551
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Koskella B, Taylor TB. Multifaceted Impacts of Bacteriophages in the Plant Microbiome. ANNUAL REVIEW OF PHYTOPATHOLOGY 2018; 56:361-380. [PMID: 29958076 DOI: 10.1146/annurev-phyto-080417-045858] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Plant-associated bacteria face multiple selection pressures within their environments and have evolved countless adaptations that both depend on and shape bacterial phenotype and their interaction with plant hosts. Explaining bacterial adaptation and evolution therefore requires considering each of these forces independently as well as their interactions. In this review, we examine how bacteriophage viruses (phages) can alter the ecology and evolution of plant-associated bacterial populations and communities. This includes influencing a bacterial population's response to both abiotic and biotic selection pressures and altering ecological interactions within the microbiome and between the bacteria and host plant. We outline specific ways in which phages can alter bacterial phenotype and discuss when and how this might impact plant-microbe interactions, including for plant pathogens. Finally, we highlight key open questions in phage-bacteria-plant research and offer suggestions for future study.
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Affiliation(s)
- Britt Koskella
- Department of Integrative Biology, University of California, Berkeley, California 94720, USA;
| | - Tiffany B Taylor
- The Milner Centre for Evolution and Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, United Kingdom;
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552
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Chen Y, Wang J, Yang N, Wen Z, Sun X, Chai Y, Ma Z. Wheat microbiome bacteria can reduce virulence of a plant pathogenic fungus by altering histone acetylation. Nat Commun 2018; 9:3429. [PMID: 30143616 PMCID: PMC6109063 DOI: 10.1038/s41467-018-05683-7] [Citation(s) in RCA: 150] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Accepted: 07/16/2018] [Indexed: 02/07/2023] Open
Abstract
Interactions between bacteria and fungi have great environmental, medical, and agricultural importance, but the molecular mechanisms are largely unknown. Here, we study the interactions between the bacterium Pseudomonas piscium, from the wheat head microbiome, and the plant pathogenic fungus Fusarium graminearum. We show that a compound secreted by the bacteria (phenazine-1-carboxamide) directly affects the activity of fungal protein FgGcn5, a histone acetyltransferase of the SAGA complex. This leads to deregulation of histone acetylation at H2BK11, H3K14, H3K18, and H3K27 in F. graminearum, as well as suppression of fungal growth, virulence, and mycotoxin biosynthesis. Therefore, an antagonistic bacterium can inhibit growth and virulence of a plant pathogenic fungus by manipulating fungal histone modification.
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Affiliation(s)
- Yun Chen
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China.
| | - Jing Wang
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Nan Yang
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Ziyue Wen
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Xuepeng Sun
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Yunrong Chai
- Department of Biology, Northeastern University, Boston, MA, 02115, USA
| | - Zhonghua Ma
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China.
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553
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Designing Reactor Microbiomes for Chemical Production from Organic Waste. Trends Biotechnol 2018; 36:747-750. [DOI: 10.1016/j.tibtech.2018.01.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Revised: 01/05/2018] [Accepted: 01/08/2018] [Indexed: 01/31/2023]
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554
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Hiruma K, Kobae Y, Toju H. Beneficial associations between Brassicaceae plants and fungal endophytes under nutrient-limiting conditions: evolutionary origins and host-symbiont molecular mechanisms. CURRENT OPINION IN PLANT BIOLOGY 2018; 44:145-154. [PMID: 29738938 DOI: 10.1016/j.pbi.2018.04.009] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Revised: 04/13/2018] [Accepted: 04/13/2018] [Indexed: 05/02/2023]
Abstract
Brassicaceae plants have lost symbiotic interactions with mutualistic mycorrhizal fungi, but, nonmycorrhizal Brassicaceae associate with diverse taxonomic groups of mutualistic root-endophytic fungi. Distantly related fungal endophytes of Brassicaceae plants transfer phosphorus to the hosts and promote plant growth, thereby suggesting that the beneficial function was independently acquired via convergent evolution. These beneficial interactions appear tightly regulated by the tryptophan-derived secondary metabolite pathway, which specifically developed in Brassicaceae. Importantly, phosphate availability and types of colonizing microbes appear to influence the metabolite pathway. Thus, endophytes of Brassicaceae may have evolved to adapt to the Brassicaceae-specific traits. Future comparative functional analyses among well-defined endophytic fungi and their relatives with distinct life strategies and host plants will help understand the mechanisms that establish and maintain beneficial interactions.
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Affiliation(s)
- Kei Hiruma
- Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan; PRESTO, Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan.
| | - Yoshihiro Kobae
- Department of Sustainable Agriculture, Rakuno Gakuen University, Ebetsu, Hokkaido 069-8501, Japan; Hokkaido Agricultural Research Center, National Agriculture and Food Research Organization (NARO) , 1 Hitsujigaoka, Toyohira-ku, Sapporo, Hokkaido 062-8555, Japan
| | - Hirokazu Toju
- PRESTO, Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan; Center for Ecological Research, Kyoto University, Otsu, Shiga 520-2113, Japan
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555
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Karasov TL, Almario J, Friedemann C, Ding W, Giolai M, Heavens D, Kersten S, Lundberg DS, Neumann M, Regalado J, Neher RA, Kemen E, Weigel D. Arabidopsis thaliana and Pseudomonas Pathogens Exhibit Stable Associations over Evolutionary Timescales. Cell Host Microbe 2018; 24:168-179.e4. [PMID: 30001519 PMCID: PMC6054916 DOI: 10.1016/j.chom.2018.06.011] [Citation(s) in RCA: 83] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Revised: 05/16/2018] [Accepted: 06/21/2018] [Indexed: 11/23/2022]
Abstract
Crop disease outbreaks are often associated with clonal expansions of single pathogenic lineages. To determine whether similar boom-and-bust scenarios hold for wild pathosystems, we carried out a multi-year, multi-site survey of Pseudomonas in its natural host Arabidopsis thaliana. The most common Pseudomonas lineage corresponded to a ubiquitous pathogenic clade. Sequencing of 1,524 genomes revealed this lineage to have diversified approximately 300,000 years ago, containing dozens of genetically identifiable pathogenic sublineages. There is differentiation at the level of both gene content and disease phenotype, although the differentiation may not provide fitness advantages to specific sublineages. The coexistence of sublineages indicates that in contrast to crop systems, no single strain has been able to overtake the studied A. thaliana populations in the recent past. Our results suggest that selective pressures acting on a plant pathogen in wild hosts are likely to be much more complex than those in agricultural systems.
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Affiliation(s)
- Talia L Karasov
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Juliana Almario
- Max Planck Research Group Fungal Biodiversity, Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, 50829 Cologne, Germany; Interfaculty Institute of Microbiology and Infection Medicine Tübingen, IMITP, University of Tübingen, 72076 Tübingen, Germany
| | - Claudia Friedemann
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Wei Ding
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Michael Giolai
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany; Earlham Institute, Norwich Research Park Innovation Centre, Colney Lane, Norwich NR4 7UZ, UK
| | - Darren Heavens
- Earlham Institute, Norwich Research Park Innovation Centre, Colney Lane, Norwich NR4 7UZ, UK
| | - Sonja Kersten
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Derek S Lundberg
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Manuela Neumann
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Julian Regalado
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Richard A Neher
- University of Basel, Klingelbergstrasse 50/70, 4056 Basel, Switzerland
| | - Eric Kemen
- Max Planck Research Group Fungal Biodiversity, Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, 50829 Cologne, Germany; Interfaculty Institute of Microbiology and Infection Medicine Tübingen, IMITP, University of Tübingen, 72076 Tübingen, Germany
| | - Detlef Weigel
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany.
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556
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Herren CM, McMahon KD. Keystone taxa predict compositional change in microbial communities. Environ Microbiol 2018; 20:2207-2217. [DOI: 10.1111/1462-2920.14257] [Citation(s) in RCA: 138] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Revised: 04/24/2018] [Accepted: 04/25/2018] [Indexed: 12/31/2022]
Affiliation(s)
- Cristina M. Herren
- Freshwater and Marine Sciences ProgramUniversity of Wisconsin ‐ MadisonMadison Wisconsin USA
- Harvard Data Science Initiative, Harvard UniversityCambridge Massachusetts USA
| | - Katherine D. McMahon
- Department of Bacteriology and Civil and Environmental EngineeringUniversity of Wisconsin ‐ MadisonMadison Wisconsin USA
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557
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Toju H, Tanabe AS, Sato H. Network hubs in root-associated fungal metacommunities. MICROBIOME 2018; 6:116. [PMID: 29935536 PMCID: PMC6015470 DOI: 10.1186/s40168-018-0497-1] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Accepted: 06/08/2018] [Indexed: 05/18/2023]
Abstract
BACKGROUND Although a number of recent studies have uncovered remarkable diversity of microbes associated with plants, understanding and managing dynamics of plant microbiomes remain major scientific challenges. In this respect, network analytical methods have provided a basis for exploring "hub" microbial species, which potentially organize community-scale processes of plant-microbe interactions. METHODS By compiling Illumina sequencing data of root-associated fungi in eight forest ecosystems across the Japanese Archipelago, we explored hubs within "metacommunity-scale" networks of plant-fungus associations. In total, the metadata included 8080 fungal operational taxonomic units (OTUs) detected from 227 local populations of 150 plant species/taxa. RESULTS Few fungal OTUs were common across all the eight forests. However, in each of the metacommunity-scale networks representing northern four localities or southern four localities, diverse mycorrhizal, endophytic, and pathogenic fungi were classified as "metacommunity hubs," which were detected from diverse host plant taxa throughout a climatic region. Specifically, Mortierella (Mortierellales), Cladophialophora (Chaetothyriales), Ilyonectria (Hypocreales), Pezicula (Helotiales), and Cadophora (incertae sedis) had broad geographic and host ranges across the northern (cool-temperate) region, while Saitozyma/Cryptococcus (Tremellales/Trichosporonales) and Mortierella as well as some arbuscular mycorrhizal fungi were placed at the central positions of the metacommunity-scale network representing warm-temperate and subtropical forests in southern Japan. CONCLUSIONS The network theoretical framework presented in this study will help us explore prospective fungi and bacteria, which have high potentials for agricultural application to diverse plant species within each climatic region. As some of those fungal taxa with broad geographic and host ranges have been known to promote the survival and growth of host plants, further studies elucidating their functional roles are awaited.
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Affiliation(s)
- Hirokazu Toju
- Center for Ecological Research, Kyoto University, Otsu, Shiga, 520-2113, Japan.
- Precursory Research for Embryonic Science and Technology (PRESTO), Japan Science and Technology Agency, Kawaguchi, Saitama, 332-0012, Japan.
| | - Akifumi S Tanabe
- Faculty of Science and Technology, Ryukoku University, Seta Oe, Otsu, Shiga, 520-2194, Japan
| | - Hirotoshi Sato
- Graduate School of Human and Environmental Studies, Kyoto University, Sakyo, Kyoto, 606-8501, Japan
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558
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Heterogeneity of interactions of microbial communities in regions of Taihu Lake with different nutrient loadings: A network analysis. Sci Rep 2018; 8:8890. [PMID: 29891905 PMCID: PMC5995825 DOI: 10.1038/s41598-018-27172-z] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Accepted: 05/25/2018] [Indexed: 11/17/2022] Open
Abstract
To investigate the differences in the interactions of microbial communities in two regions in Taihu Lake with different nutrient loadings [Meiliang Bay (MLB) and Xukou Bay (XKB)], water samples were collected and both intra- and inter-kingdom microbial community interactions were examined with network analysis. It is demonstrated that all of the bacterioplankton, microeukaryotes and inter-kingdom communities networks in Taihu Lake were non-random. For the networks of bacterioplankton and inter-kingdom community in XKB, higher clustering coefficient and average degree but lower average path length indexes were observed, indicating the nodes in XKB were more clustered and closely connected with plenty edges than those of MLB. The bacterioplankton and inter-kingdom networks were considerably larger and more complex with more module hubs and connectors in XKB compared with those of MLB, whereas the microeukaryotes networks were comparable and had no module hubs or connectors in the two lake zones. The phyla of Acidobacteria, Cyanobacteria and Planctomycetes maintained greater cooperation with other phyla in XKB, rather than competition. The relationships between microbial communities and environmental factors in MLB were weaker. Compared with the microbial community networks of XKB, less modules in networks of MLB were significantly correlated with total phosphorous and total nitrogen.
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559
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Yurgel SN, Douglas GM, Dusault A, Percival D, Langille MGI. Dissecting Community Structure in Wild Blueberry Root and Soil Microbiome. Front Microbiol 2018; 9:1187. [PMID: 29922264 PMCID: PMC5996171 DOI: 10.3389/fmicb.2018.01187] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Accepted: 05/16/2018] [Indexed: 11/16/2022] Open
Abstract
A complex network of functions and symbiotic interactions between a eukaryotic host and its microbiome is a the foundation of the ecological unit holobiont. However, little is known about how the non-fungal eukaryotic microorganisms fit in this complex network of host-microbiome interactions. In this study, we employed a unique wild blueberry ecosystem to evaluate plant-associated microbiota, encompassing both eukaryotic and bacterial communities. We found that, while soil microbiome serves as a foundation for root microbiome, plant-influenced species sorting had stronger effect on eukaryotes than on bacteria. Our study identified several fungal and protist taxa, which are correlated with decreased fruit production in wild blueberry agricultural ecosystems. The specific effect of species sorting in root microbiome resulted in an increase in relative abundance of fungi adapted to plant-associated life-style, while the relative abundance of non-fungal eukaryotes was decreased along the soil-endosphere continuum in the root, probably because of low adaptation of these microorganisms to host-plant defense responses. Analysis of community correlation networks indicated that bacterial and eukaryotic interactions became more complex along the soil-endosphere continuum and, in addition to extensive mutualistic interactions, co-exclusion also played an important role in shaping wild blueberry associated microbiome. Our study identified several potential hub taxa with important roles in soil fertility and/or plant-microbe interaction, suggesting the key role of these taxa in the interconnection between soils and plant health and overall microbial community structure. This study also provides a comprehensive view of the role of non-fungal eukaryotes in soil ecosystem.
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Affiliation(s)
- Svetlana N. Yurgel
- Department of Plant, Food, and Environmental Sciences, Dalhousie University, Truro, NS, Canada
| | - Gavin M. Douglas
- Department of Microbiology and Immunology, Dalhousie University, Halifax, NS, Canada
| | - Ashley Dusault
- Department of Plant, Food, and Environmental Sciences, Dalhousie University, Truro, NS, Canada
| | - David Percival
- Department of Plant, Food, and Environmental Sciences, Dalhousie University, Truro, NS, Canada
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560
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Manirajan BA, Maisinger C, Ratering S, Rusch V, Schwiertz A, Cardinale M, Schnell S. Diversity, specificity, co-occurrence and hub taxa of the bacterial–fungal pollen microbiome. FEMS Microbiol Ecol 2018; 94:5033679. [DOI: 10.1093/femsec/fiy112] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Accepted: 05/31/2018] [Indexed: 01/05/2023] Open
Affiliation(s)
- Binoy Ambika Manirajan
- Institute of Applied Microbiology, Research Center for BioSystems, Land Use, and Nutrition (IFZ), Justus-Liebig-University Giessen, Giessen, Germany
| | - Corinna Maisinger
- Institute of Applied Microbiology, Research Center for BioSystems, Land Use, and Nutrition (IFZ), Justus-Liebig-University Giessen, Giessen, Germany
| | - Stefan Ratering
- Institute of Applied Microbiology, Research Center for BioSystems, Land Use, and Nutrition (IFZ), Justus-Liebig-University Giessen, Giessen, Germany
| | - Volker Rusch
- Institut für Integrative Biologie, Stiftung Old Herborn University, Herborn, Germany
| | - Andreas Schwiertz
- MVZ Institut für Mikroökologie GmbH, D-35745 Herborn, Auf den Lüppen 8, Germany,
| | - Massimiliano Cardinale
- Institute of Applied Microbiology, Research Center for BioSystems, Land Use, and Nutrition (IFZ), Justus-Liebig-University Giessen, Giessen, Germany
| | - Sylvia Schnell
- Institute of Applied Microbiology, Research Center for BioSystems, Land Use, and Nutrition (IFZ), Justus-Liebig-University Giessen, Giessen, Germany
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561
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Zorner P, Farmer S, Alibek K. Quantifying Crop Rhizosphere Microbiome Ecology: The Next Frontier in Enhancing the Commercial Utility of Agricultural Microbes. Ind Biotechnol (New Rochelle N Y) 2018; 14:116-119. [PMID: 30083080 PMCID: PMC6077768 DOI: 10.1089/ind.2018.29132.pzo] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Affiliation(s)
- Paul Zorner
- Locus Agricultural Solutions, LLC, Solon, OH
| | - Sean Farmer
- Locus Agricultural Solutions, LLC, Solon, OH
| | - Ken Alibek
- Locus Agricultural Solutions, LLC, Solon, OH
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562
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Oyserman BO, Medema MH, Raaijmakers JM. Road MAPs to engineer host microbiomes. Curr Opin Microbiol 2018; 43:46-54. [DOI: 10.1016/j.mib.2017.11.023] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Revised: 11/20/2017] [Accepted: 11/21/2017] [Indexed: 01/07/2023]
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563
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Remus-Emsermann MNP, Schlechter RO. Phyllosphere microbiology: at the interface between microbial individuals and the plant host. THE NEW PHYTOLOGIST 2018; 218:1327-1333. [PMID: 29504646 DOI: 10.1111/nph.15054] [Citation(s) in RCA: 97] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Accepted: 01/12/2018] [Indexed: 05/18/2023]
Abstract
Contents Summary 1327 I. Introduction 1327 II. Individuality and the relevance of scales for the investigation of bacteria 1328 III. Bacterial aggregation and community patterning at the single-cell resolution 1329 IV. What are the effects on the plant host? 1330 V. Future directions and current questions 1331 Acknowledgements 1332 ORCID 1332 References 1332 SUMMARY: Leaf surfaces are home to diverse bacterial communities. Within these communities, every individual cell perceives its unique environment and responds accordingly. In this insight article, the perspective of the bacterial individual is assumed in an attempt to describe how the spatially heterogeneous leaf surface determines the fate of bacteria. To investigate behaviour at scales relevant to bacteria, single-cell approaches are essential. Single-cell studies provide important lessons about how current 'omics' approaches fail to give an accurate picture of the behaviour of bacterial populations in heterogeneous environments. Upcoming techniques will soon allow us to combine the power of single-cell and omics approaches.
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Affiliation(s)
- Mitja N P Remus-Emsermann
- School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch, 8140, New Zealand
- Biomolecular Interaction Centre, University of Canterbury, Private Bag 4800, Christchurch, 8140, New Zealand
| | - Rudolf O Schlechter
- School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch, 8140, New Zealand
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564
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Walker L, Zorner P. The Alignment of Science, Technology, and Need. Ind Biotechnol (New Rochelle N Y) 2018. [DOI: 10.1089/ind.2018.29137.lpw] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Larry Walker
- Co-Editor-In-Chief, Industrial Biotechnology, Mary Ann Liebert, Inc, New York, NY
| | - Paul Zorner
- President and CEO, Locus Agricultural Solutions, LLC, Solon, OH
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565
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In situ relationships between microbiota and potential pathobiota in Arabidopsis thaliana. ISME JOURNAL 2018; 12:2024-2038. [PMID: 29849170 DOI: 10.1038/s41396-018-0152-7] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Revised: 04/21/2018] [Accepted: 04/29/2018] [Indexed: 12/21/2022]
Abstract
A current challenge in microbial pathogenesis is to identify biological control agents that may prevent and/or limit host invasion by microbial pathogens. In natura, hosts are often infected by multiple pathogens. However, most of the current studies have been performed under laboratory controlled conditions and by taking into account the interaction between a single commensal species and a single pathogenic species. The next step is therefore to explore the relationships between host-microbial communities (microbiota) and microbial members with potential pathogenic behavior (pathobiota) in a realistic ecological context. In the present study, we investigated such relationships within root-associated and leaf-associated bacterial communities of 163 ecologically contrasted Arabidopsis thaliana populations sampled across two seasons in southwest of France. In agreement with the theory of the invasion paradox, we observed a significant humped-back relationship between microbiota and pathobiota α-diversity that was robust between both seasons and plant organs. In most populations, we also observed a strong dynamics of microbiota composition between seasons. Accordingly, the potential pathobiota composition was explained by combinations of season-specific microbiota operational taxonomic units. This result suggests that the potential biomarkers controlling pathogen's invasion are highly dynamic.
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566
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Banerjee S, Schlaeppi K, van der Heijden MGA. Keystone taxa as drivers of microbiome structure and functioning. Nat Rev Microbiol 2018; 16:567-576. [DOI: 10.1038/s41579-018-0024-1] [Citation(s) in RCA: 839] [Impact Index Per Article: 139.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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567
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Oberholster T, Vikram S, Cowan D, Valverde A. Key microbial taxa in the rhizosphere of sorghum and sunflower grown in crop rotation. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 624:530-539. [PMID: 29268225 DOI: 10.1016/j.scitotenv.2017.12.170] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Revised: 12/15/2017] [Accepted: 12/15/2017] [Indexed: 06/07/2023]
Abstract
Microbes are key determinants of plant health and productivity. Previous studies have characterized the rhizosphere microbiomes of numerous plant species, but little information is available on how rhizosphere microbial communities change over time under crop rotation systems. Here, we document microbial communities in the rhizosphere of sorghum and sunflower (at seedling, flowering and senescence stages) grown in crop rotation in four different soils under field conditions. A comprehensive 16S rRNA-based amplicon sequencing survey revealed that the differences in alpha-diversity between rhizosphere and bulk soils changed over time. Sorghum rhizosphere soil microbial diversity at flowering and senescence were more diverse than bulk soils, whereas the microbial diversity of sunflower rhizosphere soils at flowering were less diverse with respect to bulk soils. Sampling time was also important in explaining the variation in microbial community composition in soils grown with both crops. Temporal changes observed in the rhizosphere microbiome were both plant-driven and due to seasonal changes in the bulk soil biota. Several individual taxa were relatively more abundant in the rhizosphere and/or found to be important in maintaining rhizosphere microbial networks. Interestingly, some of these taxa showed similar patterns at different sampling times, suggesting that the same organisms may play the same functional/structural role at different plant growth stages and in different crops. Overall, we have identified prominent microbial taxa that might be used to develop microbiome-based strategies for improving the yield and productivity of sorghum and sunflower.
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Affiliation(s)
- Tanzelle Oberholster
- Department of Genetics, Centre for Microbial Ecology and Genomics, University of Pretoria, Pretoria, South Africa
| | - Surendra Vikram
- Department of Genetics, Centre for Microbial Ecology and Genomics, University of Pretoria, Pretoria, South Africa
| | - Don Cowan
- Department of Genetics, Centre for Microbial Ecology and Genomics, University of Pretoria, Pretoria, South Africa
| | - Angel Valverde
- Department of Genetics, Centre for Microbial Ecology and Genomics, University of Pretoria, Pretoria, South Africa; Department of Microbial, Biochemical and Food Biotechnology, University of the Free State, Bloemfontein, South Africa.
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568
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Schlatter DC, Burke I, Paulitz TC. Succession of Fungal and Oomycete Communities in Glyphosate-Killed Wheat Roots. PHYTOPATHOLOGY 2018; 108:582-594. [PMID: 29256828 DOI: 10.1094/phyto-06-17-0212-r] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The successional dynamics of root-colonizing microbes are hypothesized to be critical to displacing fungal pathogens that can proliferate after the use of some herbicides. Applications of glyphosate in particular, which compromises the plant defense system by interfering with the production of aromatic amino acids, are thought to promote a buildup of root pathogens and can result in a "greenbridge" between weeds or volunteers and crop hosts. By planting 2 to 3 weeks after spraying, growers can avoid most negative impacts of the greenbridge by allowing pathogen populations to decline, but with the added cost of delayed planting dates. However, the specific changes in microbial communities during this period of root death and the microbial taxa likely to be involved in displacing pathogens are poorly characterized. Using high-throughput sequencing, we characterized fungal and oomycete communities in roots after applications of herbicides with different modes of action (glyphosate or clethodim) and tracked their dynamics over 3 weeks in both naturally infested soil and soil inoculated with Rhizoctonia solani AG-8. We found that many unexpected taxa were present at high relative abundance (e.g., Pythium volutum and Myrmecridium species) in live and dying wheat roots and may play an under-recognized role in greenbridge dynamics. Moreover, communities were highly dynamic over time and had herbicide-specific successional patterns, but became relatively stable by 2 weeks after herbicide application. Network analysis of communities over time revealed patterns of interactions among taxa that were both common and unique to each herbicide treatment and identified two primary groups of taxa with many positive associations within-groups but negative associations between-groups, suggesting that these groups are antagonistic to one another in dying roots and may play a role in displacing pathogen populations during greenbridge dynamics.
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Affiliation(s)
- Daniel C Schlatter
- First and third authors: U.S. Department of Agriculture-Agriculture Research Service, Wheat Health, Genetics and Quality Research Unit, Washington State University, Pullman 99164-6430; and second author: Department of Crop and Soil Sciences, Washington State University, Pullman 99164-6420
| | - Ian Burke
- First and third authors: U.S. Department of Agriculture-Agriculture Research Service, Wheat Health, Genetics and Quality Research Unit, Washington State University, Pullman 99164-6430; and second author: Department of Crop and Soil Sciences, Washington State University, Pullman 99164-6420
| | - Timothy C Paulitz
- First and third authors: U.S. Department of Agriculture-Agriculture Research Service, Wheat Health, Genetics and Quality Research Unit, Washington State University, Pullman 99164-6430; and second author: Department of Crop and Soil Sciences, Washington State University, Pullman 99164-6420
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569
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Toju H, Peay KG, Yamamichi M, Narisawa K, Hiruma K, Naito K, Fukuda S, Ushio M, Nakaoka S, Onoda Y, Yoshida K, Schlaeppi K, Bai Y, Sugiura R, Ichihashi Y, Minamisawa K, Kiers ET. Core microbiomes for sustainable agroecosystems. NATURE PLANTS 2018; 4:247-257. [PMID: 29725101 DOI: 10.1038/s41477-018-0139-4] [Citation(s) in RCA: 374] [Impact Index Per Article: 62.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2017] [Accepted: 03/23/2018] [Indexed: 05/18/2023]
Abstract
In an era of ecosystem degradation and climate change, maximizing microbial functions in agroecosystems has become a prerequisite for the future of global agriculture. However, managing species-rich communities of plant-associated microbiomes remains a major challenge. Here, we propose interdisciplinary research strategies to optimize microbiome functions in agroecosystems. Informatics now allows us to identify members and characteristics of 'core microbiomes', which may be deployed to organize otherwise uncontrollable dynamics of resident microbiomes. Integration of microfluidics, robotics and machine learning provides novel ways to capitalize on core microbiomes for increasing resource-efficiency and stress-resistance of agroecosystems.
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Affiliation(s)
- Hirokazu Toju
- Center for Ecological Research, Kyoto University, Otsu, Shiga, Japan.
- PRESTO, Japan Science and Technology Agency, Kawaguchi, Saitama, Japan.
| | - Kabir G Peay
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Masato Yamamichi
- Department of General Systems Studies, University of Tokyo, Meguro, Tokyo, Japan
| | - Kazuhiko Narisawa
- Department of Bioresource Science, College of Agriculture, Ibaraki University, Ami, Ibaraki, Japan
| | - Kei Hiruma
- PRESTO, Japan Science and Technology Agency, Kawaguchi, Saitama, Japan
- Department of Biological Sciences, Nara Institute of Science and Technology, Nara, Japan
| | - Ken Naito
- Genetic Resource Center, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki, Japan
| | - Shinji Fukuda
- PRESTO, Japan Science and Technology Agency, Kawaguchi, Saitama, Japan
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, Japan
- Intestinal Microbiota Project, Kanagawa Institute of Industrial Science and Technology, Kawasaki, Kanagawa, Japan
- Transborder Medical Research Center, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Masayuki Ushio
- Center for Ecological Research, Kyoto University, Otsu, Shiga, Japan
- PRESTO, Japan Science and Technology Agency, Kawaguchi, Saitama, Japan
| | - Shinji Nakaoka
- PRESTO, Japan Science and Technology Agency, Kawaguchi, Saitama, Japan
- Institute of Industrial Sciences, The University of Tokyo, Tokyo, Japan
| | - Yusuke Onoda
- Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Kentaro Yoshida
- PRESTO, Japan Science and Technology Agency, Kawaguchi, Saitama, Japan
- Graduate School of Agricultural Science, Kobe University, Nada-ku, Kobe, Japan
| | - Klaus Schlaeppi
- Institute of Plant Sciences, University of Bern, Bern, Switzerland
- Department of Agroecology and Environment, Agroscope, Zurich, Switzerland
| | - Yang Bai
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Science, Beijing, China
- Centre of Excellence for Plant and Microbial Sciences (CEPAMS), Institute of Genetics and Developmental Biology, Chinese Academy of Science & John Innes Centre, Beijing, China
| | - Ryo Sugiura
- PRESTO, Japan Science and Technology Agency, Kawaguchi, Saitama, Japan
- Hokkaido Agricultural Research Center, NARO (National Agriculture and Food Research Organization), Memuro, Hokkaido, Japan
| | - Yasunori Ichihashi
- PRESTO, Japan Science and Technology Agency, Kawaguchi, Saitama, Japan
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, Japan
- RIKEN BioResource Research Center, Tsukuba, Ibaraki, Japan
| | - Kiwamu Minamisawa
- Graduate School of Life Sciences, Tohoku University, Katahira, Sendai, Japan
| | - E Toby Kiers
- Department of Ecological Science, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
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570
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Domin H, Zurita-Gutiérrez YH, Scotti M, Buttlar J, Hentschel Humeida U, Fraune S. Predicted Bacterial Interactions Affect in Vivo Microbial Colonization Dynamics in Nematostella. Front Microbiol 2018; 9:728. [PMID: 29740401 PMCID: PMC5928149 DOI: 10.3389/fmicb.2018.00728] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Accepted: 03/28/2018] [Indexed: 01/06/2023] Open
Abstract
The maintenance and resilience of host-associated microbiota during development is a fundamental process influencing the fitness of many organisms. Several host properties were identified as influencing factors on bacterial colonization, including the innate immune system, mucus composition, and diet. In contrast, the importance of bacteria–bacteria interactions on host colonization is less understood. Here, we use bacterial abundance data of the marine model organism Nematostella vectensis to reconstruct potential bacteria–bacteria interactions through co-occurrence networks. The analysis indicates that bacteria–bacteria interactions are dynamic during host colonization and change according to the host’s developmental stage. To assess the predictive power of inferred interactions, we tested bacterial isolates with predicted cooperative or competitive behavior for their ability to influence bacterial recolonization dynamics. Within 3 days of recolonization, all tested bacterial isolates affected bacterial community structure, while only competitive bacteria increased bacterial diversity. Only 1 week after recolonization, almost no differences in bacterial community structure could be observed between control and treatments. These results show that predicted competitive bacteria can influence community structure for a short period of time, verifying the in silico predictions. However, within 1 week, the effects of the bacterial isolates are neutralized, indicating a high degree of resilience of the bacterial community.
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Affiliation(s)
- Hanna Domin
- Zoological Institute, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | | | - Marco Scotti
- RD3 Experimental Ecology, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | - Jann Buttlar
- Zoological Institute, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Ute Hentschel Humeida
- RD3 Marine Microbiology, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany.,Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Sebastian Fraune
- Zoological Institute, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
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571
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Hassani MA, Durán P, Hacquard S. Microbial interactions within the plant holobiont. MICROBIOME 2018; 6:58. [PMID: 29587885 PMCID: PMC5870681 DOI: 10.1186/s40168-018-0445-0] [Citation(s) in RCA: 514] [Impact Index Per Article: 85.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Accepted: 03/13/2018] [Indexed: 05/09/2023]
Abstract
Since the colonization of land by ancestral plant lineages 450 million years ago, plants and their associated microbes have been interacting with each other, forming an assemblage of species that is often referred to as a "holobiont." Selective pressure acting on holobiont components has likely shaped plant-associated microbial communities and selected for host-adapted microorganisms that impact plant fitness. However, the high microbial densities detected on plant tissues, together with the fast generation time of microbes and their more ancient origin compared to their host, suggest that microbe-microbe interactions are also important selective forces sculpting complex microbial assemblages in the phyllosphere, rhizosphere, and plant endosphere compartments. Reductionist approaches conducted under laboratory conditions have been critical to decipher the strategies used by specific microbes to cooperate and compete within or outside plant tissues. Nonetheless, our understanding of these microbial interactions in shaping more complex plant-associated microbial communities, along with their relevance for host health in a more natural context, remains sparse. Using examples obtained from reductionist and community-level approaches, we discuss the fundamental role of microbe-microbe interactions (prokaryotes and micro-eukaryotes) for microbial community structure and plant health. We provide a conceptual framework illustrating that interactions among microbiota members are critical for the establishment and the maintenance of host-microbial homeostasis.
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Affiliation(s)
- M Amine Hassani
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany
- Environmental Genomics, Christian-Albrechts University of Kiel, 24118, Kiel, Germany
- Max Planck Institute for Evolutionary Biology, 24306, Plön, Germany
| | - Paloma Durán
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany
| | - Stéphane Hacquard
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany.
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572
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Using Cultivated Microbial Communities To Dissect Microbiome Assembly: Challenges, Limitations, and the Path Ahead. mSystems 2018; 3:mSystems00161-17. [PMID: 29629414 PMCID: PMC5881021 DOI: 10.1128/msystems.00161-17] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Accepted: 01/16/2018] [Indexed: 12/22/2022] Open
Abstract
As troves of microbiome sequencing data provide improved resolution of patterns of microbial diversity, new approaches are needed to understand what controls these patterns. Many microbial ecologists are using cultivated model microbial communities to address this challenge. As troves of microbiome sequencing data provide improved resolution of patterns of microbial diversity, new approaches are needed to understand what controls these patterns. Many microbial ecologists are using cultivated model microbial communities to address this challenge. These systems provide opportunities to identify drivers of microbiome assembly, but key challenges and limitations need to be carefully considered in their development, implementation, and interpretation. How well do model microbial communities mimic in vitro communities in terms of taxonomic diversity, trophic levels, intraspecific diversity, and the abiotic environment? What are the best ways to manipulate and measure inputs and outputs in model community experiments? In this perspective, I briefly address some of these challenges on the basis of our experience developing fermented food model communities. Future work integrating genetic and molecular approaches with cultivated model microbial communities will allow microbial ecology to develop a more mechanistic understanding of microbiome diversity.
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573
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Bayer-Santos E, Lima LDP, Ceseti LDM, Ratagami CY, de Santana ES, da Silva AM, Farah CS, Alvarez-Martinez CE. Xanthomonas citri T6SS mediates resistance to Dictyostelium predation and is regulated by an ECF σ factor and cognate Ser/Thr kinase. Environ Microbiol 2018; 20:1562-1575. [PMID: 29488354 DOI: 10.1111/1462-2920.14085] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Revised: 02/21/2018] [Accepted: 02/24/2018] [Indexed: 11/25/2022]
Abstract
Plant-associated bacteria of the genus Xanthomonas cause disease in a wide range of economically important crops. However, their ability to persist in the environment is still poorly understood. Predation by amoebas represents a major selective pressure to bacterial populations in the environment. In this study, we show that the X. citri type 6 secretion system (T6SS) promotes resistance to predation by the soil amoeba Dictyostelium discoideum. We found that an extracytoplasmic function (ECF) sigma factor (EcfK) is required for induction of T6SS genes during interaction with Dictyostelium. EcfK homologues are found in several environmental bacteria in association with a gene encoding a eukaryotic-like Ser/Thr kinase (pknS). Deletion of pknS causes sensitivity to amoeba predation and abolishes induction of T6SS genes. Phosphomimetic mutagenesis of EcfK identified a threonine residue (T51) that renders EcfK constitutively active in standard culture conditions. Moreover, susceptibility of ΔpknS to Dictyostelium predation can be overcome by expression of the constitutively active version EcfKT51E from a multicopy plasmid. Together, these results describe a new regulatory cascade in which PknS functions through activation of EcfK to promote T6SS expression. Our work reveals an important aspect of Xanthomonas physiology that affects its ability to persist in the environment.
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Affiliation(s)
- Ethel Bayer-Santos
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Brazil
| | - Lídia Dos Passos Lima
- Departamento de Genética, Evolução, Microbiologia e Imunologia, Instituto de Biologia, Universidade Estadual de Campinas, Brazil
| | - Lucas de Moraes Ceseti
- Departamento de Genética, Evolução, Microbiologia e Imunologia, Instituto de Biologia, Universidade Estadual de Campinas, Brazil
| | - Camila Yuri Ratagami
- Departamento de Genética, Evolução, Microbiologia e Imunologia, Instituto de Biologia, Universidade Estadual de Campinas, Brazil
| | - Eliane Silva de Santana
- Departamento de Genética, Evolução, Microbiologia e Imunologia, Instituto de Biologia, Universidade Estadual de Campinas, Brazil
| | - Aline Maria da Silva
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Brazil
| | - Chuck Shaker Farah
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Brazil
| | - Cristina Elisa Alvarez-Martinez
- Departamento de Genética, Evolução, Microbiologia e Imunologia, Instituto de Biologia, Universidade Estadual de Campinas, Brazil
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574
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575
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Maciá-Vicente JG, Shi YN, Cheikh-Ali Z, Grün P, Glynou K, Kia SH, Piepenbring M, Bode HB. Metabolomics-based chemotaxonomy of root endophytic fungi for natural products discovery. Environ Microbiol 2018; 20:1253-1270. [DOI: 10.1111/1462-2920.14072] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Accepted: 02/09/2018] [Indexed: 12/01/2022]
Affiliation(s)
- Jose G. Maciá-Vicente
- Institute of Ecology, Evolution and Diversity, Goethe Universität Frankfurt, Max-von-Laue-Str. 13; Frankfurt am Main 60438 Germany
- Integrative Fungal Research Cluster (IPF); Frankfurt am Main Germany
| | - Yan-Ni Shi
- Merck Stiftungsprofessur für Molekulare Biotechnologie, Fachbereich Biowissenschaften; Goethe Universität Frankfurt; Frankfurt am Main 60438 Germany
| | - Zakaria Cheikh-Ali
- Integrative Fungal Research Cluster (IPF); Frankfurt am Main Germany
- Merck Stiftungsprofessur für Molekulare Biotechnologie, Fachbereich Biowissenschaften; Goethe Universität Frankfurt; Frankfurt am Main 60438 Germany
| | - Peter Grün
- Merck Stiftungsprofessur für Molekulare Biotechnologie, Fachbereich Biowissenschaften; Goethe Universität Frankfurt; Frankfurt am Main 60438 Germany
| | - Kyriaki Glynou
- Institute of Ecology, Evolution and Diversity, Goethe Universität Frankfurt, Max-von-Laue-Str. 13; Frankfurt am Main 60438 Germany
- Integrative Fungal Research Cluster (IPF); Frankfurt am Main Germany
| | - Sevda Haghi Kia
- Institute of Ecology, Evolution and Diversity, Goethe Universität Frankfurt, Max-von-Laue-Str. 13; Frankfurt am Main 60438 Germany
- Integrative Fungal Research Cluster (IPF); Frankfurt am Main Germany
| | - Meike Piepenbring
- Institute of Ecology, Evolution and Diversity, Goethe Universität Frankfurt, Max-von-Laue-Str. 13; Frankfurt am Main 60438 Germany
- Integrative Fungal Research Cluster (IPF); Frankfurt am Main Germany
| | - Helge B. Bode
- Integrative Fungal Research Cluster (IPF); Frankfurt am Main Germany
- Merck Stiftungsprofessur für Molekulare Biotechnologie, Fachbereich Biowissenschaften; Goethe Universität Frankfurt; Frankfurt am Main 60438 Germany
- Buchmann Institute for Molecular Life Sciences (BMLS), Goethe Universität Frankfurt; Frankfurt am Main 60438 Germany
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576
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Aydogan EL, Moser G, Müller C, Kämpfer P, Glaeser SP. Long-Term Warming Shifts the Composition of Bacterial Communities in the Phyllosphere of Galium album in a Permanent Grassland Field-Experiment. Front Microbiol 2018; 9:144. [PMID: 29487575 PMCID: PMC5816784 DOI: 10.3389/fmicb.2018.00144] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2017] [Accepted: 01/23/2018] [Indexed: 11/13/2022] Open
Abstract
Global warming is currently a much discussed topic with as yet largely unexplored consequences for agro-ecosystems. Little is known about the warming effect on the bacterial microbiota inhabiting the plant surface (phyllosphere), which can have a strong impact on plant growth and health, as well as on plant diseases and colonization by human pathogens. The aim of this study was to investigate the effect of moderate surface warming on the diversity and composition of the bacterial leaf microbiota of the herbaceous plant Galium album. Leaves were collected from four control and four surface warmed (+2°C) plots located at the field site of the Environmental Monitoring and Climate Impact Research Station Linden in Germany over a 6-year period. Warming had no effect on the concentration of total number of cells attached to the leaf surface as counted by Sybr Green I staining after detachment, but changes in the diversity and phylogenetic composition of the bacterial leaf microbiota analyzed by bacterial 16S rRNA gene Illumina amplicon sequencing were observed. The bacterial phyllosphere microbiota were dominated by Proteobacteria, Bacteroidetes, and Actinobacteria. Warming caused a significant higher relative abundance of members of the Gammaproteobacteria, Actinobacteria, and Firmicutes, and a lower relative abundance of members of the Alphaproteobacteria and Bacteroidetes. Plant beneficial bacteria like Sphingomonas spp. and Rhizobium spp. occurred in significantly lower relative abundance in leaf samples of warmed plots. In contrast, several members of the Enterobacteriaceae, especially Enterobacter and Erwinia, and other potential plant or human pathogenic genera such as Acinetobacter and insect-associated Buchnera and Wolbachia spp. occurred in higher relative abundances in the phyllosphere samples from warmed plots. This study showed for the first time the long-term impact of moderate (+2°C) surface warming on the phyllosphere microbiota on plants. A reduction of beneficial bacteria and an enhancement of potential pathogenic bacteria in the phyllosphere of plants may indicate that this aspect of the ecosystem which has been largely neglected up till now, can be a potential risk for pathogen transmission in agro-ecosystems in the near future.
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Affiliation(s)
- Ebru L. Aydogan
- Institute for Applied Microbiology, Justus Liebig University Giessen, Giessen, Germany
| | - Gerald Moser
- Institute for Plant Ecology, Justus Liebig University Giessen, Giessen, Germany
| | - Christoph Müller
- Institute for Plant Ecology, Justus Liebig University Giessen, Giessen, Germany
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
| | - Peter Kämpfer
- Institute for Applied Microbiology, Justus Liebig University Giessen, Giessen, Germany
| | - Stefanie P. Glaeser
- Institute for Applied Microbiology, Justus Liebig University Giessen, Giessen, Germany
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577
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Geisen S, Mitchell EAD, Adl S, Bonkowski M, Dunthorn M, Ekelund F, Fernández LD, Jousset A, Krashevska V, Singer D, Spiegel FW, Walochnik J, Lara E. Soil protists: a fertile frontier in soil biology research. FEMS Microbiol Rev 2018; 42:293-323. [DOI: 10.1093/femsre/fuy006] [Citation(s) in RCA: 212] [Impact Index Per Article: 35.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Accepted: 02/12/2018] [Indexed: 12/27/2022] Open
Affiliation(s)
- Stefan Geisen
- Department of Terrestrial Ecology, Netherlands Institute of Ecology, 6708 PB Wageningen, The Netherlands
- Laboratory of Nematology, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Edward A D Mitchell
- Laboratory of Soil Biodiversity, University of Neuchâtel, Rue Emile-Argand 11, Neuchâtel 2000, Switzerland
- Jardin Botanique de Neuchâtel, Chemin du Perthuis-du-Sault 58, Neuchâtel 2000, Switzerland
| | - Sina Adl
- Department of Soil Sciences, College of Agriculture and Bioresources, University of Saskatchewan, 51 Campus Drive, Saskatoon, Canada
| | - Michael Bonkowski
- Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Institute of Zoology, Terrestrial Ecology, Zülpicher Straße 47b, 50674 Köln, Germany
| | - Micah Dunthorn
- Department of Ecology, University of Kaiserslautern, Erwin-Schrödinger Straße, 67663 Kaiserslautern, Germany
| | - Flemming Ekelund
- Department of Biology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark
| | - Leonardo D Fernández
- Centro de Investigación en Recursos Naturales y Sustentabilidad (CIRENYS), Universidad Bernardo O’Higgins, Avenida Viel 1497, Santiago, Chile
| | - Alexandre Jousset
- Department of Ecology and Biodiversity, Utrecht University, 3584 CH Utrecht, The Netherlands
| | - Valentyna Krashevska
- University of Göttingen, J.F. Blumenbach Institute of Zoology and Anthropology, Untere Karspüle 2, 37073 Göttingen, Germany
| | - David Singer
- Laboratory of Soil Biodiversity, University of Neuchâtel, Rue Emile-Argand 11, Neuchâtel 2000, Switzerland
| | - Frederick W Spiegel
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR, 72701, United States of America
| | - Julia Walochnik
- Molecular Parasitology, Institute of Tropical Medicine, Medical University, 1090 Vienna, Austria
| | - Enrique Lara
- Laboratory of Soil Biodiversity, University of Neuchâtel, Rue Emile-Argand 11, Neuchâtel 2000, Switzerland
- Real Jardín Botánico, CSIC, Plaza de Murillo 2, 28014 Madrid, Spain
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578
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Knelman JE, Graham EB, Prevéy JS, Robeson MS, Kelly P, Hood E, Schmidt SK. Interspecific Plant Interactions Reflected in Soil Bacterial Community Structure and Nitrogen Cycling in Primary Succession. Front Microbiol 2018; 9:128. [PMID: 29467741 PMCID: PMC5808232 DOI: 10.3389/fmicb.2018.00128] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Accepted: 01/18/2018] [Indexed: 02/01/2023] Open
Abstract
Past research demonstrating the importance plant-microbe interactions as drivers of ecosystem succession has focused on how plants condition soil microbial communities, impacting subsequent plant performance and plant community assembly. These studies, however, largely treat microbial communities as a black box. In this study, we sought to examine how emblematic shifts from early successional Alnus viridus ssp. sinuata (Sitka alder) to late successional Picea sitchensis (Sitka spruce) in primary succession may be reflected in specific belowground changes in bacterial community structure and nitrogen cycling related to the interaction of these two plants. We examined early successional alder-conditioned soils in a glacial forefield to delineate how alders alter the soil microbial community with increasing dominance. Further, we assessed the impact of late-successional spruce plants on these early successional alder-conditioned microbiomes and related nitrogen cycling through a leachate addition microcosm experiment. We show how increasingly abundant alder select for particular bacterial taxa. Additionally, we found that spruce leachate significantly alters the composition of these microbial communities in large part by driving declines in taxa that are enriched by alder, including bacterial symbionts. We found these effects to be spruce specific, beyond a general leachate effect. Our work also demonstrates a unique influence of spruce on ammonium availability. Such insights bolster theory relating the importance of plant-microbe interactions with late-successional plants and interspecific plant interactions more generally.
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Affiliation(s)
- Joseph E. Knelman
- Institute of Arctic and Alpine Research, University of Colorado Boulder, Boulder, CO, United States
| | - Emily B. Graham
- Pacific Northwest National Laboratory (U.S. Department of Energy), Richland, WA, United States
| | - Janet S. Prevéy
- Pacific Northwest Research Station, The United States Forest Service, Olympia, WA, United States
| | - Michael S. Robeson
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Patrick Kelly
- Institute of Arctic and Alpine Research, University of Colorado Boulder, Boulder, CO, United States
| | - Eran Hood
- Department of Natural Sciences, University of Alaska Southeast, Juneau, AK, United States
| | - Steve K. Schmidt
- Department of Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, CO, United States
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579
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Glynou K, Nam B, Thines M, Maciá-Vicente JG. Facultative root-colonizing fungi dominate endophytic assemblages in roots of nonmycorrhizal Microthlaspi species. THE NEW PHYTOLOGIST 2018; 217:1190-1202. [PMID: 29094363 DOI: 10.1111/nph.14873] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Accepted: 10/02/2017] [Indexed: 05/02/2023]
Abstract
There is increasing knowledge on the diversity of root-endophytic fungi, but limited information on their lifestyles and dependence on hosts hampers our understanding of their ecological functions. We compared diversity and biogeographical patterns of cultivable and noncultivable root endophytes to assess whether their occurrence is determined by distinct ecological factors. The endophytic diversity in roots of nonmycorrhizal Microthlaspi spp. growing across Europe was assessed using high-throughput sequencing (HTS) and compared with a previous dataset based on cultivation of endophytes from the same root samples. HTS revealed a large fungal richness undetected by cultivation, but which largely comprised taxa with restricted distributions and/or low representation of sequence reads. Both datasets coincided in a consistent high representation of widespread endophytes within orders Pleosporales, Hypocreales and Helotiales, as well as similar associations of community structure with spatial and environmental conditions. Likewise, distributions of particular endophytes inferred by HTS agreed with cultivation data in suggesting individual ecological preferences. Our findings support that Microthlaspi spp. roots are colonized mostly by saprotrophic and likely facultative endophytes, and that differential niche preferences and distribution ranges among fungi importantly drive the assembly of root-endophytic communities.
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Affiliation(s)
- Kyriaki Glynou
- Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Max-von-Laue-Str. 13, Frankfurt am Main, 60438, Germany
- Integrative Fungal Research Cluster (IPF), Georg-Voigt-Str. 14-16, Frankfurt am Main, 60325, Germany
| | - Bora Nam
- Biodiversity and Climate Research Centre (BiK-F), Senckenberg Gesellschaft für Naturforschung, Senckenberganlage 25, Frankfurt am Main, 60325, Germany
| | - Marco Thines
- Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Max-von-Laue-Str. 13, Frankfurt am Main, 60438, Germany
- Integrative Fungal Research Cluster (IPF), Georg-Voigt-Str. 14-16, Frankfurt am Main, 60325, Germany
- Biodiversity and Climate Research Centre (BiK-F), Senckenberg Gesellschaft für Naturforschung, Senckenberganlage 25, Frankfurt am Main, 60325, Germany
| | - Jose G Maciá-Vicente
- Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Max-von-Laue-Str. 13, Frankfurt am Main, 60438, Germany
- Integrative Fungal Research Cluster (IPF), Georg-Voigt-Str. 14-16, Frankfurt am Main, 60325, Germany
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580
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Microbial community assembly in wild populations of the fruit fly Drosophila melanogaster. ISME JOURNAL 2018; 12:959-972. [PMID: 29358735 DOI: 10.1038/s41396-017-0020-x] [Citation(s) in RCA: 97] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Revised: 09/20/2017] [Accepted: 11/15/2017] [Indexed: 02/01/2023]
Abstract
Animals are routinely colonized by microorganisms. Despite many studies documenting the microbial taxa associated with animals, the pattern and ecological determinants of among-animal variation in microbial communities are poorly understood. This study quantified the bacterial communities associated with natural populations of Drosophila melanogaster. Across five collections, each fly bore 16-78 OTUs, predominantly of the Acetobacteraceae, Lactobacillaceae, and Enterobacteriaceae. Positive relationships, mostly among related OTUs, dominated both the significant co-occurrences and co-association networks among bacteria, and OTUs with important network positions were generally of intermediate abundance and prevalence. The prevalence of most OTUs was well predicted by a neutral model suggesting that ecological drift and passive dispersal contribute significantly to microbiome composition. However, some Acetobacteraceae and Lactobacillaceae were present in more flies than predicted, indicative of superior among-fly dispersal. These taxa may be well-adapted to the Drosophila habitat from the perspective of dispersal as the principal benefit of the association to the microbial partners. Taken together, these patterns indicate that both stochastic processes and deterministic processes relating to the differential capacity for persistence in the host habitat and transmission between hosts contribute to bacterial community assembly in Drosophila melanogaster.
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581
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Hartman K, van der Heijden MGA, Wittwer RA, Banerjee S, Walser JC, Schlaeppi K. Cropping practices manipulate abundance patterns of root and soil microbiome members paving the way to smart farming. MICROBIOME 2018; 6:14. [PMID: 29338764 PMCID: PMC5771023 DOI: 10.1186/s40168-017-0389-9] [Citation(s) in RCA: 231] [Impact Index Per Article: 38.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Accepted: 12/17/2017] [Indexed: 05/20/2023]
Abstract
BACKGROUND Harnessing beneficial microbes presents a promising strategy to optimize plant growth and agricultural sustainability. Little is known to which extent and how specifically soil and plant microbiomes can be manipulated through different cropping practices. Here, we investigated soil and wheat root microbial communities in a cropping system experiment consisting of conventional and organic managements, both with different tillage intensities. RESULTS While microbial richness was marginally affected, we found pronounced cropping effects on community composition, which were specific for the respective microbiomes. Soil bacterial communities were primarily structured by tillage, whereas soil fungal communities responded mainly to management type with additional effects by tillage. In roots, management type was also the driving factor for bacteria but not for fungi, which were generally determined by changes in tillage intensity. To quantify an "effect size" for microbiota manipulation, we found that about 10% of variation in microbial communities was explained by the tested cropping practices. Cropping sensitive microbes were taxonomically diverse, and they responded in guilds of taxa to the specific practices. These microbes also included frequent community members or members co-occurring with many other microbes in the community, suggesting that cropping practices may allow manipulation of influential community members. CONCLUSIONS Understanding the abundance patterns of cropping sensitive microbes presents the basis towards developing microbiota management strategies for smart farming. For future targeted microbiota management-e.g., to foster certain microbes with specific agricultural practices-a next step will be to identify the functional traits of the cropping sensitive microbes.
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Affiliation(s)
- Kyle Hartman
- Plant-Soil Interactions, Department of Agroecology and Environment, Agroscope, Zurich, Switzerland
- Institute for Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
| | - Marcel G. A. van der Heijden
- Plant-Soil Interactions, Department of Agroecology and Environment, Agroscope, Zurich, Switzerland
- Institute for Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
- Plant-Microbe Interactions, Institute of Environmental Biology, Faculty of Science, Utrecht University, Utrecht, The Netherlands
| | - Raphaël A. Wittwer
- Plant-Soil Interactions, Department of Agroecology and Environment, Agroscope, Zurich, Switzerland
| | - Samiran Banerjee
- Plant-Soil Interactions, Department of Agroecology and Environment, Agroscope, Zurich, Switzerland
| | | | - Klaus Schlaeppi
- Plant-Soil Interactions, Department of Agroecology and Environment, Agroscope, Zurich, Switzerland
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582
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Hamonts K, Trivedi P, Garg A, Janitz C, Grinyer J, Holford P, Botha FC, Anderson IC, Singh BK. Field study reveals core plant microbiota and relative importance of their drivers. Environ Microbiol 2018; 20:124-140. [PMID: 29266641 DOI: 10.1111/1462-2920.14031] [Citation(s) in RCA: 163] [Impact Index Per Article: 27.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Accepted: 12/12/2017] [Indexed: 12/20/2022]
Abstract
Harnessing plant microbiota can assist in sustainably increasing primary productivity to meet growing global demands for food and biofuel. However, development of rational microbiome-based approaches for improving crop yield and productivity is currently hindered by a lack of understanding of the major biotic and abiotic factors shaping the crop microbiome under relevant field conditions. We examined bacterial and fungal communities associated with both aerial (leaves, stalks) and belowground (roots, soil) compartments of four commercial sugarcane varieties (Saccharum spp.) grown in several growing regions in Australia. We identified drivers of the sugarcane microbiome under field conditions and evaluated whether the plants shared a core microbiome. Sugarcane-associated microbial assemblages were primarily determined by plant compartment, followed by growing region, crop age, variety and Yellow Canopy Syndrome (YCS). We detected a core set of microbiota and identified members of the core microbiome that were influenced by YCS incidence. Our study revealed key hub microorganisms in the core microbiome networks of sugarcane leaves, stalks, roots and rhizosphere soil despite location and time-associated shifts in the community assemblages. Elucidating their functional roles and identification of the keystone core microbiota that sustain plant health could provide a technological breakthrough for a sustainable increase in crop productivity.
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Affiliation(s)
- Kelly Hamonts
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, Australia
| | - Pankaj Trivedi
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, Australia.,Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO, USA
| | - Anshu Garg
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, Australia
| | - Caroline Janitz
- Next-generation Sequencing Facility, Western Sydney University, Penrith, NSW, Australia
| | - Jasmine Grinyer
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, Australia
| | - Paul Holford
- School of Science and Health, Western Sydney University, Penrith, NSW, Australia
| | | | - Ian C Anderson
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, Australia
| | - Brajesh K Singh
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, Australia.,Global Centre for Land-based Innovation, Western Sydney University, Penrith, NSW, Australia
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583
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Biomonitoring for the 21st Century: Integrating Next-Generation Sequencing Into Ecological Network Analysis. ADV ECOL RES 2018. [DOI: 10.1016/bs.aecr.2017.12.001] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
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584
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Sasse J, Martinoia E, Northen T. Feed Your Friends: Do Plant Exudates Shape the Root Microbiome? TRENDS IN PLANT SCIENCE 2018; 23:25-41. [PMID: 29050989 DOI: 10.1016/j.tplants.2017.09.003] [Citation(s) in RCA: 760] [Impact Index Per Article: 126.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Revised: 08/25/2017] [Accepted: 09/07/2017] [Indexed: 05/18/2023]
Abstract
Plant health in natural environments depends on interactions with complex and dynamic communities comprising macro- and microorganisms. While many studies have provided insights into the composition of rhizosphere microbiomes (rhizobiomes), little is known about whether plants shape their rhizobiomes. Here, we discuss physiological factors of plants that may govern plant-microbe interactions, focusing on root physiology and the role of root exudates. Given that only a few plant transport proteins are known to be involved in root metabolite export, we suggest novel families putatively involved in this process. Finally, building off of the features discussed in this review, and in analogy to well-known symbioses, we elaborate on a possible sequence of events governing rhizobiome assembly.
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Affiliation(s)
- Joelle Sasse
- Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Enrico Martinoia
- Department of Plant and Microbial Biology, University of Zurich, Zurich 8008, Switzerland
| | - Trent Northen
- Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Joint Genome Institute, Walnut Creek, CA 94958, USA.
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585
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Sergaki C, Lagunas B, Lidbury I, Gifford ML, Schäfer P. Challenges and Approaches in Microbiome Research: From Fundamental to Applied. FRONTIERS IN PLANT SCIENCE 2018; 9:1205. [PMID: 30174681 PMCID: PMC6107787 DOI: 10.3389/fpls.2018.01205] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Accepted: 07/26/2018] [Indexed: 05/07/2023]
Abstract
We face major agricultural challenges that remain a threat for global food security. Soil microbes harbor enormous potentials to provide sustainable and economically favorable solutions that could introduce novel approaches to improve agricultural practices and, hence, crop productivity. In this review we give an overview regarding the current state-of-the-art of microbiome research by discussing new technologies and approaches. We also provide insights into fundamental microbiome research that aim to provide a deeper understanding of the dynamics within microbial communities, as well as their interactions with different plant hosts and the environment. We aim to connect all these approaches with potential applications and reflect how we can use microbial communities in modern agricultural systems to realize a more customized and sustainable use of valuable resources (e.g., soil).
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Affiliation(s)
- Chrysi Sergaki
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
- *Correspondence: Chrysi Sergaki,
| | - Beatriz Lagunas
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | - Ian Lidbury
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | - Miriam L. Gifford
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
- Warwick Integrative Synthetic Biology Centre, University of Warwick, Coventry, United Kingdom
| | - Patrick Schäfer
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
- Warwick Integrative Synthetic Biology Centre, University of Warwick, Coventry, United Kingdom
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586
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Singh BK, Trivedi P, Singh S, Macdonald CA, Verma JP. Emerging microbiome technologies for sustainable increase in farm productivity and environmental security. MICROBIOLOGY AUSTRALIA 2018. [DOI: 10.1071/ma18006] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Farming systems are under pressure to sustainably increase productivity to meet demand for food and fibre for a growing global population under shrinking arable lands and changing climatic conditions. Furthermore, conventional farming has led to declines in soil fertility and, in some cases, inappropriate and excessive use of chemical fertilisers and pesticides has caused soil degradation, negatively impacting human and environmental health. The soil and plant microbiomes are significant determinants of plant fitness and productivity. Microbes are also the main drivers of global biogeochemical cycles and thus key to sustainable agriculture. There is increasing evidence that with development of appropriate technologies, the plant microbiome can be harnessed to potentially decrease the frequency of plant diseases, increase resource use efficiencies and ultimately enhance agricultural productivity, while simultaneously decreasing the input of chemical fertilisers and pesticides, resulting in reduced greenhouse gas emissions and promoting environmental sustainability. However, to successfully translate potential to practical outcomes, both fundamental and applied research are needed to overcome current constraints. Research efforts need to be embedded in industrial requirements and policy and social frameworks to expedite the process of innovation, commercialisation and adoption. We propose that learning from the advancement in the human microbiome can significantly expedite the discovery and innovation of effective microbial products for sustainable and productive farming. This article summarises the emergence of microbiome technologies for the agriculture industry and how to facilitate the development and adoption of environmentally friendly microbiome technologies for sustainable increase in farm productivity.
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587
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Levy A, Salas Gonzalez I, Mittelviefhaus M, Clingenpeel S, Herrera Paredes S, Miao J, Wang K, Devescovi G, Stillman K, Monteiro F, Rangel Alvarez B, Lundberg DS, Lu TY, Lebeis S, Jin Z, McDonald M, Klein AP, Feltcher ME, Rio TG, Grant SR, Doty SL, Ley RE, Zhao B, Venturi V, Pelletier DA, Vorholt JA, Tringe SG, Woyke T, Dangl JL. Genomic features of bacterial adaptation to plants. Nat Genet 2017; 50:138-150. [PMID: 29255260 PMCID: PMC5957079 DOI: 10.1038/s41588-017-0012-9] [Citation(s) in RCA: 300] [Impact Index Per Article: 42.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Accepted: 11/10/2017] [Indexed: 01/10/2023]
Abstract
Plants intimately associate with diverse bacteria. Plant-associated (PA) bacteria have ostensibly evolved genes enabling adaptation to the plant environment. However, the identities of such genes are mostly unknown and their functions are poorly characterized. We sequenced 484 genomes of bacterial isolates from roots of Brassicaceae, poplar, and maize. We then compared 3837 bacterial genomes to identify thousands of PA gene clusters. Genomes of PA bacteria encode more carbohydrate metabolism functions and fewer mobile elements than related non-plant associated genomes. We experimentally validated candidates from two sets of PA genes, one involved in plant colonization, the other serving in microbe-microbe competition between PA bacteria. We also identified 64 PA protein domains that potentially mimic plant domains; some are shared with PA fungi and oomycetes. This work expands the genome-based understanding of plant-microbe interactions and provides leads for efficient and sustainable agriculture through microbiome engineering.
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Affiliation(s)
- Asaf Levy
- DOE Joint Genome Institute, Walnut Creek, CA, USA
| | - Isai Salas Gonzalez
- Department of Biology, University of North Carolina, Chapel Hill, NC, USA.,Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | | | | | - Sur Herrera Paredes
- Department of Biology, University of North Carolina, Chapel Hill, NC, USA.,Howard Hughes Medical Institute, Chevy Chase, MD, USA.,Department of Biology, Stanford University, Stanford, CA, USA
| | - Jiamin Miao
- Department of Horticulture, Virginia Tech, Blacksburg, VA, USA.,The Grassland College, Gansu Agricultural University, Lanzhou, Gansu, China
| | - Kunru Wang
- Department of Horticulture, Virginia Tech, Blacksburg, VA, USA
| | - Giulia Devescovi
- International Centre for Genetic Engineering and Biotechnology, Trieste, Italy
| | | | - Freddy Monteiro
- Department of Biology, University of North Carolina, Chapel Hill, NC, USA.,Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | | | - Derek S Lundberg
- Department of Biology, University of North Carolina, Chapel Hill, NC, USA.,Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Tse-Yuan Lu
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Sarah Lebeis
- Department of Microbiology, University of Tennessee, Knoxville, TN, USA
| | - Zhao Jin
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Meredith McDonald
- Department of Biology, University of North Carolina, Chapel Hill, NC, USA.,Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Andrew P Klein
- Department of Biology, University of North Carolina, Chapel Hill, NC, USA.,Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Meghan E Feltcher
- Department of Biology, University of North Carolina, Chapel Hill, NC, USA.,Howard Hughes Medical Institute, Chevy Chase, MD, USA.,BD Technologies and Innovation, Research Triangle Park, NC, USA
| | | | - Sarah R Grant
- Department of Biology, University of North Carolina, Chapel Hill, NC, USA
| | - Sharon L Doty
- School of Environmental and Forest Sciences, University of Washington, Seattle, WA, USA
| | - Ruth E Ley
- Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Bingyu Zhao
- Department of Horticulture, Virginia Tech, Blacksburg, VA, USA
| | - Vittorio Venturi
- International Centre for Genetic Engineering and Biotechnology, Trieste, Italy
| | - Dale A Pelletier
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | | | - Susannah G Tringe
- DOE Joint Genome Institute, Walnut Creek, CA, USA. .,School of Natural Sciences, University of California, Merced, Merced, CA, USA.
| | - Tanja Woyke
- DOE Joint Genome Institute, Walnut Creek, CA, USA. .,School of Natural Sciences, University of California, Merced, Merced, CA, USA.
| | - Jeffery L Dangl
- Department of Biology, University of North Carolina, Chapel Hill, NC, USA. .,Howard Hughes Medical Institute, Chevy Chase, MD, USA. .,The Carolina Center for Genome Sciences, University of North Carolina, Chapel Hill, NC, USA. .,Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC, USA.
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588
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Gdanetz K, Benucci GMN, Vande Pol N, Bonito G. CONSTAX: a tool for improved taxonomic resolution of environmental fungal ITS sequences. BMC Bioinformatics 2017; 18:538. [PMID: 29212440 PMCID: PMC5719527 DOI: 10.1186/s12859-017-1952-x] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2017] [Accepted: 11/22/2017] [Indexed: 01/20/2023] Open
Abstract
BACKGROUND One of the most crucial steps in high-throughput sequence-based microbiome studies is the taxonomic assignment of sequences belonging to operational taxonomic units (OTUs). Without taxonomic classification, functional and biological information of microbial communities cannot be inferred or interpreted. The internal transcribed spacer (ITS) region of the ribosomal DNA is the conventional marker region for fungal community studies. While bioinformatics pipelines that cluster reads into OTUs have received much attention in the literature, less attention has been given to the taxonomic classification of these sequences, upon which biological inference is dependent. RESULTS Here we compare how three common fungal OTU taxonomic assignment tools (RDP Classifier, UTAX, and SINTAX) handle ITS fungal sequence data. The classification power, defined as the proportion of assigned OTUs at a given taxonomic rank, varied among the classifiers. Classifiers were generally consistent (assignment of the same taxonomy to a given OTU) across datasets and ranks; a small number of OTUs were assigned unique classifications across programs. We developed CONSTAX (CONSensus TAXonomy), a Python tool that compares taxonomic classifications of the three programs and merges them into an improved consensus taxonomy. This tool also produces summary classification outputs that are useful for downstream analyses. CONCLUSIONS Our results demonstrate that independent taxonomy assignment tools classify unique members of the fungal community, and greater classification power is realized by generating consensus taxonomy of available classifiers with CONSTAX.
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Affiliation(s)
- Kristi Gdanetz
- Department of Plant Biology, Michigan State University, East Lansing, Michigan, 48824, USA
| | - Gian Maria Niccolò Benucci
- Department of Plant, Soil, & Microbial Sciences, Michigan State University, East Lansing, Michigan, 48824, USA.
| | - Natalie Vande Pol
- Department of Microbiology & Molecular Genetics, Michigan State University, East Lansing, Michigan, 48824, USA
| | - Gregory Bonito
- Department of Plant, Soil, & Microbial Sciences, Michigan State University, East Lansing, Michigan, 48824, USA
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589
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Walder F, Schlaeppi K, Wittwer R, Held AY, Vogelgsang S, van der Heijden MGA. Community Profiling of Fusarium in Combination with Other Plant-Associated Fungi in Different Crop Species Using SMRT Sequencing. FRONTIERS IN PLANT SCIENCE 2017; 8:2019. [PMID: 29234337 PMCID: PMC5712420 DOI: 10.3389/fpls.2017.02019] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/06/2017] [Accepted: 11/13/2017] [Indexed: 06/07/2023]
Abstract
Fusarium head blight, caused by fungi from the genus Fusarium, is one of the most harmful cereal diseases, resulting not only in severe yield losses but also in mycotoxin contaminated and health-threatening grains. Fusarium head blight is caused by a diverse set of species that have different host ranges, mycotoxin profiles and responses to agricultural practices. Thus, understanding the composition of Fusarium communities in the field is crucial for estimating their impact and also for the development of effective control measures. Up to now, most molecular tools that monitor Fusarium communities on plants are limited to certain species and do not distinguish other plant associated fungi. To close these gaps, we developed a sequencing-based community profiling methodology for crop-associated fungi with a focus on the genus Fusarium. By analyzing a 1600 bp long amplicon spanning the highly variable segments ITS and D1-D3 of the ribosomal operon by PacBio SMRT sequencing, we were able to robustly quantify Fusarium down to species level through clustering against reference sequences. The newly developed methodology was successfully validated in mock communities and provided similar results as the culture-based assessment of Fusarium communities by seed health tests in grain samples from different crop species. Finally, we exemplified the newly developed methodology in a field experiment with a wheat-maize crop sequence under different cover crop and tillage regimes. We analyzed wheat straw residues, cover crop shoots and maize grains and we could reveal that the cover crop hairy vetch (Vicia villosa) acts as a potent alternative host for Fusarium (OTU F.ave/tri) showing an eightfold higher relative abundance compared with other cover crop treatments. Moreover, as the newly developed methodology also allows to trace other crop-associated fungi, we found that vetch and green fallow hosted further fungal plant pathogens including Zymoseptoria tritici. Thus, besides their beneficial traits, cover crops can also entail phytopathological risks by acting as alternative hosts for Fusarium and other noxious plant pathogens. The newly developed sequencing based methodology is a powerful diagnostic tool to trace Fusarium in combination with other fungi associated to different crop species.
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Affiliation(s)
- Florian Walder
- Plant-Soil Interactions, Research Division Agroecology and Environment, Agroscope, Zurich, Switzerland
| | - Klaus Schlaeppi
- Plant-Soil Interactions, Research Division Agroecology and Environment, Agroscope, Zurich, Switzerland
| | - Raphaël Wittwer
- Plant-Soil Interactions, Research Division Agroecology and Environment, Agroscope, Zurich, Switzerland
| | - Alain Y. Held
- Plant-Soil Interactions, Research Division Agroecology and Environment, Agroscope, Zurich, Switzerland
| | - Susanne Vogelgsang
- Ecology of Noxious and Beneficial Organisms, Research Division Plant Protection, Agroscope, Zurich, Switzerland
| | - Marcel G. A. van der Heijden
- Plant-Soil Interactions, Research Division Agroecology and Environment, Agroscope, Zurich, Switzerland
- Department of Evolutionary Biology and Environmental Studies, University of Zürich, Zurich, Switzerland
- Plant-Microbe Interactions, Institute of Environmental Biology, Faculty of Science, Utrecht University, Utrecht, Netherlands
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590
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Sapp M, Ploch S, Fiore-Donno AM, Bonkowski M, Rose LE. Protists are an integral part of the Arabidopsis thaliana
microbiome. Environ Microbiol 2017; 20:30-43. [DOI: 10.1111/1462-2920.13941] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Revised: 09/19/2017] [Accepted: 09/21/2017] [Indexed: 11/29/2022]
Affiliation(s)
- Melanie Sapp
- Institute of Population Genetics, Universitätstrasse 1; Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine University; Universitätstrasse 40225 Düsseldorf Germany
- Institute of Zoology, Department of Terrestrial Ecology, Zülpicher Str 47b; Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne; Zülpicher Strasse 50674 Köln Germany
| | - Sebastian Ploch
- Institute of Population Genetics, Universitätstrasse 1; Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine University; Universitätstrasse 40225 Düsseldorf Germany
- Biodiversity and Climate Research Centre, Senckenberg Gesellschaft für Naturforschung, Senckenberganlage 25; 60325 Frankfurt am Main Germany
| | - Anna M. Fiore-Donno
- Institute of Zoology, Department of Terrestrial Ecology, Zülpicher Str 47b; Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne; Zülpicher Strasse 50674 Köln Germany
| | - Michael Bonkowski
- Institute of Zoology, Department of Terrestrial Ecology, Zülpicher Str 47b; Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne; Zülpicher Strasse 50674 Köln Germany
| | - Laura E. Rose
- Institute of Population Genetics, Universitätstrasse 1; Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine University; Universitätstrasse 40225 Düsseldorf Germany
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591
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Chong J, Xia J. Computational Approaches for Integrative Analysis of the Metabolome and Microbiome. Metabolites 2017; 7:E62. [PMID: 29156542 PMCID: PMC5746742 DOI: 10.3390/metabo7040062] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Revised: 11/14/2017] [Accepted: 11/16/2017] [Indexed: 12/31/2022] Open
Abstract
The study of the microbiome, the totality of all microbes inhabiting the host or an environmental niche, has experienced exponential growth over the past few years. The microbiome contributes functional genes and metabolites, and is an important factor for maintaining health. In this context, metabolomics is increasingly applied to complement sequencing-based approaches (marker genes or shotgun metagenomics) to enable resolution of microbiome-conferred functionalities associated with health. However, analyzing the resulting multi-omics data remains a significant challenge in current microbiome studies. In this review, we provide an overview of different computational approaches that have been used in recent years for integrative analysis of metabolome and microbiome data, ranging from statistical correlation analysis to metabolic network-based modeling approaches. Throughout the process, we strive to present a unified conceptual framework for multi-omics integration and interpretation, as well as point out potential future directions.
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Affiliation(s)
- Jasmine Chong
- Institute of Parasitology, McGill University, Montreal, QC H3A 0G4, Canada.
| | - Jianguo Xia
- Institute of Parasitology, McGill University, Montreal, QC H3A 0G4, Canada.
- Department of Animal Science, McGill University, Montreal, QC H3A 0G4, Canada.
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592
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Gouda S, Kerry RG, Das G, Paramithiotis S, Shin HS, Patra JK. Revitalization of plant growth promoting rhizobacteria for sustainable development in agriculture. Microbiol Res 2017; 206:131-140. [PMID: 29146250 DOI: 10.1016/j.micres.2017.08.016] [Citation(s) in RCA: 331] [Impact Index Per Article: 47.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Revised: 07/20/2017] [Accepted: 08/05/2017] [Indexed: 01/10/2023]
Abstract
The progression of life in all forms is not only dependent on agricultural and food security but also on the soil characteristics. The dynamic nature of soil is a direct manifestation of soil microbes, bio-mineralization, and synergistic co-evolution with plants. With the increase in world's population the demand for agriculture yield has increased tremendously and thereby leading to large scale production of chemical fertilizers. Since the use of fertilizers and pesticides in the agricultural fields have caused degradation of soil quality and fertility, thus the expansion of agricultural land with fertile soil is near impossible, hence researchers and scientists have sifted their attention for a safer and productive means of agricultural practices. Plant growth promoting rhizobacteria (PGPR) has been functioning as a co-evolution between plants and microbes showing antagonistic and synergistic interactions with microorganisms and the soil. Microbial revitalization using plant growth promoters had been achieved through direct and indirect approaches like bio-fertilization, invigorating root growth, rhizoremediation, disease resistance etc. Although, there are a wide variety of PGPR and its allies, their role and usages for sustainable agriculture remains controversial and restricted. There is also variability in the performance of PGPR that may be due to various environmental factors that might affect their growth and proliferation in the plants. These gaps and limitations can be addressed through use of modern approaches and techniques such as nano-encapsulation and micro-encapsulation along with exploring multidisciplinary research that combines applications in biotechnology, nanotechnology, agro biotechnology, chemical engineering and material science and bringing together different ecological and functional biological approaches to provide new formulations and opportunities with immense potential.
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Affiliation(s)
- Sushanto Gouda
- Amity Institute of Wildlife Science, Noida 201303, Uttar Pradesh, India
| | - Rout George Kerry
- Department of Biotechnology, AMIT College, Khurda 752057, Odisha, India
| | - Gitishree Das
- Research Institute of Biotechnology & Medical Converged Science, Dongguk University-Seoul, Ilsandong-gu, Gyeonggi-do 10326, Republic of Korea
| | - Spiros Paramithiotis
- Department of Food Science and Human Nutrition, Agricultural University of Athens, Athens, Greece
| | - Han-Seung Shin
- Department of Food Science and Biotechnology, Dongguk University, Ilsandong-gu, Goyang, Gyeonggi-do 10326, Republic of Korea
| | - Jayanta Kumar Patra
- Research Institute of Biotechnology & Medical Converged Science, Dongguk University-Seoul, Ilsandong-gu, Gyeonggi-do 10326, Republic of Korea.
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593
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Koskella B, Hall LJ, Metcalf CJE. The microbiome beyond the horizon of ecological and evolutionary theory. Nat Ecol Evol 2017; 1:1606-1615. [DOI: 10.1038/s41559-017-0340-2] [Citation(s) in RCA: 167] [Impact Index Per Article: 23.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Accepted: 09/07/2017] [Indexed: 01/16/2023]
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594
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High-Fat Diet Changes Fungal Microbiomes and Interkingdom Relationships in the Murine Gut. mSphere 2017; 2:mSphere00351-17. [PMID: 29034327 PMCID: PMC5636226 DOI: 10.1128/msphere.00351-17] [Citation(s) in RCA: 78] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Accepted: 09/22/2017] [Indexed: 02/07/2023] Open
Abstract
Recent research shows that gut microbes are involved in the development of obesity, a growing health problem in developed countries that is linked to increased risk for cardiovascular disease. However, studies showing links between microbes and metabolism have been limited to the analysis of bacteria and have ignored the potential contribution of fungi in metabolic health. This study provides evidence that ingestion of a high-fat diet is associated with changes to the fungal (and bacterial) microbiome in a mouse model. In addition, we find that interkingdom structural and functional relationships exist between fungi and bacteria within the gut and that these are perturbed by high-fat diet. Dietary fat intake and shifts in gut bacterial community composition are associated with the development of obesity. To date, characterization of microbiota in lean versus obese subjects has been dominated by studies of gut bacteria. Fungi, recently shown to affect gut inflammation, have received little study for their role in obesity. We sought to determine the effects of high-fat diet on fungal and bacterial community structures in a mouse model using the internal transcribed spacer region 2 (ITS2) of fungal ribosomal DNA (rDNA) and the 16S rRNA genes of bacteria. Mice fed a high-fat diet had significantly different abundances of 19 bacterial and 6 fungal taxa than did mice fed standard chow, with high-fat diet causing similar magnitudes of change in overall fungal and bacterial microbiome structures. We observed strong and complex diet-specific coabundance relationships between intra- and interkingdom microbial pairs and dramatic reductions in the number of coabundance correlations in mice fed a high-fat diet compared to those fed standard chow. Furthermore, predicted microbiome functional modules related to metabolism were significantly less abundant in high-fat-diet-fed than in standard-chow-fed mice. These results suggest a role for fungi and interkingdom interactions in the association between gut microbiomes and obesity. IMPORTANCE Recent research shows that gut microbes are involved in the development of obesity, a growing health problem in developed countries that is linked to increased risk for cardiovascular disease. However, studies showing links between microbes and metabolism have been limited to the analysis of bacteria and have ignored the potential contribution of fungi in metabolic health. This study provides evidence that ingestion of a high-fat diet is associated with changes to the fungal (and bacterial) microbiome in a mouse model. In addition, we find that interkingdom structural and functional relationships exist between fungi and bacteria within the gut and that these are perturbed by high-fat diet.
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595
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Hannula SE, Morriën E, de Hollander M, van der Putten WH, van Veen JA, de Boer W. Shifts in rhizosphere fungal community during secondary succession following abandonment from agriculture. THE ISME JOURNAL 2017; 11:2294-2304. [PMID: 28585935 PMCID: PMC5607372 DOI: 10.1038/ismej.2017.90] [Citation(s) in RCA: 91] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Revised: 04/20/2017] [Accepted: 04/28/2017] [Indexed: 12/14/2022]
Abstract
Activities of rhizosphere microbes are key to the functioning of terrestrial ecosystems. It is commonly believed that bacteria are the major consumers of root exudates and that the role of fungi in the rhizosphere is mostly limited to plant-associated taxa, such as mycorrhizal fungi, pathogens and endophytes, whereas less is known about the role of saprotrophs. In order to test the hypothesis that the role of saprotrophic fungi in rhizosphere processes increases with increased time after abandonment from agriculture, we determined the composition of fungi that are active in the rhizosphere along a chronosequence of ex-arable fields in the Netherlands. Intact soil cores were collected from nine fields that represent three stages of land abandonment and pulse labeled with 13CO2. The fungal contribution to metabolization of plant-derived carbon was evaluated using phospholipid analysis combined with stable isotope probing (SIP), whereas fungal diversity was analyzed using DNA-SIP combined with 454-sequencing. We show that in recently abandoned fields most of the root-derived 13C was taken up by bacteria but that in long-term abandoned fields most of the root-derived 13C was found in fungal biomass. Furthermore, the composition of the active functional fungal community changed from one composed of fast-growing and pathogenic fungal species to one consisting of beneficial and slower-growing fungal species, which may have essential consequences for the carbon flow through the soil food web and consequently nutrient cycling and plant succession.
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Affiliation(s)
- S Emilia Hannula
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
| | - Elly Morriën
- Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
- Institute for Biodiversity and Ecosystem Dynamics, Department of Ecosytem and Landscape Dynamics (IBED-ELD), University of Amsterdam, Amsterdam, The Netherlands
| | - Mattias de Hollander
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
| | - Wim H van der Putten
- Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
- Department of Nematology, Wageningen University & Research, Wageningen, The Netherlands
| | - Johannes A van Veen
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
- Insititute of Biology, Leiden University, Leiden, The Netherlands
| | - Wietse de Boer
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
- Department of Soil Quality, Wageningen University & Research, Wageningen, The Netherlands
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596
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Passari AK, Mishra VK, Singh G, Singh P, Kumar B, Gupta VK, Sarma RK, Saikia R, Donovan AO, Singh BP. Insights into the functionality of endophytic actinobacteria with a focus on their biosynthetic potential and secondary metabolites production. Sci Rep 2017; 7:11809. [PMID: 28924162 PMCID: PMC5603540 DOI: 10.1038/s41598-017-12235-4] [Citation(s) in RCA: 99] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Accepted: 09/06/2017] [Indexed: 12/20/2022] Open
Abstract
Endophytic actinobacteria play an important role in growth promotion and development of host plant by producing enormous quantities of novel bioactive natural products. In the present investigation, 169 endophytic actinobacteria were isolated from endospheric tissues of Rhynchotoechum ellipticum. Based on their antimicrobial potential, 81 strains were identified by 16rRNA gene analysis, which were taxonomically grouped into 15 genera. All identified strains were screened for their plant growth promoting attributes and, for the presence of modular polyketide synthases (PKSI, PKSII and nonribosomal peptide synthetase (NRPS) gene clusters to correlate the biosynthetic genes with their functional properties. Expression studies and antioxidant potential for four representative strains were evaluated using qRT-PCR and DPPH assay respectively. Additionally, six antibiotics (erythromycin, ketoconazole, fluconazole, chloramphenicol, rifampicin and miconazole) and nine phenolic compounds (catechin, kaempferol, chebulagic acid, chlorogenic acid, Asiatic acid, ferulic acid, arjunic acid, gallic acid and boswellic acid) were detected and quantified using UHPLC-QqQLIT-MS/MS. Furthermore, three strains (BPSAC77, 121 and 101) showed the presence of the anticancerous compound paclitaxel which was reported for the first time from endophytic actinobacteria. This study provides a holistic picture, that endophytic actinobacteria are rich bacterial resource for bioactive natural products, which has a great prospective in agriculture and pharmaceutical industries.
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Affiliation(s)
- Ajit Kumar Passari
- Molecular Microbiology and Systematics Laboratory, Department of Biotechnology, Aizawl, Mizoram University, Mizoram, 796004, India
| | - Vineet Kumar Mishra
- Molecular Microbiology and Systematics Laboratory, Department of Biotechnology, Aizawl, Mizoram University, Mizoram, 796004, India
| | - Garima Singh
- Molecular Microbiology and Systematics Laboratory, Department of Biotechnology, Aizawl, Mizoram University, Mizoram, 796004, India
| | - Pratibha Singh
- SAIF, CSIR-Central Drug Research Institute (CSIR-CDRI), Lucknow, 226012, India
| | - Brijesh Kumar
- SAIF, CSIR-Central Drug Research Institute (CSIR-CDRI), Lucknow, 226012, India
| | - Vijai Kumar Gupta
- Department of Chemistry and Biotechnology, ERA Chair of Green Chemistry, Tallinn University of Technology, 12618, Tallinn, Estonia
| | | | - Ratul Saikia
- Biotechnology Division, CSIR-NEIST, Jorhat, Assam, 785006, India
| | - Anthonia O' Donovan
- Applied Biology and Biopharmaceutical Science, School of Science & Computing, Galway-Mayo Institute of Technology, Galway, Ireland
| | - Bhim Pratap Singh
- Molecular Microbiology and Systematics Laboratory, Department of Biotechnology, Aizawl, Mizoram University, Mizoram, 796004, India.
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597
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Rybakova D, Mancinelli R, Wikström M, Birch-Jensen AS, Postma J, Ehlers RU, Goertz S, Berg G. The structure of the Brassica napus seed microbiome is cultivar-dependent and affects the interactions of symbionts and pathogens. MICROBIOME 2017; 5:104. [PMID: 28859671 PMCID: PMC5580328 DOI: 10.1186/s40168-017-0310-6] [Citation(s) in RCA: 80] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Accepted: 07/18/2017] [Indexed: 05/18/2023]
Abstract
BACKGROUND Although the plant microbiome is crucial for plant health, little is known about the significance of the seed microbiome. Here, we studied indigenous bacterial communities associated with the seeds in different cultivars of oilseed rape and their interactions with symbiotic and pathogenic microorganisms. RESULTS We found a high bacterial diversity expressed by tight bacterial co-occurrence networks within the rape seed microbiome, as identified by llumina MiSeq amplicon sequencing. In total, 8362 operational taxonomic units (OTUs) of 40 bacterial phyla with a predominance of Proteobacteria (56%) were found. The three cultivars that were analyzed shared only one third of the OTUs. The shared core of OTUs consisted mainly of Alphaproteobacteria (33%). Each cultivar was characterized by having its own unique bacterial structure, diversity, and proportion of unique microorganisms (25%). The cultivar with the lowest bacterial abundance, diversity, and the highest predicted bacterial metabolic activity rate contained the highest abundance of potential pathogens within the seed. This data corresponded with the observation that seedlings belonging to this cultivar responded more strongly to the seed treatments with bacterial inoculants than other cultivars. Cultivars containing higher indigenous diversity were characterized as having a higher colonization resistance against beneficial and pathogenic microorganisms. Our results were confirmed by microscopic images of the seed microbiota. CONCLUSIONS The structure of the seed microbiome is an important factor in the development of colonization resistance against pathogens. It also has a strong influence on the response of seedlings to biological seed treatments. These novel insights into seed microbiome structure will enable the development of next generation strategies combining both biocontrol and breeding approaches to address world agricultural challenges.
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Affiliation(s)
- Daria Rybakova
- Graz University of Technology, Institute of Environmental Biotechnology, Petersgasse 12, 8010, Graz, Austria
| | - Riccardo Mancinelli
- Graz University of Technology, Institute of Environmental Biotechnology, Petersgasse 12, 8010, Graz, Austria
- Department of Life Sciences, Università degli Studi di Trieste, Via L. Giorgeri, 34127, Trieste, Italy
| | | | | | - Joeke Postma
- Wageningen Plant Research, 6708 PB, Wageningen, Netherlands
| | - Ralf-Udo Ehlers
- E-nema GmbH, Klausdorfer Str. 28-36, 24223, Schwentinental, Germany
| | - Simon Goertz
- NPZ Innovation GmbH, Hohenlieth-Hof, 24363, Holtsee, Germany
| | - Gabriele Berg
- Graz University of Technology, Institute of Environmental Biotechnology, Petersgasse 12, 8010, Graz, Austria.
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598
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Pineda A, Kaplan I, Bezemer TM. Steering Soil Microbiomes to Suppress Aboveground Insect Pests. TRENDS IN PLANT SCIENCE 2017; 22:770-778. [PMID: 28757147 DOI: 10.1016/j.tplants.2017.07.002] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Revised: 06/30/2017] [Accepted: 07/04/2017] [Indexed: 05/18/2023]
Abstract
Soil-borne microbes affect aboveground herbivorous insects through a cascade of molecular and chemical changes in the plant, but knowledge of these microbe-plant-insect interactions is mostly limited to one or a few microbial strains. Yet, the soil microbial community comprises thousands of unique taxa interacting in complex networks, the so-called 'microbiome', which provides plants with multiple beneficial functions. There has been little exploration of the role and management of whole microbiomes in plant-insect interactions, calling for the integration of this complexity in aboveground-belowground research. Here, we propose holistic approaches to select soil microbiomes that can be used to protect plants from aboveground attackers.
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Affiliation(s)
- Ana Pineda
- Department of Terrestrial Ecology, NIOO-KNAW, Postbus 50, 6700 AB Wageningen, The Netherlands.
| | - Ian Kaplan
- Department of Entomology, Purdue University, 901 W. State Street, West Lafayette, IN 47907, USA
| | - T Martijn Bezemer
- Department of Terrestrial Ecology, NIOO-KNAW, Postbus 50, 6700 AB Wageningen, The Netherlands; Institute of Biology, Section Plant Ecology and Phytochemistry, Leiden University, PO Box 9505, 2300 RA Leiden, The Netherlands
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599
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Deines P, Lachnit T, Bosch TCG. Competing forces maintain theHydrametaorganism. Immunol Rev 2017; 279:123-136. [DOI: 10.1111/imr.12564] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Peter Deines
- Zoological Institute; Christian Albrechts University Kiel; Kiel Germany
| | - Tim Lachnit
- Zoological Institute; Christian Albrechts University Kiel; Kiel Germany
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600
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Khan Chowdhury MDE, Jeon J, Ok Rim S, Park YH, Kyu Lee S, Bae H. Composition, diversity and bioactivity of culturable bacterial endophytes in mountain-cultivated ginseng in Korea. Sci Rep 2017; 7:10098. [PMID: 28855721 PMCID: PMC5577135 DOI: 10.1038/s41598-017-10280-7] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Accepted: 07/07/2017] [Indexed: 01/09/2023] Open
Abstract
Plants harbor diverse communities of bacterial species in their internal compartments. Here we isolated and identified bacterial endophytes from mountain-cultivated ginseng (MCG, Panax ginseng Meyer) to make working collection of endophytes and exploit their potentially beneficial properties toward plants and human being. A total of 1,886 bacteria were isolated from root, stem and leaf of MCGs grown in 24 different sites across the nation, using culture-dependent approach. Sequencing of 16S rDNA allowed us to classify them into 252 distinct groups. Taxonomic binning of them resulted in 117 operational taxonomic units (OTUs). Analysis of diversity indices across sampling sites and tissues suggested that composition of bacterial endophyte community within ginseng could differ substantially from one site to the next as well as from one host compartment to another. Assessment of 252 bacterial isolates for their beneficial traits to host plants showed that some bacteria possesses the ability to promote plant growth and produce ß-glucosidase, indicating their potential roles in plant growth promotion and bio-transformation. Taken together, our work provides not only valuable resources for utilization of bacterial endophytes in ginseng but also insights into bacterial communities inside a plant of medicinal importance.
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Affiliation(s)
- M D Emran Khan Chowdhury
- Department of Biotechnology, Yeungnam University, Gyeongsan, Gyeongbook, 38541, Republic of Korea
| | - Junhyun Jeon
- Department of Biotechnology, Yeungnam University, Gyeongsan, Gyeongbook, 38541, Republic of Korea
| | - Soon Ok Rim
- Department of Biotechnology, Yeungnam University, Gyeongsan, Gyeongbook, 38541, Republic of Korea
| | - Young-Hwan Park
- Department of Biotechnology, Yeungnam University, Gyeongsan, Gyeongbook, 38541, Republic of Korea
| | - Seung Kyu Lee
- Division of Forest Diseases & Insect Pests, Korea Forest Research Institute, Seoul, 02455, Republic of Korea
| | - Hanhong Bae
- Department of Biotechnology, Yeungnam University, Gyeongsan, Gyeongbook, 38541, Republic of Korea.
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