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Wang Z, Liu J, Xu H, Liu J, Zhao Z, Gong X. Core Microbiome and Microbial Community Structure in Coralloid Roots of Cycas in Ex Situ Collection of Kunming Botanical Garden in China. Microorganisms 2023; 11:2144. [PMID: 37763988 PMCID: PMC10537389 DOI: 10.3390/microorganisms11092144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 08/12/2023] [Accepted: 08/18/2023] [Indexed: 09/29/2023] Open
Abstract
Endophytes are essential in plant succession and evolution, and essential for stress resistance. Coralloid root is a unique root structure found in cycads that has played a role in resisting adverse environments, yet the core taxa and microbial community of different Cycas species have not been thoroughly investigated. Using amplicon sequencing, we successfully elucidated the microbiomes present in coralloid roots of 10 Cycas species, representing all four sections of Cycas in China. We found that the endophytic bacteria in coralloid roots, i.e., Cyanobacteria, were mainly composed of Desmonostoc_PCC-7422, Nostoc_PCC-73102 and unclassified_f__Nostocaceae. Additionally, the Ascomycota fungi of Exophiala, Paraboeremia, Leptobacillium, Fusarium, Alternaria, and Diaporthe were identified as the core fungi taxa. The Ascomycota fungi of Nectriaceae, Herpotrichiellaceae, Cordycipitaceae, Helotiaceae, Diaporthaceae, Didymellaceae, Clavicipitaceae and Pleosporaceae were identified as the core family taxa in coralloid roots of four sections. High abundance but low diversity of bacterial community was detected in the coralloid roots, but no significant difference among species. The fungal community exhibited much higher complexity compared to bacteria, and diversity was noted among different species or sections. These core taxa, which were a subset of the microbiome that frequently occurred in all, or most, individuals of Cycas species, represent targets for the development of Cycas conservation.
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Affiliation(s)
- Zhaochun Wang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming 650091, China;
- Key Laboratory of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; (J.L.); (J.L.)
- University of Chinese Academy of Sciences, Beijing 101408, China
| | - Jian Liu
- Key Laboratory of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; (J.L.); (J.L.)
| | - Haiyan Xu
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, China Agricultural University, Beijing 100193, China;
| | - Jiating Liu
- Key Laboratory of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; (J.L.); (J.L.)
- University of Chinese Academy of Sciences, Beijing 101408, China
| | - Zhiwei Zhao
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming 650091, China;
| | - Xun Gong
- Key Laboratory of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; (J.L.); (J.L.)
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Demarquest G, Lajoie G. Bacterial endophytes of sugar maple leaves vary more idiosyncratically than epiphytes across a large geographic area. FEMS Microbiol Ecol 2023; 99:fiad079. [PMID: 37442613 DOI: 10.1093/femsec/fiad079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 07/04/2023] [Accepted: 07/12/2023] [Indexed: 07/15/2023] Open
Abstract
Bacteria from the leaf surface and the leaf tissue have been attributed with several beneficial properties for their plant host. Though physically connected, the microbial ecology of these compartments has mostly been studied separately such that we lack an integrated understanding of the processes shaping their assembly. We sampled leaf epiphytes and endophytes from the same individuals of sugar maple across the northern portion of its range to evaluate if their community composition was driven by similar processes within and across populations differing in plant traits and overall abiotic environment. Leaf compartment explained most of the variation in community diversity and composition across samples. Leaf epiphytic communities were driven more by host and site characteristics than endophytic communities, whose community composition was more idiosyncratic across samples. Our results suggest a greater importance of priority effects and opportunistic colonization in driving community assembly of leaf endophytes. Understanding the comparative assembly of bacterial communities at the surface and inside plant leaves may be particularly useful for leveraging their respective potential for improving the health of plants in natural and anthropized ecosystems.
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Affiliation(s)
- Garance Demarquest
- Institut de Recherche en Biologie Végétale, Université de Montréal, 4101 rue Sherbrooke E, H1X 2B2 Montréal, Canada
- Université de Rennes, Agro-Campus Ouest, 65 Rue de Saint-Brieuc, 35042 Rennes, France
| | - Geneviève Lajoie
- Institut de Recherche en Biologie Végétale, Université de Montréal, 4101 rue Sherbrooke E, H1X 2B2 Montréal, Canada
- Jardin Botanique de Montréal, 4101 rue Sherbrooke E, H1X 2B2 Montréal, Canada
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Kong W, Qiu L, Ishii S, Jia X, Su F, Song Y, Hao M, Shao M, Wei X. Contrasting response of soil microbiomes to long-term fertilization in various highland cropping systems. ISME COMMUNICATIONS 2023; 3:81. [PMID: 37596350 PMCID: PMC10439144 DOI: 10.1038/s43705-023-00286-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 07/17/2023] [Accepted: 07/24/2023] [Indexed: 08/20/2023]
Abstract
Soil microbiomes play important roles in supporting agricultural ecosystems. However, it is still not well-known how soil microbiomes and their functionality respond to fertilization in various cropping systems. Here we examined the effects of 36 years of phosphorus, nitrogen, and manure application on soil bacterial communities, functionality and crop productivity in three contrasting cropping systems (i.e., continuous leguminous alfalfa (AC), continuous winter wheat (WC), and grain-legume rotation of winter wheat + millet - pea - winter wheat (GLR)) in a highland region of China's Loess Plateau. We showed that long-term fertilization significantly affected soil bacterial communities and that the effects varied with cropping system. Compared with the unfertilized control, fertilization increased soil bacterial richness and diversity in the leguminous AC system, whereas it decreased those in the GLR system. Fertilization, particularly manure application, enlarged the differences in soil bacterial communities among cropping systems. Soil bacterial communities were mostly affected by the soil organic carbon and nitrogen contents in the WC and GLR systems, but by the soil available phosphorous content in the AC system. Crop productivity was closely associated with the abundance of fertilization-responsive taxa in the three cropping systems. Our study highlights that legume and non-legume cropping systems should be disentangled when assessing the responses of soil microbial communities to long-term fertilizer application.
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Affiliation(s)
- Weibo Kong
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Northwest A&F University, Yangling, 712100, Shaanxi, China
- Research Center of Soil and Water Conservation and Ecological Environment, Ministry of Education, Chinese Academy of Sciences, Yangling, 712100, China
| | - Liping Qiu
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Northwest A&F University, Yangling, 712100, Shaanxi, China
- Research Center of Soil and Water Conservation and Ecological Environment, Ministry of Education, Chinese Academy of Sciences, Yangling, 712100, China
| | - Satoshi Ishii
- BioTechnology Institute, University of Minnesota, St. Paul, MN, 55108, USA
- Department of Soil, Water, and Climate, University of Minnesota, St. Paul, MN, 55108, USA
| | - Xiaoxu Jia
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Northwest A&F University, Yangling, 712100, Shaanxi, China
- Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, 100101, Beijing, China
| | - Fuyuan Su
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Northwest A&F University, Yangling, 712100, Shaanxi, China
- Research Center of Soil and Water Conservation and Ecological Environment, Ministry of Education, Chinese Academy of Sciences, Yangling, 712100, China
| | - Yu Song
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Northwest A&F University, Yangling, 712100, Shaanxi, China
- College of Natural Resources and Environment, Northwest A&F University, Yangling, 712100, China
| | - Mingde Hao
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Northwest A&F University, Yangling, 712100, Shaanxi, China
- Research Center of Soil and Water Conservation and Ecological Environment, Ministry of Education, Chinese Academy of Sciences, Yangling, 712100, China
| | - Mingan Shao
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Northwest A&F University, Yangling, 712100, Shaanxi, China
- Research Center of Soil and Water Conservation and Ecological Environment, Ministry of Education, Chinese Academy of Sciences, Yangling, 712100, China
- CAS Center for Excellence in Quaternary Science and Global Change, Xi'an, 710061, Shaanxi, China
| | - Xiaorong Wei
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Northwest A&F University, Yangling, 712100, Shaanxi, China.
- Research Center of Soil and Water Conservation and Ecological Environment, Ministry of Education, Chinese Academy of Sciences, Yangling, 712100, China.
- CAS Center for Excellence in Quaternary Science and Global Change, Xi'an, 710061, Shaanxi, China.
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Wei X, Fu T, He G, Zhong Z, Yang M, Lou F, He T. Types of vegetables shape composition, diversity, and co-occurrence networks of soil bacteria and fungi in karst areas of southwest China. BMC Microbiol 2023; 23:194. [PMID: 37468849 PMCID: PMC10354930 DOI: 10.1186/s12866-023-02929-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 07/03/2023] [Indexed: 07/21/2023] Open
Abstract
BACKGROUND Microorganisms are of significant importance in soil. Yet their association with specific vegetable types remains poorly comprehended. This study investigates the composition of bacterial and fungal communities in soil by employing high-throughput sequencing of 16 S rRNA genes and ITS rRNA genes while considering the cultivation of diverse vegetable varieties. RESULTS The findings indicate that the presence of cultivated vegetables influenced the bacterial and fungal communities leading to discernible alterations when compared to uncultivated soil. In particular, the soil of leafy vegetables (such as cabbage and kale) exhibited higher bacterial α-diversity than melon and fruit vegetable (such as cucumber and tomato), while fungal α-diversity showed an inverse pattern. The prevailing bacterial phyla in both leafy vegetable and melon and fruit vegetable soils were Proteobacteria, Acidobacteriota, Actinobacteriota, and Chloroflexi. In leafy vegetable soil, dominant fungal phyla included Ascomycota, Olpidiomycota, Mortierellomycota, and Basidiomycota whereas in melon and fruit vegetable soil. Ascomycota, Mortierellomycota, Basidiomycota, and Rozellomycota held prominence. Notably, the relative abundance of Ascomycota was lower in leafy vegetable soil compared to melon and fruit vegetable soil. Moreover, leafy vegetable soil exhibited a more complex and stable co-occurrence network in comparison to melon and fruit vegetable soil. CONCLUSION The findings enhance our understanding of how cultivated soil bacteria and fungi respond to human disturbance, thereby providing a valuable theoretical basis for soil health in degraded karst areas of southwest China.
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Affiliation(s)
- Xiaoliao Wei
- College of Agriculture, Guizhou University, Guiyang, 550025, PR China
| | - Tianling Fu
- Institute of New Rural Development, Engineering Key Laboratory for Pollution Control and Resource Reuse Technology of Mountain Livestock Breeding, Guizhou University, Huaxi District, Guiyang City, 550025, Guizhou Province, PR China
| | - Guandi He
- College of Agriculture, Guizhou University, Guiyang, 550025, PR China
| | - Zhuoyan Zhong
- College of Agriculture, Guizhou University, Guiyang, 550025, PR China
| | - Mingfang Yang
- College of Agriculture, Guizhou University, Guiyang, 550025, PR China
| | - Fei Lou
- College of Agriculture, Guizhou University, Guiyang, 550025, PR China
| | - Tengbing He
- College of Agriculture, Guizhou University, Guiyang, 550025, PR China.
- Institute of New Rural Development, Engineering Key Laboratory for Pollution Control and Resource Reuse Technology of Mountain Livestock Breeding, Guizhou University, Huaxi District, Guiyang City, 550025, Guizhou Province, PR China.
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Sun X, Sharon O, Sharon A. Distinct Features Based on Partitioning of the Endophytic Fungi of Cereals and Other Grasses. Microbiol Spectr 2023; 11:e0061123. [PMID: 37166321 PMCID: PMC10269846 DOI: 10.1128/spectrum.00611-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 04/18/2023] [Indexed: 05/12/2023] Open
Abstract
Endophytic fungi form a significant part of the plant mycobiome. Defining core members is crucial to understanding the assembly mechanism of fungal endophytic communities (FECs) and identifying functionally important community members. We conducted a meta-analysis of FECs in stems of wheat and five wild cereal species and generated a landscape of the fungal endophytic assemblages in this group of plants. The analysis revealed that several Ascomycota members and basidiomycetous yeasts formed an important compartment of the FECs in these plants. We observed a weak spatial autocorrelation at the regional scale and high intrahost variations in the FECs, suggesting a space-related heterogeneity. Accordingly, we propose that the heterogeneity among subcommunities should be a criterion to define the core endophytic members. Analysis of the subcommunities and meta-communities showed that the core and noncore members had distinct roles in various assembly processes, such as stochasticity, universal dynamics, and network characteristics, within each host. The distinct features identified between the community partitions of endophytes aid in understanding the principles that govern the assembly and function of natural communities. These findings can assist in designing synthetic microbiomes. IMPORTANCE This study proposes a novel method for diagnosing core microbiotas based on prevalence of community members in a meta-community, which could be determined and supported statistically. Using this approach, the study found stratification in community assembly processes within fungal endophyte communities (FECs) in the stems of wheat and cereal-related wild species. The core and noncore partitions of the FECs exhibited certain degrees of determinism from different aspects. Further analysis revealed abundant and consistent interactions between rare taxa, which might contribute to the determinism process in noncore partitions. Despite minor differences in FEC compositions, wheat FECs showed distinct patterns in community assembly processes compared to wild species, suggesting the effects of domestication on FECs. Overall, our study provided a new approach for identifying core microbiota and provides insights into the community assembly processes within FECs in wheat and related wild species.
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Affiliation(s)
- Xiang Sun
- School of Life Sciences, Hebei University, Baoding, Hebei, China
| | - Or Sharon
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, Israel
| | - Amir Sharon
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, Israel
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Che J, Wu Y, Yang H, Wang S, Wu W, Lyu L, Wang X, Li W. Root Niches of Blueberry Imprint Increasing Bacterial-Fungal Interkingdom Interactions along the Soil-Rhizosphere-Root Continuum. Microbiol Spectr 2023; 11:e0533322. [PMID: 37222589 PMCID: PMC10269492 DOI: 10.1128/spectrum.05333-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Accepted: 05/10/2023] [Indexed: 05/25/2023] Open
Abstract
Plant root-associated microbiomes play critical roles in promoting plant health, productivity, and tolerance to biotic/abiotic stresses. Blueberry (Vaccinium spp.) is adapted to acidic soils, while the interactions of the root-associated microbiomes in this specific habitat under various root microenvironments remain elusive. Here, we investigated the diversity and community composition of bacterial and fungal communities in various blueberry root niches (bulk soil, rhizosphere soil, and root endosphere). The results showed that blueberry root niches significantly affected root-associated microbiome diversity and community composition compared to those of the three host cultivars. Deterministic processes gradually increased along the soil-rhizosphere-root continuum in both bacterial and fungal communities. The co-occurrence network topological features showed that both bacterial and fungal community complexity and intensive interactions decreased along the soil-rhizosphere-root continuum. Different compartment niches clearly influenced bacterial-fungal interkingdom interactions, which were significantly higher in the rhizosphere, and positive interactions gradually dominated the co-occurrence networks from the bulk soil to the endosphere. The functional predictions showed that rhizosphere bacterial and fungal communities may have higher cellulolysis and saprotrophy capacities, respectively. Collectively, the root niches not only affected microbial diversity and community composition but also enhanced the positive interkingdom interactions between bacterial and fungal communities along the soil-rhizosphere-root continuum. This provides an essential basis for manipulating synthetic microbial communities for sustainable agriculture. IMPORTANCE The blueberry root-associated microbiome plays an essential role in its adaptation to acidic soils and in limiting the uptake of soil nutrients by its poor root system. Studies on the interactions of the root-associated microbiome in the various root niches may deepen our understanding of the beneficial effects in this particular habitat. Our study extended the research on the diversity and composition of microbial communities in different blueberry root compartment niches. Root niches dominated the root-associated microbiome compared to that of the host cultivar, and deterministic processes increased from the bulk soil to the endosphere. In addition, bacterial-fungal interkingdom interactions were significantly higher in the rhizosphere, and those positive interactions progressively dominated the co-occurrence network along the soil-rhizosphere-root continuum. Collectively, root niches dominantly affected the root-associated microbiome and the positive interkingdom interactions increased, potentially providing benefits for the blueberry.
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Affiliation(s)
- Jilu Che
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Yaqiong Wu
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Nanjing, China
| | - Hao Yang
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Shaoyi Wang
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Wenlong Wu
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Nanjing, China
| | - Lianfei Lyu
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Nanjing, China
| | - Xiaomin Wang
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Nanjing, China
| | - Weilin Li
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
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Bourak K, Sare AR, Allaoui A, Jijakli MH, Massart S. Impact of Two Phosphorus Fertilizer Formulations on Wheat Physiology, Rhizosphere, and Rhizoplane Microbiota. Int J Mol Sci 2023; 24:9879. [PMID: 37373026 DOI: 10.3390/ijms24129879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 05/29/2023] [Accepted: 06/05/2023] [Indexed: 06/29/2023] Open
Abstract
Phosphorus (P) is the second most important macronutrient for crop growth and a limiting factor in food production. Choosing the right P fertilizer formulation is important for crop production systems because P is not mobile in soils, and placing phosphate fertilizers is a major management decision. In addition, root microorganisms play an important role in helping phosphorus fertilization management by regulating soil properties and fertility through different pathways. Our study evaluated the impact of two phosphorous formulations (polyphosphates and orthophosphates) on physiological traits of wheat related to yield (photosynthetic parameters, biomass, and root morphology) and its associated microbiota. A greenhouse experiment was conducted using agricultural soil deficient in P (1.49%). Phenotyping technologies were used at the tillering, stem elongation, heading, flowering, and grain-filling stages. The evaluation of wheat physiological traits revealed highly significant differences between treated and untreated plants but not between phosphorous fertilizers. High-throughput sequencing technologies were applied to analyse the wheat rhizosphere and rhizoplane microbiota at the tillering and the grain-filling growth stages. The alpha- and beta-diversity analyses of bacterial and fungal microbiota revealed differences between fertilized and non-fertilized wheat, rhizosphere, and rhizoplane, and the tillering and grain-filling growth stages. Our study provides new information on the composition of the wheat microbiota in the rhizosphere and rhizoplane during growth stages (Z39 and Z69) under polyphosphate and orthophosphate fertilization. Hence, a deeper understanding of this interaction could provide better insights into managing microbial communities to promote beneficial plant-microbiome interactions for P uptake.
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Affiliation(s)
- Kaoutar Bourak
- Terra Research Center, Integrated and Urban Plant Pathology Laboratory, Liege University, Gembloux Agro-Bio-Tech, B-5030 Gembloux, Belgium
- Microbiology Laboratory, African Genome Center (AGC), Mohammed VI Polytechnic University, Lot 660, Hay Moulay Rachid, Ben Guerir 43150, Morocco
| | - Abdoul Razack Sare
- Terra Research Center, Integrated and Urban Plant Pathology Laboratory, Liege University, Gembloux Agro-Bio-Tech, B-5030 Gembloux, Belgium
| | - Abdelmounaaim Allaoui
- Microbiology Laboratory, African Genome Center (AGC), Mohammed VI Polytechnic University, Lot 660, Hay Moulay Rachid, Ben Guerir 43150, Morocco
| | - M Haissam Jijakli
- Terra Research Center, Integrated and Urban Plant Pathology Laboratory, Liege University, Gembloux Agro-Bio-Tech, B-5030 Gembloux, Belgium
| | - Sébastien Massart
- Terra Research Center, Integrated and Urban Plant Pathology Laboratory, Liege University, Gembloux Agro-Bio-Tech, B-5030 Gembloux, Belgium
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Fu X, Ma Y, Wang D, Zhan L, Guo Z, Fan K, Yang T, Chu H. Long-term chemical fertilization results in a loss of temporal dynamics of diazotrophic communities in the wheat rhizosphere. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 875:162663. [PMID: 36894087 DOI: 10.1016/j.scitotenv.2023.162663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 03/01/2023] [Accepted: 03/02/2023] [Indexed: 06/18/2023]
Abstract
Diazotrophs are potential bacterial biofertilizers with efficacy for plant nutrition, which convert atmospheric N2 into plant available nitrogen. Although they are known to respond strongly to fertilization, little is known about the temporal dynamics of diazotrophic communities throughout plant developmental under different fertilization regimes. In this study, we investigated diazotrophic communities in the wheat rhizosphere at four developmental stages under three long-term fertilization regimes: no fertilizer (Control), chemical NPK fertilizer only (NPK), and NPK fertilizer plus cow manure (NPKM). Fertilization regime had greater effect (explained of 54.9 %) on diazotrophic community structure than developmental stage (explained of 4.8 %). NPK fertilization decreased the diazotrophic diversity and abundance to one-third of the Control, although this was largely recovered by the addition of manure. Meanwhile, Control treatment resulted in significant variation in diazotrophic abundance, diversity, and community structure (P = 0.001) depending on the developmental stage, while the NPK fertilization resulted in the loss of temporal dynamics of the diazotrophic community (P = 0.330), which could be largely recovered by the addition of manure (P = 0.011). Keystone species identified in this study were quite different among the four developmental stages under Control and NPKM treatment but were similar among stages under NPK treatment. These findings suggest that long-term chemical fertilization not only reduces diazotrophic diversity and abundance, but also results in a loss of temporal dynamics of rhizosphere diazotrophic communities.
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Affiliation(s)
- Xiao Fu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, 71 East Beijing Road, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuying Ma
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, 71 East Beijing Road, Nanjing 210008, China
| | - Daozhong Wang
- Key Laboratory of Nutrient Cycling and Resources Environment of Anhui Province, Soil and Fertilizer Research Institute, Anhui Academy of Agricultural Sciences, 40 South Nongke Road, Hefei 230001, China
| | - Linchuan Zhan
- Key Laboratory of Nutrient Cycling and Resources Environment of Anhui Province, Soil and Fertilizer Research Institute, Anhui Academy of Agricultural Sciences, 40 South Nongke Road, Hefei 230001, China
| | - Zhibin Guo
- Key Laboratory of Nutrient Cycling and Resources Environment of Anhui Province, Soil and Fertilizer Research Institute, Anhui Academy of Agricultural Sciences, 40 South Nongke Road, Hefei 230001, China
| | - Kunkun Fan
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, 71 East Beijing Road, Nanjing 210008, China
| | - Teng Yang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, 71 East Beijing Road, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Haiyan Chu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, 71 East Beijing Road, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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Dondjou DT, Diedhiou AG, Mbodj D, Mofini MT, Pignoly S, Ndiaye C, Diedhiou I, Assigbetse K, Manneh B, Laplaze L, Kane A. Rice developmental stages modulate rhizosphere bacteria and archaea co-occurrence and sensitivity to long-term inorganic fertilization in a West African Sahelian agro-ecosystem. ENVIRONMENTAL MICROBIOME 2023; 18:42. [PMID: 37198640 PMCID: PMC10193678 DOI: 10.1186/s40793-023-00500-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 05/09/2023] [Indexed: 05/19/2023]
Abstract
BACKGROUND Rhizosphere microbial communities are important components of the soil-plant continuum in paddy field ecosystems. These rhizosphere communities contribute to nutrient cycling and rice productivity. The use of fertilizers is a common agricultural practice in rice paddy fields. However, the long-term impact of the fertilizers usage on the rhizosphere microbial communities at different rice developmental stages remains poorly investigated. Here, we examined the effects of long-term (27 years) N and NPK-fertilization on bacterial and archaeal community inhabiting the rice rhizosphere at three developmental stages (tillering, panicle initiation and booting) in the Senegal River Delta. RESULTS We found that the effect of long-term inorganic fertilization on rhizosphere microbial communities varied with the rice developmental stage, and between microbial communities in their response to N and NPK-fertilization. The microbial communities inhabiting the rice rhizosphere at panicle initiation appear to be more sensitive to long-term inorganic fertilization than those at tillering and booting stages. However, the effect of developmental stage on microbial sensitivity to long-term inorganic fertilization was more pronounced for bacterial than archaeal community. Furthermore, our data reveal dynamics of bacteria and archaea co-occurrence patterns in the rice rhizosphere, with differentiated bacterial and archaeal pivotal roles in the microbial inter-kingdom networks across developmental stages. CONCLUSIONS Our study brings new insights on rhizosphere bacteria and archaea co-occurrence and the long-term inorganic fertilization impact on these communities across developmental stages in field-grown rice. It would help in developing strategies for the successful manipulation of microbial communities to improve rice yields.
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Affiliation(s)
- Donald Tchouomo Dondjou
- Département de Biologie Végétale, Faculté des Sciences et Techniques, Université Cheikh Anta Diop (UCAD), Dakar, Sénégal
- Laboratoire Mixte International Adaptation des Plantes et Microorganismes associés aux Stress Environnementaux (LAPSE), Centre de recherche de Bel-Air, Dakar, Sénégal
- Laboratoire Commun de Microbiologie (LCM), Centre de Recherche de Bel-Air, Dakar, Sénégal
- Centre d’Excellence Africain en Agriculture pour la Sécurité Alimentaire et Nutritionnelle (CEA‑AGRISAN), UCAD, Dakar, Sénégal
- Centre d’Etude Régional pour l’Amélioration de l’Adaptation à la Sécheresse (CERAAS), Institut Sénégalais de Recherches Agricoles (ISRA), Route de Khombole, Thiès, Sénégal
| | - Abdala Gamby Diedhiou
- Département de Biologie Végétale, Faculté des Sciences et Techniques, Université Cheikh Anta Diop (UCAD), Dakar, Sénégal
- Laboratoire Mixte International Adaptation des Plantes et Microorganismes associés aux Stress Environnementaux (LAPSE), Centre de recherche de Bel-Air, Dakar, Sénégal
- Laboratoire Commun de Microbiologie (LCM), Centre de Recherche de Bel-Air, Dakar, Sénégal
- Centre d’Excellence Africain en Agriculture pour la Sécurité Alimentaire et Nutritionnelle (CEA‑AGRISAN), UCAD, Dakar, Sénégal
| | - Daouda Mbodj
- Département de Biologie Végétale, Faculté des Sciences et Techniques, Université Cheikh Anta Diop (UCAD), Dakar, Sénégal
- Laboratoire Mixte International Adaptation des Plantes et Microorganismes associés aux Stress Environnementaux (LAPSE), Centre de recherche de Bel-Air, Dakar, Sénégal
- Laboratoire Commun de Microbiologie (LCM), Centre de Recherche de Bel-Air, Dakar, Sénégal
- Centre d’Excellence Africain en Agriculture pour la Sécurité Alimentaire et Nutritionnelle (CEA‑AGRISAN), UCAD, Dakar, Sénégal
- Africa Rice Center (AfricaRice), Saint-Louis, Senegal
| | - Marie-Thérèse Mofini
- Département de Biologie Végétale, Faculté des Sciences et Techniques, Université Cheikh Anta Diop (UCAD), Dakar, Sénégal
- Laboratoire Mixte International Adaptation des Plantes et Microorganismes associés aux Stress Environnementaux (LAPSE), Centre de recherche de Bel-Air, Dakar, Sénégal
- Laboratoire Commun de Microbiologie (LCM), Centre de Recherche de Bel-Air, Dakar, Sénégal
- Centre d’Excellence Africain en Agriculture pour la Sécurité Alimentaire et Nutritionnelle (CEA‑AGRISAN), UCAD, Dakar, Sénégal
- Centre d’Etude Régional pour l’Amélioration de l’Adaptation à la Sécheresse (CERAAS), Institut Sénégalais de Recherches Agricoles (ISRA), Route de Khombole, Thiès, Sénégal
| | - Sarah Pignoly
- Laboratoire Mixte International Adaptation des Plantes et Microorganismes associés aux Stress Environnementaux (LAPSE), Centre de recherche de Bel-Air, Dakar, Sénégal
- Laboratoire Commun de Microbiologie (LCM), Centre de Recherche de Bel-Air, Dakar, Sénégal
- DIADE, Université de Montpellier, IRD, CIRAD, Montpellier, France
| | - Cheikh Ndiaye
- Département de Biologie Végétale, Faculté des Sciences et Techniques, Université Cheikh Anta Diop (UCAD), Dakar, Sénégal
- Laboratoire Mixte International Adaptation des Plantes et Microorganismes associés aux Stress Environnementaux (LAPSE), Centre de recherche de Bel-Air, Dakar, Sénégal
- Laboratoire Commun de Microbiologie (LCM), Centre de Recherche de Bel-Air, Dakar, Sénégal
- Centre d’Excellence Africain en Agriculture pour la Sécurité Alimentaire et Nutritionnelle (CEA‑AGRISAN), UCAD, Dakar, Sénégal
| | - Issa Diedhiou
- Département de Biologie Végétale, Faculté des Sciences et Techniques, Université Cheikh Anta Diop (UCAD), Dakar, Sénégal
- Laboratoire Mixte International Adaptation des Plantes et Microorganismes associés aux Stress Environnementaux (LAPSE), Centre de recherche de Bel-Air, Dakar, Sénégal
- Laboratoire Commun de Microbiologie (LCM), Centre de Recherche de Bel-Air, Dakar, Sénégal
- Centre d’Excellence Africain en Agriculture pour la Sécurité Alimentaire et Nutritionnelle (CEA‑AGRISAN), UCAD, Dakar, Sénégal
| | - Komi Assigbetse
- Laboratoire Mixte International Intensification Écologique Des Sols Cultivés en Afrique de L’Ouest (IESOL), Dakar, Sénégal
- Eco&Sols, Université de Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Baboucarr Manneh
- Laboratoire Mixte International Adaptation des Plantes et Microorganismes associés aux Stress Environnementaux (LAPSE), Centre de recherche de Bel-Air, Dakar, Sénégal
- Africa Rice Center (AfricaRice), Saint-Louis, Senegal
| | - Laurent Laplaze
- Laboratoire Mixte International Adaptation des Plantes et Microorganismes associés aux Stress Environnementaux (LAPSE), Centre de recherche de Bel-Air, Dakar, Sénégal
- Laboratoire Commun de Microbiologie (LCM), Centre de Recherche de Bel-Air, Dakar, Sénégal
- Centre d’Excellence Africain en Agriculture pour la Sécurité Alimentaire et Nutritionnelle (CEA‑AGRISAN), UCAD, Dakar, Sénégal
- DIADE, Université de Montpellier, IRD, CIRAD, Montpellier, France
| | - Aboubacry Kane
- Département de Biologie Végétale, Faculté des Sciences et Techniques, Université Cheikh Anta Diop (UCAD), Dakar, Sénégal
- Laboratoire Mixte International Adaptation des Plantes et Microorganismes associés aux Stress Environnementaux (LAPSE), Centre de recherche de Bel-Air, Dakar, Sénégal
- Laboratoire Commun de Microbiologie (LCM), Centre de Recherche de Bel-Air, Dakar, Sénégal
- Centre d’Excellence Africain « Environnement, Sociétés » (CEA-AGIR), UCAD, Santé, Dakar, Sénégal
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Niu T, Zhang J, Li J, Gao X, Ma H, Gao Y, Chang Y, Xie J. Effects of exogenous glycine betaine and cycloleucine on photosynthetic capacity, amino acid composition, and hormone metabolism in Solanum melongena L. Sci Rep 2023; 13:7626. [PMID: 37165051 PMCID: PMC10172174 DOI: 10.1038/s41598-023-34509-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 05/03/2023] [Indexed: 05/12/2023] Open
Abstract
Although exogenous glycine betaine (GB) and cycloleucine (Cyc) have been reported to affect animal cell metabolism, their effects on plant growth and development have not been studied extensively. Different concentrations of exogenous glycine betaine (20, 40, and 60 mmol L-1) and cycloleucine (10, 20, and 40 mmol L-1), with 0 mmol L-1 as control, were used to investigate the effects of foliar spraying of betaine and cycloleucine on growth, photosynthesis, chlorophyll fluorescence, Calvin cycle pathway, abaxial leaf burr morphology, endogenous hormones, and amino acid content in eggplant. We found that 40 mmol L-1 glycine betaine had the best effect on plant growth and development; it increased the fresh and dry weight of plants, increased the density of abaxial leaf hairs, increased the net photosynthetic rate and Calvin cycle key enzyme activity of leaves, had an elevating effect on chlorophyll fluorescence parameters, increased endogenous indoleacetic acid (IAA) content and decreased abscisic acid (ABA) content, and increased glutamate, serine, aspartate, and phenylalanine contents. However, cycloleucine significantly inhibited plant growth; plant apical dominance disappeared, plant height and dry and fresh weights decreased significantly, the development of abaxial leaf hairs was hindered, the net photosynthetic rate and Calvin cycle key enzyme activities were inhibited, the endogenous hormones IAA and ABA content decreased, and the conversion and utilization of glutamate, arginine, threonine, and glycine were affected. Combined with the experimental results and plant growth phenotypes, 20 mmol L-1 cycloleucine significantly inhibited plant growth. In conclusion, 40 mmol L-1 glycine betaine and 20 mmol L-1 cycloleucine had different regulatory effects on plant growth and development.
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Affiliation(s)
- Tianhang Niu
- College of Horticulture, Gansu Agricultural University, Yingmen Village, Anning District, Lanzhou, 730070, China
| | - Jing Zhang
- College of Horticulture, Gansu Agricultural University, Yingmen Village, Anning District, Lanzhou, 730070, China
| | - Jing Li
- College of Horticulture, Gansu Agricultural University, Yingmen Village, Anning District, Lanzhou, 730070, China
| | - Xiaoping Gao
- College of Horticulture, Gansu Agricultural University, Yingmen Village, Anning District, Lanzhou, 730070, China
| | - Hongyan Ma
- Lanzhou New Area Agricultural Science and Technology Development Co., Ltd., Lanzhou, 730000, China
| | - Yanqiang Gao
- College of Horticulture, Gansu Agricultural University, Yingmen Village, Anning District, Lanzhou, 730070, China
| | - Youlin Chang
- College of Horticulture, Gansu Agricultural University, Yingmen Village, Anning District, Lanzhou, 730070, China
| | - Jianming Xie
- College of Horticulture, Gansu Agricultural University, Yingmen Village, Anning District, Lanzhou, 730070, China.
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61
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Liu Q, Cheng L, Nian H, Jin J, Lian T. Linking plant functional genes to rhizosphere microbes: a review. PLANT BIOTECHNOLOGY JOURNAL 2023; 21:902-917. [PMID: 36271765 PMCID: PMC10106864 DOI: 10.1111/pbi.13950] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 10/09/2022] [Accepted: 10/16/2022] [Indexed: 05/04/2023]
Abstract
The importance of rhizomicrobiome in plant development, nutrition acquisition and stress tolerance is unquestionable. Relevant plant genes corresponding to the above functions also regulate rhizomicrobiome construction. Deciphering the molecular regulatory network of plant-microbe interactions could substantially contribute to improving crop yield and quality. Here, the plant gene-related nutrient uptake, biotic and abiotic stress resistance, which may influence the composition and function of microbial communities, are discussed in this review. In turn, the influence of microbes on the expression of functional plant genes, and thereby plant growth and immunity, is also reviewed. Moreover, we have specifically paid attention to techniques and methods used to link plant functional genes and rhizomicrobiome. Finally, we propose to further explore the molecular mechanisms and signalling pathways of microbe-host gene interactions, which could potentially be used for managing plant health in agricultural systems.
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Affiliation(s)
- Qi Liu
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro‐BioresourcesSouth China Agricultural UniversityGuangzhouChina
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of AgricultureSouth China Agricultural UniversityGuangzhouChina
| | - Lang Cheng
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro‐BioresourcesSouth China Agricultural UniversityGuangzhouChina
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of AgricultureSouth China Agricultural UniversityGuangzhouChina
| | - Hai Nian
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro‐BioresourcesSouth China Agricultural UniversityGuangzhouChina
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of AgricultureSouth China Agricultural UniversityGuangzhouChina
| | - Jian Jin
- Northeast Institute of Geography and AgroecologyChinese Academy of SciencesHarbinChina
- Department of Animal, Plant and Soil Sciences, Centre for AgriBioscienceLa Trobe UniversityBundooraVictoriaAustralia
| | - Tengxiang Lian
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro‐BioresourcesSouth China Agricultural UniversityGuangzhouChina
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of AgricultureSouth China Agricultural UniversityGuangzhouChina
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62
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Jiang H, Xu X, Fang Y, Ogunyemi SO, Ahmed T, Li X, Yang Y, Yan C, Chen J, Li B. Metabarcoding reveals response of rice rhizosphere bacterial community to rice bacterial leaf blight. Microbiol Res 2023; 270:127344. [PMID: 36878090 DOI: 10.1016/j.micres.2023.127344] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 02/22/2023] [Accepted: 02/26/2023] [Indexed: 03/07/2023]
Abstract
Rice bacterial leaf blight (BLB) is a major disease affecting cultivated rice and caused by the bacterium Xanthomonas oryzae pv. oryzae (Xoo). It is well established that rhizosphere microorganisms could help improve the adaptability of plants to biotic stresses. However, it is still unclear about the response mechanism of rice rhizosphere microbial community to BLB infection. Here, we used 16S rRNA gene amplicon sequencing to explore the effect of BLB on the rice rhizosphere microbial community. The results show that the alpha diversity index of the rice rhizosphere microbial community decreased significantly at the onset of BLB and then gradually recovered to normal levels. Beta diversity analysis indicated that BLB significantly affected community composition. In addition, there were significant differences in the taxonomic composition between healthy and diseased groups. For example, ceretain genera were more abundant in diseased rhizospheres, namely Streptomyces, Sphingomonas, and Flavobacterium, among others. In addition, the size and complexity of the rhizosphere co-occurrence network increased after disease onset compared to healthy groups. Also, hub microbe Rhizobiaceae and Gemmatimonadaceae were identified in the diseased rhizosphere co-occurrence network, and these hub microbes played an important role in maintaining network stability. In conclusion, our results provide important insights into the rhizosphere microbial community response to BLB and also provide important data and ideas in using rhizosphere microbes to control BLB.
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Affiliation(s)
- Hubiao Jiang
- State Key Laboratory of Rice Biology, Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Xinyan Xu
- State Key Laboratory of Rice Biology, Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Yuan Fang
- College of Life Sciences, Zhejiang Normal University, Jinhua, 321004, China.
| | - Solabomi Olaitan Ogunyemi
- State Key Laboratory of Rice Biology, Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Temoor Ahmed
- State Key Laboratory of Rice Biology, Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Xuqing Li
- Hangzhou Academy of Agricultural Science, Hangzhou 310024, China
| | - Yong Yang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Chengqi Yan
- Institute of Biotechnology, Ningbo Academy of Agricultural Sciences, Ningbo 315040, China
| | - Jianping Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China.
| | - Bin Li
- State Key Laboratory of Rice Biology, Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China.
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Feng Y, Zhang M, Liu Y, Yang X, Wei F, Jin X, Liu D, Guo Y, Hu Y. Quantitative microbiome profiling reveals the developmental trajectory of the chicken gut microbiota and its connection to host metabolism. IMETA 2023; 2:e105. [PMID: 38868437 PMCID: PMC10989779 DOI: 10.1002/imt2.105] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 03/06/2023] [Accepted: 03/15/2023] [Indexed: 06/14/2024]
Abstract
Revealing the assembly and succession of the chicken gut microbiota is critical for a better understanding of its role in chicken physiology and metabolism. However, few studies have examined dynamic changes of absolute chicken gut microbes using the quantitative microbiome profiling (QMP) method. Here, we revealed the developmental trajectory of the broiler chicken gut bacteriome and mycobiome by combining high-throughput sequencing with a microbial load quantification assay. We showed that chicken gut microbiota abundance and diversity reached a plateau at 7 days posthatch (DPH), forming segment-specific community types after 1 DPH. The bacteriome was more impacted by deterministic processes, and the mycobiome was more affected by stochastic processes. We also observed stage-specific microbes in different gut segments, and three microbial occurrence patterns including "colonization," "disappearance," and "core" were defined. The microbial co-occurrence networks were very different among gut segments, with more positive associations than negative associations. Furthermore, we provided links between the absolute changes in chicken gut microbiota and their serum metabolite variations. Time-course untargeted metabolomics revealed six metabolite clusters with different changing patterns of abundance. The foregut microbiota had more connections with chicken serum metabolites, and the gut microbes were closely related to chicken lipid and amino acid metabolism. The present study provided a full landscape of chicken gut microbiota development in a quantitative manner, and the associations between gut microbes and chicken serum metabolites further highlight the impact of gut microbiota in chicken growth and development.
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Affiliation(s)
- Yuqing Feng
- State Key Laboratory of Animal Nutrition, College of Animal Science and TechnologyChina Agricultural UniversityBeijingChina
| | - Meihong Zhang
- State Key Laboratory of Animal Nutrition, College of Animal Science and TechnologyChina Agricultural UniversityBeijingChina
| | - Yan Liu
- State Key Laboratory of Animal Nutrition, College of Animal Science and TechnologyChina Agricultural UniversityBeijingChina
| | - Xinyue Yang
- State Key Laboratory of Animal Nutrition, College of Animal Science and TechnologyChina Agricultural UniversityBeijingChina
| | - Fuxiao Wei
- State Key Laboratory of Animal Nutrition, College of Animal Science and TechnologyChina Agricultural UniversityBeijingChina
| | - Xiaolu Jin
- State Key Laboratory of Animal Nutrition, College of Animal Science and TechnologyChina Agricultural UniversityBeijingChina
| | - Dan Liu
- State Key Laboratory of Animal Nutrition, College of Animal Science and TechnologyChina Agricultural UniversityBeijingChina
| | - Yuming Guo
- State Key Laboratory of Animal Nutrition, College of Animal Science and TechnologyChina Agricultural UniversityBeijingChina
| | - Yongfei Hu
- State Key Laboratory of Animal Nutrition, College of Animal Science and TechnologyChina Agricultural UniversityBeijingChina
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Zhang J, Liu W, Bu J, Lin Y, Bai Y. Host genetics regulate the plant microbiome. Curr Opin Microbiol 2023; 72:102268. [PMID: 36708613 DOI: 10.1016/j.mib.2023.102268] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 12/20/2022] [Accepted: 01/05/2023] [Indexed: 01/27/2023]
Abstract
Plants recruit a taxonomically diverse microbial community, collectively termed the plant microbiome, that includes mutualists, pathogens, and commensals. These myriad microorganisms are robustly intertwined with their hosts and can determine plant fate by influencing fitness and growth or offering protection from detrimental bacteria, fungi, and herbivores. Recent studies have revealed significant effects of host genome diversity on plant-microbiome assembly and how host genetics determine microbiome composition, which is crucial for beneficial functions. The few host loci identified through genome-wide association studies suggest that genes involved in plant development, immunity, nutrient uptake, and root exudates regulate plant-microbiome community structure. Elucidating the role of host genetics in plant-microbiome assembly is key to understanding how plant-microbiome interactions are evolving and how to unlock the breeding and engineering potential of the microbiome for sustainable agriculture.
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Affiliation(s)
- Jingying Zhang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, 100101 Beijing, China; CAS center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, 100049 Beijing, China; CAS-JIC Centre of Excellence for Plant and Microbial Science, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 100101 Beijing, China
| | - Weidong Liu
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, 100101 Beijing, China; CAS center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, 100049 Beijing, China; CAS-JIC Centre of Excellence for Plant and Microbial Science, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 100101 Beijing, China
| | - Jingshu Bu
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, 100101 Beijing, China; CAS center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, 100049 Beijing, China; CAS-JIC Centre of Excellence for Plant and Microbial Science, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 100101 Beijing, China; College of Life Sciences, Northwest A&F University, 712100 Shaanxi, China
| | - Yanbing Lin
- College of Life Sciences, Northwest A&F University, 712100 Shaanxi, China
| | - Yang Bai
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, 100101 Beijing, China; CAS center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, 100049 Beijing, China; CAS-JIC Centre of Excellence for Plant and Microbial Science, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 100101 Beijing, China.
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Yin L, Wang X, Li Y, Liu Z, Mei Q, Chen Z. Uptake of the Plant Agriculture-Used Antibiotics Oxytetracycline and Streptomycin by Cherry Radish─Effect on Plant Microbiome and the Potential Health Risk. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:4561-4570. [PMID: 36945880 DOI: 10.1021/acs.jafc.3c01052] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Antibiotics are used to control certain bacterial diseases in plant agriculture. Understanding antibiotic uptake by edible vegetables after application and associated risks on plant microbiome and human health is critical. In this study, oxytetracycline and streptomycin, the two most commonly used antibiotics in plant agriculture, were applied to cherry radish via continuous soil drenching to study their translocations into plant tissues, influence on radish microbiome, and the potential health risk to mice. The results demonstrated that oxytetracycline induced hormesis in radish plants and both antibiotics were translocated into the leaves, fruits, and roots of radishes from the soil, with significantly higher plant uptake of streptomycin than oxytetracycline. Interestingly, the proportion of culturable oxytetracycline or streptomycin-resistant bacteria in the antibiotic-accumulated radish tissues was significantly higher than that in the antibiotic-free radish tissues, although both bacterial and fungal communities in different radish tissues were not affected by the accumulated antibiotics, demonstrating that antibiotic application could enrich antibiotic resistance in the plant microbiome. Feeding mice with antibiotics-accumulated radish tissues did not show significant effects on the weight and blood glucose levels of mice. Overall, this study provides important insights into the risk of using antibiotics in plant agriculture.
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Affiliation(s)
- Lichun Yin
- College of Environmental Science and Engineering, Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, Nankai University, Tianjin 300071, China
| | - Xingshuo Wang
- College of Environmental Science and Engineering, Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, Nankai University, Tianjin 300071, China
| | - Yangyang Li
- College of Environmental Science and Engineering, Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, Nankai University, Tianjin 300071, China
| | - Ziyin Liu
- College of Environmental Science and Engineering, Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, Nankai University, Tianjin 300071, China
| | - Qinyuan Mei
- College of Environmental Science and Engineering, Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, Nankai University, Tianjin 300071, China
| | - Zeyou Chen
- College of Environmental Science and Engineering, Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, Nankai University, Tianjin 300071, China
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Zhang K, Zentella R, Burkey KO, Liao HL, Tisdale RH. Microbial community dynamics responding to nutrient allocation associated with soybean cultivar 'Jake' ozone adaptation. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 864:161008. [PMID: 36549524 DOI: 10.1016/j.scitotenv.2022.161008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 12/12/2022] [Accepted: 12/13/2022] [Indexed: 06/17/2023]
Abstract
Tropospheric ozone (O3), a major air pollutant, leads to significant global yield loss in soybean [Glycine max (L.) Merr.]. Soybean cultivar 'Jake' shows O3 resilient traits in above-ground organs, but the root system remains sensitive to elevated O3 (eO3). Changing carbon (C) and nitrogen (N) resource composition during eO3 stress suggests that eO3 presumably alters belowground soil microbial communities and their driven nutrient transformation. Yet, the responses of belowground microbes to eO3 and their feedback on nutrient cycling in 'Jake' are unknown. In this study, we holistically investigated soil microbial communities associated with C and N dynamics and bacterial-fungal inter-kingdom networks in the rhizosphere and bulk soil at different developmental stages of 'Jake' grown under sub-ambient O3 [charcoal-filtered (CF) air, 12 h mean: 20 ppb] or eO3 (12 h mean: 87 ppb). The results demonstrated eO3 significantly decreased fungal diversity and complexity of microbial networks at different 'Jake' developmental stages, whereas bacterial diversity was more tolerant to eO3 in both bulk soil and rhizosphere. In the bulk soil, no O3-responsive microbial biomarkers were found to be associated with C and N content, implying eO3 may stimulate niche-based processes during 'Jake' growth. In contrast, this study identified O3-responsive microbial biomarkers that may contribute to the N acquisition (Chloroflexales) and C dynamics (Caldilineales, Thermomicrobiales, and Hypocreales) in the rhizosphere, which may support the O3 resilience of the 'Jake' cultivar. However, further investigation is required to confirm their specific contributions by determining changes in microbial gene expression. Overall, these findings conduce to an expanding knowledge base that O3 induces temporal and spatial changes in the effects of microbial and nutrient networks in the O3-tolerant agriculture ecosystems.
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Affiliation(s)
- Kaile Zhang
- North Florida Research and Education Center, University of Florida, Quincy, FL 32351, USA; Department of Soil, Water, and Ecosystem Sciences, University of Florida, Gainesville, FL 32611, USA
| | - Rodolfo Zentella
- U.S. Department of Agriculture, Agricultural Research Service, Plant Science Research Unit, Raleigh, 27607, NC, USA; Department of Crop and Soil Sciences, North Carolina State University, Raleigh, 27695, NC, USA
| | - Kent O Burkey
- U.S. Department of Agriculture, Agricultural Research Service, Plant Science Research Unit, Raleigh, 27607, NC, USA; Department of Crop and Soil Sciences, North Carolina State University, Raleigh, 27695, NC, USA
| | - Hui-Ling Liao
- North Florida Research and Education Center, University of Florida, Quincy, FL 32351, USA; Department of Soil, Water, and Ecosystem Sciences, University of Florida, Gainesville, FL 32611, USA.
| | - Ripley H Tisdale
- U.S. Department of Agriculture, Agricultural Research Service, Plant Science Research Unit, Raleigh, 27607, NC, USA; Department of Crop and Soil Sciences, North Carolina State University, Raleigh, 27695, NC, USA.
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67
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Zhang Y, Cao B, Pan Y, Tao S, Zhang N. Metabolite-Mediated Responses of Phyllosphere Microbiota to Rust Infection in Two Malus Species. Microbiol Spectr 2023; 11:e0383122. [PMID: 36916990 PMCID: PMC10101083 DOI: 10.1128/spectrum.03831-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 02/24/2023] [Indexed: 03/15/2023] Open
Abstract
Plants recruit beneficial microbes to enhance their ability to fight pathogens. However, the current understanding of microbial recruitment is largely limited to belowground systems (root exudates and the rhizosphere). It remains unclear whether the changes in leaf metabolites induced by infectious pathogens can actively recruit beneficial microbes to mitigate the growth of foliar pathogens. In this study, we integrated microbiome and metabolomic analyses to systematically explore the dynamics of phyllosphere fungal and bacterial communities and key leaf metabolites in two crabapple species (Malus sp. "Flame" and Malus sp. "Kelsey") at six stages following infection with Gymnosporangium yamadae. Our results showed that the phyllosphere microbiome changed during lesion expansion, as highlighted by a reduction in bacterial alpha-diversity and an increase in fungal alpha-diversity; a decreasing and then an increasing complexity of the microbial co-occurrence network was observed in Kelsey and a decreasing complexity occurred in Flame. In addition, nucleotide sugars, diarylheptanoids, and carboxylic acids with aromatic rings were more abundant in early stages of collection, which positively regulated the abundance of bacterial orders Pseudomonadales (in Kelsey), Acidimicrobiales, Bacillales, and Flavobacteriales (in Flame). In addition, metabolites such as flavonoids, lignin precursors, terpenoids, coumarins, and quaternary ammonium salts enriched with the expansion of lesions had a positive regulatory effect on fungal families Rhynchogastremataceae and Golubeviaceae (in Flame) and the bacterial order Actinomycetales (in Kelsey). Our findings highlight that plants may also influence phyllosphere microorganisms by adjusting leaf metabolites in response to biotic stress. IMPORTANCE Our findings demonstrate the response patterns of bacterial and fungal communities in the Malus phyllosphere to rust fungus G. yamadae infection, and they also reveal how the phyllosphere microbiome changes with the expansion of lesions. We identified several metabolites whose relative abundance varied significantly with lesion expansion. Using a framework for assessing the role of leaf metabolites in shaping the phyllosphere microbiome of the two Malus species, we identified several specific metabolites that have profoundly selective effects on the microbial community. In conclusion, our study provides new evidence of the ecological niche of the phyllosphere in supporting the "cry for help" strategy for plants.
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Affiliation(s)
- Yunxia Zhang
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, Beijing Forestry University, Beijing, People’s Republic of China
- Ecological Observation and Research Station of Heilongjiang Sanjiang Plain Wetlands, National Forestry and Grassland Administration, Shuangyashan, People’s Republic of China
| | - Bin Cao
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, People’s Republic of China
| | - Yumei Pan
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, Beijing Forestry University, Beijing, People’s Republic of China
- Ecological Observation and Research Station of Heilongjiang Sanjiang Plain Wetlands, National Forestry and Grassland Administration, Shuangyashan, People’s Republic of China
| | - Siqi Tao
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, Beijing Forestry University, Beijing, People’s Republic of China
- Ecological Observation and Research Station of Heilongjiang Sanjiang Plain Wetlands, National Forestry and Grassland Administration, Shuangyashan, People’s Republic of China
| | - Naili Zhang
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, Beijing Forestry University, Beijing, People’s Republic of China
- Ecological Observation and Research Station of Heilongjiang Sanjiang Plain Wetlands, National Forestry and Grassland Administration, Shuangyashan, People’s Republic of China
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Liu S, Gao J, Wang S, Li W, Wang A. Community differentiation of rhizosphere microorganisms and their responses to environmental factors at different development stages of medicinal plant Glehnia littoralis. PeerJ 2023; 11:e14988. [PMID: 36908810 PMCID: PMC9997192 DOI: 10.7717/peerj.14988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 02/12/2023] [Indexed: 03/08/2023] Open
Abstract
Rhizosphere microorganisms play a key role in affecting plant quality and productivity through its interaction with plant root system. To figure out the bottleneck of the decline of yield and quality in the traditional Chinese medicinal herbs Glehnia littoralis they now encounter, it is important to study the dynamics of rhizosphere microbiota during the cultivation of G. littoralis. In the present study, the composition, diversity and function of rhizosphere microbes at different development stages of G. littoralis, as well as the correlation between rhizosphere microbes and environmental factors were systematically studied by high-throughput sequencing. There were significant differences between the rhizosphere microbes at early and middle-late development stages. More beneficial bacteria, such as Proteobacteria, and more symbiotic and saprophytic fungi were observed at the middle-late development stage of G. littoralis, while beneficial bacteria such as Actinobacteria and polytrophic transitional fungi were abundant at all development stages. The results of redundancy analysis show that eight environmental factors drive the changes of microflora at different development stages. pH, soil organic matter (SOM) and available phosphorus (AP) had important positive effects on the bacterial and fungal communities at the early development stage; saccharase (SC) and nitrate nitrogen (NN) showed significant positive effects on the bacterial and fungal communities at the middle and late stages; while urease (UE), available potassium (AK), and alkaline phosphatase (AKP) have different effects on bacterial and fungal communities at different development stages. Random forest analysis identified 47 bacterial markers and 22 fungal markers that could be used to distinguish G. littoralis at different development stages. Network analysis showed that the rhizosphere microbes formed a complex mutualistic symbiosis network, which is beneficial to the growth and development of G. littoralis. These results suggest that host development stage and environmental factors have profound influence on the composition, diversity, community structure and function of plant rhizosphere microorganisms. This study provides a reference for optimizing the cultivation of G. littoralis.
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Affiliation(s)
- Shuliang Liu
- Ludong University, Yantai City, Shandong Province, China
| | - Jianxin Gao
- Ludong University, Yantai City, Shandong Province, China
| | - Shimeng Wang
- Ludong University, Yantai City, Shandong Province, China
| | - Weiwei Li
- Ludong University, Yantai City, Shandong Province, China
| | - Ailan Wang
- Ludong University, Yantai City, Shandong Province, China
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Zhang F, Xu N, Zhang Z, Zhang Q, Yang Y, Yu Z, Sun L, Lu T, Qian H. Shaping effects of rice, wheat, maize, and soybean seedlings on their rhizosphere microbial community. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:35972-35984. [PMID: 36539666 DOI: 10.1007/s11356-022-24835-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 12/14/2022] [Indexed: 06/17/2023]
Abstract
The rhizosphere microbiome plays critical roles in plant growth and is an important interface for resource exchange between plants and the soil environment. Crops at various growing stages, especially the seedling stage, have strong shaping effects on the rhizosphere microbial community, and such community reconstruction will positively feed back to the plant growth. In the present study, we analyzed the variations of bacterial and fungal communities in the rhizosphere of four crop species: rice, soybean, maize, and wheat during successive cultivations (three repeats for the seedling stages) using 16S rRNA gene and internal transcribed spacer (ITS) high-throughput sequencing. We found that the relative abundances of specific microorganisms decreased after different cultivation times, e.g., Sphingomonas, Pseudomonas, Rhodanobacter, and Caulobacter, which have been reported as plant-growth beneficial bacteria. The relative abundances of potential plant pathogenic fungi Myrothecium and Ascochyta increased with the successive cultivation times. The co-occurrence network analysis showed that the bacterial and fungal communities under maize were much more stable than those under rice, soybean, and wheat. The present study explored the characteristics of bacteria and fungi in crop seedling rhizosphere and indicated that the characteristics of indigenous soil flora might determine the plant growth status. Further study will focus on the use of the critical microorganisms to control the growth and yield of specific crops.
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Affiliation(s)
- Fan Zhang
- College of Environment, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China
| | - Nuohan Xu
- College of Environment, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China
| | - Zhenyan Zhang
- College of Environment, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China
| | - Qi Zhang
- College of Environment, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China
| | - Yaohui Yang
- College of Environment, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China
| | - Zhitao Yu
- College of Environment, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China
| | - Liwei Sun
- College of Environment, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China
| | - Tao Lu
- College of Environment, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China.
| | - Haifeng Qian
- College of Environment, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China
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Cheng Z, Zheng Q, Shi J, He Y, Yang X, Huang X, Wu L, Xu J. Metagenomic and machine learning-aided identification of biomarkers driving distinctive Cd accumulation features in the root-associated microbiome of two rice cultivars. ISME COMMUNICATIONS 2023; 3:14. [PMID: 36813851 PMCID: PMC9947119 DOI: 10.1038/s43705-023-00213-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 01/03/2023] [Accepted: 01/12/2023] [Indexed: 06/18/2023]
Abstract
Developing low-cadmium (Cd) rice cultivars has emerged as a promising avenue for food safety in Cd-contaminated farmlands. The root-associated microbiomes of rice have been shown to enhance rice growth and alleviate Cd stress. However, the microbial taxon-specific Cd resistance mechanisms underlying different Cd accumulation characteristics between different rice cultivars remain largely unknown. This study compared low-Cd cultivar XS14 and hybrid rice cultivar YY17 for Cd accumulation with five soil amendments. The results showed that XS14 was characterized by more variable community structures and stable co-occurrence networks in the soil-root continuum compared to YY17. The stronger stochastic processes in assembly of the XS14 (~25%) rhizosphere community than that of YY17 (~12%) suggested XS14 may have higher resistance to changes in soil properties. Microbial co-occurrence networks and machine learning models jointly identified keystone indicator microbiota, such as Desulfobacteria in XS14 and Nitrospiraceae in YY17. Meanwhile, genes involved in sulfur cycling and nitrogen cycling were observed among the root-associated microbiome of these two cultivars, respectively. Microbiomes in the rhizosphere and root of XS14 showed a higher diversity in functioning, with the significant enrichment of functional genes related to amino acid and carbohydrate transport and metabolism, and sulfur cycling. Our findings revealed differences and similarities in the microbial communities associated with two rice cultivars, as well as bacterial biomarkers predictive of Cd-accumulation capacity. Thus, we provide new insights into taxon-specific recruitment strategies of two rice cultivars under Cd stress and highlight the utility of biomarkers in offering clues for enhancing crop resilience to Cd stresses in the future.
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Affiliation(s)
- Zhongyi Cheng
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Hangzhou, 310058, China
| | - Qiang Zheng
- Department of Mathematics and Theories, Peng Cheng Laboratory, Shenzhen, 518000, China
| | - Jiachun Shi
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China.
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Hangzhou, 310058, China.
| | - Yan He
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Hangzhou, 310058, China
| | - Xueling Yang
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Hangzhou, 310058, China
| | - Xiaowei Huang
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Hangzhou, 310058, China
| | - Laosheng Wu
- Department of Environmental Sciences, University of California, Riverside, CA, 92521, USA
| | - Jianming Xu
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Hangzhou, 310058, China
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Miao Y, Zhang X, Zhang G, Feng Z, Pei J, Liu C, Huang L. From guest to host: parasite Cistanche deserticola shapes and dominates bacterial and fungal community structure and network complexity. ENVIRONMENTAL MICROBIOME 2023; 18:11. [PMID: 36814319 PMCID: PMC9945605 DOI: 10.1186/s40793-023-00471-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Accepted: 02/10/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND Rhizosphere and plant microbiota are assumed to play an essential role in deciding the well-being of hosts, but effects of parasites on their host microbiota have been rarely studied. Also, the characteristics of the rhizosphere and root microbiota of parasites and hosts under parasitism is relatively unknown. In this study, we used Cistanche deserticola and Haloxylon ammodendron from cultivated populations as our model parasites and host plants, respectively. We collected samples from BULK soil (BULK), rhizosphere soil of H. ammodendron not parasitized (NCD) and parasitized (RHA) to study how the parasite influenced the rhizosphere microbiota of the host. We also collected samples from the rhizosphere soil and roots of C. deserticola (RCD and ECD) and Haloxylon ammodendron (RHA and EHA) to explore the difference between the microbiota of the parasite and its host under parasitism. RESULTS The parasite reduced the compositional and co-occurrence network complexities of bacterial and fungal microbiota of RHA. Additionally, the parasite increased the proportion of stochastic processes mainly belonging to dispersal limitation in the bacterial microbiota of RHA. Based on the PCoA ordinations and permutational multivariate analysis of variance, the dissimilarity between microbiota of C. deserticola and H. ammodendron were rarely evident (bacteria, R2 = 0.29971; fungi, R2 = 0.15631). Interestingly, four hub nodes of H. ammodendron in endosphere fungal microbiota were identified, while one hub node of C. deserticola in endosphere fungal microbiota was identified. It indicated that H. ammodendron played a predominant role in the co-occurrence network of endosphere fungal microbiota. Source model of plant microbiome suggested the potential source percentage from the parasite to the host (bacteria: 52.1%; fungi: 16.7%) was lower than host-to-parasite (bacteria: 76.5%; fungi: 34.3%), illustrating that microbial communication was bidirectional, mainly from the host to the parasite. CONCLUSIONS Collectively, our results suggested that the parasite C. deserticola shaped the diversity, composition, co-occurrence network, and community assembly mechanisms of the rhizosphere microbiota of H. ammodendron. Additionally, the microbiota of C. deserticola and H. ammodendron were highly similar and shared. Our findings on parasite and host microbiota provided a novel line of evidence supporting the influence of parasites on the microbiota of their hosts.
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Affiliation(s)
- Yujing Miao
- Key Laboratory of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100193, China
| | - Xinke Zhang
- Key Laboratory of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100193, China
| | - Guoshuai Zhang
- Key Laboratory of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100193, China
| | - Zhan Feng
- Key Laboratory of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100193, China
- Jiangxi University of Traditional Chinese Medicine, Nanchang, 330000, Jiangxi, China
| | - Jin Pei
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, Sichuan, China
| | - Chang Liu
- Key Laboratory of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100193, China
| | - Linfang Huang
- Key Laboratory of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100193, China.
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Fu S, Deng Y, Zou K, Zhang S, Duan Z, Wu X, Zhou J, Li S, Liu X, Liang Y. Dynamic variation of Paris polyphylla root-associated microbiome assembly with planting years. PLANTA 2023; 257:61. [PMID: 36808254 DOI: 10.1007/s00425-023-04074-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 01/12/2023] [Indexed: 06/18/2023]
Abstract
P. polyphylla selectively enriches beneficial microorganisms to help their growth. Paris polyphylla (P. polyphylla) is an important perennial plant for Chinese traditional medicine. Uncovering the interaction between P. polyphylla and the related microorganisms would help to utilize and cultivate P. polyphylla. However, studies focusing on P. polyphylla and related microbes are scarce, especially on the assembly mechanisms and dynamics of the P. polyphylla microbiome. High-throughput sequencing of the 16S rRNA genes was implemented to investigate the diversity, community assembly process and molecular ecological network of the bacterial communities in three root compartments (bulk soil, rhizosphere, and root endosphere) across three years. Our results demonstrated that the composition and assembly process of the microbial community in different compartments varied greatly and were strongly affected by planting years. Bacterial diversity was reduced from bulk soils to rhizosphere soils to root endosphere and varied over time. Microorganisms benefit to plants was selectively enriched in P. polyphylla roots as was its core microbiome, including Pseudomonas, Rhizobium, Steroidobacter, Sphingobium and Agrobacterium. The network's complexity and the proportion of stochasticity in the community assembly process increased. Besides, nitrogen metabolism, carbon metabolism, phosphonate and phosphinate metabolism genes in bulk soils increased over time. These findings suggest that P. polyphylla exerts a selective effect to enrich the beneficial microorganisms and proves the sequential increasing selection pressure with P. polyphylla growth. Our work adds to the understanding of the dynamic processes of plant-associated microbial community assembly, guides the selection and application timing of P. polyphylla-associated microbial inoculants and is vital for sustainable agriculture.
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Affiliation(s)
- Shaodong Fu
- School of Resource Processing and Bioengineering, Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, 410083, China
| | - Yan Deng
- Hunan Agricultural Biotechnology Research Institute, Hunan Academy of Agricultural Sciences, Changsha, 410125, China
| | - Kai Zou
- College of Advanced Materials Engineering, Jiaxing Nanhu University, Jiaxing, Zhejiang, China
| | - Shuangfei Zhang
- School of Resource Processing and Bioengineering, Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, 410083, China
| | - Zhenchun Duan
- School of Resource Processing and Bioengineering, Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, 410083, China
| | - Xinhong Wu
- School of Resource Processing and Bioengineering, Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, 410083, China
| | - Jin Zhou
- School of Resource Processing and Bioengineering, Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, 410083, China
| | - Shihui Li
- School of Resource Processing and Bioengineering, Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, 410083, China
| | - Xueduan Liu
- School of Resource Processing and Bioengineering, Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, 410083, China
| | - Yili Liang
- School of Resource Processing and Bioengineering, Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, 410083, China.
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Nam JH, Thibodeau A, Qian YL, Qian MC, Park SH. Multidisciplinary evaluation of plant growth promoting rhizobacteria on soil microbiome and strawberry quality. AMB Express 2023; 13:18. [PMID: 36795258 PMCID: PMC9935790 DOI: 10.1186/s13568-023-01524-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 02/04/2023] [Indexed: 02/17/2023] Open
Abstract
The natural soil environment is considered one of the most diverse habitats containing numerous bacteria, fungi, and larger organisms such as nematodes, insects, or rodents. Rhizosphere bacteria play vital roles in plant nutrition and the growth promotion of their host plant. The aim of this study was to evaluate the effects of three plant growth-promoting rhizobacteria (PGPR), Bacillus subtilis, Bacillus amyloliquefaciens, and Pseudomonas monteilii for their potential role as a biofertilizer. The effect of the PGPR was examined at a commercial strawberry farm in Dayton, Oregon. The PGPR were applied to the soil of the strawberry (Fragaria × ananassa cultivar Hood) plants in two different concentrations of PGPR, T1 (0.24% PGPR) and T2 (0.48% PGPR), and C (no PGPR). A total of 450 samples from August 2020 to May 2021 were collected, and microbiome sequencing based on the V4 region of the 16S rRNA gene was conducted. The strawberry quality was measured by sensory evaluation, total acidity (TA), total soluble solids (TSS), color (lightness and chroma), and volatile compounds. Application of the PGPR significantly increased the populations of Bacillus and Pseudomonas and promoted the growth of nitrogen-fixing bacteria. The TSS and color evaluation showed that the PGPR presumptively behaved as a ripening enhancer. The PGPR contributed to the production of fruit-related volatile compounds, while the sensory evaluation did not show significant differences among the three groups. The major finding of this study suggests that the consortium of the three PGPR have a potential role as a biofertilizer by supporting the growth of other microorganisms (nitrogen-fixing bacteria) as part of a synergetic effect and strawberry quality such as sweetness and volatile compounds.
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Affiliation(s)
- Jun Haeng Nam
- grid.4391.f0000 0001 2112 1969Department of Food Science and Technology, Oregon State University, 3051 SW Campus Way, Corvallis, OR 97331 USA
| | - Alyssa Thibodeau
- grid.4391.f0000 0001 2112 1969Department of Food Science and Technology, Oregon State University, 3051 SW Campus Way, Corvallis, OR 97331 USA
| | - Yanping L. Qian
- grid.4391.f0000 0001 2112 1969Department of Food Science and Technology, Oregon State University, 3051 SW Campus Way, Corvallis, OR 97331 USA
| | - Michael C. Qian
- grid.4391.f0000 0001 2112 1969Department of Food Science and Technology, Oregon State University, 3051 SW Campus Way, Corvallis, OR 97331 USA
| | - Si Hong Park
- Department of Food Science and Technology, Oregon State University, 3051 SW Campus Way, Corvallis, OR, 97331, USA.
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Wang L, Liu J, Zhang M, Wu T, Chai B. Ecological Processes of Bacterial and Fungal Communities Associated with Typha orientalis Roots in Wetlands Were Distinct during Plant Development. Microbiol Spectr 2023; 11:e0505122. [PMID: 36688664 PMCID: PMC9927475 DOI: 10.1128/spectrum.05051-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 12/20/2022] [Indexed: 01/24/2023] Open
Abstract
Root-associated microbiomes are essential for the ecological function of the root system. However, their assembly mechanisms in wetland are poorly understood. In this study, we explored and compared the ecological processes of bacterial and fungal communities in water, bulk soil, rhizosphere soil, and root endosphere niches for 3 developmental stages of Typha orientalis at different wetland sites, and assessed the potential functions of root endosphere microbiomes with function prediction. Our findings suggest that the microbial diversity, composition, and interaction networks along the water-soil-plant continuum are shaped predominantly by compartment niche and developmental stage, rather than by wetland site. Source tracking analysis indicated that T. orientalis' root endosphere is derived primarily from the rhizosphere soil (bacteria 39.9%, fungi 27.3%) and water (bacteria 18.9%, fungi 19.1%) niches. In addition, we found that the assembly of bacterial communities is driven primarily by deterministic processes and fungal communities by stochastic processes. The interaction network among microbes varies at different developmental stages of T. orientalis, and is accompanied by changes in microbial keystone taxa. The functional prediction data supports the distribution pattern of the bacterial and fungal microbiomes, which have different ecological roles at different plant developmental stages, where more beneficial bacterial taxa are observed in the root endosphere in the early stages, but more saprophytic fungi in the late stages. Our findings provide empirical evidence for the assembly, sources, interactions, and potential functions of wetland plant root microbial communities and have significant implications for the future applications of plant microbiomes in the wetland ecosystem. IMPORTANCE Our findings provide empirical evidence for the assembly, sources, interactions, and potential functions of wetland plant root microbial communities, and have significant implications for the future applications of plant microbiomes in the wetland ecosystem.
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Affiliation(s)
- Lixiao Wang
- Institute of Loess Plateau, Shanxi University, Shanxi Key Laboratory of Ecological Restoration for Loess Plateau, Taiyuan, China
| | - Jinxian Liu
- Institute of Loess Plateau, Shanxi University, Shanxi Key Laboratory of Ecological Restoration for Loess Plateau, Taiyuan, China
| | - Meiting Zhang
- Institute of Loess Plateau, Shanxi University, Shanxi Key Laboratory of Ecological Restoration for Loess Plateau, Taiyuan, China
| | - Tiehang Wu
- Department of Biology, Georgia Southern University, Statesboro, Georgia, USA
| | - Baofeng Chai
- Institute of Loess Plateau, Shanxi University, Shanxi Key Laboratory of Ecological Restoration for Loess Plateau, Taiyuan, China
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Plant Growth-Promoting Bacteria (PGPB) with Biofilm-Forming Ability: A Multifaceted Agent for Sustainable Agriculture. DIVERSITY 2023. [DOI: 10.3390/d15010112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Plant growth-promoting bacteria (PGPB) enhance plant growth, as well as protect plants from several biotic and abiotic stresses through a variety of mechanisms. Therefore, the exploitation of PGPB in agriculture is feasible as it offers sustainable and eco-friendly approaches to maintaining soil health while increasing crop productivity. The vital key of PGPB application in agriculture is its effectiveness in colonizing plant roots and the phyllosphere, and in developing a protective umbrella through the formation of microcolonies and biofilms. Biofilms offer several benefits to PGPB, such as enhancing resistance to adverse environmental conditions, protecting against pathogens, improving the acquisition of nutrients released in the plant environment, and facilitating beneficial bacteria–plant interactions. Therefore, bacterial biofilms can successfully compete with other microorganisms found on plant surfaces. In addition, plant-associated PGPB biofilms are capable of protecting colonization sites, cycling nutrients, enhancing pathogen defenses, and increasing tolerance to abiotic stresses, thereby increasing agricultural productivity and crop yields. This review highlights the role of biofilms in bacterial colonization of plant surfaces and the strategies used by biofilm-forming PGPB. Moreover, the factors influencing PGPB biofilm formation at plant root and shoot interfaces are critically discussed. This will pave the role of PGPB biofilms in developing bacterial formulations and addressing the challenges related to their efficacy and competence in agriculture for sustainability.
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Ranade Y, Pathak P, Chandrashekar M, Saha S. Diversity Analysis of Culturable Epiphytic Microbial Consortia of Table Grape Berry Surface. FOOD BIOTECHNOL 2023. [DOI: 10.1080/08905436.2022.2163402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Yogita Ranade
- MIT School of Bioengineering Sciences & Research, MIT ADT University, Pune, India
| | - Pranav Pathak
- MIT School of Bioengineering Sciences & Research, MIT ADT University, Pune, India
| | | | - Sujoy Saha
- Plant Pathology, ICAR-National Research Centre for Grapes, Pune, India
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Zhang C, Shi X, Zhang J, Zhang Y, Wang W. Dynamics of soil microbiome throughout the cultivation life cycle of morel ( Morchella sextelata). Front Microbiol 2023; 14:979835. [PMID: 36910237 PMCID: PMC9992412 DOI: 10.3389/fmicb.2023.979835] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 02/02/2023] [Indexed: 02/24/2023] Open
Abstract
Although Morchella sextelata (morel) is a well-known, edible, and medicinal fungus widely cultivated in China, the dynamics and roles of its soil microbiome during cultivation are unclear. Using rhizosphere soil samples collected throughout the M. sextelata cultivation life cycle, we conducted a high-throughput metagenomic sequencing analysis, with an emphasis on variations in soil microbial composition, characteristic biomarkers, and ecological functions. We found that microbial relative abundance, alpha diversity, and structure varied significantly among fungal growth stages. A total of 47 stage-associated biomarkers were identified through a linear discriminant analysis of effect size. In addition, horizontal comparison of soil microbiomes exhibiting successful and failed primordium formation further confirmed primordium-associated microbes with possible key roles in primordium formation. A microbial function analysis revealed that nutrient metabolism-related pathways were enriched during mycelium and fruiting body stages, whereas the signal transduction pathway was enriched during the primordium stage. This result indicates that diverse microbes are required at different growth stages of M. sextelata. Our research has revealed the dynamic scenario of the soil microbiome throughout the cultivation life cycle of M. sextelata. The high-resolution microbial profiles uncovered in the present study provide novel insights that should contribute to the improvement of morel cultivation using microbial inoculants.
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Affiliation(s)
- Chen Zhang
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, China
| | - Xiaofei Shi
- The Germplasm Bank of Wild Species, Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Jiexiong Zhang
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, China
| | - Yesheng Zhang
- Shandong Junsheng Biotechnologies Co., Ltd., Liaocheng, China
| | - Wen Wang
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, China
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78
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Cross Cultivation on Homologous/Heterologous Plant-Based Culture Media Empowers Host-Specific and Real Time In Vitro Signature of Plant Microbiota. DIVERSITY 2022. [DOI: 10.3390/d15010046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Alliances of microbiota with plants are masked by the inability of in vitro cultivation of their bulk. Pure cultures piled in international centers originated from dissimilar environments/hosts. Reporting that plant root/leaf-based culture media support the organ-specific growth of microbiota, it was of interest to further investigate if a plant-based medium prepared from homologous (maize) supports specific/adapted microbiota compared to another prepared from heterologous plants (sunflower). The culture-independent community of maize phyllosphere was compared to communities cross-cultivated on plant broth-based media: CFU counts and taxa prevalence (PCR-DGGE; Illumina MiSeq amplicon sequencing). Similar to total maize phyllospheric microbiota, culture-dependent communities were overwhelmed by Proteobacteria (>94.3–98.3%); followed by Firmicutes (>1.3–3.7%), Bacteroidetes (>0.01–1.58%) and Actinobacteria (>0.06–0.34%). Differential in vitro growth on homologous versus heterologous plant-media enriched/restricted various taxa. In contrast, homologous cultivation over represented members of Proteobacteria (ca. > 98.0%), mainly Pseudomonadaceae and Moraxellaceae; heterologous cultivation and R2A enriched Firmicutes (ca. > 3.0%). The present strategy simulates/fingerprints the chemical composition of host plants to expand the culturomics of plant microbiota, advance real-time in vitro cultivation and lab-keeping of compatible plant microbiota, and identify preferential pairing of plant-microbe partners toward future synthetic community (SynComs) research and use in agriculture.
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Wei Y, Quan F, Lan G, Wu Z, Yang C. Space Rather than Seasonal Changes Explained More of the Spatiotemporal Variation of Tropical Soil Microbial Communities. Microbiol Spectr 2022; 10:e0184622. [PMID: 36416607 PMCID: PMC9769686 DOI: 10.1128/spectrum.01846-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 11/03/2022] [Indexed: 11/24/2022] Open
Abstract
Soil microbiomes play an essential role in maintaining soil geochemical cycle and function. Although there have been some reports on the diversity patterns and drivers of the tropical forest soil microbial community, how space and seasonal changes affect spatiotemporal distribution at the regional scales are poorly understood. Based on 260 soil samples, we investigated the spatiotemporal patterns of rubber plantations and rainforest soil microbial communities across the whole of Hainan Island, China during the dry and rainy seasons. We examined soil bacterial and fungal composition and diversity and the main drivers of these microbes using Illumina sequencing and assembly. Our results revealed that the diversity (both alpha and beta) spatiotemporal variation in microbial communities is highly dependent on regional location rather than seasonal changes. For example, the site explained 28.5% and 37.2% of the variation in alpha diversity for soil bacteria and fungi, respectively, and explained 34.6% of the bacterial variance and 14.3% of the fungal variance in beta diversity. Soil pH, mean annual temperature, and mean annual precipitation were the most important factors associated with the distribution of soil microbial communities. Furthermore, we identified that variations in edaphic (e.g., soil pH) and climatic factors (e.g., mean annual temperature [MAT] and mean annual precipitation [MAP]) were mainly caused by regional sites (P < 0.001). Collectively, our work provides empirical evidence that space, rather than seasonal changes, explained more of the spatiotemporal variation of soil microbial communities in tropical forests, mediated by regional location-induced changes in climatic factors and edaphic properties. IMPORTANCE The soil microbiomes communities of the two forests were not only affected by environmental factors (e.g., edaphic and climatic factors), but also by different dominant geographic factors. In particular, our work showed that spatial variation in bacterial and fungal community composition was mainly dominated by edaphic properties (e.g., pH) and climatic factors (e.g., MAT and MAP). Moreover, the environmental factors were mainly explained by geographic location effect rather than by seasonal effect, and environmental dissimilarity significantly increased with geographic distance. In conclusion, our study provides solid empirical evidence that space rather than season explained more of the spatiotemporal variation of soil microbial communities in the tropical forest.
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Affiliation(s)
- Yaqing Wei
- Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou City, Hainan Province, People’s Republic of China
- Hainan Danzhou Tropical Agro-ecosystem National Observation and Research Station, Danzhou City, Hainan Province, People’s Republic of China
- College of Ecology and Environment, Hainan University, Haikou, China
| | - Fei Quan
- School of Life Sciences, Fudan University, Shanghai, People’s Republic of China
- Hainan Danzhou Tropical Agro-ecosystem National Observation and Research Station, Danzhou City, Hainan Province, People’s Republic of China
| | - Guoyu Lan
- Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou City, Hainan Province, People’s Republic of China
- Hainan Danzhou Tropical Agro-ecosystem National Observation and Research Station, Danzhou City, Hainan Province, People’s Republic of China
| | - Zhixiang Wu
- Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou City, Hainan Province, People’s Republic of China
- Hainan Danzhou Tropical Agro-ecosystem National Observation and Research Station, Danzhou City, Hainan Province, People’s Republic of China
| | - Chuan Yang
- Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou City, Hainan Province, People’s Republic of China
- Hainan Danzhou Tropical Agro-ecosystem National Observation and Research Station, Danzhou City, Hainan Province, People’s Republic of China
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80
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Sun X, Zhang X, Zhang G, Miao Y, Zeng T, Zhang M, Zhang H, Zhang L, Huang L. Environmental Response to Root Secondary Metabolite Accumulation in Paeonia lactiflora: Insights from Rhizosphere Metabolism and Root-Associated Microbial Communities. Microbiol Spectr 2022; 10:e0280022. [PMID: 36318022 PMCID: PMC9769548 DOI: 10.1128/spectrum.02800-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Accepted: 10/11/2022] [Indexed: 11/05/2022] Open
Abstract
Paeonia lactiflora is a commercial crop with horticultural and medicinal value. Although interactions between plants and microbes are increasingly evident and considered to be drivers of ecosystem service, the regulatory relationship between microbial communities and the growth and root metabolites of P. lactiflora is less well known. Here, soil metabolomics indicated that carbohydrates and organic acids were enriched in the rhizosphere (RS) with higher diversity. Moreover, the variation of root-associated microbiotas between the bulk soil (BS) and the RS of P. lactiflora was investigated via 16S rRNA and internally transcribed spacer (ITS) amplicon sequencing. The RS displayed a low-diversity community dominated by copiotrophs, whereas the BS showed an oligotroph-dominated, high-diversity community. Hierarchical partitioning showed that cation exchange capacity (CEC) was the main factor affecting microbial community diversity. The null model and the dispersion niche continuum index (DNCI) suggested that stochastic processes (dispersal limitation) dominated the community assembly of both the RS and BS. The bacterial-fungal interkingdom networks illustrated that the RS possessed more complex and stable co-occurrence patterns. Meanwhile, positive link numbers and positive cohesion results revealed more cooperative relationships among microbes in the RS. Additionally, random forest model prediction and two partial least-squares path model (PLS-PM) analyses showed that the P. lactiflora root secondary metabolites were comprehensively impacted by soil water content (SWC), mean annual precipitation (MAP), pH (abiotic), and Alternaria (biotic). Collectively, this study provides a theoretical basis for screening the microbiome associated with the active components of P. lactiflora. IMPORTANCE Determining the taxonomic and functional components of the rhizosphere microbiome, as well as how they differ from those of the bulk soil microbiome, is critical for manipulating them to improve plant growth performance and increase agricultural yields. Soil metabolic profiles can help enhance the understanding of rhizosphere exudates. Here, we explored the regulatory relationship across environmental variables (root-associated microbial communities and soil metabolism) in the accumulation of secondary metabolites of P. lactiflora. Overall, this work improves our knowledge of how the rhizosphere affects soil and microbial communities. These observations improve the understanding of plant-microbiome interactions and introduce new horizons for synthetic community investigations as well as the creation of microbiome technologies for agricultural sustainability.
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Affiliation(s)
- Xiao Sun
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Xinke Zhang
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Guoshuai Zhang
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Yujing Miao
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Tiexin Zeng
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Min Zhang
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Huihui Zhang
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Li Zhang
- College of Science, Sichuan Agricultural University, Ya’an, Sichuan, China
| | - Linfang Huang
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu, Sichuan, China
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81
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Feng J, Rana S, Liu Z, Wang Y, Cai Q, Geng X, Zhou H, Zhang T, Wang S, Xue X, Li M, Jemim RS, Li Z. Diversity Analysis of Leaf Nutrient Endophytes and Metabolites in Dioecious Idesia polycarpa Maxim Leaves during Reproductive Stages. LIFE (BASEL, SWITZERLAND) 2022; 12:life12122041. [PMID: 36556406 PMCID: PMC9785831 DOI: 10.3390/life12122041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 12/04/2022] [Accepted: 12/05/2022] [Indexed: 12/12/2022]
Abstract
Leaves are essential vegetative organs of plants. Studying the variations in leaf nutrient content and microbial communities of male and female plants at reproductive stages helps us understand allocation and adaptation strategies. This study aimed to determine the nutrient characteristics and microbial differences in the leaves of male and female Idesia polycarpa at reproductive stages. Seven-year-old female and male plants were used as test materials in this experiment. The samples were collected at three stages: flowering (May), fruit matter accumulation (July), and fruit ripening (October). The nitrogen (TN), phosphorus (TP), potassium (TK), carbon (TC), and the pH of the female and male leaves were analyzed. In addition, the leaf microbial diversity and differential metabolites were determined using the Illumina high-throughput sequencing method and the ultra-high performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) method at the reproductive developmental stages. This study found that male and female plant leaves had different TN and TK contents over time but no difference in TC and TP content. The significant differences in bacterial diversity between male and female plants and the richness of the fungi of male plants at the flowering and fruit maturity stages were observed. Proteobacteria, Pseudomonadaceae, Ascomycota, and Aspergillus were the dominant bacteria and fungi in the Idesia polycarpa leaves. The presence of microorganisms differed in the two sexes in different periods. Alphaproteobacteria and Sordariomycetes were the indicator groups for male leaves, and Pseudomonas and Sordariomycetes were the indicator groups for female leaves. Significant differences in phenolic acid were found between male and female leaves. A KEGG enrichment analysis revealed that differential metabolites were enriched in metabolic pathways, amino acid biosynthesis, and the nucleotide metabolism. According to a correlation analysis, leaf TK and TP were strongly correlated with endophytic bacteria abundance and differential metabolite composition. This study revealed the changes in substances and microorganisms in the leaves of male and female plants in their reproductive stages. It provides a theoretical basis for developing and utilizing the leaves of Idesia polycarpa and for field management.
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Affiliation(s)
- Jian Feng
- College of Forestry, Henan Agricultural University, Zhengzhou 450046, China
| | - Sohel Rana
- College of Forestry, Henan Agricultural University, Zhengzhou 450046, China
| | - Zhen Liu
- College of Forestry, Henan Agricultural University, Zhengzhou 450046, China
| | - Yanmei Wang
- College of Forestry, Henan Agricultural University, Zhengzhou 450046, China
| | - Qifei Cai
- College of Forestry, Henan Agricultural University, Zhengzhou 450046, China
| | - Xiaodong Geng
- College of Forestry, Henan Agricultural University, Zhengzhou 450046, China
| | - Huina Zhou
- College of Forestry, Henan Agricultural University, Zhengzhou 450046, China
| | - Tao Zhang
- College of Forestry, Henan Agricultural University, Zhengzhou 450046, China
| | - Shasha Wang
- College of Forestry, Henan Agricultural University, Zhengzhou 450046, China
| | - Xiaoyan Xue
- College of Forestry, Henan Agricultural University, Zhengzhou 450046, China
| | - Mingwan Li
- College of Forestry, Henan Agricultural University, Zhengzhou 450046, China
| | - Razia Sultana Jemim
- College of Life Sciences, Henan Agricultural University, Zhengzhou 450046, China
| | - Zhi Li
- College of Forestry, Henan Agricultural University, Zhengzhou 450046, China
- Correspondence: ; Tel.: +86-17752559889
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82
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Fang GY, Mu XJ, Huang BW, Wu GZ, Jiang YJ. Fungal biodiversity and interaction complexity were the important drivers of multifunctionality for flavor production in a spontaneously fermented vinegar. INNOV FOOD SCI EMERG 2022. [DOI: 10.1016/j.ifset.2022.103259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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83
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Li WJ, Li HZ, An XL, Lin CS, Li LJ, Zhu YG. Effects of manure fertilization on human pathogens in endosphere of three vegetable plants. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 314:120344. [PMID: 36206891 DOI: 10.1016/j.envpol.2022.120344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 09/26/2022] [Accepted: 09/29/2022] [Indexed: 06/16/2023]
Abstract
Pathogens can colonize plant endosphere and, be transferred into human beings through the food chain. However, our understanding of the influences of agricultural activities, such as fertilization, on endophytic microbial communities and human pathogens is still limited. Here, we conducted a microcosm experiment using the combination of 16 S rRNA gene amplicon sequencing and high-throughput qPCR array to reveal the effects of manure fertilization on microbiomes of soils and plants and how such impact is translated into endophytic pathogens. Our results showed that manure fertilization significantly altered soil microbiomes, whereas with less influence on endophytic microbial communities. Soil is a vital source of both bacterial communities and human pathogens for the plant endosphere. The abundance of pathogens was increased both in soils and endosphere under manure fertilization. These findings provide an integrated understanding of the impact of manure fertilization on endophytic pathogens.
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Affiliation(s)
- Wen-Jing Li
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen, 361021, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing, 100049, China
| | - Hong-Zhe Li
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen, 361021, China
| | - Xin-Li An
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen, 361021, China
| | - Chen-Shuo Lin
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen, 361021, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing, 100049, China
| | - Li-Juan Li
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen, 361021, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing, 100049, China
| | - Yong-Guan Zhu
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen, 361021, China; State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China.
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84
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Xiong C, Lu Y. Microbiomes in agroecosystem: Diversity, function and assembly mechanisms. ENVIRONMENTAL MICROBIOLOGY REPORTS 2022; 14:833-849. [PMID: 36184075 DOI: 10.1111/1758-2229.13126] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Accepted: 09/08/2022] [Indexed: 06/16/2023]
Abstract
Soils are a main repository of biodiversity harbouring immense diversity of microbial species that plays a central role in fundamental ecological processes and acts as the seed bank for emergence of the plant microbiome in cropland ecosystems. Crop-associated microbiomes play an important role in shaping plant performance, which includes but not limited to nutrient uptake, disease resistance, and abiotic stress tolerance. Although our understanding of structure and function of soil and plant microbiomes has been rapidly advancing, most of our knowledge comes from ecosystems in natural environment. In this review, we present an overview of the current knowledge of diversity and function of microbial communities along the soil-plant continuum in agroecosystems. To characterize the ecological mechanisms for community assembly of soil and crop microbiomes, we explore how crop host and environmental factors such as plant species and developmental stage, pathogen invasion, and land management shape microbiome structure, microbial co-occurrence patterns, and crop-microbiome interactions. Particularly, the relative importance of deterministic and stochastic processes in microbial community assembly is illustrated under different environmental conditions, and potential sources and keystone taxa of the crop microbiome are described. Finally, we highlight a few important questions and perspectives in future crop microbiome research.
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Affiliation(s)
- Chao Xiong
- College of Urban and Environmental Sciences, Peking University, Beijing, People's Republic of China
| | - Yahai Lu
- College of Urban and Environmental Sciences, Peking University, Beijing, People's Republic of China
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85
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Zhan C, Matsumoto H, Liu Y, Wang M. Pathways to engineering the phyllosphere microbiome for sustainable crop production. NATURE FOOD 2022; 3:997-1004. [PMID: 37118297 DOI: 10.1038/s43016-022-00636-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 10/12/2022] [Indexed: 04/30/2023]
Abstract
Current disease resistance breeding, which is largely dependent on the exploitation of resistance genes in host plants, faces the serious challenges of rapidly evolving phytopathogens. The phyllosphere is the largest biological surface on Earth and an untapped reservoir of functional microbiomes. The phyllosphere microbiome has the potential to defend against plant diseases. However, the mechanisms of how the microbiota assemble and function in the phyllosphere remain largely elusive, and this restricts the exploitation of the targeted beneficial microbes in the field. Here we review the endogenous and exogenous cues impacting microbiota assembly in the phyllosphere and how the phyllosphere microbiota in turn facilitate the disease resistance of host plants. We further construct a holistic framework by integrating of holo-omics, genetic manipulation, culture-dependent characterization and emerging artificial intelligence techniques, such as deep learning, to engineer the phyllosphere microbiome for sustainable crop production.
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Affiliation(s)
- Chengfang Zhan
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Laboratory of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, China
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Pesticide and Environmental Toxicology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Haruna Matsumoto
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Laboratory of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, China
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Pesticide and Environmental Toxicology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Yufei Liu
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, China
| | - Mengcen Wang
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Laboratory of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, China.
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Pesticide and Environmental Toxicology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China.
- Global Education Program for AgriScience Frontiers, Graduate School of Agriculture, Hokkaido University, Sapporo, Japan.
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86
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Ajilogba CF, Habig J, Babalola OO. Carbon source utilization pattern of soil bacterial microbiome of bambara groundnut rhizosphere at the different growth stages determines soil fertility. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2022. [DOI: 10.3389/fsufs.2022.1012818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The diversity of microbes in the soil of plants is important for sustainable agriculture as these microbes are important in carrying out different functional processes to improve the soil and invariably plant growth. Inversely the presence of the crop also affects the types of microbial communities in the soil. In this study, bambara groundnut was grown during the planting season in South Africa, from November to March 2014/2015 and 2015/2016 and soil samples were taken after every 4 weeks after planting. Soil samples were taken 15 cm deep from 2 different landraces named VBR and VL. Microbial diversity was determined by soil microbial Carbon Source Utilization Profiles (CSUP) using BIOLOG™ GN2 plates. The abundance and richness of the soil microbes was also determined using the Shannon-Weaver and Evenness diversity indices. The diversity of the soil microbial population changed over the stages of plant growth, according to cluster analysis. Bacterial abundance and diversity were higher at 4 and 8 weeks after planting (WAP). The microbial abundance (richness index) in this study ranged from 0.64 to 0.94 with cultivar VL2 at 8 WAP being the highest while bulk soil (control), R2 was the lowest. The Shannon-Weaver index varied between 2.19 and 4.00 with the lowest corresponding to control while the highest was VL2 at 8 WAP. Carbon sources utilized by bacterial communities spread across the 96 carbon sources. The highest utilization of carboxylic acids, ester, amino acids and polymers and carbohydrates was found in the bacterial communities of the different landraces across growth stages. The highest utilization of alcohols, amides, amines, aromatic chemicals, brominated chemicals and phosphorylated chemicals was found in the control landraces. This indicates that the soil samples between 4 WAP and 12 WAP were richer in diversity of microbial species and their abundance. This soil diversity and richness is an indicator of the quality of the soil in order to increase crop yields and agricultural production.
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87
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Guo Q, Liu L, Liu J, Korpelainen H, Li C. Plant sex affects plant-microbiome assemblies of dioecious Populus cathayana trees under different soil nitrogen conditions. MICROBIOME 2022; 10:191. [PMID: 36333709 PMCID: PMC9636617 DOI: 10.1186/s40168-022-01387-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 10/09/2022] [Indexed: 05/15/2023]
Abstract
BACKGROUND Dioecious plants have coevolved with diverse plant microbiomes, which are crucial for the fitness and productivity of their host. Sexual dimorphism in morphology, physiology, or gene expression may relate to different microbial compositions that affect male and female fitness in different environments. However, sex-specific impacts on ecological processes that control the microbiome assembly are not well known. In this study, Populus cathayana males and females were planted in different nitrogen conditions. It was hypothesized that males and females differently affect bacterial and fungal communities in the rhizosphere soil, roots, old leaves, and young leaves. Physiological traits and transcriptome profiles of male and female plants were investigated to reveal potential mechanisms that control the microbiome assembly. RESULTS Our results showed strong niche differentiation that shapes microbial communities leading to a rapid loss of diversity along a decreasing pH gradient from the rhizosphere soil to leaves. Sex had different impacts on the microbial assembly in each niche. Especially fungal endophytes showed great differences in the community structure, keystone species, and community complexity between P. cathayana males and females. For example, the fungal co-occurrence network was more complex and the alpha diversity was significantly higher in young female leaves compared to young male leaves. Transcriptome profiles revealed substantial differences in plant-pathogen interactions and physiological traits that clearly demonstrated divergent internal environments for endophytes inhabiting males and females. Starch and pH of young leaves significantly affected the abundance of Proteobacteria, while tannin and pH of roots showed significant effects on the abundance of Chloroflexi, Actinobacteria, and Proteobacteria, and on the bacterial Shannon diversity. CONCLUSION Our results provided important knowledge for understanding sexual dimorphism that affects microbial assemblies, thus advancing our understanding of plant-microbiome interactions. Video Abstract.
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Affiliation(s)
- Qingxue Guo
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 311121, China
| | - Lin Liu
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 311121, China
| | - Jiantong Liu
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 311121, China
| | - Helena Korpelainen
- Department of Agricultural Sciences, Viikki Plant Science Centre, University of Helsinki, P.O. Box 27, FI-00014, Helsinki, Finland
| | - Chunyang Li
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China.
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Gao J, Feng W, Yang F, Liu J, Fan W, Wang Y, Zhang Q, Yang W. Effects of water quality and bacterial community composition on dissolved organic matter structure in Daihai lake and the mechanisms. ENVIRONMENTAL RESEARCH 2022; 214:114109. [PMID: 35981612 DOI: 10.1016/j.envres.2022.114109] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 07/25/2022] [Accepted: 08/10/2022] [Indexed: 06/15/2023]
Abstract
The migration of organic matter in salinized lakes was critical in maintaining ecological balance and material circulation process of inland shallow lakes. To clarify the ecological and microbial mechanism of material transport and transformation, the microbial community structure and the characteristics of dissolved organic matter (DOM) in the sediment of Daihai Lake, a typical saline lake at the Yellow River Basin, were explored with three-dimensional excitation and emission matrix fluorescence (3DEEM), parallel factor analysis (PARAFAC) and 16 S rRNA techniques. The correlation between environmental factors, DOM composition and the bacterial community structure were also studied for identifying the key factors of community formation. DOM in the lake demonstrated both terrigenous and endogenous characteristics. Protein-like materials accounted for 74% of the total fluorescence intensity in the sediment, where 1127 species, 671 genera, 468 families, 157 classes, 317 orders, 59 phyla of microorganisms were detected. Among the top 10 abundant taxa of each level, Firmicutes, Actinobacterota, Acidimicrobiia and Alphaproteobacteria had the greatest influence on the composition and structure of DOM (|R| > 0.7, p < 0.01). Microbial metabolism was a key process of transforming sediment organic matter from terrestrial humic-like to protein-like matter, accounting for 81% of total fluorescence signal in saline lake samples, while salinity, temperature, dissolved oxygen and electrical conductivity also had significant impacts during the process (|R|>0.7, p < 0.05). The research provides fundamental data and enlightenment for the improvement of the saline inland lake environment.
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Affiliation(s)
- Jiayue Gao
- School of Space and Environment, Beihang University, Beijing, 100191, China
| | - Weiying Feng
- School of Space and Environment, Beihang University, Beijing, 100191, China; Advanced Innovation Center for Big Data-Based Precision Medicine, Beihang University, Beijing, 100191, China.
| | - Fang Yang
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China.
| | - Jing Liu
- Environment Research Institute, Shandong University, Qingdao, 266237, China
| | - Wenhong Fan
- School of Space and Environment, Beihang University, Beijing, 100191, China; Advanced Innovation Center for Big Data-Based Precision Medicine, Beihang University, Beijing, 100191, China
| | - Ying Wang
- School of Space and Environment, Beihang University, Beijing, 100191, China; Advanced Innovation Center for Big Data-Based Precision Medicine, Beihang University, Beijing, 100191, China
| | - Qi Zhang
- School of Electronic Engineering, Beijing University of Posts and Telecommunications, Beijing, 100876, China
| | - Wenhuan Yang
- School of Energy and Environment, Inner Mongolia University of Science and Technology, Baotou, 014010, China
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Shao Q, Dong C, Hu H, Huang J, Zou X, Liang Z, Han Y. Effects of Medicinal Plants on Fungal Community Structure and Function in Hospital Grassplot Soil. Curr Microbiol 2022; 79:377. [DOI: 10.1007/s00284-022-03083-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Accepted: 10/09/2022] [Indexed: 11/06/2022]
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90
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Liu L, Wang X, Chen S, Liu D, Song C, Yi S, Zhu F, Wang W, Wang F, Wang G, Song X, Jia B, Chen C, Peng H, Guo L, Han B. Fungal isolates influence the quality of Peucedanum praeruptorum Dunn. FRONTIERS IN PLANT SCIENCE 2022; 13:1011001. [PMID: 36352875 PMCID: PMC9638934 DOI: 10.3389/fpls.2022.1011001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 10/11/2022] [Indexed: 06/16/2023]
Abstract
The symbiotic relationship between beneficial microorganisms and plants plays a vital role in natural and agricultural ecosystems. Although Peucedanum praeruptorum Dunn is widely distributed, its development is greatly limited by early bolting. The reason for early bolting in P. praeruptorum remains poorly characterized. We focus on the plant related microorganisms, including endophytes and rhizosphere microorganisms, by combining the traditional isolation and culture method with metagenomic sequencing technology. We found that the OTUs of endophytes and rhizosphere microorganisms showed a positive correlation in the whole growth stage of P. praeruptorum. Meanwhile, the community diversity of endophytic and rhizosphere fungi showed an opposite change trend, and bacteria showed a similar change trend. Besides, the microbial communities differed during the pre- and post-bolting stages of P. praeruptorum. Beneficial bacterial taxa, such as Pseudomonas and Burkholderia, and fungal taxa, such as Didymella and Fusarium, were abundant in the roots in the pre-bolting stage. Further, a strain belonging to Didymella was obtained by traditional culture and was found to contain praeruptorin A, praeruptorin B, praeruptorin E. In addition, we showed that the fungus could affect its effective components when it was inoculated into P. praeruptorum. This work provided a research reference for the similar biological characteristics of perennial one-time flowering plants, such as Saposhnikovia divaricate, Angelica sinensis and Angelica dahurica.
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Affiliation(s)
- Li Liu
- College of Biological and Pharmaceutical Engineering, West Anhui University, Lu’an, China
- Anhui Engineering Research Center for Eco-agriculture of Traditional Chinese Medicine, West Anhui University, Lu’an, China
| | - Xuejun Wang
- College of Biological and Pharmaceutical Engineering, West Anhui University, Lu’an, China
- Anhui Engineering Research Center for Eco-agriculture of Traditional Chinese Medicine, West Anhui University, Lu’an, China
| | - Shaotong Chen
- College of Life Science, South China Agricultural University, Guangzhou, China
| | - Dong Liu
- College of Biological and Pharmaceutical Engineering, West Anhui University, Lu’an, China
- Anhui Engineering Research Center for Eco-agriculture of Traditional Chinese Medicine, West Anhui University, Lu’an, China
| | - Cheng Song
- College of Biological and Pharmaceutical Engineering, West Anhui University, Lu’an, China
- Anhui Engineering Research Center for Eco-agriculture of Traditional Chinese Medicine, West Anhui University, Lu’an, China
| | - Shanyong Yi
- College of Biological and Pharmaceutical Engineering, West Anhui University, Lu’an, China
- Anhui Engineering Research Center for Eco-agriculture of Traditional Chinese Medicine, West Anhui University, Lu’an, China
| | - Fucheng Zhu
- College of Biological and Pharmaceutical Engineering, West Anhui University, Lu’an, China
- Anhui Engineering Research Center for Eco-agriculture of Traditional Chinese Medicine, West Anhui University, Lu’an, China
| | - Wei Wang
- College of Biological and Pharmaceutical Engineering, West Anhui University, Lu’an, China
- Anhui Engineering Research Center for Eco-agriculture of Traditional Chinese Medicine, West Anhui University, Lu’an, China
| | - Fang Wang
- College of Biological and Pharmaceutical Engineering, West Anhui University, Lu’an, China
- Anhui Engineering Research Center for Eco-agriculture of Traditional Chinese Medicine, West Anhui University, Lu’an, China
| | - Guanglin Wang
- Analytical and Testing Center, West Anhui University, Lu’an, China
| | - Xiangwen Song
- College of Biological and Pharmaceutical Engineering, West Anhui University, Lu’an, China
- Anhui Engineering Research Center for Eco-agriculture of Traditional Chinese Medicine, West Anhui University, Lu’an, China
| | - Bin Jia
- College of Biological and Pharmaceutical Engineering, West Anhui University, Lu’an, China
- Anhui Engineering Research Center for Eco-agriculture of Traditional Chinese Medicine, West Anhui University, Lu’an, China
| | - Cunwu Chen
- College of Biological and Pharmaceutical Engineering, West Anhui University, Lu’an, China
- Anhui Engineering Research Center for Eco-agriculture of Traditional Chinese Medicine, West Anhui University, Lu’an, China
| | - Huasheng Peng
- School of Pharmacy, Anhui University of Chinese Medicine, Hefei, China
| | - Lanping Guo
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Bangxing Han
- College of Biological and Pharmaceutical Engineering, West Anhui University, Lu’an, China
- Anhui Engineering Research Center for Eco-agriculture of Traditional Chinese Medicine, West Anhui University, Lu’an, China
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91
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Yuan Z, Pang Z, Fallah N, Zhou Y, Dong F, Lin W, Hu C. Silicon fertilizer mediated structural variation and niche differentiation in the rhizosphere and endosphere bacterial microbiome and metabolites of sugarcane. Front Microbiol 2022; 13:1009505. [PMID: 36246262 PMCID: PMC9560586 DOI: 10.3389/fmicb.2022.1009505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 09/08/2022] [Indexed: 12/01/2022] Open
Abstract
The microbiomes of plant are potential determinants of plant growth, productivity, and health. They provide plants with a plethora of functional capacities, namely, phytopathogens suppression, access to low-abundance nutrients, and resistance to environmental stressors. However, a comprehensive insight into the structural compositions of the bacterial abundance, diversity, richness, and function colonizing various microenvironments of plants, and specifically their association with bioactive compounds and soil edaphic factors under silicon (Si) amendment remains largely inconclusive. Here, high-throughput sequencing technology and nontargeted metabolite profiling method were adopted to test the hypotheses regarding microbiome niche abundance, diversity, richness, function, and their association with bioactive compounds and soil edaphic factors within different ecological niches (leaf, stem, root, rhizosphere, and bulk soils) under Si amendment during cane growth were we addressed. Our results demonstrated that Si correspondingly increased sugarcane theoretical production and yield, and remarkably enhanced soil nutrient status, especially Si, AP, and AK. It was also observed that bacterial diversity demonstrated tissue-dependent distribution patterns, with the bulk soil, rhizosphere soil, and root endosphere revealing the highest amount of bacterial diversity compared with the stem and leaf tissues. Moreover, Si exhibited the advantage of considerably promoting bacterial abundance in the various plant compartments. Co-occurrence interactions demonstrated that Si application has the potential to increase bacterial diversity maintenance, coexistence, and plant–soil systems bacteria connections, thereby increasing the functional diversity in the various plant tissues, which, in turn, could trigger positive growth effects in plants. Network analysis further revealed that metabolite profiles exhibited a strong association with bacterial community structures. It was also revealed that Si content had a considerable positive association with bacterial structures. Our findings suggest that the dynamic changes in microbe’s community composition in different plant and soil compartments were compartment-specific. Our study provides comprehensive empirical evidence of the significance of Si in agriculture and illuminated on differential metabolite profiles and soil microbe’s relationship.
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Affiliation(s)
- Zhaonian Yuan
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
- College of Agricultural, Fujian Agriculture and Forestry University, Fuzhou, China
- Province and Ministry Co-sponsored Collaborative Innovation Center of Sugar Industry, Nanning, China
- *Correspondence: Zhaonian Yuan,
| | - Ziqin Pang
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
- College of Agricultural, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Nyumah Fallah
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
- College of Agricultural, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yongmei Zhou
- College of Agricultural, Fujian Agriculture and Forestry University, Fuzhou, China
- Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Fei Dong
- Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, China
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Wenxiong Lin
- College of Agricultural, Fujian Agriculture and Forestry University, Fuzhou, China
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Chaohua Hu
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
- College of Agricultural, Fujian Agriculture and Forestry University, Fuzhou, China
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92
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Wen Z, Yao W, Han M, Xu X, Wu F, Yang M, Fazal A, Yin T, Qi J, Lu G, Yang R, Song X, Yang Y. Differential assembly of root-associated bacterial and fungal communities of a dual transgenic insect-resistant maize line at different host niches and different growth stages. Front Microbiol 2022; 13:1023971. [PMID: 36246225 PMCID: PMC9557180 DOI: 10.3389/fmicb.2022.1023971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Accepted: 09/15/2022] [Indexed: 11/13/2022] Open
Abstract
Transgenic technology has been widely applied to crop development, with genetically modified (GM) maize being the world’s second-largest GM crop. Despite the fact that rhizosphere bacterial and fungal populations are critical regulators of plant performance, few studies have evaluated the influence of GM maize on these communities. Plant materials used in this study included the control maize line B73 and the mcry1Ab and mcry2Ab dual transgenic insect-resistant maize line 2A-7. The plants and soils samples were sampled at three growth stages (jointing, flowering, and maturing stages), and the sampling compartments from the outside to the inside of the root are surrounding soil (SS), rhizospheric soil (RS), and intact root (RT), respectively. In this study, the results of alpha diversity revealed that from the outside to the inside of the root, the community richness and diversity declined while community coverage increased. Morever, the different host niches of maize rhizosphere and maize development stages influenced beta diversity according to statistical analysis. The GM maize line 2A-7 had no significant influence on the composition of microbial communities when compared to B73. Compared to RS and SS, the host niche RT tended to deplete Chloroflexi, Gemmatimonadetes and Mortierellomycota at phylum level. Nitrogen-fixation bacteria Pseudomonas, Herbaspirillum huttiense, Rhizobium leguminosarum, and Sphingomonas azotifigens were found to be enriched in the niche RT in comparison to RS and SS, whilst Bacillus was found to be increased and Stenotrophomonas was found to be decreased at the maturing stage as compared to jointing and flowering stages. The nitrogen fixation protein FixH (clusters of orthologous groups, COG5456), was found to be abundant in RT. Furthermore, the pathogen fungus that causes maize stalk rot, Gaeumannomyces radicicola, was found to be abundant in RT, while the beneficial fungus Mortierella hyalina was found to be depleted in RT. Lastly, the abundance of G. radicicola gradually increased during the development of maize. In conclusion, the host niches throughout the soil-plant continuum rather than the Bt insect-resistant gene or Bt protein secretion were primarily responsible for the differential assembly of root-associated microbial communities in GM maize, which provides the theoretical basis for ecological agriculture.
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Affiliation(s)
- Zhongling Wen
- State Key Laboratory of Pharmaceutical Biotechnology, Institute for Plant Molecular Biology, School of Life Sciences, Nanjing University, Nanjing, China
- Co-innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Weixuan Yao
- State Key Laboratory of Pharmaceutical Biotechnology, Institute for Plant Molecular Biology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Mi Han
- State Key Laboratory of Pharmaceutical Biotechnology, Institute for Plant Molecular Biology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Xinhong Xu
- State Key Laboratory of Pharmaceutical Biotechnology, Institute for Plant Molecular Biology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Fengci Wu
- Jilin Provincial Key Laboratory of Agricultural Biotechnology, Agro-Biotechnology Research Institute, Jilin Academy of Agricultural Sciences, Changchun, China
| | - Minkai Yang
- State Key Laboratory of Pharmaceutical Biotechnology, Institute for Plant Molecular Biology, School of Life Sciences, Nanjing University, Nanjing, China
- Co-innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Aliya Fazal
- State Key Laboratory of Pharmaceutical Biotechnology, Institute for Plant Molecular Biology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Tongming Yin
- Co-innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Jinliang Qi
- State Key Laboratory of Pharmaceutical Biotechnology, Institute for Plant Molecular Biology, School of Life Sciences, Nanjing University, Nanjing, China
- Co-innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Guihua Lu
- State Key Laboratory of Pharmaceutical Biotechnology, Institute for Plant Molecular Biology, School of Life Sciences, Nanjing University, Nanjing, China
- Co-innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
- School of Life Sciences, Huaiyin Normal University, Huaian, China
| | - Rongwu Yang
- State Key Laboratory of Pharmaceutical Biotechnology, Institute for Plant Molecular Biology, School of Life Sciences, Nanjing University, Nanjing, China
- *Correspondence: Rongwu Yang,
| | - Xinyuan Song
- Jilin Provincial Key Laboratory of Agricultural Biotechnology, Agro-Biotechnology Research Institute, Jilin Academy of Agricultural Sciences, Changchun, China
- Xinyuan Song,
| | - Yonghua Yang
- State Key Laboratory of Pharmaceutical Biotechnology, Institute for Plant Molecular Biology, School of Life Sciences, Nanjing University, Nanjing, China
- Co-innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
- Yonghua Yang,
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93
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Birt HWG, Tharp CL, Custer GF, Dini-Andreote F. Root phenotypes as modulators of microbial microhabitats. FRONTIERS IN PLANT SCIENCE 2022; 13:1003868. [PMID: 36212354 PMCID: PMC9539067 DOI: 10.3389/fpls.2022.1003868] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 09/08/2022] [Indexed: 06/09/2023]
Abstract
Plant roots are colonized by a multitude of microbial taxa that dynamically influence plant health. Plant-microbe interactions at the root-soil interface occur at the micro-scale and are affected by variation in root phenotypes. Different root phenotypes can have distinct impacts on physical and chemical gradients at the root-soil interface, leading to heterogeneous microhabitats for microbial colonization. Microbes that influence plant physiology will establish across these heterogeneous microhabitats, and, therefore, exploiting variation in root phenotypes can allow for targeted manipulation of plant-associated microbes. In this mini-review, we discuss how changes in root anatomy and architecture can influence resource availability and the spatial configuration of microbial microhabitats. We then propose research priorities that integrate root phenotypes and microbial microhabitats for advancing the manipulation of root-associated microbiomes. We foresee the yet-unexplored potential to harness diverse root phenotypes as a new level of precision in microbiome management in plant-root systems.
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94
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Che J, Wu Y, Yang H, Wang S, Wu W, Lyu L, Li W. Long-term cultivation drives dynamic changes in the rhizosphere microbial community of blueberry. FRONTIERS IN PLANT SCIENCE 2022; 13:962759. [PMID: 36212276 PMCID: PMC9539842 DOI: 10.3389/fpls.2022.962759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 08/24/2022] [Indexed: 06/16/2023]
Abstract
Rhizosphere microbial communities profoundly affect plant health, productivity, and responses to environmental stress. Thus, it is of great significance to comprehensively understand the response of root-associated microbes to planting years and the complex interactions between plants and rhizosphere microbes under long-term cultivation. Therefore, four rabbiteye blueberries (Vaccinium ashei Reade) plantations established in 1988, 2004, 2013, and 2017 were selected to obtain the dynamic changes and assembly mechanisms of rhizosphere microbial communities with the increase in planting age. Rhizosphere bacterial and fungal community composition and diversity were determined using a high-throughput sequencing method. The results showed that the diversity and structure of bacterial and fungal communities in the rhizosphere of blueberries differed significantly among planting ages. A total of 926 operational taxonomic units (OTUs) in the bacterial community and 219 OTUs in the fungal community were identified as the core rhizosphere microbiome of blueberry. Linear discriminant analysis effect size (LEfSe) analysis revealed 36 and 56 distinct bacterial and fungal biomarkers, respectively. Topological features of co-occurrence network analysis showed greater complexity and more intense interactions in bacterial communities than in fungal communities. Soil pH is the main driver for shaping bacterial community structure, while available potassium is the main driver for shaping fungal community structure. In addition, the VPA results showed that edaphic factors and blueberry planting age contributed more to fungal community variations than bacterial community. Notably, ericoid mycorrhizal fungi were observed in cultivated blueberry varieties, with a marked increase in relative abundance with planting age, which may positively contribute to nutrient uptake and coping with environmental stress. Taken together, our study provides a basis for manipulating rhizosphere microbial communities to improve the sustainability of agricultural production during long-term cultivation.
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Affiliation(s)
- Jilu Che
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Yaqiong Wu
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing, China
| | - Hao Yang
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Shaoyi Wang
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Wenlong Wu
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing, China
| | - Lianfei Lyu
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing, China
| | - Weilin Li
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
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95
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Dynamic Fluctuation and Niche Differentiation of Fungal Pathogens Infecting Bell Pepper Plants. Appl Environ Microbiol 2022; 88:e0100322. [PMID: 36036572 PMCID: PMC9499033 DOI: 10.1128/aem.01003-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The plant microbiome is shaped by plant development and microbial interaction. Fungal pathogens infecting bell pepper plants may fluctuate across the growing seasons. Dynamic fluctuation of the microbiome and fungal pathogens in bell pepper plants is poorly understood, and the origin of fungal pathogens causing fruit rot and leaf wilt has been barely investigated. In this study, we used amplicon sequencing (i.e., 16S rRNA and internal transcribed spacer [ITS] sequencing) to explore the compositional variations of the microbiome in bell pepper plants and studied the fluctuation of fungal pathogens across the growing seasons. Co-occurrence network analysis was applied to track the origin and dissemination route of fungal pathogens that infected bell pepper plants. ITS and 16S rRNA sequencing analyses demonstrated that fungal pathogens infecting fruits and leaves probably belonged to the Penicillium, Cladosporium, Fusarium, and unclassified_Sclerotiniaceae genera rather than one specific genus. The dominant fungal pathogens were different, along with the development of bell pepper plants. Both plant development and fungal pathogens shaped microbial communities in bell pepper plants across the growing seasons. Fungal pathogens decreased species richness and diversity of fungal communities in fungus-infected fruit and leaf tissues but not the uninfected stem tissues. Bacterial metabolic functions of xenobiotics increased in fungus-infected leaves at a mature developmental stage. Competitive interaction was present between fungal and bacterial communities in leaves. Co-occurrence network analysis revealed that the origins of fungal pathogens included the greenhouse, packing house, and storage room. Niche differentiation of microbes was discovered among these locations. IMPORTANCE Bell peppers are widely consumed worldwide. Fungal pathogen infections of bell peppers lead to enormous economic loss. To control fungal pathogens and increase economic benefit, it is essential to investigate the shifting patterns of the microbiome and fungal pathogens in bell pepper plants across the growing seasons. In this study, bell pepper plant diseases observed in fruits and leaves were caused by different fungal pathogens. Fungal pathogens originated from the greenhouse, packing house, and storage room, and niche differentiation existed among microbes. This study improves the understanding of dynamic fluctuation and source of fungal pathogens infecting bell pepper plants in the farming system. It also facilitates precise management of fungal pathogens in the greenhouse.
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96
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Tao J, Yu S, Jin J, Lu P, Yang Z, Xu Y, Chen Q, Li Z, Cao P. The wilt pathogen induces different variations of root-associated microbiomes of plant. FRONTIERS IN PLANT SCIENCE 2022; 13:1023837. [PMID: 36186049 PMCID: PMC9523445 DOI: 10.3389/fpls.2022.1023837] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Accepted: 09/02/2022] [Indexed: 06/16/2023]
Abstract
Root-associated compartments, including the rhizosphere, rhizoplane, and endosphere, live with diverse microbial communities which profoundly affect plant growth and health. However, a systematic understanding of the microbiome assembly across the rhizosphere, rhizoplane, and endosphere under pathogen invasion remains elusive. Using 16S high-throughput sequencing, we studied how bacterial wilt disease affected the variation and assembly of the three continuous root-associated microbiomes of tobacco. The results indicated that microorganisms were gradually filtered from the rhizosphere to the endosphere. With the pathogen invasion, the rhizosphere, rhizoplane and endosphere microbiomes selected and recruited different beneficial bacterial taxa. Some recruited bacteria were also identified as keystone members in networks (i.e., Bosea in the endosphere). The microbiomes of endosphere and rhizoplane were more sensitive to plant disease than the rhizosphere microbiome. Still, response strategies of the rhizoplane and endosphere to disease were obviously different. Microbial networks of the rhizoplane became complex in diseased samples and genes involved in sporulation formation and cell cycle were enriched. However, microbial networks of the diseased endosphere were disrupted, and functional genes related to nitrogen utilization and chemotaxis were significantly increased, indicating the importance of nitrogen resources supply of plants for the endosphere microbiome under pathogen invasion. Our results provide novel insights for understanding the different responses of the root-associated microbiomes to plant disease.
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Affiliation(s)
- Jiemeng Tao
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou, China
| | - Shizhou Yu
- Molecular Genetics Key Laboratory of China Tobacco, Guizhou Academy of Tobacco, Guiyang, China
| | - Jingjing Jin
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou, China
| | - Peng Lu
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou, China
| | - Zhixiao Yang
- Molecular Genetics Key Laboratory of China Tobacco, Guizhou Academy of Tobacco, Guiyang, China
| | - Yalong Xu
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou, China
| | - Qiansi Chen
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou, China
| | - Zefeng Li
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou, China
| | - Peijian Cao
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou, China
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97
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Song W, Wang J, Hou L. Effects of frequency and amount of stover mulching on soil nitrogen and the microbial functional guilds of the endosphere and rhizosphere. Front Microbiol 2022; 13:976154. [PMID: 36090112 PMCID: PMC9449521 DOI: 10.3389/fmicb.2022.976154] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 08/05/2022] [Indexed: 11/20/2022] Open
Abstract
Stover mulching as a conservation and sustainable agricultural practice is beneficial for maintaining soil nitrogen (N) requirements and plant health. The microbial functional guilds of the root and rhizosphere are important factors in the soil nitrogen cycle. However, it is unclear how the frequency and amount of stover mulching influence microbial functional guilds in the root and rhizosphere. Therefore, we investigated the responses of the microbial functional guilds in the endosphere and rhizosphere to maize stover mulching amounts (0, 1/3, 2/3, and total stover mulching every year) and frequencies (once every 3 years and twice every 3 years) under 10-year no-till management. The bacterial functional guilds of nitrogen fixation, nitrification, and anaerobic nitrate oxidation displayed the significantly correlation with C/N, total nitrogen, NO3−, and NH4+. The fungal functional guilds of plant pathogens and saprotrophs showed significantly correlations with C/N, total nitrogen, and NO3−. Moreover, we found that bacterial guilds play a pivotal role in maintaining N requirements at the jointing stage, whereas root endophytic fungal guilds play a more important role than bacterial guilds in regulating plant health at the mature stage. The frequency and amount of stover mulching had significant effects on the microbial functional guilds in the root and rhizosphere. Our data suggest that stover mulch application twice every 3 years is the optimal mulching frequency because it yielded the lowest abundance of nitrifying and anaerobic nitrate-oxidising bacteria and the highest abundance of nitrogen-fixing bacteria at the jointing stage, as well as the lowest abundance of fungal plant pathogens in roots at the mature stage.
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Affiliation(s)
- Wenchen Song
- Key Laboratory of Ecology and Environment in Minority Areas, Minzu University of China, National Ethnic Affairs Commission, Beijing, China
- College of Life and Environmental Sciences, Minzu University of China, Beijing, China
- *Correspondence: Wenchen Song,
| | - Jing Wang
- College of Life and Environmental Sciences, Minzu University of China, Beijing, China
| | - Lei Hou
- Beijing Pollution Source Related Affair Management Center, Beijing, China
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98
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Qi X, Xiao S, Chen X, Ali I, Gou J, Wang D, Zhu B, Zhu W, Shang R, Han M. Biochar-based microbial agent reduces U and Cd accumulation in vegetables and improves rhizosphere microecology. JOURNAL OF HAZARDOUS MATERIALS 2022; 436:129147. [PMID: 35643000 DOI: 10.1016/j.jhazmat.2022.129147] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 05/09/2022] [Accepted: 05/10/2022] [Indexed: 06/15/2023]
Abstract
Microbial remediation of heavy metals in soil has been widely studied. However, bioremediation efficiency is limited in practical applications because of nutritional deficiency, low efficiency, and competition with indigenous microorganisms. Herein, we prepared a biochar-based microbial agent (BMA) by immobilizing the microbial agent (MA, containing Bacillus subtilis, Bacillus cereus, and Citrobacter sp.) on biochar for the remediation of U and Cd in soil. The results showed that BMA increased soil organic matter, cation exchange capacity, and fluorescein diacetate hydrolysis activity and dehydrogenase activity by 58.7%, 38.2%, 42.9%, and 51.1%. The availability of U and Cd were significantly decreased by 67.4% and 54.2% in BMA amended soil, thereby reducing their accumulation in vegetables. BMA greatly promoted vegetable growth. Additionally, BMA significantly altered the structure and function of rhizosphere soil microbial communities. Coincidently, more abundant ecologically beneficial bacteria like Nitrospira, Nitrosomonas, Lysobacter, and Bacillus were observed, whereas plant pathogenic fungi like Fusarium and Alternaria reduced in BMA amended soil. The network analysis revealed that BMA amendment increased the tightness and complexity of microbial communities. Importantly, the compatibility of niches and microbial species within co-occurrence network was enhanced after BMA addition. These findings provide a promising strategy for suppressing heavy metal accumulation in vegetables and promoting their growth.
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Affiliation(s)
- Xin Qi
- School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, Sichuan 621010, China; School of Environment and Energy, South China University of Technology, Guangzhou 510006, China
| | - Shiqi Xiao
- School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, Sichuan 621010, China; Analytical Testing Center, Sichuan University, Chengdu 610064, China
| | - Xiaoming Chen
- School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, Sichuan 621010, China; State Defense Key Laboratory of Fundamental Science on Nuclear Wastes and Environment, Southwest University of Science and Technology, Mianyang, Sichuan 621010, China.
| | - Imran Ali
- School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, Sichuan 621010, China; State Defense Key Laboratory of Fundamental Science on Nuclear Wastes and Environment, Southwest University of Science and Technology, Mianyang, Sichuan 621010, China
| | - Jialei Gou
- School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, Sichuan 621010, China; State Defense Key Laboratory of Fundamental Science on Nuclear Wastes and Environment, Southwest University of Science and Technology, Mianyang, Sichuan 621010, China
| | - Dan Wang
- School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, Sichuan 621010, China
| | - Bo Zhu
- School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, Sichuan 621010, China
| | - Wenkun Zhu
- School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, Sichuan 621010, China
| | - Ran Shang
- State Key Laboratory of NBC Protection for Civilian, Beijing 102205, China
| | - Mengwei Han
- State Key Laboratory of NBC Protection for Civilian, Beijing 102205, China.
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99
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Geng P, Ma A, Wei X, Chen X, Yin J, Hu F, Zhuang X, Song M, Zhuang G. Interaction and spatio-taxonomic patterns of the soil microbiome around oil production wells impacted by petroleum hydrocarbons. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 307:119531. [PMID: 35623572 DOI: 10.1016/j.envpol.2022.119531] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 04/26/2022] [Accepted: 05/21/2022] [Indexed: 06/15/2023]
Abstract
Numerous onshore oil production wells currently exist, and the petroleum hydrocarbon contamination of the surrounding soil caused by oil production wells is not well understood. Moreover, the impact of the distribution of the total petroleum hydrocarbons (TPH) in the soil on the microbiota requires further investigation. Accordingly, in this study, the distribution of petroleum hydrocarbons in the soils around oil production wells was investigated, and their alteration of the microbiota was revealed. The results revealed that in the horizontal direction, the heavily TPH-contaminated soils were mainly distributed within a circle with a radius of 200 cm centered on the oil production well; and in the vertical direction, the heavily TPH-contaminated soils were distributed within the 0-50 cm soil layer. A significant positive correlation was found between the microbial abundance and the TPH concentration in the soil with relatively low total carbon contents. Heavy TPH contamination (TPH concentration of >3000 mg/kg) significantly reduced the microbial diversity and altered the microbiota compared with the light TPH contamination (TPH concentration of around 1000 mg/kg). In the heavily TPH-contaminated soils, the relative abundances of the Proteobacteria and Bacteroides increased significantly; the network complexity among the soil microorganisms decreased; and the co-occurrence patterns were altered. In summary, the results of this study have reference value in the remediation of soils around oil production wells and provide guidance for the construction of microbial remediation systems for petroleum contamination.
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Affiliation(s)
- Pengxue Geng
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Anzhou Ma
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Xiaoxia Wei
- Drilling and Production Technology Research Institute, PetroChina Qinghai Oil Field, Dunhuang, 736202, China
| | - Xianke Chen
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; Sino-Danish College of University of Chinese Academy of Sciences, Beijing, 101400, China
| | - Jun Yin
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Futang Hu
- Drilling and Production Technology Research Institute, PetroChina Qinghai Oil Field, Dunhuang, 736202, China
| | - Xuliang Zhuang
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, China; Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, 100101, China
| | - Maoyong Song
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Guoqiang Zhuang
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, China
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100
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Yu Y, Li Z, Liu Y, Wang F, Liu Y, Zhao J, Li Y, Gao Y, Zhu N. Roles of plant-associated microorganisms in regulating the fate of Hg in croplands: A perspective on potential pathways in maintaining sustainable agriculture. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 834:155204. [PMID: 35421489 DOI: 10.1016/j.scitotenv.2022.155204] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 04/06/2022] [Accepted: 04/08/2022] [Indexed: 06/14/2023]
Abstract
In heavy metal-contaminated croplands, plant-associated microorganisms play important roles in the adaptation of crops to heavy metals. Plant-associated microbes can interact with Hg and stimulate plant resistance to Hg toxicity, which is crucial for impeding Hg accumulation along the food chain. The roles of rhizosphere microorganisms for the improvement of plant growth and Hg resistance have drawn great research attention. However, the interactions among plant-endophyte-Hg have been neglected although they might be important for in vivo Hg detoxification. In this study, we systematically summarized 1) the roles of plant-associated microorganisms in Hg detoxification and plant growth, 2) Hg methylation and demethylation driven by plant-associated microbes, 3) the relationships between plant-associated microbes and Hg biogeochemical cycling. The possible mechanisms underlying crop-endophyte-Hg interactions were discussed, although limited studies on this aspect are available to date. The challenges and perspectives of plant-endophytes in dampening Hg phytotoxicity and controlling Hg accumulation in croplands were proposed on the basis of the present knowledge. Taken together, this work provides evidence for further understanding the interactions between soil-plant-endophyte-Hg systems and as well as new interpretations and perspectives into regulating the fate of Hg in croplands.
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Affiliation(s)
- Yue Yu
- School of Grain Science and Technology, Jiangsu University of Science and Technology, Zhenjiang 212100, Jiangsu, China; State Environmental Protection Key Laboratory of Food Chain Pollution Control, Beijing Technology and Business University, Beijing 100048, China
| | - Zhanming Li
- School of Grain Science and Technology, Jiangsu University of Science and Technology, Zhenjiang 212100, Jiangsu, China; State Environmental Protection Key Laboratory of Food Chain Pollution Control, Beijing Technology and Business University, Beijing 100048, China; School of Environment, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China.
| | - Yonghua Liu
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, & CAS-HKU Joint Laboratory of Metallomics on Health and Environment, & Beijing Metallomics Facility, & National Consortium for Excellence in Metallomics, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, China; School of Chemical and Biological Engineering, Taiyuan University of Science and Technology, Taiyuan 030000, Shanxi, China
| | - Fang Wang
- State Environmental Protection Key Laboratory of Food Chain Pollution Control, Beijing Technology and Business University, Beijing 100048, China
| | - Yurong Liu
- State Key Laboratory of Agricultural Microbiology and College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Jiating Zhao
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, & CAS-HKU Joint Laboratory of Metallomics on Health and Environment, & Beijing Metallomics Facility, & National Consortium for Excellence in Metallomics, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, China
| | - Yufeng Li
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, & CAS-HKU Joint Laboratory of Metallomics on Health and Environment, & Beijing Metallomics Facility, & National Consortium for Excellence in Metallomics, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, China
| | - Yuxi Gao
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, & CAS-HKU Joint Laboratory of Metallomics on Health and Environment, & Beijing Metallomics Facility, & National Consortium for Excellence in Metallomics, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, China
| | - Nali Zhu
- School of Environment, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China.
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