1
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Fujita H, Yoshida S, Suzuki K, Toju H. Soil prokaryotic and fungal biome structures associated with crop disease status across the Japan Archipelago. mSphere 2024; 9:e0080323. [PMID: 38567970 PMCID: PMC11036807 DOI: 10.1128/msphere.00803-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Accepted: 02/29/2024] [Indexed: 04/24/2024] Open
Abstract
Archaea, bacteria, and fungi in the soil are increasingly recognized as determinants of agricultural productivity and sustainability. A crucial step for exploring soil microbiomes with important ecosystem functions is to perform statistical analyses on the potential relationship between microbiome structure and functions based on comparisons of hundreds or thousands of environmental samples collected across broad geographic ranges. In this study, we integrated agricultural field metadata with microbial community analyses by targeting 2,903 bulk soil samples collected along a latitudinal gradient from cool-temperate to subtropical regions in Japan (26.1-42.8 °N). The data involving 632 archaeal, 26,868 bacterial, and 4,889 fungal operational taxonomic units detected across the fields of 19 crop plant species allowed us to conduct statistical analyses (permutational analyses of variance, generalized linear mixed models, randomization analyses, and network analyses) on the relationship among edaphic factors, microbiome compositions, and crop disease prevalence. We then examined whether the diverse microbes form species sets varying in potential ecological impacts on crop plants. A network analysis suggested that the observed prokaryotes and fungi were classified into several species sets (network modules), which differed substantially in association with crop disease prevalence. Within the network of microbe-to-microbe coexistence, ecologically diverse microbes, such as an ammonium-oxidizing archaeon, an antibiotics-producing bacterium, and a potentially mycoparasitic fungus, were inferred to play key roles in shifts between crop-disease-promotive and crop-disease-suppressive states of soil microbiomes. The bird's-eye view of soil microbiome structure will provide a basis for designing and managing agroecosystems with high disease-suppressive functions.IMPORTANCEUnderstanding how microbiome structure and functions are organized in soil ecosystems is one of the major challenges in both basic ecology and applied microbiology. Given the ongoing worldwide degradation of agroecosystems, building frameworks for exploring structural diversity and functional profiles of soil microbiomes is an essential task. Our study provides an overview of cropland microbiome states in light of potential crop-disease-suppressive functions. The large data set allowed us to explore highly functional species sets that may be stably managed in agroecosystems. Furthermore, an analysis of network architecture highlighted species that are potentially used to cause shifts from disease-prevalent states of agroecosystems to disease-suppressive states. By extending the approach of comparative analyses toward broader geographic ranges and diverse agricultural practices, agroecosystem with maximized biological functions will be further explored.
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Affiliation(s)
- Hiroaki Fujita
- Center for Ecological Research, Kyoto University, Otsu, Shiga, Japan
| | - Shigenobu Yoshida
- Institute for Plant Protection, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, Japan
| | - Kenta Suzuki
- Integrated Bioresource Information Division, BioResource Research Center, Tsukuba, Ibaraki, Japan
| | - Hirokazu Toju
- Center for Ecological Research, Kyoto University, Otsu, Shiga, Japan
- Center for Living Systems Information Science (CeLiSIS), Graduate School of Biostudies, Kyoto University, Kyoto, Japan
- Laboratory of Ecosystems and Coevolution, Graduate School of Biostudies, Kyoto University, Kyoto, Japan
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2
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Ballot A, Dore J, Rey M, Meiffren G, Langin T, Joly P, Dreux-Zigha A, Taibi A, Prigent-Combaret C. Dimethylpolysulfides production as the major mechanism behind wheat fungal pathogen biocontrol, by Arthrobacter and Microbacterium actinomycetes. Microbiol Spectr 2023; 11:e0529222. [PMID: 37800942 PMCID: PMC10715130 DOI: 10.1128/spectrum.05292-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 08/07/2023] [Indexed: 10/07/2023] Open
Abstract
IMPORTANCE As the management of wheat fungal diseases becomes increasingly challenging, the use of bacterial agents with biocontrol potential against the two major wheat phytopathogens, Fusarium graminearum and Zymoseptoria tritici, may prove to be an interesting alternative to conventional pest management. Here, we have shown that dimethylpolysulfide volatiles are ubiquitously and predominantly produced by wheat-associated Microbacterium and Arthrobacter actinomycetes, displaying antifungal activity against both pathogens. By limiting pathogen growth and DON virulence factor production, the use of such DMPS-producing strains as soil biocontrol inoculants could limit the supply of pathogen inocula in soil and plant residues, providing an attractive alternative to dimethyldisulfide fumigant, which has many non-targeted toxicities. Notably, this study demonstrates the importance of bacterial volatile organic compound uptake by inhibited F. graminearum, providing new insights for the study of volatiles-mediated toxicity mechanisms within bacteria-fungus signaling crosstalk.
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Affiliation(s)
- Aline Ballot
- Laboratoire Ecologie Microbienne UMR 5557, Université Lyon 1, Villeurbanne, France
| | - Jeanne Dore
- Laboratoire Ecologie Microbienne UMR 5557, Université Lyon 1, Villeurbanne, France
| | - Marjolaine Rey
- Laboratoire Ecologie Microbienne UMR 5557, Université Lyon 1, Villeurbanne, France
| | - Guillaume Meiffren
- Laboratoire Ecologie Microbienne UMR 5557, Université Lyon 1, Villeurbanne, France
| | - Thierry Langin
- Université Clermont Auvergne, INRAE, GDEC, Clermont-Ferrand, France
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3
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Theologidis I, Karamitros T, Vichou AE, Kizis D. Nanopore-Sequencing Metabarcoding for Identification of Phytopathogenic and Endophytic Fungi in Olive ( Olea europaea) Twigs. J Fungi (Basel) 2023; 9:1119. [PMID: 37998924 PMCID: PMC10672464 DOI: 10.3390/jof9111119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 11/13/2023] [Accepted: 11/16/2023] [Indexed: 11/25/2023] Open
Abstract
Metabarcoding approaches for the identification of plant disease pathogens and characterization of plant microbial populations constitute a rapidly evolving research field. Fungal plant diseases are of major phytopathological concern; thus, the development of metabarcoding approaches for the detection of phytopathogenic fungi is becoming increasingly imperative in the context of plant disease prognosis. We developed a multiplex metabarcoding method for the identification of fungal phytopathogens and endophytes in olive young shoots, using the MinION sequencing platform (Oxford Nanopore Technologies). Selected fungal-specific primers were used to amplify three different genomic DNA loci (ITS, beta-tubulin, and 28S LSU) originating from olive twigs. A multiplex metabarcoding approach was initially evaluated using healthy olive twigs, and further assessed with naturally infected olive twig samples. Bioinformatic analysis of basecalled reads was carried out using MinKNOW, BLAST+ and R programming, and results were also evaluated using the BugSeq cloud platform. Data analysis highlighted the approaches based on ITS and their combination with beta-tubulin as the most informative ones according to diversity estimations. Subsequent implementation of the method on symptomatic samples identified major olive pathogens and endophytes including genera such as Cladosporium, Didymosphaeria, Paraconiothyrium, Penicillium, Phoma, Verticillium, and others.
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Affiliation(s)
- Ioannis Theologidis
- Laboratory of Toxicological Control of Pesticides, Scientific Directorate of Pesticides' Control & Phytopharmacy, Benaki Phytopathological Institute, 8 St. Delta Street, 14561 Athens, Attica, Greece
| | - Timokratis Karamitros
- Bioinformatics and Applied Genomics Unit, Department of Microbiology, Hellenic Pasteur Institute, 127 Vasilissis Sofias Avenue, 11521 Athens, Attica, Greece
| | - Aikaterini-Eleni Vichou
- Laboratory of Mycology, Scientific Directorate of Phytopathology, Benaki Phytopathological Institute, 8 St. Delta Street, 14561 Athens, Attica, Greece
| | - Dimosthenis Kizis
- Laboratory of Mycology, Scientific Directorate of Phytopathology, Benaki Phytopathological Institute, 8 St. Delta Street, 14561 Athens, Attica, Greece
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4
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Bernasconi A, Lorrain C, Flury P, Alassimone J, McDonald BA, Sánchez-Vallet A. Virulent strains of Zymoseptoria tritici suppress the host immune response and facilitate the success of avirulent strains in mixed infections. PLoS Pathog 2023; 19:e1011767. [PMID: 37972205 PMCID: PMC10721197 DOI: 10.1371/journal.ppat.1011767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 12/14/2023] [Accepted: 10/19/2023] [Indexed: 11/19/2023] Open
Abstract
Plants interact with a plethora of pathogenic microorganisms in nature. Pathogen-plant interaction experiments focus mainly on single-strain infections, typically ignoring the complexity of multi-strain infections even though mixed infections are common and critical for the infection outcome. The wheat pathogen Zymoseptoria tritici forms highly diverse fungal populations in which several pathogen strains often colonize the same leaf. Despite the importance of mixed infections, the mechanisms governing interactions between a mixture of pathogen strains within a plant host remain largely unexplored. Here we demonstrate that avirulent pathogen strains benefit from being in mixed infections with virulent strains. We show that virulent strains suppress the wheat immune response, allowing avirulent strains to colonize the apoplast and to reproduce. Our experiments indicate that virulent strains in mixed infections can suppress the plant immune system, probably facilitating the persistence of avirulent pathogen strains in fields planted with resistant host plants.
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Affiliation(s)
- Alessio Bernasconi
- Plant Pathology, Institute of Integrative Biology, ETH Zürich, Zürich, Switzerland
| | - Cécile Lorrain
- Plant Pathology, Institute of Integrative Biology, ETH Zürich, Zürich, Switzerland
| | - Priska Flury
- Plant Pathology, Institute of Integrative Biology, ETH Zürich, Zürich, Switzerland
| | - Julien Alassimone
- Plant Pathology, Institute of Integrative Biology, ETH Zürich, Zürich, Switzerland
| | - Bruce A. McDonald
- Plant Pathology, Institute of Integrative Biology, ETH Zürich, Zürich, Switzerland
| | - Andrea Sánchez-Vallet
- Plant Pathology, Institute of Integrative Biology, ETH Zürich, Zürich, Switzerland
- Centro de Biotecnología y Genómica de Plantas (CBGP/Universidad Politécnica de Madrid-Instituto Nacional de Investigación Agraria y Alimentaria/Centro Superior de Investigaciones Científicas (INIA/CSIC), Campus de Montegancedo, Pozuelo de Alarcón (Madrid) Spain
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5
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Dundore-Arias JP, Michalska-Smith M, Millican M, Kinkel LL. More Than the Sum of Its Parts: Unlocking the Power of Network Structure for Understanding Organization and Function in Microbiomes. ANNUAL REVIEW OF PHYTOPATHOLOGY 2023; 61:403-423. [PMID: 37217203 DOI: 10.1146/annurev-phyto-021021-041457] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Plant and soil microbiomes are integral to the health and productivity of plants and ecosystems, yet researchers struggle to identify microbiome characteristics important for providing beneficial outcomes. Network analysis offers a shift in analytical framework beyond "who is present" to the organization or patterns of coexistence between microbes within the microbiome. Because microbial phenotypes are often significantly impacted by coexisting populations, patterns of coexistence within microbiomes are likely to be especially important in predicting functional outcomes. Here, we provide an overview of the how and why of network analysis in microbiome research, highlighting the ways in which network analyses have provided novel insights into microbiome organization and functional capacities, the diverse network roles of different microbial populations, and the eco-evolutionary dynamics of plant and soil microbiomes.
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Affiliation(s)
- J P Dundore-Arias
- Department of Biology and Chemistry, California State University, Monterey Bay, Seaside, California, USA
| | - M Michalska-Smith
- Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota, USA;
- Department of Ecology, Evolution, and Behavior, University of Minnesota, St. Paul, Minnesota, USA
| | | | - L L Kinkel
- Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota, USA;
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6
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Sapkota R, Jørgensen LN, Boeglin L, Nicolaisen M. Fungal Communities of Spring Barley from Seedling Emergence to Harvest During a Severe Puccinia hordei Epidemic. MICROBIAL ECOLOGY 2023; 85:617-627. [PMID: 35229200 DOI: 10.1007/s00248-022-01985-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 02/18/2022] [Indexed: 06/14/2023]
Abstract
All plant tissues from leaves, stems, and roots are hosting a wide diversity of fungal species. Our understanding of the assembly of this diversity of fungi during the plant growth cycle is limited. Here, we characterized the mycobiome of three spring barley cultivars grown in Zealand, Denmark, at weekly intervals during a growth season from seedling emergence to senescence and seed maturity. A notable proportion of members of the fungal communities were shared among different plant organs, but community dynamics were tissue-specific. A severe attack of Puccinia hordei occurring during the vegetative stage had profound effects on the mycobiome, and P. hordei biomass displaced that of other taxa. Plant tissue type was the most important factor determining the mycobiome, but also plant age was contributing significantly. Using a random forest model, we found that specific members of the mycobiome were responding differently to plant age, for instance, Olpidium and Articulospora in roots, Dioszegia and Sporobolomyces in leaves, Pyrenophora in stems, and Epicoccum in heads. A co-occurrence network analysis revealed complex interactions among fungal OTUs, and network connectivity was changing as per plant growth stage and plant tissue type. This study contributes to the understanding of assembly of fungal communities in cereals by providing a detailed description of fungal communities associated with barley. This knowledge will be vital for microbiome assisted plant health management and our study will serve as an important baseline for future efforts to harness microbiota in cereal health.
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Affiliation(s)
- Rumakanta Sapkota
- Department of Agroecology, Faculty of Technical Sciences, Aarhus University, Forsøgsvej 1, 4200, Slagelse, Denmark
- Department of Environmental Science, Faculty of Technical Sciences, Aarhus University, Frederiksborgvej 399, 4000, Roskilde, Denmark
| | - Lise Nistrup Jørgensen
- Department of Agroecology, Faculty of Technical Sciences, Aarhus University, Forsøgsvej 1, 4200, Slagelse, Denmark
| | - Laure Boeglin
- Department of Agroecology, Faculty of Technical Sciences, Aarhus University, Forsøgsvej 1, 4200, Slagelse, Denmark
| | - Mogens Nicolaisen
- Department of Agroecology, Faculty of Technical Sciences, Aarhus University, Forsøgsvej 1, 4200, Slagelse, Denmark.
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7
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Plant litter strengthens positive biodiversity-ecosystem functioning relationships over time. Trends Ecol Evol 2023; 38:473-484. [PMID: 36599737 DOI: 10.1016/j.tree.2022.12.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 12/09/2022] [Accepted: 12/12/2022] [Indexed: 01/04/2023]
Abstract
Plant biodiversity-productivity relationships become stronger over time in grasslands, forests, and agroecosystems. Plant shoot and root litter is important in mediating these positive relationships, yet the functional role of plant litter remains overlooked in long-term experiments. We propose that plant litter strengthens biodiversity-ecosystem functioning relationships over time in four ways by providing decomposing detritus that releases nitrogen (N) over time for uptake by existing and succeeding plants, enhancing overall soil fertility, changing soil community composition, and reducing the impact of residue-borne pathogens and pests. We bring new insights into how diversity-productivity relationships may change over time and suggest that the diversification of crop residue retention through increased residue diversity from plant mixtures will improve the sustainability of food production systems.
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8
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Xiong C, Lu Y. Microbiomes in agroecosystem: Diversity, function and assembly mechanisms. ENVIRONMENTAL MICROBIOLOGY REPORTS 2022; 14:833-849. [PMID: 36184075 DOI: 10.1111/1758-2229.13126] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Accepted: 09/08/2022] [Indexed: 06/16/2023]
Abstract
Soils are a main repository of biodiversity harbouring immense diversity of microbial species that plays a central role in fundamental ecological processes and acts as the seed bank for emergence of the plant microbiome in cropland ecosystems. Crop-associated microbiomes play an important role in shaping plant performance, which includes but not limited to nutrient uptake, disease resistance, and abiotic stress tolerance. Although our understanding of structure and function of soil and plant microbiomes has been rapidly advancing, most of our knowledge comes from ecosystems in natural environment. In this review, we present an overview of the current knowledge of diversity and function of microbial communities along the soil-plant continuum in agroecosystems. To characterize the ecological mechanisms for community assembly of soil and crop microbiomes, we explore how crop host and environmental factors such as plant species and developmental stage, pathogen invasion, and land management shape microbiome structure, microbial co-occurrence patterns, and crop-microbiome interactions. Particularly, the relative importance of deterministic and stochastic processes in microbial community assembly is illustrated under different environmental conditions, and potential sources and keystone taxa of the crop microbiome are described. Finally, we highlight a few important questions and perspectives in future crop microbiome research.
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Affiliation(s)
- Chao Xiong
- College of Urban and Environmental Sciences, Peking University, Beijing, People's Republic of China
| | - Yahai Lu
- College of Urban and Environmental Sciences, Peking University, Beijing, People's Republic of China
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9
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Gökdemir FŞ, İşeri ÖD, Sharma A, Achar PN, Eyidoğan F. Metagenomics Next Generation Sequencing (mNGS): An Exciting Tool for Early and Accurate Diagnostic of Fungal Pathogens in Plants. J Fungi (Basel) 2022; 8:1195. [PMID: 36422016 PMCID: PMC9699264 DOI: 10.3390/jof8111195] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 11/08/2022] [Accepted: 11/10/2022] [Indexed: 09/19/2023] Open
Abstract
Crop output is directly impacted by infections, with fungi as the major plant pathogens, making accurate diagnosis of these threats crucial. Developing technology and multidisciplinary approaches are turning to genomic analyses in addition to traditional culture methods in diagnostics of fungal plant pathogens. The metagenomic next-generation sequencing (mNGS) method is preferred for genotyping identification of organisms, identification at the species level, illumination of metabolic pathways, and determination of microbiota. Moreover, the data obtained so far show that this new approach is promising as an emerging new trend in fungal disease detection. Another approach covered by mNGS technologies, known as metabarcoding, enables use of specific markers specific to a genetic region and allows for genotypic identification by facilitating the sequencing of certain regions. Although the core concept of mNGS remains constant across applications, the specific sequencing methods and bioinformatics tools used to analyze the data differ. In this review, we focus on how mNGS technology, including metabarcoding, is applied for detecting fungal pathogens and its promising developments for the future.
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Affiliation(s)
- Fatma Şeyma Gökdemir
- Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48824, USA
- Department of Molecular Biology and Genetics, Faculty of Science and Letters, Başkent University, Ankara 06790, Turkey
| | - Özlem Darcansoy İşeri
- Department of Molecular Biology and Genetics, Faculty of Science and Letters, Başkent University, Ankara 06790, Turkey
- Institute of Food, Agriculture and Livestock Development, Başkent University, Ankara 06790, Turkey
| | - Abhishek Sharma
- Amity Food and Agriculture Foundation, Amity University, Noida 201313, Uttar Pradesh, India
| | - Premila N. Achar
- Department of Molecular and Cellular Biology, Kennesaw State University, Kennesaw, GA 30144, USA
| | - Füsun Eyidoğan
- Department of Molecular Biology and Genetics, Faculty of Science and Letters, Başkent University, Ankara 06790, Turkey
- Institute of Food, Agriculture and Livestock Development, Başkent University, Ankara 06790, Turkey
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10
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Dynamic Fluctuation and Niche Differentiation of Fungal Pathogens Infecting Bell Pepper Plants. Appl Environ Microbiol 2022; 88:e0100322. [PMID: 36036572 PMCID: PMC9499033 DOI: 10.1128/aem.01003-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The plant microbiome is shaped by plant development and microbial interaction. Fungal pathogens infecting bell pepper plants may fluctuate across the growing seasons. Dynamic fluctuation of the microbiome and fungal pathogens in bell pepper plants is poorly understood, and the origin of fungal pathogens causing fruit rot and leaf wilt has been barely investigated. In this study, we used amplicon sequencing (i.e., 16S rRNA and internal transcribed spacer [ITS] sequencing) to explore the compositional variations of the microbiome in bell pepper plants and studied the fluctuation of fungal pathogens across the growing seasons. Co-occurrence network analysis was applied to track the origin and dissemination route of fungal pathogens that infected bell pepper plants. ITS and 16S rRNA sequencing analyses demonstrated that fungal pathogens infecting fruits and leaves probably belonged to the Penicillium, Cladosporium, Fusarium, and unclassified_Sclerotiniaceae genera rather than one specific genus. The dominant fungal pathogens were different, along with the development of bell pepper plants. Both plant development and fungal pathogens shaped microbial communities in bell pepper plants across the growing seasons. Fungal pathogens decreased species richness and diversity of fungal communities in fungus-infected fruit and leaf tissues but not the uninfected stem tissues. Bacterial metabolic functions of xenobiotics increased in fungus-infected leaves at a mature developmental stage. Competitive interaction was present between fungal and bacterial communities in leaves. Co-occurrence network analysis revealed that the origins of fungal pathogens included the greenhouse, packing house, and storage room. Niche differentiation of microbes was discovered among these locations. IMPORTANCE Bell peppers are widely consumed worldwide. Fungal pathogen infections of bell peppers lead to enormous economic loss. To control fungal pathogens and increase economic benefit, it is essential to investigate the shifting patterns of the microbiome and fungal pathogens in bell pepper plants across the growing seasons. In this study, bell pepper plant diseases observed in fruits and leaves were caused by different fungal pathogens. Fungal pathogens originated from the greenhouse, packing house, and storage room, and niche differentiation existed among microbes. This study improves the understanding of dynamic fluctuation and source of fungal pathogens infecting bell pepper plants in the farming system. It also facilitates precise management of fungal pathogens in the greenhouse.
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11
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New-Generation Sequencing Technology in Diagnosis of Fungal Plant Pathogens: A Dream Comes True? J Fungi (Basel) 2022; 8:jof8070737. [PMID: 35887492 PMCID: PMC9320658 DOI: 10.3390/jof8070737] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 07/01/2022] [Accepted: 07/11/2022] [Indexed: 02/01/2023] Open
Abstract
The fast and continued progress of high-throughput sequencing (HTS) and the drastic reduction of its costs have boosted new and unpredictable developments in the field of plant pathology. The cost of whole-genome sequencing, which, until few years ago, was prohibitive for many projects, is now so affordable that a new branch, phylogenomics, is being developed. Fungal taxonomy is being deeply influenced by genome comparison, too. It is now easier to discover new genes as potential targets for an accurate diagnosis of new or emerging pathogens, notably those of quarantine concern. Similarly, with the development of metabarcoding and metagenomics techniques, it is now possible to unravel complex diseases or answer crucial questions, such as "What's in my soil?", to a good approximation, including fungi, bacteria, nematodes, etc. The new technologies allow to redraw the approach for disease control strategies considering the pathogens within their environment and deciphering the complex interactions between microorganisms and the cultivated crops. This kind of analysis usually generates big data that need sophisticated bioinformatic tools (machine learning, artificial intelligence) for their management. Herein, examples of the use of new technologies for research in fungal diversity and diagnosis of some fungal pathogens are reported.
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12
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Nocardioides nematodiphilus sp. nov., isolated from rhizosphere of Arabidopsis thaliana. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005271] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
An actinobacterial strain, designated R-N-C8T, was isolated from the rhizosphere soil of Arabidopsis thaliana collected in Yunnan Province, south-west China. Based on the results of 16S rRNA gene sequence analysis, strain R-N-C8T had highest similarity to
Nocardioides terrae
CGMCC 1.7056T (96.5%),
Nocardioides opuntiae
KCTC 19804T (96.3%) and
Nocardioides currus
IB-3T (96.1%), and lower than 96.0 % similarity to other members of the genus
Nocardioides
. Phylogenetic trees based on 16S rRNA gene sequences indicated that strain R-N-C8T formed an isolated branch with
N. terrae
CGMCC 1.7056T and
N. opuntiae
KCTC 19804T. The polar lipids contained phosphatidylglycerol, diphosphatidylglycerol, one unidentified phosphoglycolipid and four unidentified phospholipids in the cellular membrane. The major fatty acids were identified as iso-C16 : 0, anteiso-C17 : 0, iso-C17 : 0, summed feature 9 (iso-C17 : 1 ω9c and/or C16 : 0 10-methyl) and iso-C15 : 0. The predominant respiratory quinone was MK-8(H4) and ll-diaminopimelic acid was the diagnostic diamino acid in the cell-wall peptidoglycan. The genomic DNA G+C content was 70.9 mol%. The orthologous average nucleotide identiy values between
N. terrae
CGMCC 1.7056T,
N. currus
IB-3T and strain R-N-C8T were 77.1 and 75.1 %, respectively. DNA–DNA hybridization values between
N. terrae
CGMCC 1.7056T,
N. currus
IB-3T and strain R-N-C8T were 20.7 and 19.9 % respectively. Data from phenotypic and genotypic analyses supported that strain R-N-C8T represents a new species of
Nocardioides
, for which the name Nocardioides nematodiphilus sp. nov. is proposed. The type strain is R-N-C8T (=CGMCC 1.18723T= KCTC 49528T).
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13
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Wahdan SFM, Hossen S, Tanunchai B, Sansupa C, Schädler M, Noll M, Dawoud TM, Wu YT, Buscot F, Purahong W. Life in the Wheat Litter: Effects of Future Climate on Microbiome and Function During the Early Phase of Decomposition. MICROBIAL ECOLOGY 2022; 84:90-105. [PMID: 34487212 PMCID: PMC9250916 DOI: 10.1007/s00248-021-01840-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 08/05/2021] [Indexed: 06/13/2023]
Abstract
Even though it is widely acknowledged that litter decomposition can be impacted by climate change, the functional roles of microbes involved in the decomposition and their answer to climate change are less understood. This study used a field experimental facility settled in Central Germany to analyze the effects of ambient vs. future climate that is expected in 50-80 years on mass loss and physicochemical parameters of wheat litter in agricultural cropland at the early phase of litter decomposition process. Additionally, the effects of climate change were assessed on microbial richness, community compositions, interactions, and their functions (production of extracellular enzymes), as well as litter physicochemical factors shaping their colonization. The initial physicochemical properties of wheat litter did not change between both climate conditions; however, future climate significantly accelerated litter mass loss as compared with ambient one. Using MiSeq Illumina sequencing, we found that future climate significantly increased fungal richness and altered fungal communities over time, while bacterial communities were more resistant in wheat residues. Changes on fungal richness and/or community composition corresponded to different physicochemical factors of litter under ambient (Ca2+, and pH) and future (C/N, N, P, K+, Ca2+, pH, and moisture) climate conditions. Moreover, highly correlative interactions between richness of bacteria and fungi were detected under future climate. Furthermore, the co-occurrence networks patterns among dominant microorganisms inhabiting wheat residues were strongly distinct between future and ambient climates. Activities of microbial β-glucosidase and N-acetylglucosaminidase in wheat litter were increased over time. Such increased enzymatic activities were coupled with a significant positive correlation between microbial (both bacteria and fungi) richness and community compositions with these two enzymatic activities only under future climate. Overall, we provide evidence that future climate significantly impacted the early phase of wheat litter decomposition through direct effects on fungal communities and through indirect effects on microbial interactions as well as corresponding enzyme production.
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Affiliation(s)
- Sara Fareed Mohamed Wahdan
- Department of Soil Ecology, UFZ-Helmholtz Centre for Environmental Research, Theodor-Lieser-Str. 4, 06120 Halle (Saale), Germany
- Botany Department, Faculty of Science, Suez Canal University, Ismailia, 41522 Egypt
- Botany and Microbiology Department, College of Science, King Saud University, P.O. Box 2455, Riyadh, 11451 Saudi Arabia
| | - Shakhawat Hossen
- Department of Soil Ecology, UFZ-Helmholtz Centre for Environmental Research, Theodor-Lieser-Str. 4, 06120 Halle (Saale), Germany
- Institute of Ecology and Evolution, Friedrich-Schiller-Universität Jena, Dornburger Str. 159, 07743 Jena, Germany
- Department of Applied Sciences, Institute for Bioanalysis, Coburg University of Applied Sciences and Arts, Coburg, Germany
| | - Benjawan Tanunchai
- Department of Soil Ecology, UFZ-Helmholtz Centre for Environmental Research, Theodor-Lieser-Str. 4, 06120 Halle (Saale), Germany
| | - Chakriya Sansupa
- Department of Soil Ecology, UFZ-Helmholtz Centre for Environmental Research, Theodor-Lieser-Str. 4, 06120 Halle (Saale), Germany
| | - Martin Schädler
- Department of Community Ecology, UFZ-Helmholtz Centre for Environmental Research, Theodor-Lieser-Str. 4, 06120 Halle (Saale), Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103 Leipzig, Germany
| | - Matthias Noll
- Department of Applied Sciences, Institute for Bioanalysis, Coburg University of Applied Sciences and Arts, Coburg, Germany
| | - Turki M. Dawoud
- Botany and Microbiology Department, College of Science, King Saud University, P.O. Box 2455, Riyadh, 11451 Saudi Arabia
| | - Yu-Ting Wu
- Department of Forestry, National Pingtung University of Science and Technology, Neipu, Pingtung 91201 Taiwan
| | - François Buscot
- Department of Soil Ecology, UFZ-Helmholtz Centre for Environmental Research, Theodor-Lieser-Str. 4, 06120 Halle (Saale), Germany
- Botany and Microbiology Department, College of Science, King Saud University, P.O. Box 2455, Riyadh, 11451 Saudi Arabia
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103 Leipzig, Germany
| | - Witoon Purahong
- Department of Soil Ecology, UFZ-Helmholtz Centre for Environmental Research, Theodor-Lieser-Str. 4, 06120 Halle (Saale), Germany
- Botany and Microbiology Department, College of Science, King Saud University, P.O. Box 2455, Riyadh, 11451 Saudi Arabia
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14
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Hao X, Liu X, Chen J, Wang B, Li Y, Ye Y, Ma W, Ma L. Effects on community composition and function Pinus massoniana infected by Bursaphelenchus xylophilus. BMC Microbiol 2022; 22:157. [PMID: 35690728 PMCID: PMC9188149 DOI: 10.1186/s12866-022-02569-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 06/02/2022] [Indexed: 12/14/2022] Open
Abstract
Pine wilt disease (PWD) is a worldwide forest disease caused by pine wood nematode (PWN). In this article, we investigated the composition, organization, correlation, and function of the endophytic microbial community in Pinus massoniana field with and without PWN. Samples were taken from branches, upper, middle, and lower trunks, as well as soil, from both healthy and infected trees. The results showed that the fungal diversity of healthy pines is around 1.1 times that of infected pines, while the bacterial diversity is about 0.75 times that of infected pines at the OTUs level. An increase of the abundance of pathogenic fungus such as Saitozyma, Graphilbum, Diplodia, Candida, Pseudoxanthomonas, Dyella and Pantoea was witnessed in infected pines according to the result of LEfSe. Furthermore, Ophiostoma and saprophytic fungus such as Entomocorticium, ganoderma, tomentella, entomocorticium were exclusively prominent in infected pines, which were substantially and highly connected with other species (p < 0.05), indicating the trees' vulnerability and making the wood blue. In healthy pines, the top three functional guilds are parasites, plant pathogens, and saprotrophs. Parasites (36.52%) are primarily found in the branches, plant pathogens (29.12%) are primarily found in the lower trunk, and saprotrophs (67.88%) are primarily found in the upper trunk of disease trees. Pines' immunity is being eroded due to an increase in the quantity and types of diseases. PICRUSt2 research revealed that NADH or NADPH, as well as carbon-nitrogen bonds, were more abundant in healthy pines, but acid anhydrides and transferring phosphorus-containing groups were more abundant in infected pines. The shift in resin secretion lowers the tree's potential and encourages pine wilt and mortality. In total, PWN may have disrupted the microbiological ecology and worked with the community to hasten the demise of pines.
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Affiliation(s)
- Xin Hao
- Northeast Forestry University, Harbin, China
| | - Xuefeng Liu
- Northeast Forestry University, Harbin, China
| | - Jie Chen
- Northeast Forestry University, Harbin, China.,Wageningen University & Research, Wageningen, Netherlands
| | | | - Yang Li
- Northeast Forestry University, Harbin, China
| | - Yi Ye
- Northeast Forestry University, Harbin, China
| | - Wei Ma
- Heilongjiang University of Chinese Medicine, Harbin, China.
| | - Ling Ma
- Northeast Forestry University, Harbin, China.
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15
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Chen J, Sharifi R, Khan MSS, Islam F, Bhat JA, Kui L, Majeed A. Wheat Microbiome: Structure, Dynamics, and Role in Improving Performance Under Stress Environments. Front Microbiol 2022; 12:821546. [PMID: 35095825 PMCID: PMC8793483 DOI: 10.3389/fmicb.2021.821546] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 12/23/2021] [Indexed: 11/13/2022] Open
Abstract
Wheat is an important cereal crop species consumed globally. The growing global population demands a rapid and sustainable growth of agricultural systems. The development of genetically efficient wheat varieties has solved the global demand for wheat to a greater extent. The use of chemical substances for pathogen control and chemical fertilizers for enhanced agronomic traits also proved advantageous but at the cost of environmental health. An efficient alternative environment-friendly strategy would be the use of beneficial microorganisms growing on plants, which have the potential of controlling plant pathogens as well as enhancing the host plant's water and mineral availability and absorption along with conferring tolerance to different stresses. Therefore, a thorough understanding of plant-microbe interaction, identification of beneficial microbes and their roles, and finally harnessing their beneficial functions to enhance sustainable agriculture without altering the environmental quality is appealing. The wheat microbiome shows prominent variations with the developmental stage, tissue type, environmental conditions, genotype, and age of the plant. A diverse array of bacterial and fungal classes, genera, and species was found to be associated with stems, leaves, roots, seeds, spikes, and rhizospheres, etc., which play a beneficial role in wheat. Harnessing the beneficial aspect of these microbes is a promising method for enhancing the performance of wheat under different environmental stresses. This review focuses on the microbiomes associated with wheat, their spatio-temporal dynamics, and their involvement in mitigating biotic and abiotic stresses.
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Affiliation(s)
- Jian Chen
- International Genome Center, Jiangsu University, Zhenjiang, China
| | - Rouhallah Sharifi
- Department of Plant Protection, College of Agriculture and Natural Resources, Razi University, Kermanshah, Iran
| | | | - Faisal Islam
- Zhejiang Key Laboratory of Crop Germplasm, Institute of Crop Science, Zhejiang University, Hangzhou, China
| | | | - Ling Kui
- Guangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
| | - Aasim Majeed
- Plant Molecular Genetics Laboratory, School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India
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16
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Fournier P, Pellan L, Barroso-Bergadà D, Bohan DA, Candresse T, Delmotte F, Dufour MC, Lauvergeat V, Le Marrec C, Marais A, Martins G, Masneuf-Pomarède I, Rey P, Sherman D, This P, Frioux C, Labarthe S, Vacher C. The functional microbiome of grapevine throughout plant evolutionary history and lifetime. ADV ECOL RES 2022. [DOI: 10.1016/bs.aecr.2022.09.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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17
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Zwirzitz B, Thalguter S, Wetzels SU, Stessl B, Wagner M, Selberherr E. Autochthonous fungi are central components in microbial community structure in raw fermented sausages. Microb Biotechnol 2021; 15:1392-1403. [PMID: 34739743 PMCID: PMC9049617 DOI: 10.1111/1751-7915.13950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 10/05/2021] [Accepted: 10/06/2021] [Indexed: 11/30/2022] Open
Abstract
Raw meat sausage represents a unique ecological niche rich in nutrients for microbial consumption, making it particularly vulnerable to microbial spoilage. Starter cultures are applied to improve product stability and safety as well as flavour characteristics. However, the influence of starter cultures on microbial community assembly and succession throughout the fermentation process is largely unknown. In particular the effect on the fungal community has not yet been explored. We evaluate the microbiological status of four different raw meat sausages using high‐throughput 16S rRNA gene and ITS2 gene sequencing. The objective was to study temporal changes of microbial composition during the fermentation process and to identify potential keystone species that play an important role within the microbial community. Our results suggest that fungi assigned to the species Debaryomyces hansenii and Alternaria alternata play a key role in microbial community dynamics during fermentation. In addition, bacteria related to the starter culture Lactobacillus sakei and the spoilage‐associated genera Acinetobacter, Pseudomonas and Psychrobacter are central components of the microbial ecosystem in raw fermented sausages. Elucidating the exact role and interactions of these microorganisms has the potential to have direct impacts on the quality and safety of fermented foods.
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Affiliation(s)
- Benjamin Zwirzitz
- Institute of Food Safety, Food Technology and Veterinary Public Health, University of Veterinary Medicine, Vienna, Austria.,Austrian Competence Centre for Feed and Food Quality, Safety and Innovation FFoQSI GmbH, Tulln, Austria
| | - Sarah Thalguter
- Institute of Food Safety, Food Technology and Veterinary Public Health, University of Veterinary Medicine, Vienna, Austria.,Austrian Competence Centre for Feed and Food Quality, Safety and Innovation FFoQSI GmbH, Tulln, Austria
| | - Stefanie U Wetzels
- Institute of Food Safety, Food Technology and Veterinary Public Health, University of Veterinary Medicine, Vienna, Austria.,Austrian Competence Centre for Feed and Food Quality, Safety and Innovation FFoQSI GmbH, Tulln, Austria
| | - Beatrix Stessl
- Institute of Food Safety, Food Technology and Veterinary Public Health, University of Veterinary Medicine, Vienna, Austria.,Austrian Competence Centre for Feed and Food Quality, Safety and Innovation FFoQSI GmbH, Tulln, Austria
| | - Martin Wagner
- Institute of Food Safety, Food Technology and Veterinary Public Health, University of Veterinary Medicine, Vienna, Austria.,Austrian Competence Centre for Feed and Food Quality, Safety and Innovation FFoQSI GmbH, Tulln, Austria
| | - Evelyne Selberherr
- Institute of Food Safety, Food Technology and Veterinary Public Health, University of Veterinary Medicine, Vienna, Austria.,Austrian Competence Centre for Feed and Food Quality, Safety and Innovation FFoQSI GmbH, Tulln, Austria
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18
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Yuan X, Hong S, Xiong W, Raza W, Shen Z, Wang B, Li R, Ruan Y, Shen Q, Dini-Andreote F. Development of fungal-mediated soil suppressiveness against Fusarium wilt disease via plant residue manipulation. MICROBIOME 2021; 9:200. [PMID: 34635164 PMCID: PMC8507339 DOI: 10.1186/s40168-021-01133-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 07/13/2021] [Indexed: 05/27/2023]
Abstract
BACKGROUND The development of suppressive soils is a promising strategy to protect plants against soil-borne diseases in a sustainable and viable manner. The use of crop rotation and the incorporation of plant residues into the soil are known to alleviate the stress imposed by soil pathogens through dynamics changes in soil biological and physicochemical properties. However, relatively little is known about the extent to which specific soil amendments of plant residues trigger the development of plant-protective microbiomes. Here, we investigated how the incorporation of pineapple residues in soils highly infested with the banana Fusarium wilt disease alleviates the pathogen pressure via changes in soil microbiomes. RESULTS The addition of above- and below-ground pineapple residues in highly infested soils significantly reduced the number of pathogens in the soil, thus resulting in a lower disease incidence. The development of suppressive soils was mostly related to trackable changes in specific fungal taxa affiliated with Aspergillus fumigatus and Fusarium solani, both of which displayed inhibitory effects against the pathogen. These antagonistic effects were further validated using an in vitro assay in which the pathogen control was related to growth inhibition via directly secreted antimicrobial substances and indirect interspecific competition for nutrients. The disease suppressive potential of these fungal strains was later validated using microbial inoculation in a well-controlled pot experiment. CONCLUSIONS These results mechanistically demonstrated how the incorporation of specific plant residues into the soil induces trackable changes in the soil microbiome with direct implications for disease suppression. The incorporation of pineapple residues in the soil alleviated the pathogen pressure by increasing the relative abundance of antagonistic fungal taxa causing a negative effect on pathogen growth and disease incidence. Taken together, this study provides a successful example of how specific agricultural management strategies can be used to manipulate the soil microbiome towards the development of suppressive soils against economically important soil-borne diseases. Video Abstract.
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Affiliation(s)
- Xianfu Yuan
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, People's Republic of China
- The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, People's Republic of China
| | - Shan Hong
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bio-resources, College of Tropical Crops, Hainan University, Haikou, 570228, People's Republic of China
| | - Wu Xiong
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, People's Republic of China
- The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, People's Republic of China
| | - Waseem Raza
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, People's Republic of China
- The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, People's Republic of China
- Ecology and Biodiversity Group, Department of Biology, Institute of Environmental Biology, Utrecht University, 3584 CH, Utrecht, the Netherlands
| | - Zongzhuan Shen
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, People's Republic of China
- The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, People's Republic of China
| | - Beibei Wang
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bio-resources, College of Tropical Crops, Hainan University, Haikou, 570228, People's Republic of China
| | - Rong Li
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, People's Republic of China.
- The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, People's Republic of China.
| | - Yunze Ruan
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bio-resources, College of Tropical Crops, Hainan University, Haikou, 570228, People's Republic of China
| | - Qirong Shen
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, People's Republic of China
- The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, People's Republic of China
| | - Francisco Dini-Andreote
- Department of Plant Science, The Pennsylvania State University, University Park, PA, USA
- Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA
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19
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Lyu D, Zajonc J, Pagé A, Tanney CAS, Shah A, Monjezi N, Msimbira LA, Antar M, Nazari M, Backer R, Smith DL. Plant Holobiont Theory: The Phytomicrobiome Plays a Central Role in Evolution and Success. Microorganisms 2021; 9:675. [PMID: 33805166 PMCID: PMC8064057 DOI: 10.3390/microorganisms9040675] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 03/20/2021] [Accepted: 03/23/2021] [Indexed: 12/15/2022] Open
Abstract
Under natural conditions, plants are always associated with a well-orchestrated community of microbes-the phytomicrobiome. The nature and degree of microbial effect on the plant host can be positive, neutral, or negative, and depends largely on the environment. The phytomicrobiome is integral for plant growth and function; microbes play a key role in plant nutrient acquisition, biotic and abiotic stress management, physiology regulation through microbe-to-plant signals, and growth regulation via the production of phytohormones. Relationships between the plant and phytomicrobiome members vary in intimacy, ranging from casual associations between roots and the rhizosphere microbial community, to endophytes that live between plant cells, to the endosymbiosis of microbes by the plant cell resulting in mitochondria and chloroplasts. If we consider these key organelles to also be members of the phytomicrobiome, how do we distinguish between the two? If we accept the mitochondria and chloroplasts as both members of the phytomicrobiome and the plant (entrained microbes), the influence of microbes on the evolution of plants becomes so profound that without microbes, the concept of the "plant" is not viable. This paper argues that the holobiont concept should take greater precedence in the plant sciences when referring to a host and its associated microbial community. The inclusivity of this concept accounts for the ambiguous nature of the entrained microbes and the wide range of functions played by the phytomicrobiome in plant holobiont homeostasis.
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Affiliation(s)
- Dongmei Lyu
- Department of Plant Science, Macdonald Campus, McGill University, Montréal, QC H9X 3V9, Canada; (D.L.); (J.Z.); (A.P.); (C.A.S.T.); (A.S.); (N.M.); (L.A.M.); (M.A.); (M.N.); (R.B.)
| | - Jonathan Zajonc
- Department of Plant Science, Macdonald Campus, McGill University, Montréal, QC H9X 3V9, Canada; (D.L.); (J.Z.); (A.P.); (C.A.S.T.); (A.S.); (N.M.); (L.A.M.); (M.A.); (M.N.); (R.B.)
| | - Antoine Pagé
- Department of Plant Science, Macdonald Campus, McGill University, Montréal, QC H9X 3V9, Canada; (D.L.); (J.Z.); (A.P.); (C.A.S.T.); (A.S.); (N.M.); (L.A.M.); (M.A.); (M.N.); (R.B.)
- National Research Council Canada, Aquatic and Crop Resource Development (ACRD), Montréal, QC H4P 2R2, Canada
| | - Cailun A. S. Tanney
- Department of Plant Science, Macdonald Campus, McGill University, Montréal, QC H9X 3V9, Canada; (D.L.); (J.Z.); (A.P.); (C.A.S.T.); (A.S.); (N.M.); (L.A.M.); (M.A.); (M.N.); (R.B.)
| | - Ateeq Shah
- Department of Plant Science, Macdonald Campus, McGill University, Montréal, QC H9X 3V9, Canada; (D.L.); (J.Z.); (A.P.); (C.A.S.T.); (A.S.); (N.M.); (L.A.M.); (M.A.); (M.N.); (R.B.)
| | - Nadia Monjezi
- Department of Plant Science, Macdonald Campus, McGill University, Montréal, QC H9X 3V9, Canada; (D.L.); (J.Z.); (A.P.); (C.A.S.T.); (A.S.); (N.M.); (L.A.M.); (M.A.); (M.N.); (R.B.)
| | - Levini A. Msimbira
- Department of Plant Science, Macdonald Campus, McGill University, Montréal, QC H9X 3V9, Canada; (D.L.); (J.Z.); (A.P.); (C.A.S.T.); (A.S.); (N.M.); (L.A.M.); (M.A.); (M.N.); (R.B.)
| | - Mohammed Antar
- Department of Plant Science, Macdonald Campus, McGill University, Montréal, QC H9X 3V9, Canada; (D.L.); (J.Z.); (A.P.); (C.A.S.T.); (A.S.); (N.M.); (L.A.M.); (M.A.); (M.N.); (R.B.)
| | - Mahtab Nazari
- Department of Plant Science, Macdonald Campus, McGill University, Montréal, QC H9X 3V9, Canada; (D.L.); (J.Z.); (A.P.); (C.A.S.T.); (A.S.); (N.M.); (L.A.M.); (M.A.); (M.N.); (R.B.)
| | - Rachel Backer
- Department of Plant Science, Macdonald Campus, McGill University, Montréal, QC H9X 3V9, Canada; (D.L.); (J.Z.); (A.P.); (C.A.S.T.); (A.S.); (N.M.); (L.A.M.); (M.A.); (M.N.); (R.B.)
| | - Donald L. Smith
- Department of Plant Science, Macdonald Campus, McGill University, Montréal, QC H9X 3V9, Canada; (D.L.); (J.Z.); (A.P.); (C.A.S.T.); (A.S.); (N.M.); (L.A.M.); (M.A.); (M.N.); (R.B.)
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20
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Kavamura VN, Mendes R, Bargaz A, Mauchline TH. Defining the wheat microbiome: Towards microbiome-facilitated crop production. Comput Struct Biotechnol J 2021; 19:1200-1213. [PMID: 33680361 PMCID: PMC7902804 DOI: 10.1016/j.csbj.2021.01.045] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 01/29/2021] [Accepted: 01/30/2021] [Indexed: 12/17/2022] Open
Abstract
Wheat is one of the world's most important crops, but its production relies heavily on agrochemical inputs which can be harmful to the environment when used excessively. It is well known that a multitude of microbes interact with eukaryotic organisms, including plants, and the sum of microbes and their functions associated with a given host is termed the microbiome. Plant-microbe interactions can be beneficial, neutral or harmful to the host plant. Over the last decade, with the development of next generation DNA sequencing technology, our understanding of the plant microbiome structure has dramatically increased. Considering that defining the wheat microbiome is key to leverage crop production in a sustainable way, here we describe how different factors drive microbiome assembly in wheat, including crop management, edaphic-environmental conditions and host selection. In addition, we highlight the benefits to take a multidisciplinary approach to define and explore the wheat core microbiome to generate solutions based on microbial (synthetic) communities or single inoculants. Advances in plant microbiome research will facilitate the development of microbial strategies to guarantee a sustainable intensification of crop production.
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Affiliation(s)
- Vanessa N. Kavamura
- Sustainable Agriculture Sciences, Rothamsted Research, Harpenden, Hertfordshire, UK
| | - Rodrigo Mendes
- Laboratory of Environmental Microbiology, Embrapa Environment, Jaguariúna, SP, Brazil
| | - Adnane Bargaz
- Agrobiosciences, Mohammed VI Polytechnic University, Benguerir, Morocco
| | - Tim H. Mauchline
- Sustainable Agriculture Sciences, Rothamsted Research, Harpenden, Hertfordshire, UK
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21
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Chaudhry V, Runge P, Sengupta P, Doehlemann G, Parker JE, Kemen E. Shaping the leaf microbiota: plant-microbe-microbe interactions. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:36-56. [PMID: 32910810 PMCID: PMC8210630 DOI: 10.1093/jxb/eraa417] [Citation(s) in RCA: 71] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 09/07/2020] [Indexed: 05/28/2023]
Abstract
The aerial portion of a plant, namely the leaf, is inhabited by pathogenic and non-pathogenic microbes. The leaf's physical and chemical properties, combined with fluctuating and often challenging environmental factors, create surfaces that require a high degree of adaptation for microbial colonization. As a consequence, specific interactive processes have evolved to establish a plant leaf niche. Little is known about the impact of the host immune system on phyllosphere colonization by non-pathogenic microbes. These organisms can trigger plant basal defenses and benefit the host by priming for enhanced resistance to pathogens. In most disease resistance responses, microbial signals are recognized by extra- or intracellular receptors. The interactions tend to be species specific and it is unclear how they shape leaf microbial communities. In natural habitats, microbe-microbe interactions are also important for shaping leaf communities. To protect resources, plant colonizers have developed direct antagonistic or host manipulation strategies to fight competitors. Phyllosphere-colonizing microbes respond to abiotic and biotic fluctuations and are therefore an important resource for adaptive and protective traits. Understanding the complex regulatory host-microbe-microbe networks is needed to transfer current knowledge to biotechnological applications such as plant-protective probiotics.
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Affiliation(s)
- Vasvi Chaudhry
- Department of Microbial Interactions, IMIT/ZMBP, University of
Tübingen, Tübingen, Germany
| | - Paul Runge
- Department of Microbial Interactions, IMIT/ZMBP, University of
Tübingen, Tübingen, Germany
- Max Planck Institute for Plant Breeding Research, Köln, Germany
| | - Priyamedha Sengupta
- Institute for Plant Sciences and Cluster of Excellence on Plant Sciences
(CEPLAS), University of Cologne, Center for Molecular Biosciences, Cologne,
Germany
| | - Gunther Doehlemann
- Institute for Plant Sciences and Cluster of Excellence on Plant Sciences
(CEPLAS), University of Cologne, Center for Molecular Biosciences, Cologne,
Germany
| | - Jane E Parker
- Max Planck Institute for Plant Breeding Research, Köln, Germany
- Institute for Plant Sciences and Cluster of Excellence on Plant Sciences
(CEPLAS), University of Cologne, Center for Molecular Biosciences, Cologne,
Germany
| | - Eric Kemen
- Department of Microbial Interactions, IMIT/ZMBP, University of
Tübingen, Tübingen, Germany
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22
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Kerdraon L, Barret M, Balesdent M, Suffert F, Laval V. Impact of a resistance gene against a fungal pathogen on the plant host residue microbiome: The case of the Leptosphaeria maculans-Brassica napus pathosystem. MOLECULAR PLANT PATHOLOGY 2020; 21:1545-1558. [PMID: 32975002 PMCID: PMC7694673 DOI: 10.1111/mpp.12994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 04/20/2020] [Accepted: 08/21/2020] [Indexed: 06/11/2023]
Abstract
Oilseed rape residues are a crucial determinant of stem canker epidemiology as they support the sexual reproduction of the fungal pathogen Leptosphaeria maculans. The aim of this study was to characterize the impact of a resistance gene against L. maculans infection on residue microbial communities and to identify microorganisms interacting with this pathogen during residue degradation. We used near-isogenic lines to obtain healthy and infected host plants. The microbiome associated with the two types of plant residues was characterized by metabarcoding. A combination of linear discriminant analysis and ecological network analysis was used to compare the microbial communities and to identify microorganisms interacting with L. maculans. Fungal community structure differed between the two lines at harvest, but not subsequently, suggesting that the presence/absence of the resistance gene influences the microbiome at the base of the stem whilst the plant is alive, but that this does not necessarily lead to differential colonization of the residues by fungi. Direct interactions with other members of the community involved many fungal and bacterial amplicon sequence variants (ASVs). L. maculans appeared to play a minor role in networks, whereas one ASV affiliated to Plenodomus biglobosus (synonym Leptosphaeria biglobosa) from the Leptosphaeria species complex may be considered a keystone taxon in the networks at harvest. This approach could be used to identify and promote microorganisms with beneficial effects against residue-borne pathogens and, more broadly, to decipher the complex interactions between multispecies pathosystems and other microbial components in crop residues.
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Affiliation(s)
- Lydie Kerdraon
- Université Paris‐SaclayINRAE, UMR BIOGERThiverval‐GrignonFrance
| | | | | | | | - Valérie Laval
- Université Paris‐SaclayINRAE, UMR BIOGERThiverval‐GrignonFrance
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Yang P, Tan C, Han M, Cheng L, Cui X, Ning K. Correlation-Centric Network (CCN) representation for microbial co-occurrence patterns: new insights for microbial ecology. NAR Genom Bioinform 2020; 2:lqaa042. [PMID: 33575595 PMCID: PMC7671402 DOI: 10.1093/nargab/lqaa042] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Revised: 05/29/2020] [Accepted: 06/05/2020] [Indexed: 12/27/2022] Open
Abstract
Mainstream studies of microbial community focused on critical organisms and their physiology. Recent advances in large-scale metagenome analysis projects initiated new researches in the complex correlations between large microbial communities. Specifically, previous studies focused on the nodes (i.e. species) of the Species-Centric Networks (SCNs). However, little was understood about the change of correlation between network members (i.e. edges of the SCNs) when the network was disturbed. Here, we introduced a Correlation-Centric Network (CCN) to the microbial research based on the concept of edge networks. In CCN, each node represented a species-species correlation, and edge represented the species shared by two correlations. In this research, we investigated the CCNs and their corresponding SCNs on two large cohorts of microbiome. The results showed that CCNs not only retained the characteristics of SCNs, but also contained information that cannot be detected by SCNs. In addition, when the members of microbial communities were decreased (i.e. environmental disturbance), the CCNs fluctuated within a small range in terms of network connectivity. Therefore, by highlighting the important species correlations, CCNs could unveil new insights when studying not only the functions of target species, but also the stabilities of their residing microbial communities.
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Affiliation(s)
- Pengshuo Yang
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Chongyang Tan
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Maozhen Han
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Lin Cheng
- Department of Engineering, Trinity College, 300 Summit Street, Hartford, CT 06106, USA
| | - Xuefeng Cui
- School of Computer Science and Technology, Shandong University, Qingdao, Shandong 250100, China
| | - Kang Ning
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
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Fareed Mohamed Wahdan S, Hossen S, Tanunchai B, Schädler M, Buscot F, Purahong W. Future Climate Significantly Alters Fungal Plant Pathogen Dynamics during the Early Phase of Wheat Litter Decomposition. Microorganisms 2020; 8:microorganisms8060908. [PMID: 32560135 PMCID: PMC7356542 DOI: 10.3390/microorganisms8060908] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Revised: 05/25/2020] [Accepted: 06/09/2020] [Indexed: 12/13/2022] Open
Abstract
Returning wheat residues to the soil is a common practice in modern agricultural systems and is considered to be a sustainable practice. However, the negative contribution of these residues in the form of “residue-borne pathogens” is recognized. Here, we aimed to investigate the structure and ecological functions of fungal communities colonizing wheat residues during the early phase of decomposition in a conventional farming system. The experiment was conducted under both ambient conditions and a future climate scenario expected in 50–70 years from now. Using MiSeq Illumina sequencing of the fungal internal transcribed spacer 2 (ITS2), we found that plant pathogenic fungi dominated (~87% of the total sequences) within the wheat residue mycobiome. Destructive wheat fungal pathogens such as Fusarium graminearum, Fusarium tricinctum, and Zymoseptoria tritci were detected under ambient and future climates. Moreover, future climate enhanced the appearance of new plant pathogenic fungi in the plant residues. Our results based on the bromodeoxyuridine (BrdU) immunocapture technique demonstrated that almost all detected pathogens are active at the early stage of decomposition under both climate scenarios. In addition, future climate significantly changed both the richness patterns and the community dynamics of the total, plant pathogenic and saprotrophic fungi in wheat residues as compared with the current ambient climate. We conclude that the return of wheat residues can increase the pathogen load, and therefore have negative consequences for wheat production in the future.
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Affiliation(s)
- Sara Fareed Mohamed Wahdan
- Department of Soil Ecology, UFZ-Helmholtz Centre for Environmental Research, Theodor-Lieser-Str. 4, 06120 Halle (Saale), Germany; (S.H.); (B.T.); (F.B.)
- Department of Botany, Faculty of Science, Suez Canal University, 41522 Ismailia, Egypt
- Correspondence: or (S.F.M.W.); (W.P.); Tel.: +49-345-558-5207 (S.F.M.W.)
| | - Shakhawat Hossen
- Department of Soil Ecology, UFZ-Helmholtz Centre for Environmental Research, Theodor-Lieser-Str. 4, 06120 Halle (Saale), Germany; (S.H.); (B.T.); (F.B.)
- Friedrich-Schiller-Universität Jena, Institute of Ecology and Evolution, Dornburger Str. 159, 07743 Jena, Germany
| | - Benjawan Tanunchai
- Department of Soil Ecology, UFZ-Helmholtz Centre for Environmental Research, Theodor-Lieser-Str. 4, 06120 Halle (Saale), Germany; (S.H.); (B.T.); (F.B.)
| | - Martin Schädler
- Department of Community Ecology, UFZ-Helmholtz Centre for Environmental Research, Theodor-Lieser-Str. 4, 06120 Halle (Saale), Germany;
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103 Leipzig, Germany
| | - François Buscot
- Department of Soil Ecology, UFZ-Helmholtz Centre for Environmental Research, Theodor-Lieser-Str. 4, 06120 Halle (Saale), Germany; (S.H.); (B.T.); (F.B.)
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103 Leipzig, Germany
| | - Witoon Purahong
- Department of Soil Ecology, UFZ-Helmholtz Centre for Environmental Research, Theodor-Lieser-Str. 4, 06120 Halle (Saale), Germany; (S.H.); (B.T.); (F.B.)
- Correspondence: or (S.F.M.W.); (W.P.); Tel.: +49-345-558-5207 (S.F.M.W.)
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