers in lake sediment nutrient cycling. Our results suggested that nutrient content variation in autumn and spring changes interkingdom networks' topological structure between bacteria and microeukaryotes. Microalgae and protostomes are essential in freshwater lake nutrient cycling and may be targeted to modulate nutrient cycling in large freshwater ecosystems.
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Affiliation(s)
- Zhidan Li
- College of Biological and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, P.R. China
| | - Liang Sun
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211816, P.R. China
| | - Sijie Liu
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211816, P.R. China
| | - Peng Lei
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211816, P.R. China
| | - Rui Wang
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211816, P.R. China
| | - Sha Li
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211816, P.R. China
| | - Yian Gu
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211816, P.R. China
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46
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Li X, Chou MY, Bonito GM, Last RL. Anti-fungal bioactive terpenoids in the bioenergy crop switchgrass (Panicum virgatum) may contribute to ecotype-specific microbiome composition. Commun Biol 2023; 6:917. [PMID: 37679469 PMCID: PMC10485007 DOI: 10.1038/s42003-023-05290-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 08/25/2023] [Indexed: 09/09/2023] Open
Abstract
Plant derived bioactive small molecules have attracted attention of scientists across fundamental and applied scientific disciplines. We seek to understand the influence of these phytochemicals on rhizosphere and root-associated fungi. We hypothesize that - consistent with accumulating evidence that switchgrass genotype impacts microbiome assembly - differential terpenoid accumulation contributes to switchgrass ecotype-specific microbiome composition. An initial in vitro Petri plate-based disc diffusion screen of 18 switchgrass root derived fungal isolates revealed differential responses to upland- and lowland-isolated metabolites. To identify specific fungal growth-modulating metabolites, we tested fractions from root extracts on three ecologically important fungal isolates - Linnemania elongata, Trichoderma sp. and Fusarium sp. Saponins and diterpenoids were identified as the most prominent antifungal metabolites. Finally, analysis of liquid chromatography-purified terpenoids revealed fungal inhibition structure - activity relationships (SAR). Saponin antifungal activity was primarily determined by the number of sugar moieties - saponins glycosylated at a single core position were inhibitory whereas saponins glycosylated at two core positions were inactive. Saponin core hydroxylation and acetylation were also associated with reduced activity. Diterpenoid activity required the presence of an intact furan ring for strong fungal growth inhibition. These results inform future breeding and biotechnology strategies for crop protection with reduced pesticide application.
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Affiliation(s)
- Xingxing Li
- DOE Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI, 48824, USA
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, 48824, USA
| | - Ming-Yi Chou
- DOE Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI, 48824, USA
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, 48824, USA
- Department of Plant Biology, Rutgers University, New Brunswick, NJ, 08901, USA
| | - Gregory M Bonito
- DOE Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI, 48824, USA
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, 48824, USA
| | - Robert L Last
- DOE Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI, 48824, USA.
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, 48824, USA.
- Department Plant Biology, Michigan State University, East Lansing, MI, 48824, USA.
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47
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Dundore-Arias JP, Michalska-Smith M, Millican M, Kinkel LL. More Than the Sum of Its Parts: Unlocking the Power of Network Structure for Understanding Organization and Function in Microbiomes. ANNUAL REVIEW OF PHYTOPATHOLOGY 2023; 61:403-423. [PMID: 37217203 DOI: 10.1146/annurev-phyto-021021-041457] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Plant and soil microbiomes are integral to the health and productivity of plants and ecosystems, yet researchers struggle to identify microbiome characteristics important for providing beneficial outcomes. Network analysis offers a shift in analytical framework beyond "who is present" to the organization or patterns of coexistence between microbes within the microbiome. Because microbial phenotypes are often significantly impacted by coexisting populations, patterns of coexistence within microbiomes are likely to be especially important in predicting functional outcomes. Here, we provide an overview of the how and why of network analysis in microbiome research, highlighting the ways in which network analyses have provided novel insights into microbiome organization and functional capacities, the diverse network roles of different microbial populations, and the eco-evolutionary dynamics of plant and soil microbiomes.
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Affiliation(s)
- J P Dundore-Arias
- Department of Biology and Chemistry, California State University, Monterey Bay, Seaside, California, USA
| | - M Michalska-Smith
- Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota, USA;
- Department of Ecology, Evolution, and Behavior, University of Minnesota, St. Paul, Minnesota, USA
| | | | - L L Kinkel
- Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota, USA;
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Hou M, Zhao X, Wang Y, Lv X, Chen Y, Jiao X, Sui Y. Pedogenesis of typical zonal soil drives belowground bacterial communities of arable land in the Northeast China Plain. Sci Rep 2023; 13:14555. [PMID: 37666914 PMCID: PMC10477331 DOI: 10.1038/s41598-023-41401-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 08/25/2023] [Indexed: 09/06/2023] Open
Abstract
Belowground bacterial communities play essential roles in maintaining ecosystem multifunction, while our understanding of how and why their distribution patterns and community compositions may change with the distinct pedogenetic conditions of different soil types is still limited. Here, we evaluated the roles of soil physiochemical properties and biotic interactions in driving belowground bacterial community composition across three typical zonal soil types, including black calcium soil (QS), typical black soil (HL) and dark brown soil (BQL), with distinct pedogenesis on the Northeast China Plain. Changes in soil bacterial diversity and community composition in these three zonal soil types were strongly correlated with soil pedogenetic features. SOC concentrations in HL were higher than in QS and BQL, but bacterial diversity was low, and the network structure revealed greater stability and connectivity. The composition of the bacterial community correlated significantly with soil pH in QS but with soil texture in BQL. The bacterial co-occurrence network of HL had higher density and clustering coefficients but lower edges, and different keystone species of networks were also detected. This work provides a basic understanding of the driving mechanisms responsible for belowground bacterial biodiversity and distribution patterns over different pedogenetic conditions in agroecosystems.
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Affiliation(s)
- Meng Hou
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, 150081, Harbin, People's Republic of China
- University of Chinese Academy of Sciences, 100049, Beijing, People's Republic of China
| | - Xiaorui Zhao
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, 150081, Harbin, People's Republic of China
| | - Yao Wang
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, 150081, Harbin, People's Republic of China
- University of Chinese Academy of Sciences, 100049, Beijing, People's Republic of China
| | - Xuemei Lv
- College of Modern Agriculture and Eco-Environment, Heilongjiang University, 150080, Harbin, People's Republic of China
| | - Yimin Chen
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, 150081, Harbin, People's Republic of China
| | - Xiaoguang Jiao
- College of Modern Agriculture and Eco-Environment, Heilongjiang University, 150080, Harbin, People's Republic of China.
| | - Yueyu Sui
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, 150081, Harbin, People's Republic of China.
- University of Chinese Academy of Sciences, 100049, Beijing, People's Republic of China.
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49
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Yang K, Fu R, Feng H, Jiang G, Finkel O, Sun T, Liu M, Huang B, Li S, Wang X, Yang T, Wang Y, Wang S, Xu Y, Shen Q, Friman VP, Jousset A, Wei Z. RIN enhances plant disease resistance via root exudate-mediated assembly of disease-suppressive rhizosphere microbiota. MOLECULAR PLANT 2023; 16:1379-1395. [PMID: 37563832 DOI: 10.1016/j.molp.2023.08.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Revised: 05/06/2023] [Accepted: 08/07/2023] [Indexed: 08/12/2023]
Abstract
The RIPENING-INHIBITOR (RIN) transcriptional factor is a key regulator governing fruit ripening. While RIN also affects other physiological processes, its potential roles in triggering interactions with the rhizosphere microbiome and plant health are unknown. Here we show that RIN affects microbiome-mediated disease resistance via root exudation, leading to recruitment of microbiota that suppress the soil-borne, phytopathogenic Ralstonia solanacearum bacterium. Compared with the wild-type (WT) plant, RIN mutants had different root exudate profiles, which were associated with distinct changes in microbiome composition and diversity. Specifically, the relative abundances of antibiosis-associated genes and pathogen-suppressing Actinobacteria (Streptomyces) were clearly lower in the rhizosphere of rin mutants. The composition, diversity, and suppressiveness of rin plant microbiomes could be restored by the application of 3-hydroxyflavone and riboflavin, which were exuded in much lower concentrations by the rin mutant. Interestingly, RIN-mediated effects on root exudates, Actinobacteria, and disease suppression were evident from the seedling stage, indicating that RIN plays a dual role in the early assembly of disease-suppressive microbiota and late fruit development. Collectively, our work suggests that, while plant disease resistance is a complex trait driven by interactions between the plant, rhizosphere microbiome, and the pathogen, it can be indirectly manipulated using "prebiotic" compounds that promote the recruitment of disease-suppressive microbiota.
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Affiliation(s)
- Keming Yang
- Key Lab of Organic-based Fertilizers of China, Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China; College of Agro-grassland Science, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Ruixin Fu
- Key Lab of Organic-based Fertilizers of China, Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China; School of Biology and Food, Shangqiu Normal University, Shangqiu 476000, China
| | - Haichao Feng
- College of Agriculture, Henan University, Zhengzhou 450046, China
| | - Gaofei Jiang
- Key Lab of Organic-based Fertilizers of China, Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Omri Finkel
- Department of Plant and Environmental Sciences, Institute of Life Science, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Tianyu Sun
- Key Lab of Organic-based Fertilizers of China, Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Mingchun Liu
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu 610064, China
| | - Baowen Huang
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, Chongqing, China
| | - Shan Li
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
| | - Xiaofang Wang
- Key Lab of Organic-based Fertilizers of China, Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Tianjie Yang
- Key Lab of Organic-based Fertilizers of China, Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China.
| | - Yikui Wang
- Institute of Vegetable Research, Guangxi Academy of Agricultural Sciences, Nanning, China.
| | - Shimei Wang
- Key Lab of Organic-based Fertilizers of China, Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Yangchun Xu
- Key Lab of Organic-based Fertilizers of China, Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Qirong Shen
- Key Lab of Organic-based Fertilizers of China, Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Ville-Petri Friman
- Key Lab of Organic-based Fertilizers of China, Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China; Department of Biology, University of York, York YO10 5DD, UK; Department of Microbiology, University of Helsinki, 00014 Helsinki, Finland
| | - Alexandre Jousset
- Key Lab of Organic-based Fertilizers of China, Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Zhong Wei
- Key Lab of Organic-based Fertilizers of China, Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China.
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Feng H, Fu R, Luo J, Hou X, Gao K, Su L, Xu Y, Miao Y, Liu Y, Xu Z, Zhang N, Shen Q, Xun W, Zhang R. Listening to plant's Esperanto via root exudates: reprogramming the functional expression of plant growth-promoting rhizobacteria. THE NEW PHYTOLOGIST 2023; 239:2307-2319. [PMID: 37357338 DOI: 10.1111/nph.19086] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2023] [Accepted: 05/31/2023] [Indexed: 06/27/2023]
Abstract
Rhizomicrobiome plays important roles in plant growth and health, contributing to the sustainable development of agriculture. Plants recruit and assemble the rhizomicrobiome to satisfy their functional requirements, which is widely recognized as the 'cry for help' theory, but the intrinsic mechanisms are still limited. In this study, we revealed a novel mechanism by which plants reprogram the functional expression of inhabited rhizobacteria, in addition to the de novo recruitment of soil microbes, to satisfy different functional requirements as plants grow. This might be an efficient and low-cost strategy and a substantial extension to the rhizomicrobiome recruitment theory. We found that the plant regulated the sequential expression of genes related to biocontrol and plant growth promotion in two well-studied rhizobacteria Bacillus velezensis SQR9 and Pseudomonas protegens CHA0 through root exudate succession across the plant developmental stages. Sixteen key chemicals in root exudates were identified to significantly regulate the rhizobacterial functional gene expression by high-throughput qPCR. This study not only deepens our understanding of the interaction between the plant-rhizosphere microbiome, but also provides a novel strategy to regulate and balance the different functional expression of the rhizomicrobiome to improve plant health and growth.
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Affiliation(s)
- Haichao Feng
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Nanjing Agricultural University, Nanjing, 210095, China
- College of Agriculture, Henan University, Zhengzhou, 450046, China
| | - Ruixin Fu
- School of Biology and Food, Shangqiu Normal University, Shangqiu, 476000, China
| | - Jiayu Luo
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xueqin Hou
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Nanjing Agricultural University, Nanjing, 210095, China
| | - Kun Gao
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Nanjing Agricultural University, Nanjing, 210095, China
| | - Lv Su
- State Key Laboratory of Efficient Utilization of Arid and Semi-arid Arable Land in Northern China, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yu Xu
- Hebei Key Laboratory of Soil Ecology, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 286 Huaizhong Road, Yuhua District, Shijiazhuang, 050021, China
| | - Youzhi Miao
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yunpeng Liu
- State Key Laboratory of Efficient Utilization of Arid and Semi-arid Arable Land in Northern China, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Zhihui Xu
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Nanjing Agricultural University, Nanjing, 210095, China
| | - Nan Zhang
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Nanjing Agricultural University, Nanjing, 210095, China
| | - Qirong Shen
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Nanjing Agricultural University, Nanjing, 210095, China
| | - Weibing Xun
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Nanjing Agricultural University, Nanjing, 210095, China
| | - Ruifu Zhang
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Nanjing Agricultural University, Nanjing, 210095, China
- State Key Laboratory of Efficient Utilization of Arid and Semi-arid Arable Land in Northern China, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
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