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Liu W, Zhang Z, Zhang B, Zhu Y, Zhu C, Chen C, Zhang F, Liu F, Ai J, Wang W, Kong W, Xiang H, Wang W, Gong D, Meng D, Zhu L. Role of bacterial pathogens in microbial ecological networks in hydroponic plants. FRONTIERS IN PLANT SCIENCE 2024; 15:1403226. [PMID: 39290732 PMCID: PMC11405252 DOI: 10.3389/fpls.2024.1403226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Accepted: 07/15/2024] [Indexed: 09/19/2024]
Abstract
Plant-associated microbial communities are crucial for plant growth and health. However, assembly mechanisms of microbial communities and microbial interaction patterns remain elusive across vary degrees of pathogen-induced diseases. By using 16S rRNA high-throughput sequencing technology, we investigated the impact of wildfire disease on the microbial composition and interaction network in plant three different compartments. The results showed that pathogen infection significantly affect the phyllosphere and rhizosphere microbial community. We found that the primary sources of microbial communities in healthy and mildly infected plants were from the phyllosphere and hydroponic solution community. Mutual exchanges between phyllosphere and rhizosphere communities were observed, but microbial species migration from the leaf to the root was rarely observed in severely infected plants. Moreover, wildfire disease reduced the diversity and network complexity of plant microbial communities. Interactions among pathogenic bacterial members suggested that Caulobacter and Bosea might be crucial "pathogen antagonists" inhibiting the spread of wildfire disease. Our study provides deep insights into plant pathoecology, which is helpful for the development of novel strategies for phyllosphere disease prediction or prevention.
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Affiliation(s)
- Wenyi Liu
- College of Environment and Ecology, Hunan Agricultural University, Changsha, China
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
| | - Zhihua Zhang
- Changde Tobacco Company of Hunan Province, Changde, China
| | - Bin Zhang
- College of Chemistry and Bioengineering, Hunan University of Science and Engineering, Yongzhou, China
| | - Yi Zhu
- Changde Tobacco Company of Hunan Province, Changde, China
| | - Chongwen Zhu
- Changde Tobacco Company of Hunan Province, Changde, China
| | - Chaoyong Chen
- Changde Tobacco Company of Hunan Province, Changde, China
| | - Fangxu Zhang
- Changde Tobacco Company of Hunan Province, Changde, China
| | - Feng Liu
- Changde Tobacco Company of Hunan Province, Changde, China
| | - Jixiang Ai
- Changde Tobacco Company of Hunan Province, Changde, China
| | - Wei Wang
- Changde Tobacco Company of Hunan Province, Changde, China
| | - Wuyuan Kong
- Changde Tobacco Company of Hunan Province, Changde, China
| | - Haoming Xiang
- Changde Tobacco Company of Hunan Province, Changde, China
| | - Weifeng Wang
- Changde Tobacco Company of Hunan Province, Changde, China
| | - Daoxin Gong
- College of Environment and Ecology, Hunan Agricultural University, Changsha, China
| | - Delong Meng
- College of Chemistry and Bioengineering, Hunan University of Science and Engineering, Yongzhou, China
| | - Li Zhu
- Changde Tobacco Company of Hunan Province, Changde, China
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Harmsen N, Vesga P, Glauser G, Klötzli F, Heiman CM, Altenried A, Vacheron J, Muller D, Moënne-Loccoz Y, Steinger T, Keel C, Garrido-Sanz D. Natural plant disease suppressiveness in soils extends to insect pest control. MICROBIOME 2024; 12:127. [PMID: 39014485 PMCID: PMC11251354 DOI: 10.1186/s40168-024-01841-w] [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: 03/20/2024] [Accepted: 05/19/2024] [Indexed: 07/18/2024]
Abstract
BACKGROUND Since the 1980s, soils in a 22-km2 area near Lake Neuchâtel in Switzerland have been recognized for their innate ability to suppress the black root rot plant disease caused by the fungal pathogen Thielaviopsis basicola. However, the efficacy of natural disease suppressive soils against insect pests has not been studied. RESULTS We demonstrate that natural soil suppressiveness also protects plants from the leaf-feeding pest insect Oulema melanopus. Plants grown in the most suppressive soil have a reduced stress response to Oulema feeding, reflected by dampened levels of herbivore defense-related phytohormones and benzoxazinoids. Enhanced salicylate levels in insect-free plants indicate defense-priming operating in this soil. The rhizosphere microbiome of suppressive soils contained a higher proportion of plant-beneficial bacteria, coinciding with their microbiome networks being highly tolerant to the destabilizing impact of insect exposure observed in the rhizosphere of plants grown in the conducive soils. We suggest that presence of plant-beneficial bacteria in the suppressive soils along with priming, conferred plant resistance to the insect pest, manifesting also in the onset of insect microbiome dysbiosis by the displacement of the insect endosymbionts. CONCLUSIONS Our results show that an intricate soil-plant-insect feedback, relying on a stress tolerant microbiome network with the presence of plant-beneficial bacteria and plant priming, extends natural soil suppressiveness from soilborne diseases to insect pests. Video Abstract.
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Affiliation(s)
- Nadine Harmsen
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
- Institute of Earth Sciences, University of Lausanne, Lausanne, Switzerland
| | - Pilar Vesga
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Madrid, Spain
| | - Gaétan Glauser
- Neuchâtel Platform of Analytical Chemistry, University of Neuchâtel, Neuchâtel, Switzerland
| | | | - Clara M Heiman
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Aline Altenried
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Jordan Vacheron
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Daniel Muller
- Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR5557 Ecologie Microbienne, Villeurbanne, France
| | - Yvan Moënne-Loccoz
- Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR5557 Ecologie Microbienne, Villeurbanne, France
| | | | - Christoph Keel
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland.
| | - Daniel Garrido-Sanz
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland.
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Wang HL, Chen ZZ, Koski TM, Zhang B, Wang XF, Zhang RB, Li RQ, Wang SX, Zeng JY, Li HP. Emerald Ash Borer Infestation-Induced Elevated Negative Correlations and Core Genera Shift in the Endophyte Community of Fraxinus bungeana. INSECTS 2024; 15:534. [PMID: 39057267 PMCID: PMC11277034 DOI: 10.3390/insects15070534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2024] [Revised: 07/10/2024] [Accepted: 07/10/2024] [Indexed: 07/28/2024]
Abstract
Endophytes, prevalent in plants, mediate plant-insect interactions. Nevertheless, our understanding of the key members of endophyte communities involved in inhibiting or assisting EAB infestation remains limited. Employing ITS and 16S rRNA high-throughput sequencing, along with network analysis techniques, we conducted a comprehensive investigation into the reaction of endophytic fungi and bacteria within F. bungeana phloem by comparing EAB-infested and uninfected samples. Our findings reveal that EAB infestation significantly impacts the endophytic communities, altering both their diversity and overall structure. Interestingly, both endophytic fungi and bacteria exhibited distinct patterns in response to the infestation. For instance, in the EAB-infested phloem, the fungi abundance remained unchanged, but diversity decreased significantly. Conversely, bacterial abundance increased, without significant diversity changes. The fungi community structure altered significantly, which was not observed in bacteria. The bacterial composition in the infested phloem underwent significant changes, characterized by a substantial decrease in beneficial species abundance, whereas the fungal composition remained largely unaffected. In network analysis, the endophytes in infested phloem exhibited a modular topology, demonstrating greater complexity due to an augmented number of network nodes, elevated negative correlations, and a core genera shift compared to those observed in healthy phloem. Our findings increase understanding of plant-insect-microorganism relationships, crucial for pest control, considering endophytic roles in plant defense.
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Affiliation(s)
- Hua-Ling Wang
- College of Forestry, Hebei Agricultural University, Baoding 071001, China
- Hebei Urban Forest Health Technology Innovation Center, Hebei Agricultural University, Baoding 071001, China
| | - Zhen-Zhu Chen
- College of Forestry, Hebei Agricultural University, Baoding 071001, China
| | | | - Bin Zhang
- College of Life Sciences, Hebei University, Baoding 071002, China
| | - Xue-Fei Wang
- College of Forestry, Hebei Agricultural University, Baoding 071001, China
| | - Rui-Bo Zhang
- College of Forestry, Hebei Agricultural University, Baoding 071001, China
| | - Ruo-Qi Li
- College of Forestry, Hebei Agricultural University, Baoding 071001, China
| | - Shi-Xian Wang
- College of Forestry, Hebei Agricultural University, Baoding 071001, China
| | - Jian-Yong Zeng
- College of Forestry, Hebei Agricultural University, Baoding 071001, China
- Key Laboratory of Forest Germplasm Resources and Protection of Hebei Province, Hebei Agricultural University, Baoding 071001, China
| | - Hui-Ping Li
- College of Forestry, Hebei Agricultural University, Baoding 071001, China
- Hebei Urban Forest Health Technology Innovation Center, Hebei Agricultural University, Baoding 071001, China
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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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Huang L, Fu Y, Liu Y, Chen Y, Wang T, Wang M, Lin X, Feng Y. Global insights into endophytic bacterial communities of terrestrial plants: Exploring the potential applications of endophytic microbiota in sustainable agriculture. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 927:172231. [PMID: 38608902 DOI: 10.1016/j.scitotenv.2024.172231] [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: 10/23/2023] [Revised: 04/01/2024] [Accepted: 04/03/2024] [Indexed: 04/14/2024]
Abstract
Endophytic microorganisms are indispensable symbionts during plant growth and development and often serve functions such as growth promotion and stress resistance in plants. Therefore, an increasing number of researchers have applied endophytes for multifaceted phytoremediation (e.g., organic pollutants and heavy metals) in recent years. With the availability of next-generation sequencing technologies, an increasing number of studies have shifted the focus from culturable bacteria to total communities. However, information on the composition, structure, and function of bacterial endophytic communities is still not widely synthesized. To explore the general patterns of variation in bacterial communities between plant niches, we reanalyzed data from 1499 samples in 30 individual studies from different continents and provided comprehensive insights. A group of bacterial genera were commonly found in most plant roots and shoots. Our analysis revealed distinct variations in the diversity, composition, structure, and function of endophytic bacterial communities between plant roots and shoots. These variations underscore the sophisticated mechanisms by which plants engage with their endophytic microbiota, optimizing these interactions to bolster growth, health, and resilience against stress. Highlighting the strategic role of endophytic bacteria in promoting sustainable agricultural practices and environmental stewardship, our study not only offers global insights into the endophytic bacterial communities of terrestrial plants but also underscores the untapped potential of these communities as invaluable resources for future research.
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Affiliation(s)
- Lukuan Huang
- Key Laboratory of Environment Remediation and Ecological Health of Ministry of Education, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yingyi Fu
- Key Laboratory of Environment Remediation and Ecological Health of Ministry of Education, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yaru Liu
- Key Laboratory of Environment Remediation and Ecological Health of Ministry of Education, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yijie Chen
- IDEO Play Lab, CA 91006, United States of America
| | - Tingzhang Wang
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou 310012, China
| | - Meixia Wang
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou 310012, China
| | - Xianyong Lin
- Key Laboratory of Environment Remediation and Ecological Health of Ministry of Education, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Ying Feng
- Key Laboratory of Environment Remediation and Ecological Health of Ministry of Education, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China.
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Gao Z, Zheng Y, Li Z, Ruan A. Effects of 17β-Estradiol Pollution on Microbial Communities and Methane Emissions in Aerobic Water Bodies. TOXICS 2024; 12:373. [PMID: 38787152 PMCID: PMC11126138 DOI: 10.3390/toxics12050373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Revised: 05/16/2024] [Accepted: 05/17/2024] [Indexed: 05/25/2024]
Abstract
17β-Estradiol (E2) is a widely present trace pollutant in aquatic environments. However, its impact on microbial communities in aerobic lake waters, which are crucial for methane (CH4) production, remains unclear. This study conducted an E2 contamination experiment by constructing laboratory-simulated aerobic microecosystems. Using 16S rRNA high-throughput sequencing, the effects of E2 on bacterial and archaeal communities were systematically examined. Combined with gas chromatography, the patterns and mechanisms of E2's impact on CH4 emissions in aerobic aquatic systems were uncovered for the first time. Generally, E2 contamination increased the randomness of bacterial and archaeal community assemblies and weakened microbial interactions. Furthermore, changes occurred in the composition and ecological functions of bacterial and archaeal communities under E2 pollution. Specifically, two days after exposure to E2, the relative abundance of Proteobacteria in the low-concentration (L) and high-concentration (H) groups decreased by 6.99% and 4.01%, respectively, compared to the control group (C). Conversely, the relative abundance of Planctomycetota was 1.81% and 1.60% higher in the L and H groups, respectively. E2 contamination led to an increase in the relative abundance of the methanogenesis functional group and a decrease in that of the methanotrophy functional group. These changes led to an increase in CH4 emissions. This study comprehensively investigated the ecotoxicological effects of E2 pollution on microbial communities in aerobic water bodies and filled the knowledge gap regarding aerobic methane production under E2 contamination.
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Affiliation(s)
- Zihao Gao
- The National Key Laboratory of Water Disaster Prevention, Hohai University, Nanjing 210098, China; (Z.G.); (Y.Z.); (Z.L.)
- College of Hydrology and Water Resources, Hohai University, Nanjing 210098, China
| | - Yu Zheng
- The National Key Laboratory of Water Disaster Prevention, Hohai University, Nanjing 210098, China; (Z.G.); (Y.Z.); (Z.L.)
- College of Hydrology and Water Resources, Hohai University, Nanjing 210098, China
| | - Zhendong Li
- The National Key Laboratory of Water Disaster Prevention, Hohai University, Nanjing 210098, China; (Z.G.); (Y.Z.); (Z.L.)
- College of Hydrology and Water Resources, Hohai University, Nanjing 210098, China
| | - Aidong Ruan
- The National Key Laboratory of Water Disaster Prevention, Hohai University, Nanjing 210098, China; (Z.G.); (Y.Z.); (Z.L.)
- College of Geography and Remote Sensing, Hohai University, Nanjing 210098, China
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Wu CD, Fan YB, Chen X, Cao JW, Ye JY, Feng ML, Liu XX, Sun WJ, Liu RN, Wang AY. Analysis of endophytic bacterial diversity in seeds of different genotypes of cotton and the suppression of Verticillium wilt pathogen infection by a synthetic microbial community. BMC PLANT BIOLOGY 2024; 24:263. [PMID: 38594616 PMCID: PMC11005247 DOI: 10.1186/s12870-024-04910-2] [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: 01/16/2024] [Accepted: 03/15/2024] [Indexed: 04/11/2024]
Abstract
BACKGROUND In agricultural production, fungal diseases significantly impact the yield and quality of cotton (Gossypium spp.) with Verticillium wilt posing a particularly severe threat. RESULTS This study is focused on investigating the effectiveness of endophytic microbial communities present in the seeds of disease-resistant cotton genotypes in the control of cotton Verticillium wilt. The technique of 16S ribosomal RNA (16S rRNA) amplicon sequencing identified a significant enrichment of the Bacillus genus in the resistant genotype Xinluzao 78, which differed from the endophytic bacterial community structure in the susceptible genotype Xinluzao 63. Specific enriched strains were isolated and screened from the seeds of Xinluzao 78 to further explore the biological functions of seed endophytes. A synthetic microbial community (SynCom) was constructed using the broken-rod model, and seeds of the susceptible genotype Xinluzao 63 in this community that had been soaked with the SynCom were found to significantly control the occurrence of Verticillium wilt and regulate the growth of cotton plants. Antibiotic screening techniques were used to preliminarily identify the colonization of strains in the community. These techniques revealed that the strains can colonize plant tissues and occupy ecological niches in cotton tissues through a priority effect, which prevents infection by pathogens. CONCLUSION This study highlights the key role of seed endophytes in driving plant disease defense and provides a theoretical basis for the future application of SynComs in agriculture.
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Affiliation(s)
- Chong-Die Wu
- College of Life Sciences, Shihezi University, Shihezi, China
- Key Laboratory of Oasis Town and Mountain-Basin System Ecology, Xinjiang Production and Construction Corps, Shihezi, China
| | - Yong-Bin Fan
- College of Life Sciences, Shihezi University, Shihezi, China
- Key Laboratory of Oasis Town and Mountain-Basin System Ecology, Xinjiang Production and Construction Corps, Shihezi, China
| | - Xue Chen
- College of Life Sciences, Shihezi University, Shihezi, China
| | - Jiang-Wei Cao
- College of Life Sciences, Shihezi University, Shihezi, China
- Key Laboratory of Oasis Town and Mountain-Basin System Ecology, Xinjiang Production and Construction Corps, Shihezi, China
| | - Jing-Yi Ye
- College of Life Sciences, Shihezi University, Shihezi, China
- Key Laboratory of Oasis Town and Mountain-Basin System Ecology, Xinjiang Production and Construction Corps, Shihezi, China
| | - Meng-Lei Feng
- College of Life Sciences, Shihezi University, Shihezi, China
- Key Laboratory of Oasis Town and Mountain-Basin System Ecology, Xinjiang Production and Construction Corps, Shihezi, China
| | - Xing-Xing Liu
- College of Life Sciences, Shihezi University, Shihezi, China
- Key Laboratory of Oasis Town and Mountain-Basin System Ecology, Xinjiang Production and Construction Corps, Shihezi, China
| | - Wen-Jing Sun
- College of Life Sciences, Shihezi University, Shihezi, China
- Key Laboratory of Oasis Town and Mountain-Basin System Ecology, Xinjiang Production and Construction Corps, Shihezi, China
| | - Rui-Na Liu
- College of Life Sciences, Shihezi University, Shihezi, China
- Key Laboratory of Oasis Town and Mountain-Basin System Ecology, Xinjiang Production and Construction Corps, Shihezi, China
| | - Ai-Ying Wang
- College of Life Sciences, Shihezi University, Shihezi, China.
- Key Laboratory of Oasis Town and Mountain-Basin System Ecology, Xinjiang Production and Construction Corps, Shihezi, China.
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Wang G, Feng Z, Yin X, Chen D, Zhao N, Yuan Y, Chen C, Liu C, Ao M, Chen L, Chen Z, Yang W, Li D, Morel JL, Chao Y, Wang P, Tang Y, Qiu R, Wang S. Biogenic manganese oxides promote metal(loid) remediation by shaping microbial communities in biological aqua crust. WATER RESEARCH 2024; 253:121287. [PMID: 38387264 DOI: 10.1016/j.watres.2024.121287] [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: 11/06/2023] [Revised: 02/05/2024] [Accepted: 02/06/2024] [Indexed: 02/24/2024]
Abstract
Biological aqua crust (biogenic aqua crust-BAC) is a potentially sustainable solution for metal(loid) bioremediation in global water using solar energy. However, the key geochemical factors and underlying mechanisms shaping microbial communities in BAC remain poorly understood. The current study aimed at determining the in situ metal(loid) distribution and the key geochemical factors related to microbial community structure and metal(loid)-related genes in BAC of a representative Pb/Zn tailing pond. Here we showed that abundant metal(loid)s (e.g. Pb, As) were co-distributed with Mn/Fe-rich minerals (e.g. biogenic Mn oxide, FeOOH) in BAC. Biogenic Mn oxide (i.e. Mn) was the most dominant factor in shaping microbial community structure in BAC and source tailings. Along with the fact that keystone species (e.g. Burkholderiales, Haliscomenobacter) have the potential to promote Mn ion oxidization and particle agglomeration, as well as Mn is highly associated with metal(loid)-related genes, especially genes related to As redox (e.g. arsC, aoxA), and Cd transport (e.g. zipB), biogenic Mn oxides thus effectively enhance metal(loid) remediation by accelerating the formation of organo-mineral aggregates in biofilm-rich BAC system. Our study indicated that biogenic Mn oxides may play essential roles in facilitating in situ metal(loid) bioremediation in BAC of mine drainage.
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Affiliation(s)
- Guobao Wang
- Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, 510006, PR China; College of Chemistry and Environmental Engineering, Yangtze University, Jingzhou, 434023, PR China
| | - Zekai Feng
- Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, 510006, PR China
| | - Xiuran Yin
- Microbial Ecophysiology Group, University of Bremen, Bremen, Germany
| | - Daijie Chen
- Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, 510006, PR China
| | - Nan Zhao
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou, 510650, PR China
| | - Yongqiang Yuan
- Key Laboratory of Karst Georesources and Environment, Ministry of Education, College of Resources and Environmental Engineering, Guizhou University, Guiyang, PR China
| | - Chiyu Chen
- Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, 510006, PR China
| | - Chong Liu
- Institute of Agricultural Resources and Environment, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, PR China
| | - Ming Ao
- Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, 510006, PR China
| | - Lei Chen
- Key Laboratory for New Technology Research of Vegetable, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, PR China
| | - Ziwu Chen
- Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, 510006, PR China
| | - Wenjun Yang
- Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, 510006, PR China
| | - Dantong Li
- Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, 510006, PR China
| | - Jean Louis Morel
- Laboratoire Sols et Environnement, UMR 1120, Université de Lorraine, INRAE, 54518, Vandoeuvre-lès-Nancy, France
| | - Yuanqing Chao
- Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, 510006, PR China
| | - Peng Wang
- Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, 510006, PR China
| | - Yetao Tang
- Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, 510006, PR China
| | - Rongliang Qiu
- Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, 510006, PR China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Provincial Key Laboratory of Agricultural & Rural Pollution Abatement and Environmental Safety, College of Natural Resources and Environment, South China Agricultural University, Guangzhou, 510642, PR China
| | - Shizhong Wang
- Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, 510006, PR China.
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Peng D, Wang Z, Tian J, Wang W, Guo S, Dai X, Yin H, Li L. Phyllosphere bacterial community dynamics in response to bacterial wildfire disease: succession and interaction patterns. FRONTIERS IN PLANT SCIENCE 2024; 15:1331443. [PMID: 38533399 PMCID: PMC10963427 DOI: 10.3389/fpls.2024.1331443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 02/08/2024] [Indexed: 03/28/2024]
Abstract
Plants interact with complex microbial communities in which microorganisms play different roles in plant development and health. While certain microorganisms may cause disease, others promote nutrient uptake and resistance to stresses through a variety of mechanisms. Developing plant protection measures requires a deeper comprehension of the factors that influence multitrophic interactions and the organization of phyllospheric communities. High-throughput sequencing was used in this work to investigate the effects of climate variables and bacterial wildfire disease on the bacterial community's composition and assembly in the phyllosphere of tobacco (Nicotiana tabacum L.). The samples from June (M1), July (M2), August (M3), and September (M4) formed statistically separate clusters. The assembly of the whole bacterial population was mostly influenced by stochastic processes. PICRUSt2 predictions revealed genes enriched in the M3, a period when the plant wildfire disease index reached climax, were associated with the development of the wildfire disease (secretion of virulence factor), the enhanced metabolic capacity and environmental adaption. The M3 and M4 microbial communities have more intricate molecular ecological networks (MENs), bursting with interconnections within a densely networked bacterial population. The relative abundances of plant-beneficial and antagonistic microbes Clostridiales, Bacillales, Lactobacillales, and Sphingobacteriales, showed significant decrease in severally diseased sample (M3) compared to the pre-diseased samples (M1/M2). Following the results of MENs, we further test if the correlating bacterial pairs within the MEN have the possibility to share functional genes and we have unraveled 139 entries of such horizontal gene transfer (HGT) events, highlighting the significance of HGT in shaping the adaptive traits of plant-associated bacteria across the MENs, particularly in relation to host colonization and pathogenicity.
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Affiliation(s)
- Deyuan Peng
- Zhangjiajie Tobacco Company of Hunan Province, Zhangjiajie, China
| | - Zhenhua Wang
- Zhangjiajie Tobacco Company of Hunan Province, Zhangjiajie, China
| | - Jinyan Tian
- Zhangjiajie Tobacco Company of Hunan Province, Zhangjiajie, China
| | - Wei Wang
- Zhangjiajie Tobacco Company of Hunan Province, Zhangjiajie, China
| | - Shijie Guo
- Zhangjiajie Tobacco Company of Hunan Province, Zhangjiajie, China
| | - Xi Dai
- Zhangjiajie Tobacco Company of Hunan Province, Zhangjiajie, China
| | - Huaqun Yin
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
| | - Liangzhi Li
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
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10
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Jayasinghe H, Chang HX, Knobloch S, Yang SH, Hendalage DPB, Ariyawansa KGSU, Liu PY, Stadler M, Ariyawansa HA. Metagenomic insight to apprehend the fungal communities associated with leaf blight of Welsh onion in Taiwan. FRONTIERS IN PLANT SCIENCE 2024; 15:1352997. [PMID: 38495366 PMCID: PMC10941342 DOI: 10.3389/fpls.2024.1352997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2023] [Accepted: 02/12/2024] [Indexed: 03/19/2024]
Abstract
Plants are associated with a large diversity of microbes, and these complex plant-associated microbial communities are critical for plant health. Welsh onion (Allium fistulosum L.) is one of the key and oldest vegetable crops cultivated in Taiwan. The leaf of the Welsh onion is one of the famous spices in Taiwanese cuisine, thus, it is crucial to control foliar diseases. In recent years, Welsh onion cultivation in Taiwan has been severely threatened by the occurrence of leaf blight disease, greatly affecting their yield and quality. However, the overall picture of microbiota associated with the Welsh onion plant is still not clear as most of the recent etiological investigations were heavily based on the isolation of microorganisms from diseased plants. Therefore, studying the diversity of fungal communities associated with the leaf blight symptoms of Welsh onion may provide information regarding key taxa possibly involved in the disease. Therefore, this investigation was mainly designed to understand the major fungal communities associated with leaf blight to identify key taxa potentially involved in the disease and further evaluate any shifts in both phyllosphere and rhizosphere mycobiome assembly due to foliar pathogen infection by amplicon sequencing targeting the Internal Transcribed Spacer (ITS) 1 region of the rRNA. The alpha and beta-diversity analyses were used to compare the fungal communities and significant fungal groups were recognized based on linear discriminant analyses. Based on the results of relative abundance data and co-occurrence networks in symptomatic plants we revealed that the leaf blight of Welsh onion in Sanxing, is a disease complex mainly involving Stemphylium and Colletotrichum taxa. In addition, genera such as Aspergillus, Athelia and Colletotrichum were abundantly found associated with the symptomatic rhizosphere. Alpha-diversity in some fields indicated a significant increase in species richness in the symptomatic phyllosphere compared to the asymptomatic phyllosphere. These results will broaden our knowledge of pathogens of Welsh onion associated with leaf blight symptoms and will assist in developing effective disease management strategies to control the progress of the disease.
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Affiliation(s)
- Himanshi Jayasinghe
- Department of Plant Pathology and Microbiology, National Taiwan University, Taipei, Taiwan
| | - Hao-Xun Chang
- Department of Plant Pathology and Microbiology, National Taiwan University, Taipei, Taiwan
| | - Stephen Knobloch
- Department of Food Technology, Fulda University of Applied Sciences, Fulda, Germany
| | - Shan-Hua Yang
- Institute of Fisheries Science, National Taiwan University, Taipei, Taiwan
| | - D. P. Bhagya Hendalage
- Department of Plant Sciences, Faculty of Science, University of Colombo, Colombo, Sri Lanka
| | | | - Po-Yu Liu
- School of Medicine, College of Medicine, National Sun Yat-Sen University, Kaohsiung, Taiwan
| | - Marc Stadler
- Department Microbial Drugs, Helmholtz Centre for Infection Research GmbH (HZI), Braunschweig, Germany
| | - Hiran A. Ariyawansa
- Department of Plant Pathology and Microbiology, National Taiwan University, Taipei, Taiwan
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11
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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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12
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Yang H, Zhang X, Qiu X, Chen J, Wang Y, Zhang G, Jia S, Shen X, Ye W, Yan Z. Fusarium Wilt Invasion Results in a Strong Impact on Strawberry Microbiomes. PLANTS (BASEL, SWITZERLAND) 2023; 12:4153. [PMID: 38140478 PMCID: PMC10747085 DOI: 10.3390/plants12244153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 12/11/2023] [Accepted: 12/12/2023] [Indexed: 12/24/2023]
Abstract
Plant-endophytic microbes affect plant growth, development, nutrition, and resistance to pathogens. However, how endophytic microbial communities change in different strawberry plant compartments after Fusarium pathogen infection has remained elusive. In this study, 16S and internal transcribed spacer rRNA amplicon sequencing were used to systematically investigate changes in the bacterial and fungal diversity and composition in the endophytic compartments (roots, stems, and leaves) of healthy strawberries and strawberries with Fusarium wilt, respectively. The analysis of the diversity, structure, and composition of the bacterial and fungal communities revealed a strong effect of pathogen invasion on the endophytic communities. The bacterial and fungal community diversity was lower in the Fusarium-infected endophytic compartments than in the healthy samples. The relative abundance of certain bacterial and fungal genera also changed after Fusarium wilt infection. The relative abundance of the beneficial bacterial genera Bacillus, Bradyrhizobium, Methylophilus, Sphingobium, Lactobacillus, and Streptomyces, as well as fungal genera Acremonium, Penicillium, Talaromyces, and Trichoderma, were higher in the healthy samples than in the Fusarium wilt samples. The relative abundance of Fusarium in the infected samples was significantly higher than that in the healthy samples, consistent with the field observations and culture isolation results for strawberry wilt. Our findings provide a theoretical basis for the isolation, identification, and control of strawberry wilt disease.
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Affiliation(s)
- Hongjun Yang
- College of Agronomy and Horticulture, Jiangsu Vocational College of Agriculture and Forestry, Zhenjiang 212400, China; (H.Y.); (X.Q.); (Y.W.); (G.Z.); (S.J.); (X.S.)
- Jiangsu Engineering and Technology Center for Modern Horticulture, Zhenjiang 212400, China
| | - Xu Zhang
- College of Agronomy and Horticulture, Jiangsu Vocational College of Agriculture and Forestry, Zhenjiang 212400, China; (H.Y.); (X.Q.); (Y.W.); (G.Z.); (S.J.); (X.S.)
- Jiangsu Engineering and Technology Center for Modern Horticulture, Zhenjiang 212400, China
| | - Xiaohong Qiu
- College of Agronomy and Horticulture, Jiangsu Vocational College of Agriculture and Forestry, Zhenjiang 212400, China; (H.Y.); (X.Q.); (Y.W.); (G.Z.); (S.J.); (X.S.)
| | - Jiajia Chen
- College of Landscape Architecture, Jiangsu Vocational College of Agriculture and Forestry, Zhenjiang 212400, China;
| | - Yuanhua Wang
- College of Agronomy and Horticulture, Jiangsu Vocational College of Agriculture and Forestry, Zhenjiang 212400, China; (H.Y.); (X.Q.); (Y.W.); (G.Z.); (S.J.); (X.S.)
- Jiangsu Engineering and Technology Center for Modern Horticulture, Zhenjiang 212400, China
| | - Geng Zhang
- College of Agronomy and Horticulture, Jiangsu Vocational College of Agriculture and Forestry, Zhenjiang 212400, China; (H.Y.); (X.Q.); (Y.W.); (G.Z.); (S.J.); (X.S.)
- Jiangsu Engineering and Technology Center for Modern Horticulture, Zhenjiang 212400, China
| | - Sizhen Jia
- College of Agronomy and Horticulture, Jiangsu Vocational College of Agriculture and Forestry, Zhenjiang 212400, China; (H.Y.); (X.Q.); (Y.W.); (G.Z.); (S.J.); (X.S.)
| | - Xiangqi Shen
- College of Agronomy and Horticulture, Jiangsu Vocational College of Agriculture and Forestry, Zhenjiang 212400, China; (H.Y.); (X.Q.); (Y.W.); (G.Z.); (S.J.); (X.S.)
| | - Wenwu Ye
- Key Laboratory of Plant Immunity, Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China;
| | - Zhiming Yan
- College of Agronomy and Horticulture, Jiangsu Vocational College of Agriculture and Forestry, Zhenjiang 212400, China; (H.Y.); (X.Q.); (Y.W.); (G.Z.); (S.J.); (X.S.)
- Jiangsu Engineering and Technology Center for Modern Horticulture, Zhenjiang 212400, China
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13
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He R, Hu S, Li Q, Zhao D, Wu QL, Zeng J. Greater transmission capacities and small-world characteristics of bacterial communities in the above- than those in the below- ground niches of a typical submerged macrophyte, Vallisneria natans. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 903:166229. [PMID: 37586539 DOI: 10.1016/j.scitotenv.2023.166229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 08/06/2023] [Accepted: 08/09/2023] [Indexed: 08/18/2023]
Abstract
Leaves and roots of submerged macrophytes provide extended surfaces and stable internal tissues for distinct microorganisms to rest, but how these microorganisms interact with each other across different niches and ultimately drive the distribution through horizontal and vertical transmissions remains largely undetermined. Knowledge of the mechanisms of assemblage and transmission in aquatic macrophytes-associated microbial communities will help to better understanding their important roles in plant fitness and benefit ecological functions. Here, we conducted a microcosmic experiment based on in situ lake samples to investigate the bacterial community assemblage, transmission, and co-occurrence patterns in different niches of a typical submerged macrophyte, Vallisneria natans (V. natans), including seed endosphere, as well as environmental (water and bulk sediment), epiphytic (phyllosphere and rhizosphere), and endophytic (leaf and root endosphere) microhabitats of both leaves and roots representatives of the above- and below- ground niches (AGNs and BGNs), respectively. We found the bacterial communities colonized in epiphytic niches not only exhibited the highest diversity compared to adjacent environmental and endophytic niches, but also dominated the interactions between those bacterial members of neighboring niches in both AGNs and BGNs. The host plants promoted niche specificity at bacterial community-level, as confirmed by the proportion of bacterial specialists increased with plant proximity, especially in the BGNs. Furthermore, the bacterial taxa colonized in the AGNs exhibited higher horizontal and vertical transmission capacities than those in the BGNs, especially in the vertical transmission from seeds to leaves (41.38 %) than roots (0.42 %). Meanwhile, the bacterial co-occurrence network in AGNs was shown to have stronger small-world characteristics but weaker stability than those in the BGNs. Overall, this study cast new light on the plant microbiome in the aquatic environment, thus better promoting the potential development of strategies for breeding aquatic macrophyte holobiont with enhanced water purification and pollutant removal capabilities in the future.
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Affiliation(s)
- Rujia He
- State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Joint International Research Laboratory of Global Change and Water Cycle, Hohai University, Nanjing 210098, China; State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China
| | - Siwen Hu
- State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Joint International Research Laboratory of Global Change and Water Cycle, Hohai University, Nanjing 210098, China; State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China
| | - Qisheng Li
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China
| | - Dayong Zhao
- State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Joint International Research Laboratory of Global Change and Water Cycle, Hohai University, Nanjing 210098, China
| | - Qinglong L Wu
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China; Center for Evolution and Conservation Biology, Southern Marine Sciences and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China; Sino-Danish Centre for Education and Research, University of Chinese Academy of Sciences, Beijing 100039, China
| | - Jin Zeng
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China; Sino-Danish Centre for Education and Research, University of Chinese Academy of Sciences, Beijing 100039, China.
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14
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Li T, Gao J. Attribution of dispersal limitation can better explain the assembly patterns of plant microbiota. FRONTIERS IN PLANT SCIENCE 2023; 14:1168760. [PMID: 37941678 PMCID: PMC10628812 DOI: 10.3389/fpls.2023.1168760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Accepted: 10/05/2023] [Indexed: 11/10/2023]
Abstract
Disentangling community assembly processes is crucial for fully understanding the function of microbiota in agricultural ecosystems. However, numerous plant microbiome surveys have gradually revealed that stochastic processes dominate the assembly of the endophytic root microbiota in conflict with strong host filtering effects, which is an important issue. Resolving such conflicts or inconsistencies will not only help accurately predict the composition and structure of the root endophytic microbiota and its driving mechanisms, but also provide important guidance on the correlation between the relative importance of deterministic and stochastic processes in the assembly of the root endophytic microbiota, and crop productivity and nutritional quality. Here, we propose that the inappropriate division of dispersal limitation may be the main reason for such inconsistency, which can be resolved after the proportion of dispersal limitation is incorporated into the deterministic processes. The rationality of this adjustment under the framework of the formation of a holobiont between the microbiome and the plant host is herein explained, and a potential theoretical framework for dynamic assembly patterns of endophytic microbiota along the soil-plant continuum is proposed. Considering that the assembly of root endophytic microbiota is complicated, we suggest caution and level-by-level verification from deterministic processes to neutral components to stochastic processes when deciding on the attribution of dispersal limitation in the future to promote the expansion and application of microbiome engineering in sustainable agricultural development based on community assembly patterns.
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Affiliation(s)
| | - Jiangyun Gao
- Institute of Biodiversity, School of Ecology and Environmental Science, Yunnan University, Kunming, China
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15
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Li P, Gu S, Zhu Y, Xu T, Yang Y, Wang Z, Deng X, Wang B, Li W, Mei W, Hu Q. Soil microbiota plays a key regulatory role in the outbreak of tobacco root rot. Front Microbiol 2023; 14:1214167. [PMID: 37779693 PMCID: PMC10540700 DOI: 10.3389/fmicb.2023.1214167] [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: 05/03/2023] [Accepted: 09/01/2023] [Indexed: 10/03/2023] Open
Abstract
Introduction Root rot caused by the fungal pathogen Fusarium sp. poses significant challenges to tobacco cultivation in China, leading to major economic setbacks. The interplay between this pathogen and the wider soil microbial community remains poorly understood. Methods High-throughput sequencing technology was utilized to evaluate soil prokaryotic, fungal, and protistan communities. We compared microbial communities in infected soils to those in healthy soils from the same field. Additionally, the influence of pH on the microbial communities was assessed. Results Infected soils displayed elevated levels of soil nutrients but diminished observed richness across prokaryotic, fungal, and protistan groups. The pathogenic fungi Fusarium solani f sp. eumartii's abundance was notably increased in infected soils. Infection with F. solani significantly altered the soil's microbial community structure and interactions, manifested as a decrease in network scale and the number of keystone species. An evaluation of prokaryotes' role in F. solani's invasion revealed an increased number of connecting nodes in infected soils. Additionally, relationships between predatory protists and fungi were augmented, whereas predation on F. solani declined. Discussion The study underscores the significance of comprehending the interactions among soil microorganisms and brings to light the susceptibility of soil microbial communities to pathogen invasion. It offers insights into the multifaceted relationships and potential vulnerabilities within the soil ecosystem in the context of Fusarium sp. invasion.
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Affiliation(s)
- Pengfei Li
- Wenshan Tobacco Company of Yunnan Province, Wenshan, Yunnan, China
| | - Songsong Gu
- Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Yanmei Zhu
- Wenshan Tobacco Company of Yunnan Province, Wenshan, Yunnan, China
| | - Tianyang Xu
- Wenshan Tobacco Company of Yunnan Province, Wenshan, Yunnan, China
| | - Yishuai Yang
- College of Horticulture and Landscape Architecture, Hunan Agricultural University, Changsha, Hunan, China
| | - Zhengqiang Wang
- College of Horticulture and Landscape Architecture, Hunan Agricultural University, Changsha, Hunan, China
| | - Xiangdong Deng
- College of Horticulture and Landscape Architecture, Hunan Agricultural University, Changsha, Hunan, China
| | - Bin Wang
- Wenshan Tobacco Company of Yunnan Province, Wenshan, Yunnan, China
| | - Wei Li
- Wenshan Tobacco Company of Yunnan Province, Wenshan, Yunnan, China
| | - Wenqiang Mei
- Wenshan Tobacco Company of Yunnan Province, Wenshan, Yunnan, China
| | - Qiulong Hu
- College of Horticulture and Landscape Architecture, Hunan Agricultural University, Changsha, Hunan, China
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16
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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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Kashyap S, Sharma I, Dowarah B, Barman R, Gill SS, Agarwala N. Plant and soil-associated microbiome dynamics determine the fate of bacterial wilt pathogen Ralstonia solanacearum. PLANTA 2023; 258:57. [PMID: 37524889 DOI: 10.1007/s00425-023-04209-w] [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: 04/24/2023] [Accepted: 07/18/2023] [Indexed: 08/02/2023]
Abstract
MAIN CONCLUSION Plant and the soil-associated microbiome is important for imparting bacterial wilt disease tolerance in plants. Plants are versatile organisms that are endowed with the capacity to withstand various biotic and abiotic stresses despite having no locomotory abilities. Being the agent for bacterial wilt (BW) disease, Ralstonia solanacearum (RS) colonizes the xylem vessels and limits the water supply to various plant parts, thereby causing wilting. The havoc caused by RS leads to heavy losses in crop productivity around the world, for which a sustainable mitigation strategy is urgently needed. As several factors can influence plant-microbe interactions, comprehensive understanding of plant and soil-associated microbiome under the influence of RS and various environmental/edaphic conditions is important to control this pathogen. This review mainly focuses on microbiome dynamics associated with BW disease and also provide update on microbial/non-microbial approaches employed to control BW disease in crop plants.
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Affiliation(s)
- Sampurna Kashyap
- Department of Botany, Gauhati University, Gopinath Bordoloi Nagar, Jalukbari, Guwahati, Assam, 781014, India
| | - Indrani Sharma
- Department of Botany, Gauhati University, Gopinath Bordoloi Nagar, Jalukbari, Guwahati, Assam, 781014, India
| | - Bhaskar Dowarah
- Department of Botany, Bahona College, Bahona, Jorhat, Assam, 785101, India
| | - Ramen Barman
- Department of Botany, Gauhati University, Gopinath Bordoloi Nagar, Jalukbari, Guwahati, Assam, 781014, India
| | - Sarvajeet Singh Gill
- Centre for Biotechnology, Maharshi Dayanand University, Rohtak, Haryana, 124001, India.
| | - Niraj Agarwala
- Department of Botany, Gauhati University, Gopinath Bordoloi Nagar, Jalukbari, Guwahati, Assam, 781014, India.
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18
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Park S, Zhang T, Kang S. Fecal Microbiota Composition, Their Interactions, and Metagenome Function in US Adults with Type 2 Diabetes According to Enterotypes. Int J Mol Sci 2023; 24:ijms24119533. [PMID: 37298483 DOI: 10.3390/ijms24119533] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Revised: 05/24/2023] [Accepted: 05/30/2023] [Indexed: 06/12/2023] Open
Abstract
T2DM etiology differs among Asians and Caucasians and may be associated with gut microbiota influenced by different diet patterns. However, the association between fecal bacterial composition, enterotypes, and T2DM susceptibility remained controversial. We investigated the fecal bacterial composition, co-abundance network, and metagenome function in US adults with T2DM compared to healthy adults based on enterotypes. We analyzed 1911 fecal bacterial files of 1039 T2DM and 872 healthy US adults from the Human Microbiome Projects. Operational taxonomic units were obtained after filtering and cleaning the files using Qiime2 tools. Machine learning and network analysis identified primary bacteria and their interactions influencing T2DM incidence, clustered into enterotypes, Bacteroidaceae (ET-B), Lachnospiraceae (ET-L), and Prevotellaceae (ET-P). ET-B showed higher T2DM incidence. Alpha-diversity was significantly lower in T2DM in ET-L and ET-P (p < 0.0001), but not in ET-B. Beta-diversity revealed a distinct separation between T2DM and healthy groups across all enterotypes (p < 0.0001). The XGBoost model exhibited high accuracy and sensitivity. Enterocloster bolteae, Facalicatena fissicatena, Clostridium symbiosum, and Facalibacterium prausnitizii were more abundant in the T2DM group than in the healthy group. Bacteroides koreensis, Oscillibacter ruminantium, Bacteroides uniformis, and Blautia wexlerae were lower in the T2DM than in the healthy group regardless of the enterotypes in the XGBoost model (p < 0.0001). However, the patterns of microbial interactions varied among different enterotypes affecting T2DM risk. The interaction between fecal bacteria was more tightly regulated in the ET-L than in the ET-B and ET-P groups (p < 0.001). Metagenomic analysis revealed an inverse association between bacteria abundance in T2DM, energy utility, butanoate and propanoate metabolism, and the insulin signaling pathway (p < 0.0001). In conclusion, fecal bacteria play a role in T2DM pathogenesis, particularly within different enterotypes, providing valuable insights into the link between gut microbiota and T2DM in the US population.
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Affiliation(s)
- Sunmin Park
- Department of Food and Nutrition, Obesity/Diabetes Research Center, Hoseo University, 165 Sechul-Ri, Asan 31499, Republic of Korea
- Department of Bioconvergence, Hoseo University, Asan 31499, Republic of Korea
| | - Ting Zhang
- Department of Bioconvergence, Hoseo University, Asan 31499, Republic of Korea
| | - Suna Kang
- Department of Food and Nutrition, Obesity/Diabetes Research Center, Hoseo University, 165 Sechul-Ri, Asan 31499, Republic of Korea
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19
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Wang L, Ye X, Shen Z, Zhang Y, Lin J. Identifying the effects of cropping with different pear cultivars on microbial community composition and networks in orchard soils. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:66157-66169. [PMID: 37097572 DOI: 10.1007/s11356-023-26944-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 04/06/2023] [Indexed: 05/17/2023]
Abstract
The role of plant genotype in determining the assembly of soil microorganisms is widely accepted; however, the effects of cropping with different cultivars of perennial crop plants on the composition of soil microbial communities are not fully understood. In the current study, high-throughput amplicon sequencing and real-time PCR were used to investigate the major features of bacterial community composition, ecological networks, and soil physicochemical properties in three replicate pear orchards, each planted with monocultures of pear cultivars Hosui (HS) or Sucui (SC) of similar ages. A distinct difference in the composition of microbial communities was observed between soils of HS and SC orchards. A significantly greater relative abundance of Verrucomicrobia and Alphaproteobacteria whereas a significantly lower relative abundance of Betaproteobacteria were found in soils of HS cropped orchards than that in SC orchards. Sphingomonas sp., belonging to the Alphaproteobacteria, was recognized as a key species in the co-occurrence network of the microbial interactions. Moreover, redundancy analysis, the Mantel correlation test, and random forest analysis showed that soil pH was the dominant driver in determining microbial community composition in HS soils, whereas soil organic matter was the primary factor determining microbial community composition in SC soils. Altogether, we provide evidence that soils in HS orchards harbor unique microbial communities enriched with respect to microbial groups associated with nutrient cycling, whereas soils in SC orchards are dominated by a group of beneficial microbes exhibiting plant growth promotion. These findings have implications for science-based guidance for manipulation of the soil microbiome to achieve sustainable food production.
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Affiliation(s)
- Li Wang
- Institute of Animal Science, Key Laboratory of Crop and Livestock Integrated Farming, Ministry of Agriculture and Rural Affairs, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
| | - Xiaomei Ye
- Institute of Animal Science, Key Laboratory of Crop and Livestock Integrated Farming, Ministry of Agriculture and Rural Affairs, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China.
| | - Zongzhuan Shen
- 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, The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yingpeng Zhang
- Institute of Animal Science, Key Laboratory of Crop and Livestock Integrated Farming, Ministry of Agriculture and Rural Affairs, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
| | - Jing Lin
- Institute of Pomology, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
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20
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Bhandari R, Sanz-Saez A, Leisner CP, Potnis N. Xanthomonas infection and ozone stress distinctly influence the microbial community structure and interactions in the pepper phyllosphere. ISME COMMUNICATIONS 2023; 3:24. [PMID: 36973329 PMCID: PMC10043289 DOI: 10.1038/s43705-023-00232-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 03/08/2023] [Accepted: 03/15/2023] [Indexed: 03/29/2023]
Abstract
While the physiological and transcriptional response of the host to biotic and abiotic stresses have been intensely studied, little is known about the resilience of associated microbiomes and their contribution towards tolerance or response to these stresses. We evaluated the impact of elevated tropospheric ozone (O3), individually and in combination with Xanthomonas perforans infection, under open-top chamber field conditions on overall disease outcome on resistant and susceptible pepper cultivars, and their associated microbiome structure, function, and interaction network across the growing season. Pathogen infection resulted in a distinct microbial community structure and functions on the susceptible cultivar, while concurrent O3 stress did not further alter the community structure, and function. However, O3 stress exacerbated the disease severity on resistant cultivar. This altered diseased severity was accompanied by enhanced heterogeneity in associated Xanthomonas population counts, although no significant shift in overall microbiota density, microbial community structure, and function was evident. Microbial co-occurrence networks under simultaneous O3 stress and pathogen challenge indicated a shift in the most influential taxa and a less connected network, which may reflect the altered stability of interactions among community members. Increased disease severity on resistant cultivar may be explained by such altered microbial co-occurrence network, indicating the altered microbiome-associated prophylactic shield against pathogens under elevated O3. Our findings demonstrate that microbial communities respond distinctly to individual and simultaneous stressors, in this case, O3 stress and pathogen infection, and can play a significant role in predicting how plant-pathogen interactions would change in the face of climate change.
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Affiliation(s)
- Rishi Bhandari
- Department of Entomology and Plant Pathology, Auburn University, Auburn, AL, 36849, USA
| | - Alvaro Sanz-Saez
- Department of Crop, Soil and Environmental Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Courtney P Leisner
- Department of Biological Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Neha Potnis
- Department of Entomology and Plant Pathology, Auburn University, Auburn, AL, 36849, USA.
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21
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Lv N, Tao C, Ou Y, Wang J, Deng X, Liu H, Shen Z, Li R, Shen Q. Root-Associated Antagonistic Pseudomonas spp. Contribute to Soil Suppressiveness against Banana Fusarium Wilt Disease of Banana. Microbiol Spectr 2023; 11:e0352522. [PMID: 36786644 PMCID: PMC10100972 DOI: 10.1128/spectrum.03525-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 01/24/2023] [Indexed: 02/15/2023] Open
Abstract
Members of the microbiotas colonizing the plant endophytic compartments and the surrounding bulk and rhizosphere soil play an important role in determining plant health. However, the relative contributions of the soil and endophytic microbiomes and their mechanistic roles in achieving disease suppression remain elusive. To disentangle the relative importance of the different microbiomes in the various plant compartments in inhibiting pathogen infection, we conducted a field experiment to track changes in the composition of microbial communities in bulk and rhizosphere soil and of root endophytes and leaf endosphere collected from bananas planted on Fusarium-infested orchards in disease-suppressive and disease-conducive soils. We found that the rhizosphere and roots were the two dominant plant parts whose bacterial communities contributed to pathogen suppression. We further observed that Pseudomonas was potentially a key organism acting as a pathogen antagonist, as illustrated by microbial community composition and network analysis. Subsequently, culturable pathogen-antagonistic Pseudomonas strains were isolated, and their potential suppressive functions or possible antibiosis in terms of auxin or siderophore synthesis and phosphate solubilization were screened to analyze the mode of action of candidate disease-suppressive Pseudomonas strains. In a follow-up in vivo and greenhouse experiment, we revealed that microbial consortia of culturable Pseudomonas strains P8 and S25 (or S36), isolated from banana plantlet rhizosphere and roots, respectively, significantly suppressed the survival of pathogens in the soil, manipulated the soil microbiome, and stimulated indigenous beneficial microbes. Overall, our study demonstrated that root-associated microbiomes, especially the antagonistic Pseudomonas sp. components, contribute markedly to soil suppression of banana Fusarium wilt. IMPORTANCE Soil suppression of Fusarium wilt disease has been proven to be linked with the local microbial community. However, the contribution of endophytic microbes to disease suppression in wilt-suppressive soils remains unclear. Moreover, the key microbes involving in Fusarium wilt-suppressive soils and in the endophytic populations have not been fully characterized. In this study, we demonstrate that root-associated microbes play vitally important roles in disease suppression. Root-associated Pseudomonas consortia were recognized as a key component in inhibiting pathogen abundance associated with the host banana plants. This finding is crucial to developing alternate strategies for soilborne disease management by harnessing the plant microbiome.
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Affiliation(s)
- Nana Lv
- 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, The Key Laboratory of Plant Immunity, Joint International Research Laboratory of Soil Health, Nanjing Agricultural University, Nanjing, Jiangsu, People’s Republic of China
| | - Chengyuan Tao
- 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, The Key Laboratory of Plant Immunity, Joint International Research Laboratory of Soil Health, Nanjing Agricultural University, Nanjing, Jiangsu, People’s Republic of China
| | - Yannan Ou
- 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, The Key Laboratory of Plant Immunity, Joint International Research Laboratory of Soil Health, Nanjing Agricultural University, Nanjing, Jiangsu, People’s Republic of China
| | - Jiabao Wang
- 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, The Key Laboratory of Plant Immunity, Joint International Research Laboratory of Soil Health, Nanjing Agricultural University, Nanjing, Jiangsu, People’s Republic of China
- The Sanya Institute of the Nanjing Agricultural University, Sanya, Hainan, People’s Republic of China
| | - Xuhui Deng
- 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, The Key Laboratory of Plant Immunity, Joint International Research Laboratory of Soil Health, Nanjing Agricultural University, Nanjing, Jiangsu, People’s Republic of China
| | - Hongjun Liu
- 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, The Key Laboratory of Plant Immunity, Joint International Research Laboratory of Soil Health, Nanjing Agricultural University, Nanjing, Jiangsu, People’s Republic of China
| | - Zongzhuan Shen
- 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, The Key Laboratory of Plant Immunity, Joint International Research Laboratory of Soil Health, Nanjing Agricultural University, Nanjing, Jiangsu, People’s Republic of China
- The Sanya Institute of the Nanjing Agricultural University, Sanya, Hainan, People’s Republic of China
| | - Rong Li
- 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, The Key Laboratory of Plant Immunity, Joint International Research Laboratory of Soil Health, Nanjing Agricultural University, Nanjing, Jiangsu, People’s Republic of China
- The Sanya Institute of the Nanjing Agricultural University, Sanya, Hainan, People’s Republic of China
| | - Qirong Shen
- 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, The Key Laboratory of Plant Immunity, Joint International Research Laboratory of Soil Health, Nanjing Agricultural University, Nanjing, Jiangsu, People’s Republic of China
- The Sanya Institute of the Nanjing Agricultural University, Sanya, Hainan, People’s Republic of China
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22
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Chen J, He J, Zhang Y, Huang J, Chen Z, Zeng W, Deng X, Hu Q. Effects of tobacco plant residue return on rhizosphere soil microbial community. ANN MICROBIOL 2022. [DOI: 10.1186/s13213-022-01699-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abstract
Purpose
Based on the recycling principle, returning of tobacco crop residues into the field is a common agronomic practice. However, comprehensive knowledge about the effects of tobacco plant residue return on the rhizosphere soil microbial community is very limited.
Methods
After tobacco crop residue returning into the potted soil, 16S ribosomal RNA (rRNA) and internal transcribed spacer (ITS) amplicon sequencing were employed to investigate the bacterial and fungal communities, respectively, from the tobacco rhizosphere soils.
Results
The results showed that tobacco residue returning increased the diversity of microbial communities (bacteria and fungi) and changed the species composition. It further increased the relative abundance of beneficial microorganisms. After tobacco residue returning, the structure of the rhizosphere soil microbial community network was found more complex with strong interactions among microbial species. In addition, the keystone species of bacterial and fungal communities associated with tobacco rhizosphere soil were altered. This had exerted a driving force to the beneficial bacteria such as Sphiningomonas and Psathyrella to the keystone microorganisms which played important roles in microbial species interaction.
Conclusions
Tobacco residue return into soil showed significant effects on the microbial diversity, community composition, network structure, keystone microorganisms, and ecosystem functions of tobacco rhizosphere soils. This study provides a scientific basis for the improvement of tobacco field ecosystem functioning and ensuring soil health.
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23
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Gu S, Xiong X, Tan L, Deng Y, Du X, Yang X, Hu Q. Soil microbial community assembly and stability are associated with potato ( Solanum tuberosum L.) fitness under continuous cropping regime. FRONTIERS IN PLANT SCIENCE 2022; 13:1000045. [PMID: 36262646 PMCID: PMC9574259 DOI: 10.3389/fpls.2022.1000045] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 09/16/2022] [Indexed: 06/16/2023]
Abstract
Continuous cropping obstacles caused by the over-cultivation of a single crop trigger soil degradation, yield reduction and the occurrence of plant disease. However, the relationships among stability, complexity and the assembly process of soil microbial community with continuous cropping obstacles remains unclear. In this study, molecular ecological networks analysis (MENs) and inter-domain ecological networks analysis (IDENs), and a new index named cohesion tools were used to calculate the stability and complexity of soil microbial communities from eight potato cultivars grown under a continuous cropping regime by using the high-throughput sequencing data. The results showed that the stability (i.e., robustness index) of the bacterial and fungal communities for cultivar ZS5 was significantly higher, and that the complexity (i.e., cohesion values) was also significantly higher in the bacterial, fungal and inter-domain communities (i.e., bacterial-fungal community) of cultivar ZS5 than other cultivars. Network analysis also revealed that Actinobacteria and Ascomycota were the dominant phyla within intra-domain networks of continuous cropping potato soil communities, while the phyla Proteobacteria and Ascomycota dominated the correlation of the bacterial-fungal network. Infer community assembly mechanism by phylogenetic-bin-based null model analysis (iCAMP) tools were used to calculate the soil bacterial and fungal communities' assembly processes of the eight potato cultivars under continuous cropping regime, and the results showed that the bacterial community was mainly dominated by deterministic processes (64.19% - 81.31%) while the fungal community was mainly dominated by stochastic processes (78.28% - 98.99%), indicating that the continuous-cropping regime mainly influenced the potato soil bacterial community assembly process. Moreover, cultivar ZS5 possessed a relatively lower homogeneous selection, and a higher TP, TN, AP and yield than other cultivars. Our results indicated that the soil microbial network stability and complexity, and community assemble might be associated with yield and soil properties, which would be helpful in the study for resistance to potato continuous cropping obstacles.
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Affiliation(s)
- Songsong Gu
- Hunan Agricultural University, Changsha, China
- Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing, China
| | - Xingyao Xiong
- Hunan Agricultural University, Changsha, China
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Lin Tan
- Hunan Agricultural University, Changsha, China
| | - Ye Deng
- Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing, China
| | - Xiongfeng Du
- Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing, China
| | - Xingxing Yang
- Hunan Center of Crop Germplasm Resources and Breeding Crop, Changsha, China
| | - Qiulong Hu
- Hunan Agricultural University, Changsha, China
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24
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Tao J, Yu S, Jin J, Lu P, Yang Z, Xu Y, Chen Q, Li Z, Cao P. The wilt pathogen induces different variations of root-associated microbiomes of plant. FRONTIERS IN PLANT SCIENCE 2022; 13:1023837. [PMID: 36186049 PMCID: PMC9523445 DOI: 10.3389/fpls.2022.1023837] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Accepted: 09/02/2022] [Indexed: 06/16/2023]
Abstract
Root-associated compartments, including the rhizosphere, rhizoplane, and endosphere, live with diverse microbial communities which profoundly affect plant growth and health. However, a systematic understanding of the microbiome assembly across the rhizosphere, rhizoplane, and endosphere under pathogen invasion remains elusive. Using 16S high-throughput sequencing, we studied how bacterial wilt disease affected the variation and assembly of the three continuous root-associated microbiomes of tobacco. The results indicated that microorganisms were gradually filtered from the rhizosphere to the endosphere. With the pathogen invasion, the rhizosphere, rhizoplane and endosphere microbiomes selected and recruited different beneficial bacterial taxa. Some recruited bacteria were also identified as keystone members in networks (i.e., Bosea in the endosphere). The microbiomes of endosphere and rhizoplane were more sensitive to plant disease than the rhizosphere microbiome. Still, response strategies of the rhizoplane and endosphere to disease were obviously different. Microbial networks of the rhizoplane became complex in diseased samples and genes involved in sporulation formation and cell cycle were enriched. However, microbial networks of the diseased endosphere were disrupted, and functional genes related to nitrogen utilization and chemotaxis were significantly increased, indicating the importance of nitrogen resources supply of plants for the endosphere microbiome under pathogen invasion. Our results provide novel insights for understanding the different responses of the root-associated microbiomes to plant disease.
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Affiliation(s)
- Jiemeng Tao
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou, China
| | - Shizhou Yu
- Molecular Genetics Key Laboratory of China Tobacco, Guizhou Academy of Tobacco, Guiyang, China
| | - Jingjing Jin
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou, China
| | - Peng Lu
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou, China
| | - Zhixiao Yang
- Molecular Genetics Key Laboratory of China Tobacco, Guizhou Academy of Tobacco, Guiyang, China
| | - Yalong Xu
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou, China
| | - Qiansi Chen
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou, China
| | - Zefeng Li
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou, China
| | - Peijian Cao
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou, China
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25
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Garcia J, Gannett M, Wei L, Cheng L, Hu S, Sparks J, Giovannoni J, Kao-Kniffin J. Selection pressure on the rhizosphere microbiome can alter nitrogen use efficiency and seed yield in Brassica rapa. Commun Biol 2022; 5:959. [PMID: 36104398 PMCID: PMC9474469 DOI: 10.1038/s42003-022-03860-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 08/18/2022] [Indexed: 01/03/2023] Open
Abstract
Microbial experimental systems provide a platform to observe how networks of groups emerge to impact plant development. We applied selection pressure for microbiome enhancement of Brassica rapa biomass to examine adaptive bacterial group dynamics under soil nitrogen limitation. In the 9th and final generation of the experiment, selection pressure enhanced B. rapa seed yield and nitrogen use efficiency compared to our control treatment, with no effect between the random selection and control treatments. Aboveground biomass increased for both the high biomass selection and random selection plants. Soil bacterial diversity declined under high B. rapa biomass selection, suggesting a possible ecological filtering mechanism to remove bacterial taxa. Distinct sub-groups of interactions emerged among bacterial phyla such as Proteobacteria and Bacteroidetes in response to selection. Extended Local Similarity Analysis and NetShift indicated greater connectivity of the bacterial community, with more edges, shorter path lengths, and altered modularity through the course of selection for enhanced plant biomass. In contrast, bacterial communities under random selection and no selection showed less complex interaction profiles of bacterial taxa. These results suggest that group-level bacterial interactions could be modified to collectively shift microbiome functions impacting the growth of the host plant under soil nitrogen limitation.
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Affiliation(s)
- Joshua Garcia
- School of Integrative Plant Science, Cornell University, Ithaca, NY, USA
| | - Maria Gannett
- School of Integrative Plant Science, Cornell University, Ithaca, NY, USA
| | - LiPing Wei
- School of Integrative Plant Science, Cornell University, Ithaca, NY, USA
| | - Liang Cheng
- School of Integrative Plant Science, Cornell University, Ithaca, NY, USA
| | - Shengyuan Hu
- Machine Learning Department, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Jed Sparks
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA
| | | | - Jenny Kao-Kniffin
- School of Integrative Plant Science, Cornell University, Ithaca, NY, USA.
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26
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Xing B, Zheng Y, Zhang M, Liu X, Li L, Mou C, Wu Q, Guo H, Shao Q. Biocontrol: Endophytic bacteria could be crucial to fight soft rot disease in the rare medicinal herb, Anoectochilus roxburghii. Microb Biotechnol 2022; 15:2929-2941. [PMID: 36099393 PMCID: PMC9733646 DOI: 10.1111/1751-7915.14142] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 08/21/2022] [Accepted: 08/26/2022] [Indexed: 12/14/2022] Open
Abstract
Microbial destabilization induced by pathogen infection has severely affected plant quality and output, such as Anoectochilus roxburghii, an economically important herb. Soft rot is the main disease that occurs during A. roxburghii culturing. However, the key members of pathogens and their interplay with non-detrimental microorganisms in diseased plants remain largely unsolved. Here, by utilizing a molecular ecological network approach, the interactions within bacterial communities in endophytic compartments and the surrounding soils during soft rot infection were investigated. Significant differences in bacterial diversity and community composition between healthy and diseased plants were observed, indicating that the endophytic communities were strongly influenced by pathogen invasion. Endophytic stem communities of the diseased plants were primarily derived from roots and the root endophytes were largely derived from rhizosphere soils, which depicts a possible pathogen migration image from soils to roots and finally the stems. Furthermore, interactions among microbial members indicated that pathogen invasion might be aided by positively correlated native microbial members, such as Enterobacter and Microbacterium, who may assist in colonization and multiplication through a mutualistic relationship in roots during the pathogen infection process. Our findings will help open new avenues for developing more accurate strategies for biological control of A. roxburghii bacterial soft rot disease.
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Affiliation(s)
- Bingcong Xing
- State Key Laboratory of Subtropical SilvicultureZhejiang A&F UniversityHangzhouChina,Zhejiang Provincial Key Laboratory of Resources Protection and Innovation of Traditional Chinese MedicineZhejiang A&F UniversityHangzhouChina
| | - Ying Zheng
- State Key Laboratory of Subtropical SilvicultureZhejiang A&F UniversityHangzhouChina,Zhejiang Provincial Key Laboratory of Resources Protection and Innovation of Traditional Chinese MedicineZhejiang A&F UniversityHangzhouChina
| | - Man Zhang
- Zhejiang Provincial Key Laboratory of Resources Protection and Innovation of Traditional Chinese MedicineZhejiang A&F UniversityHangzhouChina
| | - Xinting Liu
- State Key Laboratory of Subtropical SilvicultureZhejiang A&F UniversityHangzhouChina,Zhejiang Provincial Key Laboratory of Resources Protection and Innovation of Traditional Chinese MedicineZhejiang A&F UniversityHangzhouChina
| | - Lihong Li
- State Key Laboratory of Subtropical SilvicultureZhejiang A&F UniversityHangzhouChina,Zhejiang Provincial Key Laboratory of Resources Protection and Innovation of Traditional Chinese MedicineZhejiang A&F UniversityHangzhouChina
| | - Chenhao Mou
- State Key Laboratory of Subtropical SilvicultureZhejiang A&F UniversityHangzhouChina,Zhejiang Provincial Key Laboratory of Resources Protection and Innovation of Traditional Chinese MedicineZhejiang A&F UniversityHangzhouChina
| | - Qichao Wu
- State Key Laboratory of Subtropical SilvicultureZhejiang A&F UniversityHangzhouChina,Zhejiang Provincial Key Laboratory of Resources Protection and Innovation of Traditional Chinese MedicineZhejiang A&F UniversityHangzhouChina
| | - Haipeng Guo
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro‐Products, School of Marine SciencesNingbo UniversityNingboChina
| | - Qingsong Shao
- State Key Laboratory of Subtropical SilvicultureZhejiang A&F UniversityHangzhouChina,Zhejiang Provincial Key Laboratory of Resources Protection and Innovation of Traditional Chinese MedicineZhejiang A&F UniversityHangzhouChina
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27
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Liu S, Wu J, Wang H, Lukianova A, Tokmakova A, Jin Z, Tan S, Chen S, Wang Y, Du Y, Miroshnikov KA, Xie J. Soil Layers Impact Lithocarpus Soil Microbial Composition in the Ailao Mountains Subtropical Forest, Yunnan, China. J Fungi (Basel) 2022; 8:jof8090948. [PMID: 36135673 PMCID: PMC9504396 DOI: 10.3390/jof8090948] [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] [Received: 07/07/2022] [Revised: 09/05/2022] [Accepted: 09/06/2022] [Indexed: 11/16/2022] Open
Abstract
Plant litter decomposition is a complex, long-term process. The decomposition of litterfall is a major process influencing nutrient balance in forest soil. The soil microbiome is exceptionally diverse and is an essential regulator of litter decomposition. However, the microbiome composition and the interaction with litterfall and soil remain poorly understood. In this study, we examined the bacterial and fungal community composition of Lithocarpus across soil samples from different sampling seasons. Our results displayed that the microbiome assembly along the soil layer is influenced predominantly by the soil layer rather than by the sampling season. We identified that the soil layer strongly affected network complexity and that bacterial and fungal microbiomes displayed different patterns in different soil layers. Furthermore, source tracking and community composition analysis indicated that there are significantly different between soil and litter. Moreover, our results demonstrate that few dominant taxa (2% and 4% of bacterial and fungal phylotypes) dominated in the different soil layers. Hydnodontaceae was identified as the most important biomarker taxa for humic fragmented litter fungal microbiome and Nigrospora and Archaeorhizomycetaceae for organic soil and the organic mineral soil layer, and the phylum of Acidobacteria for the bacteria microbiome. Our work provides comprehensive evidence of significant microbiome differences between soil layers and has important implications for further studying soil microbiome ecosystem functions.
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Affiliation(s)
- Sijia Liu
- National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Forestry University, Beijing 100083, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, College of Biological Sciences and Technology, Beijing Forestry University, Ministry of Education, Beijing 100083, China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, Beijing Forestry University, Beijing 100083, China
| | - Jiadong Wu
- National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Forestry University, Beijing 100083, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, College of Biological Sciences and Technology, Beijing Forestry University, Ministry of Education, Beijing 100083, China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, Beijing Forestry University, Beijing 100083, China
| | - Haofei Wang
- National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Forestry University, Beijing 100083, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, College of Biological Sciences and Technology, Beijing Forestry University, Ministry of Education, Beijing 100083, China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, Beijing Forestry University, Beijing 100083, China
| | - Anna Lukianova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia
| | - Anna Tokmakova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia
| | - Zhelun Jin
- National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Forestry University, Beijing 100083, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, College of Biological Sciences and Technology, Beijing Forestry University, Ministry of Education, Beijing 100083, China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, Beijing Forestry University, Beijing 100083, China
| | - Shuxian Tan
- National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Forestry University, Beijing 100083, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, College of Biological Sciences and Technology, Beijing Forestry University, Ministry of Education, Beijing 100083, China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, Beijing Forestry University, Beijing 100083, China
| | - Sisi Chen
- National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Forestry University, Beijing 100083, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, College of Biological Sciences and Technology, Beijing Forestry University, Ministry of Education, Beijing 100083, China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, Beijing Forestry University, Beijing 100083, China
| | - Yue Wang
- National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Forestry University, Beijing 100083, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, College of Biological Sciences and Technology, Beijing Forestry University, Ministry of Education, Beijing 100083, China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, Beijing Forestry University, Beijing 100083, China
| | - Yuxin Du
- National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Forestry University, Beijing 100083, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, College of Biological Sciences and Technology, Beijing Forestry University, Ministry of Education, Beijing 100083, China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, Beijing Forestry University, Beijing 100083, China
| | - Konstantin A. Miroshnikov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia
| | - Jianbo Xie
- National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Forestry University, Beijing 100083, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, College of Biological Sciences and Technology, Beijing Forestry University, Ministry of Education, Beijing 100083, China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, Beijing Forestry University, Beijing 100083, China
- Correspondence: ; Tel./Fax: +86-10-62336007
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Diwan D, Rashid MM, Vaishnav A. Current understanding of plant-microbe interaction through the lenses of multi-omics approaches and their benefits in sustainable agriculture. Microbiol Res 2022; 265:127180. [PMID: 36126490 DOI: 10.1016/j.micres.2022.127180] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 08/26/2022] [Accepted: 08/27/2022] [Indexed: 11/28/2022]
Abstract
The success of sustainable agricultural practices has now become heavily dependent on the interactions between crop plants and their associated microbiome. Continuous advancement in high throughput sequencing platforms, omics-based approaches, and gene editing technologies has remarkably accelerated this area of research. It has enabled us to characterize the interactions of plants with associated microbial communities more comprehensively and accurately. Furthermore, the genomic and post-genomic era has significantly refined our perspective toward the complex mechanisms involved in those interactions, opening new avenues for efficiently deploying the knowledge in developing sustainable agricultural practices. This review focuses on our fundamental understanding of plant-microbe interactions and the contribution of existing multi-omics approaches, including those under active development and their tremendous success in unraveling different aspects of the complex network between plant hosts and microbes. In addition, we have also discussed the importance of sustainable and eco-friendly agriculture and the associated outstanding challenges ahead.
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Affiliation(s)
- Deepti Diwan
- Washington University School of Medicine, Saint Louis, MO 63110, USA.
| | - Md Mahtab Rashid
- Department of Plant Pathology, Bihar Agricultural University, Sabour, Bhagalpur, Bihar 813210, India; Department of Mycology and Plant Pathology, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi, Uttar Pradesh 221005, India
| | - Anukool Vaishnav
- Department of Biotechnology, GLA University, Mathura, Uttar Pradesh 281121, India; Department of Plant and Microbial Biology, University of Zürich, Zollikerstrasse 107, Zürich CH-8008, Switzerland; Plant-Soil Interaction Group, Agroscope (Reckenholz), Reckenholzstrasse 191, Zürich 8046, Switzerland
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Huang K, Sun X, Zou Y, Li H, Xu P, Zhang W, Zhang Y, Li H, Sun H, Wang W, Pang M, Luo J. Comparison of the Endophytic Bacterial Microbiota of Asymptomatic and Symptomatic Ginger Rhizomes During the Activation of Adventitious Bud Development. PLANT DISEASE 2022; 106:2470-2479. [PMID: 35286131 DOI: 10.1094/pdis-09-21-2069-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Bacterial infections are the cause of rhizome rot in ginger (Zingiber officinale). Key members of the endophytic microbial community in ginger rhizomes have not been identified, and their impact on the decay of rhizomes during the activation of adventitious bud development has not been investigated. High-throughput, 16S rRNA amplicon sequencing and inoculation experiments were used to analyze the microbial diversity, community structure and composition, and pathogenicity of isolated bacteria. Our results indicated that the composition of the endophytic microbiota underwent a shift during the progression of rhizome rot disease. Enterobacteriaceae, Lachnospiraceae, and the bacterial genera Clostridium, Bacteroides, Acrobacter, Dysgonomonas, Anaerosinus, Pectobacterium, and Lactococcus were relatively abundant in the bacterial community of rhizomes exhibiting bacterial decay symptoms but were also present in asymptomatic rhizomes. The presence of Enterobacteriaceae and Pseudomonadaceae were positively correlated (ρ = 0.83) at the beginning of the sampling period in the symptomatic group, while a positive correlation (ρ = 0.89) was only observed after 20 days in the asymptomatic group. These data indicate that the co-occurrence of Enterobacteriaceae and Pseudomonadaceae may be associated with the development of ginger rot. Bacterial taxa isolated from ginger rhizomes, such as Enterobacter cloacae, E. hormaechei, and Pseudomonas putida, induced obvious rot symptoms when they were inoculated on ginger rhizomes. Notably, antibiotic-producing bacterial taxa in the Streptococcaceae and Flavobacteriaceae were also relatively abundant in rhizomes with rot and appeared to be linked to the onset of rhizome rot disease. Our results provide important information on the establishment and management of disease in ginger rhizomes.
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Affiliation(s)
- Ke Huang
- College of Landscape Architecture and Life Science/Institute of Special Plants, Chongqing University of Arts & Sciences, Yongchuan, 402160, China
- Institute of Microbial Ecology, Chongqing University of Arts & Sciences, Yongchuan, 402160, China
| | - Xiangcheng Sun
- West China Biopharm Research Institute, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Yong Zou
- College of Landscape Architecture and Life Science/Institute of Special Plants, Chongqing University of Arts & Sciences, Yongchuan, 402160, China
| | - Huihe Li
- College of Landscape Architecture and Life Science/Institute of Special Plants, Chongqing University of Arts & Sciences, Yongchuan, 402160, China
| | - Panpan Xu
- College of Life Sciences, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Wenlin Zhang
- College of Landscape Architecture and Life Science/Institute of Special Plants, Chongqing University of Arts & Sciences, Yongchuan, 402160, China
| | - Yin Zhang
- Agricultural and Rural Committee of Chongqing Rongchang District, Rongchang, 402460, China
| | - Honglei Li
- College of Landscape Architecture and Life Science/Institute of Special Plants, Chongqing University of Arts & Sciences, Yongchuan, 402160, China
| | - Hanchang Sun
- College of Landscape Architecture and Life Science/Institute of Special Plants, Chongqing University of Arts & Sciences, Yongchuan, 402160, China
| | - Wei Wang
- College of Landscape Architecture and Life Science/Institute of Special Plants, Chongqing University of Arts & Sciences, Yongchuan, 402160, China
- Institute of Microbial Ecology, Chongqing University of Arts & Sciences, Yongchuan, 402160, China
| | - Min Pang
- College of Landscape Architecture and Life Science/Institute of Special Plants, Chongqing University of Arts & Sciences, Yongchuan, 402160, China
| | - Jie Luo
- Department of Pharmaceutical, Chongqing University of Arts and Sciences, Chongqing University of Arts & Sciences, Yongchuan, 402160, China
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Dastogeer KMG, Yasuda M, Okazaki S. Microbiome and pathobiome analyses reveal changes in community structure by foliar pathogen infection in rice. Front Microbiol 2022; 13:949152. [PMID: 35983324 PMCID: PMC9379101 DOI: 10.3389/fmicb.2022.949152] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 07/12/2022] [Indexed: 12/11/2022] Open
Abstract
Increasing evidence suggests that the plant rhizosphere may recruit beneficial microbes to suppress soil-borne pathogens, but microbiome assembly due to foliar pathogen infection and ecological mechanisms that govern microbiome assembly and functions in the diseased host are not fully understood. To provide a comprehensive view of the rice-associated microbiome, we compared bacterial and fungal communities of healthy rice and those infected with Magnaporthe oryzae, the causal agent of blast disease. We found that the soil had a greater diversity of bacterial and fungal communities than plant endospheric communities. There was no significant dysbiosis of bacterial and fungal microbiome diversity due to disease, but it caused a substantial alteration of bacterial community structure in the root and rhizosphere compartments. The pathobiome analysis showed that the microbiome community structure of leaf and grain tissues was changed markedly at the pathogen infection site, although the alpha diversity did not change. Correspondingly, the relative abundances of some bacteria and fungi were clearly altered in symptomatic tissues. We noted an increase in Rhizobium bacteria and a decline of Tylospora, Clohesyomyces, and Penicillium fungi in the symptomatic leaf and grain tissues from both locations. According to the inferred microbial network, several direct interactions between M. oryzae and other microbes were identified. The majority of edges in the interaction network were positive in diseased samples; contrastingly, the number of edges was much lower in the healthy samples. With source tracking analysis, we observed a sharp contrast in the source of root endosphere bacteria due to Magnaporthe infection. Whereas the majority (71%) of healthy root bacteria could be tracked from the soil, only a very small portion (17%) could be tracked from the soil for diseased samples. These results advanced our understanding and provided potential ideas and a theoretical basis for studying pathobiome and exploiting the microbiome for sustainable agriculture.
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Affiliation(s)
- Khondoker M. G. Dastogeer
- Plant Microbiology Laboratory, Tokyo University of Agriculture and Technology, Tokyo, Japan
- Department of Plant Pathology, Bangladesh Agricultural University, Mymensingh, Bangladesh
- *Correspondence: Khondoker M. G. Dastogeer
| | - Michiko Yasuda
- Plant Microbiology Laboratory, Tokyo University of Agriculture and Technology, Tokyo, Japan
| | - Shin Okazaki
- Plant Microbiology Laboratory, Tokyo University of Agriculture and Technology, Tokyo, Japan
- Shin Okazaki
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31
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Zhao Y, Lou Y, Qin W, Cai J, Zhang P, Hu B. Interval aeration improves degradation and humification by enhancing microbial interactions in the composting process. BIORESOURCE TECHNOLOGY 2022; 358:127296. [PMID: 35562028 DOI: 10.1016/j.biortech.2022.127296] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 05/06/2022] [Accepted: 05/07/2022] [Indexed: 06/15/2023]
Abstract
Five full-scale food waste composts were conducted under different aeration frequencies (no aeration, aeration at different intervals, and continuous aeration) to reveal the optimal strategy and its microbial mechanisms. The highest degradation rate (77.2%) and humus content (29.3%) were observed in Treatment D with interval aeration (aeration 20 min, pause 10 min). Aeration influenced the degradation and humification rate by regulating microbial interactions. The microbial interactions peaked in Treatment D, with a 1.30-fold increase. In terms of the microbial community, Thermobifida was a key genus for improving positive cohesion, fulfilling three criteria (high abundance, high occurrence frequency, and significant differences between treatments). The aeration strategy employed in Treatment D not only increased relative abundance of Thermobifida (1.2 times higher) but also strengthened interaction between it and functional genera (34 nodes). Overall, interval aeration, featured by 20 min aeration and 10 min pause, could increase microbial interactions and improve composting efficiency.
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Affiliation(s)
- Yuxiang Zhao
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China
| | - Yicheng Lou
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China
| | - Weizhen Qin
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China
| | - Jingjie Cai
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China
| | - Pan Zhang
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China
| | - Baolan Hu
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China; Zhejiang Province Key Laboratory for Water Pollution Control and Environmental Safety, Hangzhou, China; Key Laboratory of Environment Remediation and Ecological Health, Ministry of Education, College of Environmental Resource Sciences, Zhejiang University, Hangzhou, China.
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32
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Zeng Q, Man X, Dai Y, Liu H. Pseudomonas spp. Enriched in Endophytic Community of Healthy Cotton Plants Inhibit Cotton Verticillium Wilt. Front Microbiol 2022; 13:906732. [PMID: 35923406 PMCID: PMC9339998 DOI: 10.3389/fmicb.2022.906732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 06/21/2022] [Indexed: 11/29/2022] Open
Abstract
The plant microbiome plays a fundamental role in plant growth and health. However, detailed information regarding the plant endophytic microbiome during the infection period of a pathogen is largely unknown. Here, we investigated the microbial community of healthy and diseased cotton plants and the root exudate profiles of susceptible and resistant cultivars utilizing high-throughput sequencing and metabolomics. The results showed that the pathogen infection reduced bacterial diversity and significantly affected the bacterial community composition. The microbiome assembly is shaped predominantly by cultivars. The endophytic microbiome of the infected plants showed greater complexity than the healthy plants in network analysis. The results displayed that a total of 76 compounds were significantly different in the two groups, with 18 compounds showing a higher relative abundance in the resistant cultivars and 58 compounds in the susceptible cultivars. Pathway enrichment analysis showed that pathways related to plant hormone signal transduction, biosynthesis of various secondary metabolites, and biosynthesis and metabolism of amino acids were prominently altered. We also demonstrate that plants inoculated with Pseudomonas sp. strains showed increased resistance to the cotton Verticillium wilt compared with the control plants in pot experiments. Overall, it showed that the pathogen infection affected the community composition, and healthy plants displayed an enriched beneficial microbiome to combat the plant disease. These findings significantly advance our understanding of the endophytic microbiome assembly under the pathogen infection and develop microbiome-based solutions for sustainable crop production systems.
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Affiliation(s)
- Qingchao Zeng
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China
| | - Xiaowu Man
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China
| | - Yucheng Dai
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China
| | - Haiyang Liu
- Institute of Plant Protection, Xinjiang Academy of Agricultural Sciences, Ürümqi, China
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Wang Z, Zhang Y, Bo G, Zhang Y, Chen Y, Shen M, Zhang P, Li G, Zhou J, Li Z, Yang J. Ralstonia solanacearum Infection Disturbed the Microbiome Structure Throughout the Whole Tobacco Crop Niche as Well as the Nitrogen Metabolism in Soil. Front Bioeng Biotechnol 2022; 10:903555. [PMID: 35800334 PMCID: PMC9253565 DOI: 10.3389/fbioe.2022.903555] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 05/27/2022] [Indexed: 01/23/2023] Open
Abstract
Infections of Ralstonia solanacearum result in huge agricultural and economic losses. As known, the proposal of effective biological measures for the control of soil disease depends on the complex interactions between pathogens, soil microbiota and soil properties, which remains to be studied. Previous studies have shown that the phosphorus availability increased pathobiome abundance and infection of rhizosphere microbial networks by Ralstonia. Similarly, as a nutrient necessary for plant growth, nitrogen has also been suggested to be strongly associated with Ralstonia infection. To further reveal the relationship between soil nitrogen content, soil nitrogen metabolism and Ralstonia pathogens, we investigated the effects of R. solanacearum infection on the whole tobacco niche and its soil nitrogen metabolism. The results demonstrated that Ralstonia infection resulted in a reduction of the ammonium nitrogen in soil and the total nitrogen in plant. The microbes in rhizosphere and the plant’s endophytes were also significantly disturbed by the infection. Rhodanobacter which is involved in nitrogen metabolism significantly decreased. Moreover, the load of microbial nitrogen metabolism genes in the rhizosphere soil significantly varied after the infection, resulting in a stronger denitrification process in the diseased soil. These results suggest that the application management strategies of nitrogen fertilizing and a balanced regulation of the rhizosphere and the endophytic microbes could be promising strategies in the biological control of soil-borne secondary disasters.
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Affiliation(s)
- Zhaobao Wang
- Energy-Rich Compounds Production by Photosynthetic Carbon Fixation Research Center, Shandong Key Lab of Applied Mycology, College of Life Sciences, Qingdao Agricultural University, Qingdao, China
| | - Yuzhen Zhang
- Energy-Rich Compounds Production by Photosynthetic Carbon Fixation Research Center, Shandong Key Lab of Applied Mycology, College of Life Sciences, Qingdao Agricultural University, Qingdao, China
| | - Guodong Bo
- Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Yanping Zhang
- Energy-Rich Compounds Production by Photosynthetic Carbon Fixation Research Center, Shandong Key Lab of Applied Mycology, College of Life Sciences, Qingdao Agricultural University, Qingdao, China
| | - Yu Chen
- Grassland Agri-Husbandry Research Center, College of Grassland Science, Qingdao Agricultural University, Qingdao, China
| | - Minchong Shen
- Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Peng Zhang
- Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Guitong Li
- Energy-Rich Compounds Production by Photosynthetic Carbon Fixation Research Center, Shandong Key Lab of Applied Mycology, College of Life Sciences, Qingdao Agricultural University, Qingdao, China
| | - Jie Zhou
- Energy-Rich Compounds Production by Photosynthetic Carbon Fixation Research Center, Shandong Key Lab of Applied Mycology, College of Life Sciences, Qingdao Agricultural University, Qingdao, China
| | - Zhengfeng Li
- China Tobacco Yunnan Industrial Co., Ltd., Kunming, China
| | - Jianming Yang
- Energy-Rich Compounds Production by Photosynthetic Carbon Fixation Research Center, Shandong Key Lab of Applied Mycology, College of Life Sciences, Qingdao Agricultural University, Qingdao, China
- *Correspondence: Jianming Yang,
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Feng K, Peng X, Zhang Z, Gu S, He Q, Shen W, Wang Z, Wang D, Hu Q, Li Y, Wang S, Deng Y. iNAP: An integrated network analysis pipeline for microbiome studies. IMETA 2022; 1:e13. [PMID: 38868563 PMCID: PMC10989900 DOI: 10.1002/imt2.13] [Citation(s) in RCA: 136] [Impact Index Per Article: 68.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 01/28/2022] [Accepted: 01/29/2022] [Indexed: 02/05/2023]
Abstract
Integrated network analysis pipeline (iNAP) is an online analysis pipeline for generating and analyzing comprehensive ecological networks in microbiome studies. It is implemented in two sections, that is, network construction and network analysis, and integrates many open-access tools. Network construction contains multiple feasible alternatives, including correlation-based approaches (Pearson's correlation and Spearman's rank correlation along with random matrix theory, and sparse correlations for compositional data) and conditional dependence-based methods (extended local similarity analysis and sparse inverse covariance estimation for ecological association inference), while network analysis provides topological structures at different levels and the potential effects of environmental factors on network structures. Considering the full workflow, from microbiome data set to network result, iNAP contains the molecular ecological network analysis pipeline and interdomain ecological network analysis pipeline (IDENAP), which correspond to the intradomain and interdomain associations of microbial species at multiple taxonomic levels. Here, we describe the detailed workflow by taking IDENAP as an example and show the comprehensive steps to assist researchers to conduct the relevant analyses using their own data sets. Afterwards, some auxiliary tools facilitating the pipeline are introduced to effectively aid in the switch from local analysis to online operations. Therefore, iNAP, as an easy-to-use platform that provides multiple network-associated tools and approaches, can enable researchers to better understand the organization of microbial communities. iNAP is available at http://mem.rcees.ac.cn:8081 with free registration.
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Affiliation(s)
- Kai Feng
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco‐Environmental SciencesChinese Academy of SciencesBeijingChina
| | - Xi Peng
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco‐Environmental SciencesChinese Academy of SciencesBeijingChina
- Collegeof Resources and EnvironmentUniversity of Chinese Academy of SciencesBeijingChina
| | - Zheng Zhang
- Institute for Marine Science and TechnologyShandong UniversityQingdaoChina
| | - Songsong Gu
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco‐Environmental SciencesChinese Academy of SciencesBeijingChina
| | - Qing He
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco‐Environmental SciencesChinese Academy of SciencesBeijingChina
- Collegeof Resources and EnvironmentUniversity of Chinese Academy of SciencesBeijingChina
| | - Wenli Shen
- Institute for Marine Science and TechnologyShandong UniversityQingdaoChina
| | - Zhujun Wang
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco‐Environmental SciencesChinese Academy of SciencesBeijingChina
- Collegeof Resources and EnvironmentUniversity of Chinese Academy of SciencesBeijingChina
| | - Danrui Wang
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco‐Environmental SciencesChinese Academy of SciencesBeijingChina
- Collegeof Resources and EnvironmentUniversity of Chinese Academy of SciencesBeijingChina
| | - Qiulong Hu
- College of HorticultureHunan Agricultural UniversityChangshaChina
| | - Yan Li
- West China Hospital of Stomatology, State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral DiseasesSichuan UniversityChengduChina
| | - Shang Wang
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco‐Environmental SciencesChinese Academy of SciencesBeijingChina
| | - Ye Deng
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco‐Environmental SciencesChinese Academy of SciencesBeijingChina
- Collegeof Resources and EnvironmentUniversity of Chinese Academy of SciencesBeijingChina
- Institute for Marine Science and TechnologyShandong UniversityQingdaoChina
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35
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Zhao Y, Weng Q, Hu B. Microbial interaction promote the degradation rate of organic matter in thermophilic period. WASTE MANAGEMENT (NEW YORK, N.Y.) 2022; 144:11-18. [PMID: 35299060 DOI: 10.1016/j.wasman.2022.03.006] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 02/19/2022] [Accepted: 03/08/2022] [Indexed: 06/14/2023]
Abstract
Composting is an efficient, microbe-driven method for the biodegradation of solid organic substrates. In such a complex engineering ecosystem, microbial interaction is more important to function than relative abundance and alpha diversity. However, microbial interaction and its driving force in the composting process has been rarely reported. Thus, we combined network analysis and positive cohesion to analyze the relationship between cooperation among bacteria taxa and the degradation of organic matter in ten industrial-scale food waste composting piles. The results showed that although the complexity of network and microbial diversity were inhibited by high temperature, microbial cooperation was stimulated in the thermophilic period. The positive cohesion, which reflected the degree of microbial cooperation, tended to be positively correlated with the degradation rate of organic matter, functional genera, and genes associated with organic matter degradation. Thus, microbial cooperation was a key factor in the promotion of the degradation of organic matter. From the insight microbial community, Thermobifida was the genera with high abundance, high occurrence frequency, and high contributions to microbial structure. Additionally, it was not only highly associated with the degree of cooperation but was also highly linked with the functional genera in the composting, implying that it might play an important role in regulating cooperation to promote the functional genera. Our research provides a deep understanding of the interaction among bacteria taxa during the composting process. Focusing on the abundance of Thermobifida might be an efficient way to improve composting quality by enhancing the cooperation of microbes.
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Affiliation(s)
- Yuxiang Zhao
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China
| | - Qin Weng
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China
| | - Baolan Hu
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China; Zhejiang Province Key Laboratory for Water Pollution Control and Environmental Safety, Hangzhou, China; Key Laboratory of Environment Remediation and Ecological Health, Ministry of Education, College of Environmental Resource Sciences, Zhejiang University, Hangzhou, China.
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Dal’Rio I, Mateus JR, Seldin L. Unraveling the Tropaeolum majus L. (Nasturtium) Root-Associated Bacterial Community in Search of Potential Biofertilizers. Microorganisms 2022; 10:638. [PMID: 35336212 PMCID: PMC8950702 DOI: 10.3390/microorganisms10030638] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 03/14/2022] [Accepted: 03/15/2022] [Indexed: 01/27/2023] Open
Abstract
Although Tropaeolum majus (nasturtium) is an agriculturally and economically important plant, especially due to the presence of edible flowers and its medicinal properties, its microbiome is quite unexplored. Here, the structure of the total bacterial community associated with the rhizosphere, endosphere and bulk soil of T. majus was determined by 16S rRNA amplicon metagenomic sequencing. A decrease in diversity and richness from bulk soil to the rhizosphere and from the rhizosphere to the endosphere was observed in the alpha diversity analyses. The phylum Proteobacteria was the most dominant in the bacteriome of the three sites evaluated, whereas the genera Pseudomonas and Ralstonia showed a significantly higher relative abundance in the rhizosphere and endosphere communities, respectively. Plant growth-promoting bacteria (236 PGPB) were also isolated from the T. majus endosphere, and 76 strains belonging to 11 different genera, mostly Serratia, Raoultella and Klebsiella, showed positive results for at least four out of six plant growth-promoting tests performed. The selection of PGPB associated with T. majus can result in the development of a biofertilizer with activity against phytopathogens and capable of favoring the development of this important plant.
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Affiliation(s)
| | | | - Lucy Seldin
- Laboratório de Genética Microbiana, Departamento de Microbiologia Geral, Instituto de Microbiologia Paulo de Góes, Centro de Ciências da Saúde, Universidade Federal do Rio de Janeiro, Bloco I, Ilha do Fundão, Rio de Janeiro CEP 21941-902, Brazil; (I.D.); (J.R.M.)
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Li M, Pommier T, Yin Y, Wang J, Gu S, Jousset A, Keuskamp J, Wang H, Wei Z, Xu Y, Shen Q, Kowalchuk GA. Indirect reduction of Ralstonia solanacearum via pathogen helper inhibition. THE ISME JOURNAL 2022; 16:868-875. [PMID: 34671104 PMCID: PMC8857195 DOI: 10.1038/s41396-021-01126-2] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/04/2021] [Revised: 09/02/2021] [Accepted: 09/20/2021] [Indexed: 11/26/2022]
Abstract
The rhizosphere microbiome forms a first line of defense against soilborne pathogens. To date, most microbiome enhancement strategies have relied on bioaugmentation with antagonistic microorganisms that directly inhibit pathogens. Previous studies have shown that some root-associated bacteria are able to facilitate pathogen growth. We therefore hypothesized that inhibiting such pathogen helpers may help reduce pathogen densities. We examined tripartite interactions between a model pathogen, Ralstonia solanacearum, two model helper strains and a collection of 46 bacterial isolates recovered from the tomato rhizosphere. This system allowed us to examine the importance of direct (effects of rhizobacteria on pathogen growth) and indirect (effects of rhizobacteria on helper growth) pathways affecting pathogen growth. We found that the interaction between rhizosphere isolates and the helper strains was the major determinant of pathogen suppression both in vitro and in vivo. We therefore propose that controlling microbiome composition to prevent the growth of pathogen helpers may become part of sustainable strategies for pathogen control.
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Affiliation(s)
- Mei Li
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Key Lab of Plant Immunity, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, National Engineering Research Center for Organic-based Fertilizers, Nanjing Agricultural University, 210095, Nanjing, PR China
- Institute for Environmental Biology, Ecology & Biodiversity, Utrecht University, Padualaan 8, 3584CH, Utrecht, The Netherlands
| | - Thomas Pommier
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR Ecologie Microbienne, F-69622, Villeurbanne, France
| | - Yue Yin
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Key Lab of Plant Immunity, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, National Engineering Research Center for Organic-based Fertilizers, Nanjing Agricultural University, 210095, Nanjing, PR China
| | - Jianing Wang
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Key Lab of Plant Immunity, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, National Engineering Research Center for Organic-based Fertilizers, Nanjing Agricultural University, 210095, Nanjing, PR China
| | - Shaohua Gu
- Center for Quantitative Biology and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, PR China
| | - Alexandre Jousset
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Key Lab of Plant Immunity, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, National Engineering Research Center for Organic-based Fertilizers, Nanjing Agricultural University, 210095, Nanjing, PR China
| | - Joost Keuskamp
- Institute for Environmental Biology, Ecology & Biodiversity, Utrecht University, Padualaan 8, 3584CH, Utrecht, The Netherlands
- Biont Research, Abeelstraat 33, 3552 RC, Utrecht, The Netherlands
| | - Honggui Wang
- School of Environmental Science and Engineering, Yangzhou University, 225127, Yangzhou, Jiangsu, PR China
| | - Zhong Wei
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Key Lab of Plant Immunity, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, National Engineering Research Center for Organic-based Fertilizers, Nanjing Agricultural University, 210095, Nanjing, PR China.
| | - Yangchun Xu
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Key Lab of Plant Immunity, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, National Engineering Research Center for Organic-based Fertilizers, Nanjing Agricultural University, 210095, Nanjing, PR China
| | - Qirong Shen
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Key Lab of Plant Immunity, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, National Engineering Research Center for Organic-based Fertilizers, Nanjing Agricultural University, 210095, Nanjing, PR China
| | - George A Kowalchuk
- Institute for Environmental Biology, Ecology & Biodiversity, Utrecht University, Padualaan 8, 3584CH, Utrecht, The Netherlands
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38
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Gómez-Lama Cabanás C, Wentzien NM, Zorrilla-Fontanesi Y, Valverde-Corredor A, Fernández-González AJ, Fernández-López M, Mercado-Blanco J. Impacts of the Biocontrol Strain Pseudomonas simiae PICF7 on the Banana Holobiont: Alteration of Root Microbial Co-occurrence Networks and Effect on Host Defense Responses. Front Microbiol 2022; 13:809126. [PMID: 35242117 PMCID: PMC8885582 DOI: 10.3389/fmicb.2022.809126] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Accepted: 01/10/2022] [Indexed: 12/18/2022] Open
Abstract
The impact of the versatile biocontrol and plant-growth-promoting rhizobacteria Pseudomonas simiae PICF7 on the banana holobiont under controlled conditions was investigated. We examine the fate of this biological control agent (BCA) upon introduction in the soil, the effect on the banana root microbiota, and the influence on specific host genetic defense responses. While the presence of strain PICF7 significantly altered neither the composition nor the structure of the root microbiota, a significant shift in microbial community interactions through co-occurrence network analysis was observed. Despite the fact that PICF7 did not constitute a keystone, the topology of this network was significantly modified-the BCA being identified as a constituent of one of the main network modules in bacterized plants. Gene expression analysis showed the early suppression of several systemic acquired resistance and induced systemic resistance (ISR) markers. This outcome occurred at the time in which the highest relative abundance of PICF7 was detected. The absence of major and permanent changes on the banana holobiont upon PICF7 introduction poses advantages regarding the use of this beneficial rhizobacteria under field conditions. Indeed a BCA able to control the target pathogen while altering as little as possible the natural host-associated microbiome should be a requisite when developing effective bio-inoculants.
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Affiliation(s)
- Carmen Gómez-Lama Cabanás
- Departamento de Protección de Cultivos, Instituto de Agricultura Sostenible, Consejo Superior de Investigaciones Científicas, Córdoba, Spain
| | - Nuria M. Wentzien
- Departamento de Microbiología del Suelo y Sistemas Simbióticos, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | | | - Antonio Valverde-Corredor
- Departamento de Protección de Cultivos, Instituto de Agricultura Sostenible, Consejo Superior de Investigaciones Científicas, Córdoba, Spain
| | - Antonio J. Fernández-González
- Departamento de Microbiología del Suelo y Sistemas Simbióticos, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Manuel Fernández-López
- Departamento de Microbiología del Suelo y Sistemas Simbióticos, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Jesús Mercado-Blanco
- Departamento de Protección de Cultivos, Instituto de Agricultura Sostenible, Consejo Superior de Investigaciones Científicas, Córdoba, Spain
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Wang SS, Liu JM, Sun J, Huang YT, Jin N, Li MM, Liang YT, Fan B, Wang FZ. Analysis of Endophytic Bacterial Diversity From Different Dendrobium Stems and Discovery of an Endophyte Produced Dendrobine-Type Sesquiterpenoid Alkaloids. Front Microbiol 2022; 12:775665. [PMID: 35069479 PMCID: PMC8767021 DOI: 10.3389/fmicb.2021.775665] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 11/25/2021] [Indexed: 11/13/2022] Open
Abstract
As the unique component of Dendrobium, dendrobine-type sesquiterpenoid alkaloids (DSAs) possess a variety of medicinal properties. It has been well documented that plant endophytes can in vitro synthesize secondary metabolites identical or similar to metabolites produced by their host plants. This study aimed to investigate the composition and distribution of endophytic bacteria of Dendrobium stems by Illumina MiSeq platform sequencing and cultivation-dependent methods and then to assess the potential for endophytic bacteria to produce DSAs. Results indicated that it was necessary to combine both cultivation-dependent and cultivation-independent methods to analyze the community structure of endophytic bacterial in plants comprehensively. The length of the Dendrobium stems influenced the endophytic bacterial community. The diversity and richness of endophytic bacteria in group J10_15cm of stems were the highest, which showed a significant difference from the other stem groups. However, there was no certain connection between the diversity and richness of endophytic bacteria and the content of dendrobine. It was most likely due to the influence of several specific endophytic bacteria genera, such as Sphingomonas and Rhodococcus. Athelia rolfsii, Myrothecium roridum, as pathogenic fungi, and Pectobacterium carotovorum subsp. actinidiae, as pathogenic bacteria of Dendrobium, were used to determine the antimicrobial activities. In these assays, six strains belonging to five genera showed antimicrobial activity against at least two phytopathogens. The strain BL-YJ10_15-29 (Paracoccus pueri THG-N2.35, 98.98%) showed the best antimicrobial activity against the three phytopathogens. In addition, 2 DSAs (6-hydroxydendrobine and nobilonine) were identified in the fermentation supernatant of the strain CM-YJ10_15-44 (Pseudomonas protegens CHA0, 99.24%), whereas the whole-genome analysis results further demonstrated that the precursors of the two DSAs [geranyl-PP and (E, E)-famesyl-PP] were synthesized mainly through the methyl-D-erythritol 4-phosphate pathway in this strain. This study provides new insight into the studies on the biosynthesis of DSAs and provides potential biocontrol bacteria.
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Affiliation(s)
- Shan-Shan Wang
- Key Laboratory of Agro-Products Quality and Safety Control in Storage and Transport Process, Ministry of Agriculture and Rural Affairs/Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jia-Meng Liu
- Key Laboratory of Agro-Products Quality and Safety Control in Storage and Transport Process, Ministry of Agriculture and Rural Affairs/Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jing Sun
- Key Laboratory of Agro-Products Quality and Safety Control in Storage and Transport Process, Ministry of Agriculture and Rural Affairs/Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Ya-Tao Huang
- Key Laboratory of Agro-Products Quality and Safety Control in Storage and Transport Process, Ministry of Agriculture and Rural Affairs/Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Nuo Jin
- Key Laboratory of Agro-Products Quality and Safety Control in Storage and Transport Process, Ministry of Agriculture and Rural Affairs/Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Min-Min Li
- Key Laboratory of Agro-Products Quality and Safety Control in Storage and Transport Process, Ministry of Agriculture and Rural Affairs/Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yan-Tian Liang
- Key Laboratory of Agro-Products Quality and Safety Control in Storage and Transport Process, Ministry of Agriculture and Rural Affairs/Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Bei Fan
- Key Laboratory of Agro-Products Quality and Safety Control in Storage and Transport Process, Ministry of Agriculture and Rural Affairs/Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Feng-Zhong Wang
- Key Laboratory of Agro-Products Quality and Safety Control in Storage and Transport Process, Ministry of Agriculture and Rural Affairs/Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing, China
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40
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Kong X, Bai Z, Jin T, Jin D, Pan J, Yu X, Cernava T. Arthrobacter is a universal responder to di-n-butyl phthalate (DBP) contamination in soils from various geographical locations. JOURNAL OF HAZARDOUS MATERIALS 2022; 422:126914. [PMID: 34419851 DOI: 10.1016/j.jhazmat.2021.126914] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 08/12/2021] [Accepted: 08/13/2021] [Indexed: 06/13/2023]
Abstract
Plasticizer phthalic acid esters (PAEs) are commonly found as contaminants in various soils. Previous studies indicated that their natural degradation can substantially differ among soil types; however, potential implications of the soil microbiome remained largely unexplored. Here, we have collected ten soil types from nine different geographical regions of China to investigate the degradation of DBP therein and role of bacteria in this process. Results showed that the degradation rate of DBP was lowest in nutrient-poor red soils from Jiangxi Province, while it was highest in fluvo-aquatic soil from Hebei Province. Bacterial community responses to DBP substantially differed in each of the analyzed soils. Arthrobacter is known for its broad-spectrum activity in terms of DBP degradation in soil and was therefore implemented as bioremediating inoculant in many polluted environments. In the present study, network analyses indicated that synergism between soil bacteria increased following exposure to DBP. Arthrobacter and Sphingomonas were found to expand their positive interactions with other members of the microbiome in DBP-contaminated soils. The overall findings of our study provide a basis for biomarker development for detection of DBP contaminations and an extended basis for future bioremediation approaches based on beneficial bacteria.
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Affiliation(s)
- Xiao Kong
- School of Public Health, Qingdao University, Qingdao 266021, China; Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Zhanbing Bai
- Hunan Vegetable Research Institute, Hunan Academy of Agricultural Sciences, Changsha 410125, China
| | - Tuo Jin
- Rural Energy and Environment Agency, Ministry of Agriculture and Rural Affairs, Beijing 100125, China
| | - Decai Jin
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Jiangang Pan
- School of Life Science and Technology, Inner Mongolia University of Science and Technology, Baotou 014010, China
| | - Xiangyang Yu
- Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base, Ministry of Science and Technology, Nanjing 210014, China
| | - Tomislav Cernava
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12, Graz 8010, Austria
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41
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Gómez-Godínez LJ, Martínez-Romero E, Banuelos J, Arteaga-Garibay RI. Tools and challenges to exploit microbial communities in agriculture. CURRENT RESEARCH IN MICROBIAL SCIENCES 2021; 2:100062. [PMID: 34841352 PMCID: PMC8610360 DOI: 10.1016/j.crmicr.2021.100062] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 08/12/2021] [Accepted: 08/18/2021] [Indexed: 12/13/2022] Open
Abstract
Plants contain diverse microbial communities. The associated microorganisms confer advantages to the host plant, which include growth promotion, nutrient absorption, stress tolerance, and pathogen and disease resistance. In this review, we explore how agriculture is implementing the use of microbial inoculants (single species or consortia) to improve crop yields, and discuss current strategies to study plant-associated microorganisms and how their diversity varies under unconventional agriculture. It is predicted that microbial inoculation will continue to be used in agriculture.
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Affiliation(s)
- Lorena Jacqueline Gómez-Godínez
- Laboratorio de Recursos Genéticos Microbianos, Centro Nacional de Recursos Genéticos. Instituto Nacional de Investigación Forestales, Agrícolas y Pecuarios. Boulevard de la Biodiversidad 400, Rancho las Cruces, C.P. 47600. Tepatitlán de Morelos, Jalisco, México
| | - Esperanza Martínez-Romero
- Centro de Ciencias genómicas, Universidad Nacional Autónoma de México Campus Morelos, Cuernavaca, Morelos México
| | - Jacob Banuelos
- Laboratorio de Organismos Benéficos, Facultad de Ciencias Agrícolas, Universidad Veracruzana. Circuito Aguirre Beltrán SN, Col. Universitaria, CP 91000, Xalapa, Veracruz, México
| | - Ramón I. Arteaga-Garibay
- Laboratorio de Recursos Genéticos Microbianos, Centro Nacional de Recursos Genéticos. Instituto Nacional de Investigación Forestales, Agrícolas y Pecuarios. Boulevard de la Biodiversidad 400, Rancho las Cruces, C.P. 47600. Tepatitlán de Morelos, Jalisco, México
- Corresponding authors.
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42
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Wei G, Ning K, Zhang G, Yu H, Yang S, Dai F, Dong L, Chen S. Compartment Niche Shapes the Assembly and Network of Cannabis sativa-Associated Microbiome. Front Microbiol 2021; 12:714993. [PMID: 34675893 PMCID: PMC8524047 DOI: 10.3389/fmicb.2021.714993] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 09/06/2021] [Indexed: 11/13/2022] Open
Abstract
Interactions between plants and microbes may promote the growth of plants and regulate the production of secondary metabolites. Hemp (Cannabis sativa) is an annual herb and an important commercial crop. However, the assembly and network of hemp-associated microbiomes inhabiting in soil and plant compartments have not been comprehensively understood. This work investigated the assembly and network of bacterial and fungal communities living in soils (bulk and rhizosphere) and plant compartments (root, stem, leaf, and flower) of four hemp ecotypes cultivated in the same habitat. Microbiome assembly was predominantly shaped by compartment niche. Microbial alpha diversity was the highest in soil, continually decreased from root to flower. Core bacterial genera Pseudomonas, Bacillus, Rhizobium, Planococcus, and Sphingomonas were mostly enriched in aerial endosphere niches; Clitopilus, Plectosphaerella, and Mortierella were enriched in belowground endosphere. Microbial network complexity and connectivity decreased from root to flower. According to source tracking analysis, hemp microbiota primarily originated from soil and were subsequently filtered in different plant compartments. This work provides details on hemp-associated microbiome along the soil-plant continuum and a comprehensive understanding of the origin and transmission mode of endophytes in hemp.
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Affiliation(s)
- Guangfei Wei
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Kang Ning
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Guozhuang Zhang
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Haibin Yu
- Yunnan Industrial Investment Group, Yunnan Hemp Seed Industry Co., Ltd., Kunming, China
| | - Shuming Yang
- Yunnan Industrial Investment Group, Yunnan Hemp Seed Industry Co., Ltd., Kunming, China
| | - Fei Dai
- Yunnan Industrial Investment Group, Yunnan Hemp Seed Industry Co., Ltd., Kunming, China
| | - Linlin Dong
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Shilin Chen
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
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43
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Tan L, Zeng WA, Xiao Y, Li P, Gu S, Wu S, Zhai Z, Feng K, Deng Y, Hu Q. Fungi-Bacteria Associations in Wilt Diseased Rhizosphere and Endosphere by Interdomain Ecological Network Analysis. Front Microbiol 2021; 12:722626. [PMID: 34552573 PMCID: PMC8450586 DOI: 10.3389/fmicb.2021.722626] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 08/11/2021] [Indexed: 11/13/2022] Open
Abstract
In the plant rhizosphere and endosphere, some fungal and bacterial species regularly co-exist, however, our knowledge about their co-existence patterns is quite limited, especially during invasion by bacterial wilt pathogens. In this study, the fungal communities from soil to endophytic compartments were surveyed during an outbreak of tobacco wilt disease caused by Ralstonia solanacearum. It was found that the stem endophytic fungal community was significantly altered by pathogen invasion in terms of community diversity, structure, and composition. The associations among fungal species in the rhizosphere and endosphere infected by R. solanacearum showed more complex network structures than those of healthy plants. By integrating the bacterial dataset, associations between fungi and bacteria were inferred by Inter-Domain Ecological Network (IDEN) approach. It also revealed that infected samples, including both the rhizosphere and endosphere, had more complex interdomain networks than the corresponding healthy samples. Additionally, the bacterial wilt pathogenic Ralstonia members were identified as the keystone genus within the IDENs of both root and stem endophytic compartments. Ralstonia members was negatively correlated with the fungal genera Phoma, Gibberella, and Alternaria in infected roots, as well as Phoma, Gibberella, and Diaporthe in infected stems. This suggested that those endophytic fungi may play an important role in resisting the invasion of R. solanacearum.
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Affiliation(s)
- Lin Tan
- Hunan Agricultural University, Changsha, China
| | - Wei-Ai Zeng
- Changsha Tobacco Company of Hunan Province, Changsha, China
| | - Yansong Xiao
- Chenzhou Tobacco Company of Hunan Province, Chenzhou, China
| | - Pengfei Li
- Wenshan Tobacco Company of Yunnan Province, Wenshan, China
| | - Songsong Gu
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China.,Institute for Marine Science and Technology, Shandong University, Qingdao, China
| | - Shaolong Wu
- Tobacco Company of Hunan Province, Changsha, China
| | | | - Kai Feng
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China.,College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Ye Deng
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China.,Institute for Marine Science and Technology, Shandong University, Qingdao, China.,College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Qiulong Hu
- Hunan Agricultural University, Changsha, China
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44
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Wu M, Li G, Li P, Jiang N, Wei S, Petropoulos E, Li Z. Assessing the ecological risk of pesticides should not ignore the impact of their transformation byproducts - The case of chlorantraniliprole. JOURNAL OF HAZARDOUS MATERIALS 2021; 418:126270. [PMID: 34102368 DOI: 10.1016/j.jhazmat.2021.126270] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 05/10/2021] [Accepted: 05/28/2021] [Indexed: 06/12/2023]
Abstract
Risk assessments for pesticides typically focus on the compound itself ignoring the impact of its transformation byproducts. Challenges in isolating such byproducts (i.e. after application of pesticide in soil) often lead to underestimation of the real risk from such substances. The toxicological properties of these byproducts may differ from those of the parent pesticides; hence, special attention is required for these new emerging contaminants. In this study, two transformation byproducts of chlorantraniliprole were isolated from soil and identified, using nuclear magnetic resonance and high resolution mass spectrometry, as products of dechlorination (Z1) and bromination (Z2). Kinetic experiments revealed both byproducts degrade faster than chlorantraniliprole in soil (half-lives 38 & 43 d vs. 58 d). The ecological risk evaluation of chlorantraniliprole and its byproducts on soil bacterial community showed that they were all potentially harmful but they imposed different impacts on both alpha and beta diversities and co-occurrence networks of the bacterial community. Z2 had the biggest potential impact on soil bacteria and accounted as a high potential risk. By comparing their impacts on soil bacterial community, we confirm that ecological risk assessment necessitates the understanding of the environmental impacts of a substance as well as of its transformation byproducts.
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Affiliation(s)
- Meng Wu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, PR China
| | - Guilong Li
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, PR China
| | - Pengfa Li
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, PR China
| | - Nan Jiang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, PR China
| | - Shiping Wei
- Jiangsu Engineering and Technology Center for Modern Horticulture, Jiangsu Polytechnic College of Agriculture and Forestry, Zhenjiang, Jiangsu 212400, PR China
| | | | - Zhongpei Li
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, PR China.
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45
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Li P, Liu M, Li G, Liu K, Liu T, Wu M, Saleem M, Li Z. Phosphorus availability increases pathobiome abundance and invasion of rhizosphere microbial networks by Ralstonia. Environ Microbiol 2021; 23:5992-6003. [PMID: 34347357 DOI: 10.1111/1462-2920.15696] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 07/26/2021] [Accepted: 07/28/2021] [Indexed: 12/16/2022]
Abstract
Soil disease-suppressiveness depends on complex interactions among pathogens, native microbiota, and physicochemical properties, while these interactions remain understudied. Comparing field and microcosm experiments, we investigated the significance of these interactions in disease emergence or suppression using structural equation modelling (SEM) and receiver operating characteristic curve (ROC) analyses. We observed significant differences in the relative abundance of pathogenic and beneficial microbes, alpha and beta diversity indices between disease-conducive and -suppressive rhizosphere soils. The pathogenic (Ralstonia) and beneficial (Bacillus) taxa dominated disease-conducive and -suppressive rhizosphere soils, respectively. Moreover, the co-occurrences of Ralstonia with native microorganisms were positive and negative in the disease-conducive and -suppressive soils, respectively. These results suggest the supportive (Rudaea) and suppressive (Enterobacter, Bacillus) role of indigenous microbes in the invasion of soil and plant systems by Ralstonia. The SEM and ROC analysis predicted that Ralstonia invaded rhizospheric microbial networks and caused peanut wilt under high than low soil phosphorus conditions. Our results suggest the importance of soil phosphorus availability in altering the microbial interactions, thus leading to soil invasion by Ralstonia. Thus, we conclude by saying that feeding soil with high amounts of available phosphorus could deplete plant-beneficial microbes and increase the pathobiome abundance that may compromise plant health.
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Affiliation(s)
- Pengfa Li
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ming Liu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Guilong Li
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Kai Liu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Tianshun Liu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Meng Wu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Muhammad Saleem
- Department of Biological Sciences, Alabama State University, Montgomery, AL, 36104, USA
| | - Zhongpei Li
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
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46
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Shi M, Zhao Y, Zhang A, Zhao M, Zhai W, Wei Z, Song Y, Tang X, He P. Factoring distinct materials and nitrogen-related microbes into assessments of nitrogen pollution risks during composting. BIORESOURCE TECHNOLOGY 2021; 329:124896. [PMID: 33657502 DOI: 10.1016/j.biortech.2021.124896] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 02/17/2021] [Accepted: 02/20/2021] [Indexed: 06/12/2023]
Abstract
The aim of this study was to evaluate nitrogen pollution risks from distinct materials composting with the discrepancy of component, including chicken manure, municipal solid and straw waste (CM, MSW, SW). Results showed total nitrogen maximum mean concentrations were observed in CM (39.57 g/kg). Pollution risks in CM were continuous, while MSW and SW mainly concentrated during heating phases. Microbial analysis confirmed that pollution risks from ammonification and nitrification were more prevalent in CM. The risks of pollution caused by nitrate reduction accompanied N2O were the most serious in MSW. The multifunctional nitrogen-related microbes Pseudomonas and Bacillus were affected by microenvironments and contributed to different pollution risks. Furthermore, PICRUSt analysis identified the "inferred" key genes (pmoC-amoC, nrfH, nifD etc.) related to nitrogen pollution risks. This study evaluated nitrogen pollution risks and proposed the future directions, providing theoretical basis and feasible optimization measures for the mitigation of nitrogen pollution during composting.
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Affiliation(s)
- Mingzi Shi
- College of Life Science, Northeast Agricultural University, Harbin 150030, China
| | - Yue Zhao
- College of Life Science, Northeast Agricultural University, Harbin 150030, China
| | - An Zhang
- College of Life Science, Northeast Agricultural University, Harbin 150030, China
| | - Maoyuan Zhao
- College of Life Science, Northeast Agricultural University, Harbin 150030, China
| | - Wenhao Zhai
- College of Life Science, Northeast Agricultural University, Harbin 150030, China
| | - Zimin Wei
- College of Life Science, Northeast Agricultural University, Harbin 150030, China.
| | - Yangyang Song
- College of Life Science, Northeast Agricultural University, Harbin 150030, China
| | - Xiaofei Tang
- Heilongjiang Province Environmental Science Research Institute, Harbin 150056, China
| | - Pingping He
- Heilongjiang Province Environmental Science Research Institute, Harbin 150056, China
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47
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Wu T, Li XB, Xu J, Liu LX, Ren LL, Dong B, Li W, Xie WJ, Yao ZG, Chen QF, Xia JB. Diversity and functional characteristics of endophytic bacteria from two grass species growing on an oil-contaminated site in the Yellow River Delta, China. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 767:144340. [PMID: 33429273 DOI: 10.1016/j.scitotenv.2020.144340] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 12/01/2020] [Accepted: 12/02/2020] [Indexed: 06/12/2023]
Abstract
Phragmites australis and Chloris virgata are native, dominant, salt-tolerant grass species that grow in the Yellow River Delta, China, and have potential applications in the phytoremediation of petroleum-polluted saline soil. The characteristics of endophytic bacterial communities of Phragmites australis and Chloris virgata and their functions in hydrocarbon degradation and plant growth promotion have been studied using both high-throughput sequencing and conventional microbial techniques. Through 16S rRNA gene amplicon sequencing, we found five bacterial phyla that were dominant among the endophytic bacterial communities of the two grass species, including Proteobacteria, Actinobacteria, Firmicutes, Bacteroidetes, and Tenericutes. The phylum Proteobacteria was common among the endophytic bacterial communities of the two grass species. The diversity in the endophytic bacterial community of Chloris virgata was generally higher than that in the community of Phragmites australis. Thirty-eight hydrocarbon-degrading endophytic bacteria were isolated from the two grasses via culturing techniques. Based on phylogenetic analyses, the bacterial isolates were classified into the phyla Proteobacteria, Firmicutes, and Actinobacteria. The majority of strains belonged to the genera Bacillus and Pseudomonas. More than 70% of the isolates of hydrocarbon-degrading endophytes exhibited the ability to stimulate plant growth. These isolates mainly belonged to Bacillus sp., Pseudomonas sp., Beijerinckia sp., Serratia sp., Acinetobacter sp., Microbacterium sp., and Rhizobium sp. Altogether, the present study revealed that Phragmites australis and Chloris virgata growing on petroleum-polluted saline soil in the Yellow River Delta harbor several diverse species of endophytic bacteria and serve as novel sources of beneficial bacteria and hydrocarbon degradation.
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Affiliation(s)
- Tao Wu
- Shandong Provincial Engineering and Technology Research Center for Wild Plant Resources Development and Application of Yellow River Delta, College of Biological and Environmental Engineering, Binzhou University, Binzhou 256603, China; Shandong Key Laboratory of Eco-Environmental Science for the Yellow River Delta, Binzhou University, Binzhou 256603, China
| | - Xiao-Bin Li
- Zhuhai Precision Medical Center, Zhuhai People's Hospital (Zhuhai hospital affiliated with Jinan University), Zhuhai 519000, China
| | - Jie Xu
- Department of Bioengineering, Binzhou Vocational College, Binzhou 256600, China
| | - Long-Xiang Liu
- Shandong Provincial Engineering and Technology Research Center for Wild Plant Resources Development and Application of Yellow River Delta, College of Biological and Environmental Engineering, Binzhou University, Binzhou 256603, China
| | - Li-Li Ren
- Shandong Provincial Engineering and Technology Research Center for Wild Plant Resources Development and Application of Yellow River Delta, College of Biological and Environmental Engineering, Binzhou University, Binzhou 256603, China
| | - Bin Dong
- Shandong Provincial Engineering and Technology Research Center for Wild Plant Resources Development and Application of Yellow River Delta, College of Biological and Environmental Engineering, Binzhou University, Binzhou 256603, China
| | - Wang Li
- Shandong Provincial Engineering and Technology Research Center for Wild Plant Resources Development and Application of Yellow River Delta, College of Biological and Environmental Engineering, Binzhou University, Binzhou 256603, China
| | - Wen-Jun Xie
- Shandong Provincial Engineering and Technology Research Center for Wild Plant Resources Development and Application of Yellow River Delta, College of Biological and Environmental Engineering, Binzhou University, Binzhou 256603, China; Shandong Key Laboratory of Eco-Environmental Science for the Yellow River Delta, Binzhou University, Binzhou 256603, China
| | - Zhi-Gang Yao
- Shandong Provincial Engineering and Technology Research Center for Wild Plant Resources Development and Application of Yellow River Delta, College of Biological and Environmental Engineering, Binzhou University, Binzhou 256603, China
| | - Qing-Feng Chen
- College of Geography and Environment, Shandong Normal University, Jinan 250014, China.
| | - Jiang-Bao Xia
- Shandong Provincial Engineering and Technology Research Center for Wild Plant Resources Development and Application of Yellow River Delta, College of Biological and Environmental Engineering, Binzhou University, Binzhou 256603, China; Shandong Key Laboratory of Eco-Environmental Science for the Yellow River Delta, Binzhou University, Binzhou 256603, China.
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48
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Evaluation of seed associated endophytic bacteria from tolerant chilli cv. Firingi Jolokia for their biocontrol potential against bacterial wilt disease. Microbiol Res 2021; 248:126751. [PMID: 33839507 DOI: 10.1016/j.micres.2021.126751] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Revised: 03/05/2021] [Accepted: 03/19/2021] [Indexed: 12/26/2022]
Abstract
In this study, the seed endosphere of a bacterial wilt tolerant chilli cv. Firingi Jolokia was explored in order to find effective agents for bacterial wilt disease biocontrol. A total of 32 endophytic bacteria were isolated from freshly collected seeds and six isolates were selected based on R. solanacearum inhibition assay. These isolates were identified as Bacillus subtilis (KJ-2), Bacillus velezensis (KJ-4), Leuconostoc mesenteroides (KP-1), Lactococcus lactis (LB-3), Bacillus amyloliquefaciens (WK-2), and Bacillus subtilis (WK-3) by 16S rRNA gene sequencing. In the in planta R. solanacearum inhibition assay carried out by seedling root bacterization method, Bacillus subtilis (KJ-2) exhibited highest biocontrol efficacy of 86.6 % on 7th day post R. solanacearum inoculation and a minimum biocontrol efficacy of 52.9 % was noted for Leuconostoc mesenteroides (KP-1). GC-HRMS analysis detected several known antimicrobial compounds in the extract of the culture supernatant of Bacillus subtilis (KJ-2); which may contribute to inhibition of R. solanacearum. In the growth promotion assay conducted using these isolates, only two of them namely Bacillus subtilis (KJ-2) and Bacillus amyloliquefaciens (WK-2) showed growth promotion in true leafed tomato plants. All the selected seed endophytic isolates were able to control bacterial wilt of tomato at the seedling stage and Bacillus subtilis (KJ-2) was found to be most effective in controlling the disease. The results of the present study highlighted that seed endosphere of bacterial wilt tolerant cultivar is a rich source of R. solanacearum antagonizing bacterial isolates.
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49
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Wang P, Kong X, Chen H, Xiao Y, Liu H, Li X, Zhang Z, Tan X, Wang D, Jin D, Deng Y, Cernava T. Exploration of Intrinsic Microbial Community Modulators in the Rice Endosphere Indicates a Key Role of Distinct Bacterial Taxa Across Different Cultivars. Front Microbiol 2021; 12:629852. [PMID: 33664718 PMCID: PMC7920960 DOI: 10.3389/fmicb.2021.629852] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 01/20/2021] [Indexed: 11/22/2022] Open
Abstract
Microbial communities associated with the plant phyllosphere and endosphere can have both beneficial as well as detrimental effects on their hosts. There is an ongoing debate to which extend the phyllosphere and endosphere microbiome assembly is controlled by the host plant how pronounced cultivar effects are. We investigated the bacterial and fungal communities from the phyllosphere and endosphere of 10 different rice cultivars grown under identical environmental conditions in the frame of a targeted approach to identify drivers of community assembly. The results indicated that the endophytic bacterial communities were clearly separated into two groups. The α-diversity and microbial network complexity within Group I were significantly lower than in Group II. Moreover, the genera Nocardioides, Microvirga, and Gaiella were significantly more abundant in Group II and only present in the interaction networks of this group. These three genera were significantly correlated with α- and β-diversity of the endophytic bacterial community and thus identified as major drivers of the endosphere community. We have identified keystone taxa that shape endophytic bacterial communities of different rice cultivars. Our overall findings provide new insights into plant-microbe interactions, and may contribute to targeted improvements of rice varieties in the future.
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Affiliation(s)
- Pei Wang
- College of Plant Protection, Hunan Agricultural University, Changsha, China
- Hunan Plant Protection Institute, Hunan Academy of Agricultural Sciences, Changsha, China
| | - Xiao Kong
- School of Public Health, Qingdao University, Qingdao, China
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Hongsong Chen
- Guangxi Key Laboratory for Biology of Crop Diseases and Insect Pests, Institute of Plant Protection, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Youlun Xiao
- Hunan Plant Protection Institute, Hunan Academy of Agricultural Sciences, Changsha, China
| | - Huijun Liu
- Beijing Key Laboratory of Detection and Control of Spoilage Organisms and Pesticide Residues in Agricultural Products, Beijing University of Agriculture, Beijing, China
| | - Xiaojuan Li
- Hunan Plant Protection Institute, Hunan Academy of Agricultural Sciences, Changsha, China
| | - Zhuo Zhang
- College of Plant Protection, Hunan Agricultural University, Changsha, China
- Hunan Plant Protection Institute, Hunan Academy of Agricultural Sciences, Changsha, China
| | - Xinqiu Tan
- Hunan Plant Protection Institute, Hunan Academy of Agricultural Sciences, Changsha, China
| | - Diandong Wang
- College of Life Science and Technology, Yangtze Normal University, Chongqing, China
| | - Decai Jin
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Ye Deng
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Tomislav Cernava
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
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50
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Shi W, Su G, Li M, Wang B, Lin R, Yang Y, Wei T, Zhou B, Gao Z. Distribution of Bacterial Endophytes in the Non-lesion Tissues of Potato and Their Response to Potato Common Scab. Front Microbiol 2021; 12:616013. [PMID: 33633704 PMCID: PMC7900429 DOI: 10.3389/fmicb.2021.616013] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 01/13/2021] [Indexed: 11/24/2022] Open
Abstract
The response of plant endophytes to disease within infected tissues has been well demonstrated, but the corresponding response of endophytes in non-lesion tissues remains unclear. Here, we studied the composition and distribution of bacterial endophytes in potato roots (RE), stems (SE), and tubers (TE), and explored the response of endophytes in non-lesion tissues to potato common scab (PCS), which is a soil-borne disease caused by pathogenic Streptomyces and results in serious losses to the global economy every year. Via high-throughput sequencing, it was seen that the composition of endophytes in roots, stems, and tubers had significant differences (P < 0.05) and the distribution of the bacterial communities illustrated a gradient from soil to root to tuber/stem. PCS significantly reduced bacterial endophytes α-diversity indexes, including ACE and the number of observed operational taxonomic units (OTUs), of RE without significantly reducing the indexes of SE and TE. No significant effect on the composition of endophytes were caused by PCS in roots, tubers, or stems between high PCS severity (H) and low PCS severity (L) infections at the community level, but PCS did have a substantial impact on the relative abundance of several specific endophytes. Rhizobium and Sphingopyxis were significantly enriched in root endophytes with low PCS severity (REL); Delftia and Ochrobactrum were significantly enriched in stem endophytes with low PCS severity (SEL); Pedobacter, Delftia, and Asticcacaulis were significantly enriched in tuber endophytes with high PCS severity (TEH). OTU62, a potential PCS pathogen in this study, was capable of colonizing potato tubers, roots, and stems with few or no symptoms present. Co-occurrence networks showed that the number of correlations to OTU62 was higher than average in these three tissue types, suggesting the importance of OTU62 in endophytic communities. This study clarified the distribution and composition of potato endophytes in tubers, roots, and stems, and demonstrated the response of endophytes in non-lesion tissues to PCS.
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Affiliation(s)
- Wencong Shi
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, China.,College of Life Sciences, Shandong Agricultural University, Tai'an, China
| | - Gaoya Su
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, China.,College of Life Sciences, Shandong Agricultural University, Tai'an, China
| | - Mingcong Li
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, China.,College of Life Sciences, Shandong Agricultural University, Tai'an, China
| | - Bing Wang
- College of Life Sciences, Shandong Agricultural University, Tai'an, China.,National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Tai'an, China
| | - Rongshan Lin
- College of Life Sciences, Shandong Agricultural University, Tai'an, China.,National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Tai'an, China
| | - Yutian Yang
- Agriculture Research Institute of Zaozhuang, Zaozhuang, China
| | - Tao Wei
- Agriculture Research Institute of Zaozhuang, Zaozhuang, China
| | - Bo Zhou
- College of Life Sciences, Shandong Agricultural University, Tai'an, China.,National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Tai'an, China
| | - Zheng Gao
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, China.,College of Life Sciences, Shandong Agricultural University, Tai'an, China
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