201
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Wu C, Wang F, Zhang H, Chen G, Deng Y, Chen J, Yang J, Ge T. Enrichment of beneficial rhizosphere microbes in Chinese wheat yellow mosaic virus-resistant cultivars. Appl Microbiol Biotechnol 2021; 105:9371-9383. [PMID: 34767052 DOI: 10.1007/s00253-021-11666-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 10/24/2021] [Accepted: 10/25/2021] [Indexed: 01/04/2023]
Abstract
The microbial community within the root system, the rhizosphere closely connected to the root, and their symbiotic relationship with the host are increasingly seen as possible drivers of natural pathogen resistance. Resistant cultivars have the most effective strategy in controlling the Chinese wheat yellow mosaic disease, but the roles of the root and rhizosphere microbial interactions among different taxonomic levels of resistant cultivars are still unknown. Thus, we aimed to investigate whether these microbial community composition and network characteristics are related to disease resistance and to analyze the belowground plant-associated microflora. Relatively high microbial diversity and stable community structure for the resistant cultivars were detected. Comparison analysis showed that some bacterial phyla were significantly enriched in the wheat root or rhizosphere of the resistant wheat cultivar. Furthermore, the root and rhizosphere of the resistant cultivars greatly recruited many known beneficial bacterial and fungal taxa. In contrast, the relative abundance of potential pathogens was higher for the susceptible cultivar than for the resistant cultivar. Network co-occurrence analysis revealed that a much more complex, more mutually beneficial, and a higher number of bacterial keystone taxa in belowground microbial networks were displayed in the resistant cultivar, which may have been responsible for maintaining the stability and ecological balance of the microbial community. Overall, compared with the susceptible cultivar, the resistant cultivar tends to recruit more potential beneficial microbial groups for plant and rhizosphere microbial community interactions. These findings indicate that beneficial rhizosphere microbiomes for cultivars should be targeted and evaluated using community compositional profiles. KEY POINTS: • Different resistance levels in cultivars affect the rhizosphere microbiome.. • Resistant cultivars tend to recruit more potential beneficial microbial groups. • Bacteria occupy a high proportion and core position in the microflora network.
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Affiliation(s)
- Chuanfa Wu
- State Key Laboratory for Managing Biotic and Chemical Threats To the Quality and Safety of Agro-Products, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China
| | - Fangyan Wang
- State Key Laboratory for Managing Biotic and Chemical Threats To the Quality and Safety of Agro-Products, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China
| | - Haoqing Zhang
- State Key Laboratory for Managing Biotic and Chemical Threats To the Quality and Safety of Agro-Products, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China
| | - Guixian Chen
- State Key Laboratory for Managing Biotic and Chemical Threats To the Quality and Safety of Agro-Products, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China.,School of Resources and Environmental Engineering, Jiangxi University of Science and Technology, Ganzhou, 341000, China
| | - Yangwu Deng
- School of Resources and Environmental Engineering, Jiangxi University of Science and Technology, Ganzhou, 341000, China
| | - Jianping Chen
- State Key Laboratory for Managing Biotic and Chemical Threats To the Quality and Safety of Agro-Products, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China.
| | - Jian Yang
- State Key Laboratory for Managing Biotic and Chemical Threats To the Quality and Safety of Agro-Products, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China.
| | - Tida Ge
- State Key Laboratory for Managing Biotic and Chemical Threats To the Quality and Safety of Agro-Products, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China.
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202
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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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203
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Lu T, Zhang Z, Li Y, Zhang Q, Cui H, Sun L, Peijnenburg WJGM, Peñuelas J, Zhu L, Zhu YG, Chen J, Qian H. Does biological rhythm transmit from plants to rhizosphere microbes? Environ Microbiol 2021; 23:6895-6906. [PMID: 34658124 DOI: 10.1111/1462-2920.15820] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Accepted: 10/07/2021] [Indexed: 11/28/2022]
Abstract
Plant physiological and metabolic processes are modulated by rhythmic gene expression in a large part. Meanwhile, plants are also regulated by rhizosphere microorganisms, which are fed by root exudates and provide beneficial functions to their plant host. Whether the biorhythms in plants would transfer to the rhizosphere microbial community is still uncertain and their intricate connection remains poorly understood. Here, we investigated the role of the Arabidopsis circadian clock in shaping the rhizosphere microbial community using wild-type plants and clock mutants (cca1-1 and toc1-101) with transcriptomic, metabolomic and 16S rRNA gene sequencing analysis throughout a 24-h period. Deficiencies of the central circadian clock led to abnormal diurnal rhythms for thousands of expressed genes and dozens of root exudates. The bacterial community failed to follow obvious patterns in the 24-h period, and there was lack of coordination with plant growth in the clock mutants. Our results suggest that the robust rhythmicity of genes and root exudation due to circadian clock in plants is an important driving force for the positive succession of rhizosphere communities, which will feedback on plant development.
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Affiliation(s)
- Tao Lu
- College of Environment, Zhejiang University of Technology, Hangzhou, 310032, People's Republic of China
| | - Zhenyan Zhang
- College of Environment, Zhejiang University of Technology, Hangzhou, 310032, People's Republic of China
| | - Yan Li
- College of Environment, Zhejiang University of Technology, Hangzhou, 310032, People's Republic of China
| | - Qi Zhang
- College of Environment, Zhejiang University of Technology, Hangzhou, 310032, People's Republic of China
| | - Hengzheng Cui
- College of Environment, Zhejiang University of Technology, Hangzhou, 310032, People's Republic of China
| | - Liwei Sun
- College of Environment, Zhejiang University of Technology, Hangzhou, 310032, People's Republic of China
| | - W J G M Peijnenburg
- Institute of Environmental Sciences (CML), Leiden University, Leiden, 2300 RA, The Netherlands
| | - Josep Peñuelas
- CSIC, Global Ecology Unit, CREAF- CSIC-UAB, Barcelona, Catalonia, Spain.,CREAF, Cerdanyola del Vallès, Barcelona, Catalonia, Spain
| | - Lizhong Zhu
- Department of Environmental Science, Zhejiang University, Hangzhou, 310058, People's Republic of China
| | - Yong-Guan Zhu
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, People's Republic of China
| | - Jianmeng Chen
- College of Environment, Zhejiang University of Technology, Hangzhou, 310032, People's Republic of China
| | - Haifeng Qian
- College of Environment, Zhejiang University of Technology, Hangzhou, 310032, People's Republic of China
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204
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Ha J, Gao Y, Zhang R, Li K, Zhang Y, Niu X, Chen X, Luo K, Chen Y. Diversity of the Bacterial Microbiome Associated With the Endosphere and Rhizosphere of Different Cassava ( Manihot esculenta Crantz) Genotypes. Front Microbiol 2021; 12:729022. [PMID: 34659156 PMCID: PMC8515189 DOI: 10.3389/fmicb.2021.729022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 09/01/2021] [Indexed: 11/13/2022] Open
Abstract
Root-associated microbial communities play important roles in plant growth and development. However, little attention has been paid to the microbial community structures associated with cassava, which is a staple food for approximately 800 million people worldwide. Here, we studied the diversity and structure of tuber endosphere and rhizosphere bacterial communities in fourteen cassava genotypes: SC5, SC8, SC9, SC205, KU50, R72, XL1, FX01, SC16, 4612, 587, 045, S0061, and 1110. The results of bacterial 16S rDNA sequencing showed that the richness and diversity of bacteria in the rhizosphere were higher than those in the tuber endosphere across the 14 cassava genotypes. After sequencing, 21 phyla and 310 genera were identified in the tuberous roots, and 36 phyla and 906 genera were identified in the rhizosphere soils. The dominant phylum across all tuber samples was Firmicutes, and the dominant phyla across all rhizosphere samples were Actinobacteria, Proteobacteria, and Acidobacteria. The numbers of core bacterial taxa within the tuber endospheres and the rhizospheres of all cassava genotypes were 11 and 236, respectively. Principal coordinate analysis and hierarchical cluster analysis demonstrated significant differences in the compositions of rhizosphere soil microbiota associated with the different cassava genotypes. Furthermore, we investigated the metabolic changes in tuber roots of three genotypes, KU50, SC205, and SC9. The result showed that the abundances of Firmicutes, Proteobacteria, and Actinobacteria in tuber samples were positively correlated with organic acids and lipids and negatively correlated with vitamins and cofactors. These results strongly indicate that there are clear differences in the structure and diversity of the bacterial communities associated with different cassava genotypes.
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Affiliation(s)
- Jingwen Ha
- Hainan Key Laboratory for the Sustainable Utilization of Tropical Bioresources, Hainan University, Haikou, China
| | - Yu Gao
- Hainan Key Laboratory for the Sustainable Utilization of Tropical Bioresources, Hainan University, Haikou, China
| | - Rui Zhang
- Hainan Key Laboratory for the Sustainable Utilization of Tropical Bioresources, Hainan University, Haikou, China
| | - Ke Li
- Hainan Key Laboratory for the Sustainable Utilization of Tropical Bioresources, Hainan University, Haikou, China
| | - Yijie Zhang
- Hainan Key Laboratory for the Sustainable Utilization of Tropical Bioresources, Hainan University, Haikou, China
| | - Xiaolei Niu
- Hainan Key Laboratory for the Sustainable Utilization of Tropical Bioresources, Hainan University, Haikou, China
| | - Xin Chen
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Kai Luo
- Hainan Key Laboratory for the Sustainable Utilization of Tropical Bioresources, Hainan University, Haikou, China
| | - Yinhua Chen
- Hainan Key Laboratory for the Sustainable Utilization of Tropical Bioresources, Hainan University, Haikou, China
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205
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Wu N, Shi W, Liu W, Gao Z, Han L, Wang X. Differential impact of Bt-transgenic rice plantings on bacterial community in three niches over consecutive years. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2021; 223:112569. [PMID: 34352582 DOI: 10.1016/j.ecoenv.2021.112569] [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: 03/11/2021] [Revised: 06/11/2021] [Accepted: 07/25/2021] [Indexed: 05/26/2023]
Abstract
Transgenic-Bacillus thuringiensis (Bt) crops express insecticidal proteins, which can accumulate in plants and soil where they may influence microbial populations. The impact of Bt crops on bacterial communities has only been assessed under short-term, and results have been contradictory. Here, we analyzed the bacterial communities in three niches, rhizosphere soil (RS), root endosphere (RE) and leaf endosphere (LE), of three Bt rice and their non-Bt parental lines for three consecutive years by high-throughput sequencing. In principal coordinate analysis (PCoA) and PERMANOVA (Adonis) analysis, operational taxonomic units (OTUs) were clustered primarily by niche type and differed significantly in the RE and LE but not in the RS between each of three Bt lines compared with the non-Bt rice line, and not in each respective niche among the three Bt rice lines. The bacterial communities in the RS of different rice lines over the 3 years were clustered mainly by year rather than by lines. The differential bacterial taxa among the lines did not overlap between years, presumably because Cry proteins are rapidly degraded in the soil. A network analysis of RS bacterial communities showed that the network complexity and density for the three Bt rice lines did not decrease compared with those for the non-Bt line. In conclusion, our results demonstrated that bacterial communities differed significantly in RE and LE between Bt and non-Bt rice lines, but the differences were mild and transient, and had no adverse impact on RS over the 3 years. This study provides favorable evidence in support of the commercialization of Bt rice.
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Affiliation(s)
- Nan Wu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Wencong Shi
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an 271018, China
| | - Wenwen Liu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Zheng Gao
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an 271018, China
| | - Lanzhi Han
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| | - Xifeng Wang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
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206
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Lewin S, Francioli D, Ulrich A, Kolb S. Crop host signatures reflected by co-association patterns of keystone Bacteria in the rhizosphere microbiota. ENVIRONMENTAL MICROBIOME 2021; 16:18. [PMID: 34641981 PMCID: PMC8513244 DOI: 10.1186/s40793-021-00387-w] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 09/28/2021] [Indexed: 05/28/2023]
Abstract
BACKGROUND The native crop bacterial microbiota of the rhizosphere is envisioned to be engineered for sustainable agriculture. This requires the identification of keystone rhizosphere Bacteria and an understanding on how these govern crop-specific microbiome assembly from soils. We identified the metabolically active bacterial microbiota (SSU RNA) inhabiting two compartments of the rhizosphere of wheat (Triticum aestivum L.), barley (Hordeum vulgare L.), rye (Secale cereale), and oilseed rape (Brassica napus L.) at different growth stages. RESULTS Based on metabarcoding analysis the bacterial microbiota was shaped by the two rhizosphere compartments, i.e. close and distant. Thereby implying a different spatial extent of bacterial microbiota acquirement by the cereals species versus oilseed rape. We derived core microbiota of each crop species. Massilia (barley and wheat) and unclassified Chloroflexi of group 'KD4-96' (oilseed rape) were identified as keystone Bacteria by combining LEfSe biomarker and network analyses. Subsequently, differential associations between networks of each crop species' core microbiota revealed host plant-specific interconnections for specific genera, such as the unclassified Tepidisphaeraceae 'WD2101 soil group'. CONCLUSIONS Our results provide keystone rhizosphere Bacteria derived from for crop hosts and revealed that cohort subnetworks and differential associations elucidated host species effect that was not evident from differential abundance of single bacterial genera enriched or unique to a specific plant host. Thus, we underline the importance of co-occurrence patterns within the rhizosphere microbiota that emerge in crop-specific microbiomes, which will be essential to modify native crop microbiomes for future agriculture and to develop effective bio-fertilizers.
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Affiliation(s)
- Simon Lewin
- Microbial Biogeochemistry, Research Area Landscape Functioning, Leibniz Centre for Agricultural Landscape Research e.V. (ZALF), Müncheberg, Germany
| | - Davide Francioli
- Microbial Biogeochemistry, Research Area Landscape Functioning, Leibniz Centre for Agricultural Landscape Research e.V. (ZALF), Müncheberg, Germany
| | - Andreas Ulrich
- Microbial Biogeochemistry, Research Area Landscape Functioning, Leibniz Centre for Agricultural Landscape Research e.V. (ZALF), Müncheberg, Germany
| | - Steffen Kolb
- Microbial Biogeochemistry, Research Area Landscape Functioning, Leibniz Centre for Agricultural Landscape Research e.V. (ZALF), Müncheberg, Germany.
- Thaer Institute, Faculty of Life Sciences, Humboldt University of Berlin, Berlin, Germany.
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207
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Mauger S, Ricono C, Mony C, Chable V, Serpolay E, Biget M, Vandenkoornhuyse P. Differentiation of endospheric microbiota in ancient and modern wheat cultivar roots. PLANT-ENVIRONMENT INTERACTIONS (HOBOKEN, N.J.) 2021; 2:235-248. [PMID: 37284513 PMCID: PMC10168034 DOI: 10.1002/pei3.10062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 08/26/2021] [Accepted: 09/17/2021] [Indexed: 06/08/2023]
Abstract
Modern plant breeding and agrosystems artificialization could have altered plants' ability to filter and recruit beneficial microorganisms in its microbiota. Thus, compared to modern cultivars, we hypothesized that root-endosphere microbiota in modern wheat cultivars are less resistant to colonization by fungi and bacteria and thus more susceptible to also recruit more pathogens. We used an in-field experimental design including six wheat varieties (three ancient vs. three modern) grown in monoculture and in mixture (three replicates each). Endospheric microbiota of wheat roots were analyzed on four individuals sampled randomly in each plot. Composition-based clustering of sequences was then characterized from amplicon mass-sequencing. We show that the bacterial and fungal microbiota composition in wheat roots differed between ancient and modern wheat cultivar categories. However, the responses observed varied with the group considered. Modern cultivars harbored higher richness of bacterial and fungal pathogens than ancient cultivars. Both cultivar types displayed specific indicator species. A synergistic effect was identified in mixtures of modern cultivars with a higher root endospheric mycobiota richness than expected from a null model. The present study shows the effect of plant breeding on the microbiota associated plant roots. The results call for making a diagnosis of the cultivar's endospheric-microbiota composition. These new results also suggest the importance of a holobiont-vision while considering plant selection in crops and call for better integration of symbiosis in the development of next-generation agricultural practices.
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Affiliation(s)
- Solène Mauger
- Université de Rennes 1CNRSUMR6553 ECOBIORennes CedexFrance
| | - Claire Ricono
- Université de Rennes 1CNRSUMR6553 ECOBIORennes CedexFrance
| | - Cendrine Mony
- Université de Rennes 1CNRSUMR6553 ECOBIORennes CedexFrance
| | | | | | - Marine Biget
- Université de Rennes 1CNRSUMR6553 ECOBIORennes CedexFrance
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208
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Gao M, Xiong C, Gao C, Tsui CKM, Wang MM, Zhou X, Zhang AM, Cai L. Disease-induced changes in plant microbiome assembly and functional adaptation. MICROBIOME 2021; 9:187. [PMID: 34526096 PMCID: PMC8444440 DOI: 10.1186/s40168-021-01138-2] [Citation(s) in RCA: 109] [Impact Index Per Article: 36.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 07/27/2021] [Indexed: 05/20/2023]
Abstract
BACKGROUND The plant microbiome is an integral part of the host and increasingly recognized as playing fundamental roles in plant growth and health. Increasing evidence indicates that plant rhizosphere recruits beneficial microbes to the plant to suppress soil-borne pathogens. However, the ecological processes that govern plant microbiome assembly and functions in the below- and aboveground compartments under pathogen invasion are not fully understood. Here, we studied the bacterial and fungal communities associated with 12 compartments (e.g., soils, roots, stems, and fruits) of chili pepper (Capsicum annuum L.) using amplicons (16S and ITS) and metagenomics approaches at the main pepper production sites in China and investigated how Fusarium wilt disease (FWD) affects the assembly, co-occurrence patterns, and ecological functions of plant-associated microbiomes. RESULTS The amplicon data analyses revealed that FWD affected less on the microbiome of pepper reproductive organs (fruit) than vegetative organs (root and stem), with the strongest impact on the upper stem epidermis. Fungal intra-kingdom networks were less stable and their communities were more sensitive to FWD than the bacterial communities. The analysis of microbial interkingdom network further indicated that FWD destabilized the network and induced the ecological importance of fungal taxa. Although the diseased plants were more susceptible to colonization by other pathogenic fungi, their below- and aboveground compartments can also recruit potential beneficial bacteria. Some of the beneficial bacterial taxa enriched in the diseased plants were also identified as core taxa for plant microbiomes and hub taxa in networks. On the other hand, metagenomic analysis revealed significant enrichment of several functional genes involved in detoxification, biofilm formation, and plant-microbiome signaling pathways (i.e., chemotaxis) in the diseased plants. CONCLUSIONS Together, we demonstrate that a diseased plant could recruit beneficial bacteria and mitigate the changes in reproductive organ microbiome to facilitate host or its offspring survival. The host plants may attract the beneficial microbes through the modulation of plant-microbiome signaling pathways. These findings significantly advance our understanding on plant-microbiome interactions and could provide fundamental and important data for harnessing the plant microbiome in sustainable agriculture. Video abstract.
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Affiliation(s)
- Min Gao
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chao Xiong
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 100085, Beijing, China
| | - Cheng Gao
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Clement K M Tsui
- Department of Pathology, Sidra Medicine, Doha, Qatar
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine-Qatar, Doha, Qatar
- Division of Infectious Diseases, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Meng-Meng Wang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xin Zhou
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ai-Min Zhang
- Pepper Research Institute, Guizhou Provincial Academy of Agricultural Sciences, 550009, Guiyang, China
| | - Lei Cai
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China.
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209
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Zhao J, Ma J, Yang Y, Yu H, Zhang S, Chen F. Response of Soil Microbial Community to Vegetation Reconstruction Modes in Mining Areas of the Loess Plateau, China. Front Microbiol 2021; 12:714967. [PMID: 34512593 PMCID: PMC8424123 DOI: 10.3389/fmicb.2021.714967] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 07/30/2021] [Indexed: 11/25/2022] Open
Abstract
Vegetation reconstruction and restoration is vital to the health of the mine land ecosystem. Different vegetations might change microbial community structure and function of soil, mediating the biogeochemical cycle and nutrition supply to the soil. To clarify the response of soil microbes to different vegetation reconstruction modes in the mining areas of the Loess Plateau, China, soil microbial community structures and functions were determined by the MiSeq high-throughput sequencing along with PICRUSt2 and FUNGuild tools. The fungal community richness was observed to be the highest in grassland soil and positively correlated with soil organic matter, total nitrogen, and nitrate-nitrogen. The bacterial and fungal community structures were similar in grassland and brushland areas, but were significantly differentiated in the coniferous and broadleaf forest, and the leading factors were soil pH and nitrate-nitrogen. Actinobacteriota, Proteobacteria, and Acidobacteriota were the dominant bacterial phyla under different vegetation reconstruction modes. The dominant phyla of fungi were Ascomycota, Basidiomycota, and Mortierellomycota. Different vegetation reconstruction modes did not affect the bacterial functional communities but shaped different functional groups of fungi. The grassland soil was dominated by saprotrophic fungi, while symbiotrophic fungi dominated the coniferous and broadleaf forests. The results suggested that shifts in vegetation reconstruction modes may alter the mining soil bacterial and fungal community structures and function. These findings improve the understanding of microbial ecology in the reclaimed mine soil and provide a reference for the ecological restoration of fragile mining ecosystems.
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Affiliation(s)
- Jiao Zhao
- Engineering Research Center of Ministry of Education for Mine Ecological Restoration, Xuzhou, China.,Low Carbon Energy Institute, China University of Mining and Technology, Xuzhou, China
| | - Jing Ma
- Low Carbon Energy Institute, China University of Mining and Technology, Xuzhou, China
| | - Yongjun Yang
- Engineering Research Center of Ministry of Education for Mine Ecological Restoration, Xuzhou, China
| | - Haochen Yu
- Engineering Research Center of Ministry of Education for Mine Ecological Restoration, Xuzhou, China
| | - Shaoliang Zhang
- Engineering Research Center of Ministry of Education for Mine Ecological Restoration, Xuzhou, China
| | - Fu Chen
- Engineering Research Center of Ministry of Education for Mine Ecological Restoration, Xuzhou, China.,Low Carbon Energy Institute, China University of Mining and Technology, Xuzhou, China
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210
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The assembly of wheat-associated fungal community differs across growth stages. Appl Microbiol Biotechnol 2021; 105:7427-7438. [PMID: 34505913 DOI: 10.1007/s00253-021-11550-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 08/03/2021] [Accepted: 08/22/2021] [Indexed: 02/04/2023]
Abstract
Plant-associated fungal communities play a vital role in plant adaptations, physiological functions, and productivity. Therefore, it is important to reveal the mechanisms driving the assembly of these communities. Yet it is still not fully understood how community assembly and structure differentiate in plant compartments, growth seasons, and varieties at large geographic distances. In this study, we analyzed bulk soil and plant-associated fungal communities of five wheat varieties across two growth stages in three biogeographic sites with distances of about 324, 534, or 800 km apart between any two locations. Our results indicated that the fungal community varied primarily across the sample types (leaf endosphere, root endosphere, rhizosphere, and bulk soil), followed by growth stage. Compared with the regreening stage, lower α-diversity and more dominance by abundant species in the fungal community were observed in wheat-associated compartments (four sample types except for bulk soil) at the heading stage. Additionally, within each wheat-associated compartment across every growth stage, location had stronger effects on fungal community assembly than the wheat variety. The effects of variety on fungal community assembly were location specific as were the growth-stage patterns of varietal effects on leaf endosphere and rhizosphere fungal communities. We further detected a less diverse but abundant core fungal taxa that could be grouped into three clusters associated mainly with location. This study characterized the interplay effects between plant selection (compartment, growth stage, variety) and environment (location) on wheat-associated mycobiomes by determining drivers of fungal community assembly and core fungal taxa in field conditions. KEY POINTS: • Fungal community assembly was mainly shaped by sample type and growth stage • A lower diversity and more abundant core fungal taxa were shown at heading stage • Location had stronger effects on fungal community assembly than variety.
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211
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He X, Zhang Q, Li B, Jin Y, Jiang L, Wu R. Network mapping of root-microbe interactions in Arabidopsis thaliana. NPJ Biofilms Microbiomes 2021; 7:72. [PMID: 34493731 PMCID: PMC8423736 DOI: 10.1038/s41522-021-00241-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2021] [Accepted: 08/04/2021] [Indexed: 02/07/2023] Open
Abstract
Understanding how plants interact with their colonizing microbiota to determine plant phenotypes is a fundamental question in modern plant science. Existing approaches for genome-wide association studies (GWAS) are often focused on the association analysis between host genes and the abundance of individual microbes, failing to characterize the genetic bases of microbial interactions that are thought to be important for microbiota structure, organization, and function. Here, we implement a behavioral model to quantify various patterns of microbe-microbe interactions, i.e., mutualism, antagonism, aggression, and altruism, and map host genes that modulate microbial networks constituted by these interaction types. We reanalyze a root-microbiome data involving 179 accessions of Arabidopsis thaliana and find that the four networks differ structurally in the pattern of bacterial-fungal interactions and microbiome complexity. We identify several fungus and bacterial hubs that play a central role in mediating microbial community assembly surrounding A. thaliana root systems. We detect 1142 significant host genetic variants throughout the plant genome and then implement Bayesian networks (BN) to reconstruct epistatic networks involving all significant SNPs, of which 91 are identified as hub QTLs. Results from gene annotation analysis suggest that most of the hub QTLs detected are in proximity to candidate genes, executing a variety of biological functions in plant growth and development, resilience against pathogens, root development, and abiotic stress resistance. This study provides a new gateway to understand how genetic variation in host plants influences microbial communities and our results could help improve crops by harnessing soil microbes.
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Affiliation(s)
- Xiaoqing He
- grid.66741.320000 0001 1456 856XBeijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China ,grid.66741.320000 0001 1456 856XCenter for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Qi Zhang
- grid.66741.320000 0001 1456 856XCenter for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Beibei Li
- grid.66741.320000 0001 1456 856XCenter for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Yi Jin
- grid.66741.320000 0001 1456 856XCenter for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Libo Jiang
- grid.66741.320000 0001 1456 856XBeijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China ,grid.66741.320000 0001 1456 856XCenter for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Rongling Wu
- grid.66741.320000 0001 1456 856XBeijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China ,grid.66741.320000 0001 1456 856XCenter for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China ,grid.29857.310000 0001 2097 4281Center for Statistical Genetics, Departments of Public Health Sciences and Statistics, The Pennsylvania State University, Hershey, PA USA
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212
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Xiong C, Singh BK, He JZ, Han YL, Li PP, Wan LH, Meng GZ, Liu SY, Wang JT, Wu CF, Ge AH, Zhang LM. Plant developmental stage drives the differentiation in ecological role of the maize microbiome. MICROBIOME 2021; 9:171. [PMID: 34389047 PMCID: PMC8364065 DOI: 10.1186/s40168-021-01118-6] [Citation(s) in RCA: 110] [Impact Index Per Article: 36.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Accepted: 06/21/2021] [Indexed: 05/04/2023]
Abstract
BACKGROUND Plants live with diverse microbial communities which profoundly affect multiple facets of host performance, but if and how host development impacts the assembly, functions and microbial interactions of crop microbiomes are poorly understood. Here we examined both bacterial and fungal communities across soils, epiphytic and endophytic niches of leaf and root, and plastic leaf of fake plant (representing environment-originating microbes) at three developmental stages of maize at two contrasting sites, and further explored the potential function of phylloplane microbiomes based on metagenomics. RESULTS Our results suggested that plant developmental stage had a much stronger influence on the microbial diversity, composition and interkingdom networks in plant compartments than in soils, with the strongest effect in the phylloplane. Phylloplane microbiomes were co-shaped by both plant growth and seasonal environmental factors, with the air (represented by fake plants) as its important source. Further, we found that bacterial communities in plant compartments were more strongly driven by deterministic processes at the early stage but a similar pattern was for fungal communities at the late stage. Moreover, bacterial taxa played a more important role in microbial interkingdom network and crop yield prediction at the early stage, while fungal taxa did so at the late stage. Metagenomic analyses further indicated that phylloplane microbiomes possessed higher functional diversity at the early stage than the late stage, with functional genes related to nutrient provision enriched at the early stage and N assimilation and C degradation enriched at the late stage. Coincidently, more abundant beneficial bacterial taxa like Actinobacteria, Burkholderiaceae and Rhizobiaceae in plant microbiomes were observed at the early stage, but more saprophytic fungi at the late stage. CONCLUSIONS Our results suggest that host developmental stage profoundly influences plant microbiome assembly and functions, and the bacterial and fungal microbiomes take a differentiated ecological role at different stages of plant development. This study provides empirical evidence for host exerting strong effect on plant microbiomes by deterministic selection during plant growth and development. These findings have implications for the development of future tools to manipulate microbiome for sustainable increase in primary productivity. Video Abstract.
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Affiliation(s)
- Chao Xiong
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Brajesh K Singh
- Global Centre for Land-Based Innovation, Western Sydney University, Penrith, NSW, 2751, Australia
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, 2751, Australia
| | - Ji-Zheng He
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Yan-Lai Han
- College of Resource and Environmental Sciences, Henan Agricultural University, Zhengzhou, 450002, China
| | - Pei-Pei Li
- College of Resource and Environmental Sciences, Henan Agricultural University, Zhengzhou, 450002, China
| | - Li-Hua Wan
- Soil and Fertilizer Station of Qilin District, Qujing, Yunnan Province, Qujing, 655000, China
| | - Guo-Zhong Meng
- Soil and Fertilizer Station of Qilin District, Qujing, Yunnan Province, Qujing, 655000, China
| | - Si-Yi Liu
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jun-Tao Wang
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chuan-Fa Wu
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
- College of Resource and Environmental Sciences, Henan Agricultural University, Zhengzhou, 450002, China
| | - An-Hui Ge
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Li-Mei Zhang
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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213
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Xing L, Yang J, Jia Y, Hu X, Liu Y, Xu H, Yin H, Li J, Yi Z. Effects of ecological environment and host genotype on the phyllosphere bacterial communities of cigar tobacco ( Nicotiana tabacum L.). Ecol Evol 2021; 11:10892-10903. [PMID: 34429888 PMCID: PMC8366869 DOI: 10.1002/ece3.7861] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 06/05/2021] [Accepted: 06/10/2021] [Indexed: 12/03/2022] Open
Abstract
Microorganisms of plant phyllosphere play an important role in plant health and productivity and are influenced by abiotic and biotic factors. In this study, we investigated the phyllosphere bacterial communities of three cigar tobacco varieties cultivated in Guangcun (GC) and Wuzhishan (WZS), Hainan, China. Metagenomic DNA was extracted from tobacco leaf samples and sequenced by 16S rDNA amplicon sequencing. Our results showed that bacterial communities of cigar tobacco phyllosphere in GC exhibited remarkably higher alpha diversity than that in WZS. There was slight effect of tobacco genotype variations on the alpha diversity in both cultivation sites, and beta diversity and structure of bacterial community were not influenced significantly by the cultivation sites and tobacco varieties. Statistical analyses of species diversity unraveled that the dominant species in bacterial communities of cigar tobacco phyllosphere among all these samples were phylogenetically affiliated to Proteobacteria and Cyanobacteria. At the genus level, the most abundant microorganism was Limnobacter, followed by Brevundimonas, unidentified_Cyanobacteria, and Pseudomonas. Additionally, environmental conditions except for humidity were negatively correlated with the relative abundance of bacterial genera. Further analyses revealed that influence of site-specific factors on tobacco bacterial community was relatively higher than genotype-specific factors. In short, this study may contribute to the knowledge base of practical applications of bacterial inoculants for tobacco leaf production.
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Affiliation(s)
- Lei Xing
- College of AgronomyHunan Agricultural UniversityChangshaChina
- Greatwall Cigar FactoryChina Tobacco Sichuan Industrial Co., LtdShifangChina
| | - Jianlei Yang
- School of Minerals Processing and BioengineeringCentral South UniversityChangshaChina
| | - Yuhong Jia
- Greatwall Cigar FactoryChina Tobacco Sichuan Industrial Co., LtdShifangChina
| | - Xi Hu
- Greatwall Cigar FactoryChina Tobacco Sichuan Industrial Co., LtdShifangChina
| | - Yi Liu
- Greatwall Cigar FactoryChina Tobacco Sichuan Industrial Co., LtdShifangChina
| | - Heng Xu
- Greatwall Cigar FactoryChina Tobacco Sichuan Industrial Co., LtdShifangChina
| | - Huaqun Yin
- School of Minerals Processing and BioengineeringCentral South UniversityChangshaChina
| | - Juan Li
- College of AgronomyHunan Agricultural UniversityChangshaChina
| | - Zhenxie Yi
- College of AgronomyHunan Agricultural UniversityChangshaChina
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214
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Zai X, Luo W, Bai W, Li Y, Xiao X, Gao X, Wang E, Wei G, Chen W. Effect of Root Diameter on the Selection and Network Interactions of Root-Associated Bacterial Microbiomes in Robinia pseudoacacia L. MICROBIAL ECOLOGY 2021; 82:391-402. [PMID: 33449130 DOI: 10.1007/s00248-020-01678-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2020] [Accepted: 12/29/2020] [Indexed: 05/06/2023]
Abstract
The high plasticity of root morphology, physiology, and function influences root-associated microbiomes. However, the variation in root-associated microbiome diversity and structures in response to root diameter at different root depths remains poorly understood. Here, we selected black locust (Robinia pseudoacacia L.) as a model plant to investigate the selection and network interactions of rhizospheric and root endophytic bacterial microbiomes associated with roots of different diameters (1, 1-2, and > 2 mm) among root depths of 0-100 cm via the Illumina sequencing of the 16S rRNA gene. The results showed that the alpha diversity of the root-associated bacterial communities decreased with increasing root diameters among different root depths; fewer orders with higher relative abundance, especially in the endosphere, were enriched in association with coarse roots (> 2 mm) than fine roots among root depths. Furthermore, the variation in the enriched bacterial orders associated with different root diameters was explained by bulk soil properties. Higher co-occurrence network complexity and stability emerged in the rhizosphere microbiomes of fine roots than those of coarse roots, in contrast to the situation in the endosphere microbiomes. In particular, the endosphere of roots with a diameter of 1-2 mm exhibited the lowest network complexity and stability and a high proportion of keystone taxa (e.g., Cytophagia, Flavobacteriia, Sphingobacteriia, β-Proteobacteria, and γ-Proteobacteria), suggesting a keystone taxon-reliant strategy in this transitional stage. In summary, this study indicated that root diameter at different root depths differentially affects rhizospheric and endophytic bacterial communities, which implies a close relationship between the bacterial microbiome, root function, and soil properties.
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Affiliation(s)
- Xiaoyu Zai
- Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, 3 Taicheng Road, Yangling, Xianyang, 712100, Shaanxi, People's Republic of China
| | - Wen Luo
- Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, 3 Taicheng Road, Yangling, Xianyang, 712100, Shaanxi, People's Republic of China
| | - Wenqing Bai
- Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, 3 Taicheng Road, Yangling, Xianyang, 712100, Shaanxi, People's Republic of China
| | - Yuhua Li
- Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, 3 Taicheng Road, Yangling, Xianyang, 712100, Shaanxi, People's Republic of China
| | - Xiao Xiao
- Department of Microbiology, School of Basic Medical Sciences, Hubei University of Medicine, Shiyan, 442000, Hubei, People's Republic of China
| | - Xuee Gao
- Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, 3 Taicheng Road, Yangling, Xianyang, 712100, Shaanxi, People's Republic of China
| | - Entao Wang
- Depatamento de Microbiología, Escuela Nacional de Ciencias Biologicas, Instituto Politécnico Nacional, 11340, Mexico, D.F., Mexico
| | - Gehong Wei
- Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, 3 Taicheng Road, Yangling, Xianyang, 712100, Shaanxi, People's Republic of China
| | - Weimin Chen
- Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, 3 Taicheng Road, Yangling, Xianyang, 712100, Shaanxi, People's Republic of China.
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215
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Zuo Y, Li X, Yang J, Liu J, Zhao L, He X. Fungal Endophytic Community and Diversity Associated with Desert Shrubs Driven by Plant Identity and Organ Differentiation in Extremely Arid Desert Ecosystem. J Fungi (Basel) 2021; 7:jof7070578. [PMID: 34356957 PMCID: PMC8306007 DOI: 10.3390/jof7070578] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 07/15/2021] [Accepted: 07/16/2021] [Indexed: 12/23/2022] Open
Abstract
Despite desert ecosystem being crucial to our understanding of natural geography, species evolution and global climate change, there is limited information on the dynamics of their composition and the diversity of endophytic fungi communities driven by plant identity and organ differentiation. Here, an extensive investigation of endophytic fungal microbiome in root, stem, and leaf organs associated with five xerophyte shrubs in an extremely arid desert, Northwest China, were examined. The fungal community dominated by Dothideomycetes and Pleosporales. Shrub species strongly drive the niche-based processes of endophytic fungi across the root, stem and leaf compartments. The diversity and composition of endophytic fungi in stem showed higher variability among plant species than leaf and root. The fungal communities in root libraries were more diverse and exhibited a remarkable differentiation of community composition. We further demonstrated the significant host preferences and tissue specificity of desert endophytic fungi, and unique specific taxa were also observed. The co-occurrence network revealed the coexistence of fungal endophytes in arid desert, and the root fungal network harbored the highest interspecies connectivity. Members of Pleosporales were the most common keystone species in the root fungal network. This is the first report of mycobiota in both plant species and organ differentiation in an extremely arid desert ecosystem.
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Affiliation(s)
| | | | | | | | | | - Xueli He
- Correspondence: ; Tel.: +86-31-2507-9364
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216
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Jiang Y, Chen X, Zhao G, Liu J, Xie Y, Li Y, Gu H, Zou C. Endophytic Fungal Community of Tobacco Leaves and Their Potential Role in the Formation of "Cherry-Red" Tobacco. Front Microbiol 2021; 12:658116. [PMID: 34335492 PMCID: PMC8323715 DOI: 10.3389/fmicb.2021.658116] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 05/17/2021] [Indexed: 11/13/2022] Open
Abstract
"Cherry-red" tobacco is the superior variant of tobacco, appearing with the apperance of red dapples on cured leaves due to the demethylation of nicotine to nornicotine during maturation and curing. Fungi are known to have the capacity to convert nicotine to nornicotine. However, an endophytic fungal community of "cherry-red" tobacco has never been reported to our best knowledge. Here, we sampled mature leaves from both "cherry-red" and ordinary tobacco at lower, center, and upper plant sections, and we analyzed the ITS diversity using high-throughput sequencing. Results revealed a significantly different fungal community of foliar endophyte in "cherry-red" and ordinary tobacco. In comparison to the ordinary control, higher diversity and a co-occurrence network complex were found in "cherry-red" samples, especially in the center and upper leaves, where the red dapples mainly emerged. More taxa were enriched in the "cherry-red" than ordinary tobacco leaves at all plant sections. In particular, Aspergillus, some strains of which are reported capable of converting nicotine to nornicotine, was specifically enriched in upper "cherry-red" tobacco leaves, which showed most red dapples after curing. A less robust network structure was detected in the "cherry-red" tobacco compared to ordinary tobacco. The nearest taxon index (NTI) and β NTI indicated that the local community structuration of tobacco endophytic fungi mainly driven by deterministic process, while the community turnover among plant sections was stochastic. In conclusion, our study provides the earliest information of endophytic fungal community in "cherry-red" tobacco leaf, and the community diversity, composition, and network features are synchronously varied with the appearance of red dapples, which is suggestive of their relationship to the formation of "cherry-red" tobacco.
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Affiliation(s)
- Yonglei Jiang
- Yunnan Academy of Tobacco Agricultural Sciences, Kunming, China
| | - Xing Chen
- Yunnan Academy of Tobacco Agricultural Sciences, Kunming, China
| | - Gaokun Zhao
- Yunnan Academy of Tobacco Agricultural Sciences, Kunming, China
| | - Jiahong Liu
- Qujing Branch, Yunnan Tobacco Company, Qujing, China
| | - Yan Xie
- Qujing Branch, Yunnan Tobacco Company, Qujing, China
| | - Yong Li
- Yunnan Academy of Tobacco Agricultural Sciences, Kunming, China
| | - Huaguo Gu
- Yunnan Academy of Tobacco Agricultural Sciences, Kunming, China
| | - Congming Zou
- Yunnan Academy of Tobacco Agricultural Sciences, Kunming, China
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217
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Wei G, Chen Z, Wang B, Wei F, Zhang G, Wang Y, Zhu G, Zhou Y, Zhao Q, He M, Dong L, Chen S. Endophytes isolated from Panax notoginseng converted ginsenosides. Microb Biotechnol 2021; 14:1730-1746. [PMID: 34081833 PMCID: PMC8313278 DOI: 10.1111/1751-7915.13842] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Revised: 05/02/2021] [Accepted: 05/13/2021] [Indexed: 01/02/2023] Open
Abstract
Endophytes may participate in the conversion of metabolites within medicinal plants, influencing the efficacy of host. However, the distribution of endophytes within medicinal plants P. notoginseng and how it contributes to the conversion of saponins are not well understood. Here, we determined the distribution of saponins and endophytes within P. notoginseng compartments and further confirm the saponin conversion by endophytes. We found metabolites showed compartment specificity within P. notoginseng. Potential saponin biomarkers, such as Rb1, Rg1, Re, Rc and Rd, were obtained. Endophytic diversity, composition and co-occurrence networks also showed compartment specificity, and bacterial alpha diversity values were highest in root compartment, consistently decreased in the stem and leaf compartments, whereas those of fungi showed the opposite trend. Potential bacterial biomarkers, such as Rhizobium, Bacillus, Pseudomonas, Enterobacter, Klebsiella, Pantoea and fungal biomarkers Phoma, Epicoccum, Xylariales, were also obtained. Endophytes related to saponin contents were found by Spearman correlation analysis, and further verification experiments showed that Enterobacter chengduensis could convert ginsenoside Rg1 to F1 at a rate of 13.24%; Trichoderma koningii could convert ginsenoside Rb1 to Rd at a rate of 40.00% and to Rg3 at a rate of 32.31%; Penicillium chermesinum could convert ginsenoside Rb1 to Rd at a rate of 74.24%.
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Affiliation(s)
- Guangfei Wei
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese MedicineInstitute of Chinese Materia MedicaChina Academy of Chinese Medical SciencesNo.16 Nanxiaojie, Dongzhimennei AveBeijing100700China
| | - Zhongjian Chen
- Institute of Sanqi ResearchWenshan UniversityWenshan663000China
| | - Bo Wang
- Hubei Institute for Drug ControlWuhan430012China
| | - Fugang Wei
- Wenshan Miaoxiang Notoginseng Technology, Co., Ltd.Wenshan663000China
| | - Guozhuang Zhang
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese MedicineInstitute of Chinese Materia MedicaChina Academy of Chinese Medical SciencesNo.16 Nanxiaojie, Dongzhimennei AveBeijing100700China
| | - Yong Wang
- Institute of Sanqi ResearchWenshan UniversityWenshan663000China
| | - Guangwei Zhu
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese MedicineInstitute of Chinese Materia MedicaChina Academy of Chinese Medical SciencesNo.16 Nanxiaojie, Dongzhimennei AveBeijing100700China
| | - Yuxin Zhou
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese MedicineInstitute of Chinese Materia MedicaChina Academy of Chinese Medical SciencesNo.16 Nanxiaojie, Dongzhimennei AveBeijing100700China
- Hubei Institute for Drug ControlWuhan430012China
| | - Qinghe Zhao
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese MedicineInstitute of Chinese Materia MedicaChina Academy of Chinese Medical SciencesNo.16 Nanxiaojie, Dongzhimennei AveBeijing100700China
| | - Mingjun He
- Hainan Branch Institute of Medicinal PlantChinese Academy of Medical Sciences & Peking Union Medical CollegeWanning571533China
| | - Linlin Dong
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese MedicineInstitute of Chinese Materia MedicaChina Academy of Chinese Medical SciencesNo.16 Nanxiaojie, Dongzhimennei AveBeijing100700China
| | - Shilin Chen
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese MedicineInstitute of Chinese Materia MedicaChina Academy of Chinese Medical SciencesNo.16 Nanxiaojie, Dongzhimennei AveBeijing100700China
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218
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Noman M, Ahmed T, Ijaz U, Shahid M, Azizullah, Li D, Manzoor I, Song F. Plant-Microbiome Crosstalk: Dawning from Composition and Assembly of Microbial Community to Improvement of Disease Resilience in Plants. Int J Mol Sci 2021; 22:6852. [PMID: 34202205 PMCID: PMC8269294 DOI: 10.3390/ijms22136852] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 06/18/2021] [Accepted: 06/23/2021] [Indexed: 02/06/2023] Open
Abstract
Plants host diverse but taxonomically structured communities of microorganisms, called microbiome, which colonize various parts of host plants. Plant-associated microbial communities have been shown to confer multiple beneficial advantages to their host plants, such as nutrient acquisition, growth promotion, pathogen resistance, and environmental stress tolerance. Systematic studies have provided new insights into the economically and ecologically important microbial communities as hubs of core microbiota and revealed their beneficial impacts on the host plants. Microbiome engineering, which can improve the functional capabilities of native microbial species under challenging agricultural ambiance, is an emerging biotechnological strategy to improve crop yield and resilience against variety of environmental constraints of both biotic and abiotic nature. This review highlights the importance of indigenous microbial communities in improving plant health under pathogen-induced stress. Moreover, the potential solutions leading towards commercialization of proficient bioformulations for sustainable and improved crop production are also described.
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Affiliation(s)
- Muhammad Noman
- State Key Laboratory of Rice Biology and Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China; (M.N.); (T.A.); (U.I.); (A.); (D.L.)
| | - Temoor Ahmed
- State Key Laboratory of Rice Biology and Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China; (M.N.); (T.A.); (U.I.); (A.); (D.L.)
| | - Usman Ijaz
- State Key Laboratory of Rice Biology and Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China; (M.N.); (T.A.); (U.I.); (A.); (D.L.)
| | - Muhammad Shahid
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad 38000, Pakistan;
| | - Azizullah
- State Key Laboratory of Rice Biology and Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China; (M.N.); (T.A.); (U.I.); (A.); (D.L.)
| | - Dayong Li
- State Key Laboratory of Rice Biology and Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China; (M.N.); (T.A.); (U.I.); (A.); (D.L.)
| | - Irfan Manzoor
- Department of Biology, Indiana University, Bloomington, IN 47405, USA; or
| | - Fengming Song
- State Key Laboratory of Rice Biology and Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China; (M.N.); (T.A.); (U.I.); (A.); (D.L.)
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Wang S, Guo Z, Wang L, Zhang Y, Jiang F, Wang X, Yin L, Liu B, Liu H, Wang H, Wang A, Ren Y, Liu C, Fan W, Wang Z. Wheat Rhizosphere Metagenome Reveals Newfound Potential Soil Zn-Mobilizing Bacteria Contributing to Cultivars' Variation in Grain Zn Concentration. Front Microbiol 2021; 12:689855. [PMID: 34248914 PMCID: PMC8261137 DOI: 10.3389/fmicb.2021.689855] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 05/24/2021] [Indexed: 11/24/2022] Open
Abstract
An effective solution to global human zinc (Zn) deficiency is Zn biofortification of staple food crops, which has been hindered by the low available Zn in calcareous soils worldwide. Many culturable soil microbes have been reported to increase Zn availability in the laboratory, while the status of these microbes in fields and whether there are unculturable Zn-mobilizing microbes remain unexplored. Here, we use the culture-independent metagenomic sequencing to investigate the rhizosphere microbiome of three high-Zn (HZn) and three low-Zn (LZn) wheat cultivars in a field experiment with calcareous soils. The average grain Zn concentration of HZn was higher than the Zn biofortification target 40 mg kg–1, while that of LZn was lower than 40 mg kg–1. Metagenomic sequencing and analysis showed large microbiome difference between wheat rhizosphere and bulk soil but small difference between HZn and LZn. Most of the rhizosphere-enriched microbes in HZn and LZn were in common, including many of the previously reported soil Zn-mobilizing microbes. Notably, 30 of the 32 rhizosphere-enriched species exhibiting different abundances between HZn and LZn possess the functional genes involved in soil Zn mobilization, especially the synthesis and exudation of organic acids and siderophores. Most of the abundant potential Zn-mobilizing species were positively correlated with grain Zn concentration and formed a module with strong interspecies relations in the co-occurrence network of abundant rhizosphere-enriched microbes. The potential Zn-mobilizing species, especially Massilia and Pseudomonas, may contribute to the cultivars’ variation in grain Zn concentration, and they deserve further investigation in future studies on Zn biofortification.
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Affiliation(s)
- Sen Wang
- Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Zikang Guo
- State Key Laboratory of Crop Stress Biology in Arid Areas, Northwest A&F University, Yangling, China.,Key Laboratory of Plant Nutrition and Agri-Environment in Northwest China, Ministry of Agriculture, College of Natural Resources and Environment, Northwest A&F University, Yangling, China
| | - Li Wang
- State Key Laboratory of Crop Stress Biology in Arid Areas, Northwest A&F University, Yangling, China.,Key Laboratory of Plant Nutrition and Agri-Environment in Northwest China, Ministry of Agriculture, College of Natural Resources and Environment, Northwest A&F University, Yangling, China
| | - Yan Zhang
- Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Fan Jiang
- Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Xingshu Wang
- State Key Laboratory of Crop Stress Biology in Arid Areas, Northwest A&F University, Yangling, China.,Key Laboratory of Plant Nutrition and Agri-Environment in Northwest China, Ministry of Agriculture, College of Natural Resources and Environment, Northwest A&F University, Yangling, China
| | - Lijuan Yin
- Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Bo Liu
- Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Hangwei Liu
- Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Hengchao Wang
- Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Anqi Wang
- Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Yuwei Ren
- Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Conghui Liu
- Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Wei Fan
- Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Zhaohui Wang
- State Key Laboratory of Crop Stress Biology in Arid Areas, Northwest A&F University, Yangling, China.,Key Laboratory of Plant Nutrition and Agri-Environment in Northwest China, Ministry of Agriculture, College of Natural Resources and Environment, Northwest A&F University, Yangling, China
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220
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Lei F, Liu X, Huang H, Fu S, Zou K, Zhang S, Zhou L, Zeng J, Liu H, Jiang L, Miao B, Liang Y. The Macleaya cordata Symbiont: Revealing the Effects of Plant Niches and Alkaloids on the Bacterial Community. Front Microbiol 2021; 12:681210. [PMID: 34177865 PMCID: PMC8219869 DOI: 10.3389/fmicb.2021.681210] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 05/07/2021] [Indexed: 11/13/2022] Open
Abstract
Endophytes are highly associated with plant growth and health. Exploring the variation of bacterial communities in different plant niches is essential for understanding microbe-plant interactions. In this study, high-throughput gene sequencing was used to analyze the composition and abundance of bacteria from the rhizospheric soil and different parts of the Macleaya cordata. The results indicated that the bacterial community structure varied widely among compartments. Bacterial diversity was observed to be the highest in the rhizospheric soil and the lowest in fruits. Proteobacteria, Actinobacteria, and Bacteroidetes were found as the dominant phyla. The genera Sphingomonas (∼47.77%) and Methylobacterium (∼45.25%) dominated in fruits and leaves, respectively. High-performance liquid chromatography (HPLC) was employed to measure the alkaloid content of different plant parts. Significant correlations were observed between endophytic bacteria and alkaloids. Especially, Sphingomonas showed a significant positive correlation with sanguinarine and chelerythrine. All four alkaloids were negatively correlated with the microbiota of stems. The predicted result of PICRUST2 revealed that the synthesis of plant alkaloids might lead to a higher abundance of endophytic microorganisms with genes related to alkaloid synthesis, further demonstrated the correlation between bacterial communities and alkaloids. This study provided the first insight into the bacterial community composition in different parts of Macleaya cordata and the correlation between the endophytic bacteria and alkaloids.
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Affiliation(s)
- Fangying Lei
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China.,Key Laboratory of Biometallurgy, Ministry of Education, Changsha, China
| | - Xueduan Liu
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China.,Key Laboratory of Biometallurgy, Ministry of Education, Changsha, China
| | - Haonan Huang
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China.,Key Laboratory of Biometallurgy, Ministry of Education, Changsha, China
| | - Shaodong Fu
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China.,Key Laboratory of Biometallurgy, Ministry of Education, Changsha, China
| | - Kai Zou
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China.,Key Laboratory of Biometallurgy, Ministry of Education, Changsha, China
| | - Shuangfei Zhang
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China.,Key Laboratory of Biometallurgy, Ministry of Education, Changsha, China
| | - Li Zhou
- Hunan Key Laboratory of Traditional Chinese Veterinary Medicine, Hunan Agricultural University, Changsha, China
| | - Jianguo Zeng
- Hunan Key Laboratory of Traditional Chinese Veterinary Medicine, Hunan Agricultural University, Changsha, China
| | - Hongwei Liu
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China.,Key Laboratory of Biometallurgy, Ministry of Education, Changsha, China
| | - Luhua Jiang
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China.,Key Laboratory of Biometallurgy, Ministry of Education, Changsha, China
| | - Bo Miao
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China.,Key Laboratory of Biometallurgy, Ministry of Education, Changsha, China
| | - Yili Liang
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China.,Key Laboratory of Biometallurgy, Ministry of Education, Changsha, China
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221
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Assembly of the Populus Microbiome Is Temporally Dynamic and Determined by Selective and Stochastic Factors. mSphere 2021; 6:e0131620. [PMID: 34106767 PMCID: PMC8265678 DOI: 10.1128/msphere.01316-20] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Recent work shows that the plant microbiome, particularly the initial assembly of this microbiome, influences plant health, survival, and fitness. Here, we characterize the initial assembly of the Populus microbiome across ten genotypes belonging to two poplar species in a common garden using 16S rRNA gene and ITS2 region amplicon sequencing of the leaf endosphere, leaf surface, root endosphere, and rhizosphere. We sampled these microbiomes three times throughout the first growing season and found that the composition of the microbiome changed dramatically over time across all plant-associated habitats and host genotypes. For archaea and bacteria, these changes were dominated by strong homogenizing selection (accounting for 29 to 62% of pairwise comparisons). However, fungal assembly was generally characterized by multiple ecological assembly processes (i.e., a mix of weak selective and dispersal processes). Interestingly, genotype, while a significant moderator of microbiome composition, generally explained less variation than sample date across plant-associated habitats. We defined a set of core genera that accounted for, on average, 36% of the microbiome. The relative abundance of this core community was consistent over time. Additionally, using source tracking modeling, we determined that new microbial taxa colonize from both aboveground and belowground sources, and combined with our ecological assembly null models, we found that both selective and dispersal processes explained the differences between exo- (i.e., leaf surface and rhizosphere) and endospheric microbiomes. Taken together, our results suggest that the initial assembly of the Populus microbiome is time-, genotype-, and habitat-dependent and is moderated by both selective and stochastic factors. IMPORTANCE The initial assembly of the plant microbiome may establish the trajectory of forthcoming microbiome states, which could determine the overall future health of the plant. However, while much is known about the initial microbiome assembly of grasses and agricultural crops, less is known about the initial microbiome of long-lived trees, such as poplar (Populus spp.). Thus, a greater understanding of initial plant microbiome assembly in an ecologically and economically important plant such as Populus is highly desirable. Here, we show that the initial microbiome community composition and assembly in the first growing season of Populus is temporally dynamic and is determined by a combination of both selective and stochastic factors. Our findings could be used to prescribe ecologically informed microbial inoculations and better predict the composition of the Populus microbiome into the future and to better understand its influence on plant health.
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Kavamura VN, Mendes R, Bargaz A, Mauchline TH. Defining the wheat microbiome: Towards microbiome-facilitated crop production. Comput Struct Biotechnol J 2021; 19:1200-1213. [PMID: 33680361 PMCID: PMC7902804 DOI: 10.1016/j.csbj.2021.01.045] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 01/29/2021] [Accepted: 01/30/2021] [Indexed: 12/17/2022] Open
Abstract
Wheat is one of the world's most important crops, but its production relies heavily on agrochemical inputs which can be harmful to the environment when used excessively. It is well known that a multitude of microbes interact with eukaryotic organisms, including plants, and the sum of microbes and their functions associated with a given host is termed the microbiome. Plant-microbe interactions can be beneficial, neutral or harmful to the host plant. Over the last decade, with the development of next generation DNA sequencing technology, our understanding of the plant microbiome structure has dramatically increased. Considering that defining the wheat microbiome is key to leverage crop production in a sustainable way, here we describe how different factors drive microbiome assembly in wheat, including crop management, edaphic-environmental conditions and host selection. In addition, we highlight the benefits to take a multidisciplinary approach to define and explore the wheat core microbiome to generate solutions based on microbial (synthetic) communities or single inoculants. Advances in plant microbiome research will facilitate the development of microbial strategies to guarantee a sustainable intensification of crop production.
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Affiliation(s)
- Vanessa N. Kavamura
- Sustainable Agriculture Sciences, Rothamsted Research, Harpenden, Hertfordshire, UK
| | - Rodrigo Mendes
- Laboratory of Environmental Microbiology, Embrapa Environment, Jaguariúna, SP, Brazil
| | - Adnane Bargaz
- Agrobiosciences, Mohammed VI Polytechnic University, Benguerir, Morocco
| | - Tim H. Mauchline
- Sustainable Agriculture Sciences, Rothamsted Research, Harpenden, Hertfordshire, UK
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224
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Haworth M, Marino G, Loreto F, Centritto M. Integrating stomatal physiology and morphology: evolution of stomatal control and development of future crops. Oecologia 2021; 197:867-883. [PMID: 33515295 PMCID: PMC8591009 DOI: 10.1007/s00442-021-04857-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 01/11/2021] [Indexed: 11/29/2022]
Abstract
Stomata are central players in the hydrological and carbon cycles, regulating the uptake of carbon dioxide (CO2) for photosynthesis and transpirative loss of water (H2O) between plants and the atmosphere. The necessity to balance water-loss and CO2-uptake has played a key role in the evolution of plants, and is increasingly important in a hotter and drier world. The conductance of CO2 and water vapour across the leaf surface is determined by epidermal and stomatal morphology (the number, size, and spacing of stomatal pores) and stomatal physiology (the regulation of stomatal pore aperture in response to environmental conditions). The proportion of the epidermis allocated to stomata and the evolution of amphistomaty are linked to the physiological function of stomata. Moreover, the relationship between stomatal density and [CO2] is mediated by physiological stomatal behaviour; species with less responsive stomata to light and [CO2] are most likely to adjust stomatal initiation. These differences in the sensitivity of the stomatal density—[CO2] relationship between species influence the efficacy of the ‘stomatal method’ that is widely used to infer the palaeo-atmospheric [CO2] in which fossil leaves developed. Many studies have investigated stomatal physiology or morphology in isolation, which may result in the loss of the ‘overall picture’ as these traits operate in a coordinated manner to produce distinct mechanisms for stomatal control. Consideration of the interaction between stomatal morphology and physiology is critical to our understanding of plant evolutionary history, plant responses to on-going climate change and the production of more efficient and climate-resilient food and bio-fuel crops.
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Affiliation(s)
- Matthew Haworth
- National Research Council of Italy, Institute of Sustainable Plant Protection (CNR-IPSP), Via Madonna del Piano 10, 50019, Sesto Fiorentino, FI, Italy.
| | - Giovanni Marino
- National Research Council of Italy, Institute of Sustainable Plant Protection (CNR-IPSP), Via Madonna del Piano 10, 50019, Sesto Fiorentino, FI, Italy
| | - Francesco Loreto
- Department of Biology, Agriculture and Food Sciences (CNR-DiSBA), National Research Council of Italy, Rome, Italy
- Department of Biology, University of Naples Federico II, Naples, Italy
| | - Mauro Centritto
- National Research Council of Italy, Institute of Sustainable Plant Protection (CNR-IPSP), Via Madonna del Piano 10, 50019, Sesto Fiorentino, FI, Italy
- ENI-CNR Water Research Center "Hypatia of Alexandria", Research Center Metapontum Agrobios, Metaponto, Italy
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225
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Taskin E, Misci C, Bandini F, Fiorini A, Pacini N, Obiero C, Sila DN, Tabaglio V, Puglisi E. Smallholder Farmers' Practices and African Indigenous Vegetables Affect Soil Microbial Biodiversity and Enzyme Activities in Lake Naivasha Basin, Kenya. BIOLOGY 2021; 10:biology10010044. [PMID: 33440642 PMCID: PMC7826984 DOI: 10.3390/biology10010044] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 01/08/2021] [Accepted: 01/08/2021] [Indexed: 01/03/2023]
Abstract
Simple Summary Smallholder farmers in Sub-Saharan Africa (SSA) are food insecure. Underexploited African indigenous vegetables (AIVs) are consumed locally without being considered a primary source of food and income. However, AIVs hold great potential for the future challenges of food security and climate change. We investigated the effects of different cropping systems and inclusion of AIVs in farming on the soil biodiversity and fertility status of smallholder farmers in Naivasha, Kenya. Compared to mainstream farming approaches, soil microorganisms under AIV cultivations differed significantly. Tillage, fertilization, soil amendments, and traditional homemade plant protection were singled out as the most important factors. The soil alteration index based on enzyme activity offered a reliable way to determine the alteration status for the first time in SSA. These findings could be useful for farmers to integrate AIVs with correct sustainable practices for a sustainable future and may contribute to the mitigation of food insecurity. Abstract Loss of soil biodiversity and fertility in Sub-Saharan Africa (SSA) may put the food security of smallholder farmers in peril. Food systems in SSA are seeing the rise of African indigenous vegetables (AIVs) that are underexploited but locally consumed without being considered a primary source of food and income. Here we present a field study, a first of its kind, in which we investigated the effects of different cropping systems and inclusion of AIVs in the farming approach on bacterial and fungal biodiversity and community structures, enzymatic activity, and the alteration status of soils of the smallholder farmers in Kenya. When compared to mainstream farming approaches, the composition and biodiversity of bacteria and fungi under AIV cultivations was significantly different. Tillage had a significant impact only on the fungal communities. Fertilization and soil amendments caused shifts in microbial communities towards specialized degraders and revealed the introduction of specific microorganisms from amendments. Traditional homemade plant protection products did not cause any disturbance to either of soil bacteria or fungi. The soil alteration index based on enzyme activity successfully differentiated the alteration status for the first time in SSA. These findings could be useful for farmers to integrate AIVs with correct sustainable practices for a sustainable future.
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Affiliation(s)
- Eren Taskin
- Dipartimento di Scienze e Tecnologie Alimentari per la Sostenibilità della Filiera Agro-Alimentare (DISTAS), Facoltà di Scienze Agrarie Alimentari ed Ambientali, Università Cattolica del Sacro Cuore, Via Emilia Parmense 84, 29122 Piacenza, Italy; (E.T.); (C.M.); (F.B.); (E.P.)
| | - Chiara Misci
- Dipartimento di Scienze e Tecnologie Alimentari per la Sostenibilità della Filiera Agro-Alimentare (DISTAS), Facoltà di Scienze Agrarie Alimentari ed Ambientali, Università Cattolica del Sacro Cuore, Via Emilia Parmense 84, 29122 Piacenza, Italy; (E.T.); (C.M.); (F.B.); (E.P.)
| | - Francesca Bandini
- Dipartimento di Scienze e Tecnologie Alimentari per la Sostenibilità della Filiera Agro-Alimentare (DISTAS), Facoltà di Scienze Agrarie Alimentari ed Ambientali, Università Cattolica del Sacro Cuore, Via Emilia Parmense 84, 29122 Piacenza, Italy; (E.T.); (C.M.); (F.B.); (E.P.)
| | - Andrea Fiorini
- Dipartimento di Scienze delle Produzioni Vegetali Sostenibili (DI.PRO.VE.S.), Facoltà di Scienze Agrarie Alimentari ed Ambientali, Università Cattolica del Sacro Cuore, Via Emilia Parmense 84, 29122 Piacenza, Italy;
| | - Nic Pacini
- Dipartimento di Ingegneria dell’Ambiente (DIAm), Università della Calabria, Via Pietro Bucci, 87036 Arcavacata di Rende, Italy;
- School of Geography, Geology and Environment, University of Leicester, Leicester LE1 7RH, UK
| | - Clifford Obiero
- Land Resource Planning and Management, College of Agriculture and Natural Resources, Jomo Kenyatta University of Agriculture and Technology, Nairobi P.O. Box 62000, Kenya;
| | - Daniel Ndaka Sila
- School of Food and Nutritional Sciences, College of Agriculture and Natural Resources, Jomo Kenyatta University of Agriculture and Technology, Nairobi P.O. Box 62000, Kenya;
| | - Vincenzo Tabaglio
- Dipartimento di Scienze delle Produzioni Vegetali Sostenibili (DI.PRO.VE.S.), Facoltà di Scienze Agrarie Alimentari ed Ambientali, Università Cattolica del Sacro Cuore, Via Emilia Parmense 84, 29122 Piacenza, Italy;
- Correspondence: ; Tel.: +39-0523-599-222
| | - Edoardo Puglisi
- Dipartimento di Scienze e Tecnologie Alimentari per la Sostenibilità della Filiera Agro-Alimentare (DISTAS), Facoltà di Scienze Agrarie Alimentari ed Ambientali, Università Cattolica del Sacro Cuore, Via Emilia Parmense 84, 29122 Piacenza, Italy; (E.T.); (C.M.); (F.B.); (E.P.)
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