101
|
|
102
|
Egidi E, Delgado-Baquerizo M, Plett JM, Wang J, Eldridge DJ, Bardgett RD, Maestre FT, Singh BK. A few Ascomycota taxa dominate soil fungal communities worldwide. Nat Commun 2019; 10:2369. [PMID: 31147554 PMCID: PMC6542806 DOI: 10.1038/s41467-019-10373-z] [Citation(s) in RCA: 215] [Impact Index Per Article: 43.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Accepted: 04/30/2019] [Indexed: 12/22/2022] Open
Abstract
Despite having key functions in terrestrial ecosystems, information on the dominant soil fungi and their ecological preferences at the global scale is lacking. To fill this knowledge gap, we surveyed 235 soils from across the globe. Our findings indicate that 83 phylotypes (<0.1% of the retrieved fungi), mostly belonging to wind dispersed, generalist Ascomycota, dominate soils globally. We identify patterns and ecological drivers of dominant soil fungal taxa occurrence, and present a map of their distribution in soils worldwide. Whole-genome comparisons with less dominant, generalist fungi point at a significantly higher number of genes related to stress-tolerance and resource uptake in the dominant fungi, suggesting that they might be better in colonising a wide range of environments. Our findings constitute a major advance in our understanding of the ecology of fungi, and have implications for the development of strategies to preserve them and the ecosystem functions they provide. Soil fungi play essential roles in ecosystems worldwide. Here, the authors sequence and analyze 235 soil samples collected from across the globe, and identify dominant fungal taxa and their associated environmental attributes.
Collapse
Affiliation(s)
- Eleonora Egidi
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, NSW, 2753, Australia.
| | - Manuel Delgado-Baquerizo
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, NSW, 2753, Australia. .,Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, CO, 80309, USA. .,Departamento de Biología y Geología, Física y Química Inorgánica, Escuela Superior de Ciencias Experimentales y Tecnología. Universidad Rey Juan Carlos, c/Tulipán s/n, 28933, Móstoles, Spain.
| | - Jonathan M Plett
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, NSW, 2753, Australia
| | - Juntao Wang
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, NSW, 2753, Australia.,State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - David J Eldridge
- Centre for Ecosystem Science, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Richard D Bardgett
- School of Earth and Environmental Sciences, Michael Smith Building, The University of Manchester, Oxford Road, Manchester, M13 9PT, UK
| | - Fernando T Maestre
- Departamento de Biología y Geología, Física y Química Inorgánica, Escuela Superior de Ciencias Experimentales y Tecnología. Universidad Rey Juan Carlos, c/Tulipán s/n, 28933, Móstoles, Spain.,Departamento de Ecología and Instituto Multidisciplinar para el Estudio del Medio "Ramon Margalef", Universidad de Alicante, Alicante, Spain
| | - Brajesh K Singh
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, NSW, 2753, Australia. .,Global Centre for Land-Based Innovation, Western Sydney University, Penrith South DC, NSW, 2751, Australia.
| |
Collapse
|
103
|
Duhamel M, Wan J, Bogar LM, Segnitz RM, Duncritts NC, Peay KG. Plant selection initiates alternative successional trajectories in the soil microbial community after disturbance. ECOL MONOGR 2019. [DOI: 10.1002/ecm.1367] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Marie Duhamel
- Department of Biology Stanford University Stanford California 94305 USA
| | - Joe Wan
- Department of Biology Stanford University Stanford California 94305 USA
| | - Laura M. Bogar
- Department of Biology Stanford University Stanford California 94305 USA
| | - R. Max Segnitz
- Department of Biology Stanford University Stanford California 94305 USA
| | - Nora C. Duncritts
- Department of Botany University of Wisconsin Madison Wisconsin 53706 USA
| | - Kabir G. Peay
- Department of Biology Stanford University Stanford California 94305 USA
| |
Collapse
|
104
|
Inglis GD, Duke GM, Goettel MS, Kabaluk JT, Ortega-Polo R. Biogeography and genotypic diversity of Metarhizium brunneum and Metarhizium robertsii in northwestern North American soils. Can J Microbiol 2019; 65:261-281. [DOI: 10.1139/cjm-2018-0297] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The biogeography and genotype diversity of Metarhizium species in northwestern North American soils was examined; 20 ecoregions were sampled, including 58 agricultural and 80 natural habitat subsites, and areas that were glaciated during the Pleistocene epoch. One hundred and twenty-nine isolates of M. brunneum, 26 isolates of M. robertsii, four isolates of M. guizhouense, one isolate of M. flavoviride, and 55 isolates of Beauveria were recovered. Metarhizium and Beauveria species were isolated in diverse ecoregions within the study area, but a trend for increased isolation of Metarhizium species in western regions of the study area was observed. Consistent with this observation, the prevalence of M. brunneum and M. robertsii decreased at higher elevations, and the opposite was true for Beauveria. Both M. brunneum and M. robertsii were more commonly isolated from agricultural and natural habitat subsites, and considerable genotypic diversity was observed in both habitats and within the same subsite. Metarhizium robertsii, but not M. brunneum, was more commonly isolated from nonglaciated locations; however, less diversity and richness was observed for M. brunneum recovered from glaciated versus nonglaciated locations consistent with insular biogeography. The study has implications for microbial control strategies in the region.
Collapse
Affiliation(s)
| | - Grant M. Duke
- Agriculture and Agri-Food Canada, Lethbridge, AB T1J 4B1, Canada
| | - Mark S. Goettel
- Agriculture and Agri-Food Canada, Lethbridge, AB T1J 4B1, Canada
| | - J. Todd Kabaluk
- Agriculture and Agri-Food Canada, Agassiz, BC V0M 1A0, Canada
| | | |
Collapse
|
105
|
Host Phylogenetic Relatedness and Soil Nutrients Shape Ectomycorrhizal Community Composition in Native and Exotic Pine Plantations. FORESTS 2019. [DOI: 10.3390/f10030263] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Exotic non-native Pinus species have been widely planted or become naturalized in many parts of the world. Pines rely on ectomycorrhizal (ECM) fungi mutualisms to overcome barriers to establishment, yet the degree to which host specificity and edaphic preferences influence ECM community composition remains poorly understood. In this study, we used high-throughput sequencing coupled with soil analyses to investigate the effect of host plant identity, spatial distance and edaphic factors on ECM community composition in young (30-year-old) native (Pinus massoniana Lamb.) and exotic (Pinus elliottii Engelm.) pine plantations in China. The ECM fungal communities comprised 43 species with the majority belonging to the Thelephoraceae and Russulaceae. Most species were found associated with both host trees while certain native ECM taxa (Suillus) showed host specificity to the native P. massoniana. ECM fungi that are known to occur exclusively with Pinus (e.g., Rhizopogon) were uncommon. We found no significant effect of host identity on ECM communities, i.e., phylogenetically related pines shared similar ECM fungal communities. Instead, ECM fungal community composition was strongly influenced by site-specific abiotic factors and dispersal. These findings reinforce the idea that taxonomic relatedness might be a factor promoting ECM colonization in exotic pines but that shifts in ECM communities may also be context-dependent.
Collapse
|
106
|
Shelef O, Hahn PG, Getman-Pickering Z, Martinez Medina A. Coming to Common Ground: The Challenges of Applying Ecological Theory Developed Aboveground to Rhizosphere Interactions. Front Ecol Evol 2019. [DOI: 10.3389/fevo.2019.00058] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
|
107
|
Cuellar-Gempeler C, Leibold MA. Key colonist pools and habitat filters mediate the composition of fiddler crab-associated bacterial communities. Ecology 2019; 100:e02628. [PMID: 30657600 DOI: 10.1002/ecy.2628] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Revised: 11/27/2018] [Accepted: 12/20/2018] [Indexed: 12/18/2022]
Abstract
The diversity and composition of local communities depends strongly on the pool of species that have been able to colonize that community from elsewhere. Typically this is thought to depend on a larger regional species pool that is subject to local environmental constraints that act as "filters." Often, however, colonists arrive from multiple sources that differ in habitat conditions and have therefore already experienced distinct "prefiltering." Consequently, it is the interaction of species from these distinct pools that determine the composition of local communities. This interaction is particularly important when certain colonist pools provide keystone species with disproportionate roles on community assembly. We propose to identify these key colonist pools and their interaction with local habitat filters by quantifying community-level responses to colonist pool manipulation. We tested this framework to assess the contribution of surface and burrow sediment bacteria to bacterial communities associated with the fiddler crab, Uca panacea. In a mesocosm experiment, we combined normal and autoclaved surface and burrow sediment in a factorial experimental design, and we evaluated the community-level responses of carapace and gut microbial assemblages to sediment treatments with next-generation sequencing of the 16S rRNA gene. Results from carapace bacterial communities indicate that burrow sediments contribute most recruits, but surface sediments provide a few key colonizers that become established in the carapace community. In contrast, the composition of gut-associated microbial communities responded only to surface bacteria manipulation, despite being highly dissimilar from the community composition in both the surface and burrow source pools. These results suggest that assembly in the gut depends primarily on colonization from the surface sediment and regulation by habitat filtering. For fiddler crab-associated bacteria, we can conclude that key colonist pools and habitat filters regulate the influence of multiple colonist pools. Incorporating and distinguishing the contribution of multiple sources of species, rather than a single regional species pool, may better explain community dynamics in many systems, especially those with weak habitat filters.
Collapse
Affiliation(s)
- Catalina Cuellar-Gempeler
- Department of Biological Sciences, Humboldt State University, 1st Harpst Street, Arcata, California, 95521, USA
| | - Mathew A Leibold
- Department of Biology, University of Florida, Gainesville, Florida, 32611, USA
| |
Collapse
|
108
|
Alzarhani AK, Clark DR, Underwood GJC, Ford H, Cotton TEA, Dumbrell AJ. Are drivers of root-associated fungal community structure context specific? ISME JOURNAL 2019; 13:1330-1344. [PMID: 30692628 PMCID: PMC6474305 DOI: 10.1038/s41396-019-0350-y] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Revised: 11/22/2018] [Accepted: 12/25/2018] [Indexed: 12/01/2022]
Abstract
The composition and structure of plant-root-associated fungal communities are determined by local abiotic and biotic conditions. However, the relative influence and identity of relationships to abiotic and biotic factors may differ across environmental and ecological contexts, and fungal functional groups. Thus, understanding which aspects of root-associated fungal community ecology generalise across contexts is the first step towards a more predictive framework. We investigated how the relative importance of biotic and abiotic factors scale across environmental and ecological contexts using high-throughput sequencing (ca. 55 M Illumina metabarcoding sequences) of >260 plant-root-associated fungal communities from six UK salt marshes across two geographic regions (South-East and North-West England) in winter and summer. Levels of root-associated fungal diversity were comparable with forests and temperate grasslands, quadrupling previous estimates of salt-marsh fungal diversity. Whilst abiotic variables were generally most important, a range of site- and spatial scale-specific abiotic and biotic drivers of diversity and community composition were observed. Consequently, predictive models of diversity trained on one site, extrapolated poorly to others. Fungal taxa from the same functional groups responded similarly to the specific drivers of diversity and composition. Thus site, spatial scale and functional group are key factors that, if accounted for, may lead to a more predictive understanding of fungal community ecology.
Collapse
Affiliation(s)
- A Khuzaim Alzarhani
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester, Essex, CO4 3SQ, UK.,Faculty of Science, Northern Border University, Arar, Saudi Arabia
| | - Dave R Clark
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester, Essex, CO4 3SQ, UK
| | - Graham J C Underwood
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester, Essex, CO4 3SQ, UK
| | - Hilary Ford
- School of Environment, Natural Resources and Geography, Thoday buildings, Bangor University, Bangor, LL57 2DG, UK
| | - T E Anne Cotton
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester, Essex, CO4 3SQ, UK.,Department of Animal and Plant Sciences, The University of Sheffield, Alfred Denny Building, Sheffield, SY, S10 2TN, UK
| | - Alex J Dumbrell
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester, Essex, CO4 3SQ, UK.
| |
Collapse
|
109
|
Effects of host species, environmental filtering and forest age on community assembly of ectomycorrhizal fungi in fragmented forests. FUNGAL ECOL 2018. [DOI: 10.1016/j.funeco.2018.08.003] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
|
110
|
Corrales A, Henkel TW, Smith ME. Ectomycorrhizal associations in the tropics - biogeography, diversity patterns and ecosystem roles. THE NEW PHYTOLOGIST 2018; 220:1076-1091. [PMID: 29689121 DOI: 10.1111/nph.15151] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Accepted: 02/20/2018] [Indexed: 06/08/2023]
Abstract
Contents Summary 1076 I. Introduction 1076 II. Historical overview 1077 III. Identities and distributions of tropical ectomycorrhizal plants 1077 IV. Dominance of tropical forests by ECM trees 1078 V. Biogeography of tropical ECM fungi 1081 VI. Beta diversity patterns in tropical ECM fungal communities 1082 VII. Conclusions and future research 1086 Acknowledgements 1087 References 1087 SUMMARY: Ectomycorrhizal (ECM) associations were historically considered rare or absent from tropical ecosystems. Although most tropical forests are dominated by arbuscular mycorrhizal (AM) trees, ECM associations are widespread and found in all tropical regions. Here, we highlight emerging patterns of ECM biogeography, diversity and ecosystem functions, identify knowledge gaps, and offer direction for future research. At the continental and regional scales, tropical ECM systems are highly diverse and vary widely in ECM plant and fungal abundance, diversity, composition and phylogenetic affinities. We found strong regional differences among the dominant host plant families, suggesting that biogeographical factors strongly influence tropical ECM symbioses. Both ECM plants and fungi also exhibit strong turnover along altitudinal and soil fertility gradients, suggesting niche differentiation among taxa. Ectomycorrhizal fungi are often more abundant and diverse in sites with nutrient-poor soils, suggesting that ECM associations can optimize plant nutrition and may contribute to the maintenance of tropical monodominant forests. More research is needed to elucidate the diversity patterns of ECM fungi and plants in the tropics and to clarify the role of this symbiosis in nutrient and carbon cycling.
Collapse
Affiliation(s)
- Adriana Corrales
- Department of Plant Pathology, University of Florida, Gainesville, FL, 32611, USA
| | - Terry W Henkel
- Department of Biological Sciences, Humboldt State University, Arcata, CA, 95521, USA
| | - Matthew E Smith
- Department of Plant Pathology, University of Florida, Gainesville, FL, 32611, USA
| |
Collapse
|
111
|
Zinger L, Taberlet P, Schimann H, Bonin A, Boyer F, De Barba M, Gaucher P, Gielly L, Giguet‐Covex C, Iribar A, Réjou‐Méchain M, Rayé G, Rioux D, Schilling V, Tymen B, Viers J, Zouiten C, Thuiller W, Coissac E, Chave J. Body size determines soil community assembly in a tropical forest. Mol Ecol 2018; 28:528-543. [DOI: 10.1111/mec.14919] [Citation(s) in RCA: 90] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Revised: 10/02/2018] [Accepted: 10/14/2018] [Indexed: 01/02/2023]
Affiliation(s)
- Lucie Zinger
- CNRS, IRDUMR 5174 Evolution et Diversité Biologique (EDB)Université Toulouse 3 Paul Sabatier Toulouse France
| | - Pierre Taberlet
- CNRSLaboratoire d'Ecologie Alpine (LECA)Univ. Grenoble Alpes Grenoble France
| | - Heidy Schimann
- UMR Ecologie des Forets de Guyane (AgroParisTech, CIRAD, CNRS, Université des Antilles, Université de la Guyane)INRA Kourou France
| | - Aurélie Bonin
- CNRSLaboratoire d'Ecologie Alpine (LECA)Univ. Grenoble Alpes Grenoble France
| | - Frédéric Boyer
- CNRSLaboratoire d'Ecologie Alpine (LECA)Univ. Grenoble Alpes Grenoble France
| | - Marta De Barba
- CNRSLaboratoire d'Ecologie Alpine (LECA)Univ. Grenoble Alpes Grenoble France
| | - Philippe Gaucher
- USR 3456CNRSCentre de recherche de Montabo IRDCNRS‐Guyane Cayenne France
| | - Ludovic Gielly
- CNRSLaboratoire d'Ecologie Alpine (LECA)Univ. Grenoble Alpes Grenoble France
| | | | - Amaia Iribar
- CNRS, IRDUMR 5174 Evolution et Diversité Biologique (EDB)Université Toulouse 3 Paul Sabatier Toulouse France
| | - Maxime Réjou‐Méchain
- CNRS, IRDUMR 5174 Evolution et Diversité Biologique (EDB)Université Toulouse 3 Paul Sabatier Toulouse France
- UMR AMAP, IRD Montpellier France
| | - Gilles Rayé
- CNRSLaboratoire d'Ecologie Alpine (LECA)Univ. Grenoble Alpes Grenoble France
| | - Delphine Rioux
- CNRSLaboratoire d'Ecologie Alpine (LECA)Univ. Grenoble Alpes Grenoble France
| | - Vincent Schilling
- CNRS, IRDUMR 5174 Evolution et Diversité Biologique (EDB)Université Toulouse 3 Paul Sabatier Toulouse France
| | - Blaise Tymen
- CNRS, IRDUMR 5174 Evolution et Diversité Biologique (EDB)Université Toulouse 3 Paul Sabatier Toulouse France
| | - Jérôme Viers
- CNRS, IRDUMR 5563 GETUniversité Toulouse 3 Paul Sabatier Toulouse France
| | - Cyril Zouiten
- CNRS, IRDUMR 5563 GETUniversité Toulouse 3 Paul Sabatier Toulouse France
| | - Wilfried Thuiller
- CNRSLaboratoire d'Ecologie Alpine (LECA)Univ. Grenoble Alpes Grenoble France
| | - Eric Coissac
- CNRSLaboratoire d'Ecologie Alpine (LECA)Univ. Grenoble Alpes Grenoble France
| | - Jérôme Chave
- CNRS, IRDUMR 5174 Evolution et Diversité Biologique (EDB)Université Toulouse 3 Paul Sabatier Toulouse France
| |
Collapse
|
112
|
Schröter K, Wemheuer B, Pena R, Schöning I, Ehbrecht M, Schall P, Ammer C, Daniel R, Polle A. Assembly processes of trophic guilds in the root mycobiome of temperate forests. Mol Ecol 2018; 28:348-364. [PMID: 30276908 DOI: 10.1111/mec.14887] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Revised: 09/05/2018] [Accepted: 09/17/2018] [Indexed: 01/09/2023]
Abstract
Root-associated mycobiomes (RAMs) link plant and soil ecological processes, thereby supporting ecosystem functions. Understanding the forces that govern the assembly of RAMs is key to sustainable ecosystem management. Here, we dissected RAMs according to functional guilds and combined phylogenetic and multivariate analyses to distinguish and quantify the forces driving RAM assembly processes. Across large biogeographic scales (>1,000 km) in temperate forests (>100 plots), RAMs were taxonomically highly distinct but composed of a stable trophic structure encompassing symbiotrophic, ectomycorrhizal (55%), saprotrophic (7%), endotrophic (3%) and pathotrophic fungi (<1%). Taxonomic community composition of RAMs is explained by abiotic factors, forest management intensity, dominant tree family (Fagaceae, Pinaceae) and root resource traits. Local RAM assemblies are phylogenetically clustered, indicating stronger habitat filtering on roots in dry, acid soils and in conifer stands than in other forest types. The local assembly of ectomycorrhizal communities is driven by forest management intensity. At larger scales, root resource traits and soil pH shift the assembly process of ectomycorrhizal fungi from deterministic to neutral. Neutral or weak deterministic assembly processes are prevalent in saprotrophic and endophytic guilds. The remarkable consistency of the trophic composition of the RAMs suggests that temperate forests attract fungal assemblages that afford functional resilience under the current range of climatic and edaphic conditions. At local scales, the filtering processes that structure symbiotrophic assemblies can be influenced by forest management and tree selection, but at larger scales, environmental cues and host resource traits are the most prevalent forces.
Collapse
Affiliation(s)
- Kristina Schröter
- Forest Botany and Tree Physiology, University of Goettingen, Göttingen, Germany
| | - Bernd Wemheuer
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, University of Goettingen, Göttingen, Germany.,Centre for Marine Bio-Innovation, School of Biological Earth and Environmental Sciences, The University of New South Wales, Sydney, NSW, Australia
| | - Rodica Pena
- Forest Botany and Tree Physiology, University of Goettingen, Göttingen, Germany
| | - Ingo Schöning
- Max Planck Institute for Biogeochemistry, Jena, Germany
| | - Martin Ehbrecht
- Silviculture and Forest Ecology of the Temperate Zones, University of Goettingen, Göttingen, Germany
| | - Peter Schall
- Silviculture and Forest Ecology of the Temperate Zones, University of Goettingen, Göttingen, Germany
| | - Christian Ammer
- Silviculture and Forest Ecology of the Temperate Zones, University of Goettingen, Göttingen, Germany
| | - Rolf Daniel
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, University of Goettingen, Göttingen, Germany
| | - Andrea Polle
- Forest Botany and Tree Physiology, University of Goettingen, Göttingen, Germany
| |
Collapse
|
113
|
Wu BW, Gao C, Chen L, Buscot F, Goldmann K, Purahong W, Ji NN, Wang YL, Lü PP, Li XC, Guo LD. Host Phylogeny Is a Major Determinant of Fagaceae-Associated Ectomycorrhizal Fungal Community Assembly at a Regional Scale. Front Microbiol 2018; 9:2409. [PMID: 30364168 PMCID: PMC6191505 DOI: 10.3389/fmicb.2018.02409] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Accepted: 09/20/2018] [Indexed: 01/28/2023] Open
Abstract
Environmental filtering (niche process) and dispersal limitation (neutral process) are two of the primary forces driving community assembly in ecosystems, but how these processes affect the Fagaceae-associated ectomycorrhizal (EM) fungal community at regional scales is so far poorly documented. We examined the EM fungal communities of 61 plant species in six genera belonging to the Fagaceae distributed across Chinese forest ecosystems (geographic distance up to ∼3,757 km) using Illumina Miseq sequencing of ITS2 sequences. The relative effects of environmental filtering (e.g., host plant phylogeny, soil and climate) and dispersal limitation (e.g., spatial distance) on the EM fungal community were distinguished using multiple models. In total, 2,706 operational taxonomic units (OTUs) of EM fungi, corresponding to 54 fungal lineages, were recovered at a 97% sequence similarity level. The EM fungal OTU richness was significantly affected by soil pH and nutrients and by host phylogeny. The EM fungal community composition was significantly influenced by combinations of host phylogeny, spatial distance, soil and climate. Furthermore, host phylogeny had the greatest effect on EM fungal community. The study suggests that the assembly of the EM fungal community is governed by both environmental filtering and dispersal limitation, with host effect being the most important determinant at the regional scale.
Collapse
Affiliation(s)
- Bin-Wei Wu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
- Department of Soil Ecology, UFZ-Helmholtz Centre for Environmental Research, Halle, Germany
| | - Cheng Gao
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Liang Chen
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - François Buscot
- Department of Soil Ecology, UFZ-Helmholtz Centre for Environmental Research, Halle, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
- Institute of Biology, Leipzig University, Leipzig, Germany
| | - Kezia Goldmann
- Department of Soil Ecology, UFZ-Helmholtz Centre for Environmental Research, Halle, Germany
| | - Witoon Purahong
- Department of Soil Ecology, UFZ-Helmholtz Centre for Environmental Research, Halle, Germany
| | - Niu-Niu Ji
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Yong-Long Wang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Peng-Peng Lü
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Xing-Chun Li
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Liang-Dong Guo
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| |
Collapse
|
114
|
Wang J, Chen C, Ye Z, Li J, Feng Y, Lu Q. Relationships Between Fungal and Plant Communities Differ Between Desert and Grassland in a Typical Dryland Region of Northwest China. Front Microbiol 2018; 9:2327. [PMID: 30333808 PMCID: PMC6176009 DOI: 10.3389/fmicb.2018.02327] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Accepted: 09/11/2018] [Indexed: 11/13/2022] Open
Abstract
The relationships between soil fungal and plant communities in the dryland have been well documented, yet the associated difference in relationships between soil fungal and plant communities among different habitats remains unclear. Here, we explored the relationships between plant and fungal functional communities, and the dominant factors of these fungal communities in the desert and grassland. Soil fungal functional communities were assessed based on fungal ITS sequence data which were obtained from our previous study. The results showed that the total, saprotrophic and pathotrophic fungal richness were predominantly determined by plant species richness and/or soil nutrients in the desert, but by MAP or soil CN in the grassland. AM fungal richness was only significantly related to soil nutrients in two habitats. The total and saprotrophic fungal species compositions were mainly shaped by abiotic and spatial factors in the desert, but by plant and abiotic factors in the grassland. Pathotrophic fungal species composition was more strongly correlated with plant and spatial factors in the desert, but with spatial and abiotic factors in the grassland. AM fungal species composition was more strongly correlated with MAP in the grassland, but with no factors in the desert. These results provide robust evidence that the relationships between soil fungal and plant communities, and the drivers of soil fungal communities differ between the desert and grassland. Furthermore, we highlight that the linkages between soil fungal and plant communities, and the drivers of soil fungal communities may also be affected by fungal traits (e.g., functional groups).
Collapse
Affiliation(s)
- Jianming Wang
- College of Forestry, Beijing Forestry University, Beijing, China
| | - Chen Chen
- College of Forestry, Beijing Forestry University, Beijing, China
| | - Ziqi Ye
- College of Forestry, Beijing Forestry University, Beijing, China
| | - Jingwen Li
- College of Forestry, Beijing Forestry University, Beijing, China
| | - Yiming Feng
- Institute of Desertification Studies, Chinese Academy of Forestry, Beijing, China
| | - Qi Lu
- Institute of Desertification Studies, Chinese Academy of Forestry, Beijing, China
| |
Collapse
|
115
|
Pozzi AC, Roy M, Nagati M, Schwob G, Manzi S, Gardes M, Moreau PA, Fernandez MP. Patterns of diversity, endemism and specialization in the root symbiont communities of alder species on the island of Corsica. THE NEW PHYTOLOGIST 2018; 219:336-349. [PMID: 29377140 DOI: 10.1111/nph.14996] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2017] [Accepted: 12/07/2017] [Indexed: 06/07/2023]
Abstract
We investigated whether the diversity, endemicity and specificity of alder symbionts could be changed by isolation in a Mediterranean glacial refugium. We studied both ectomycorrhizal (EM) fungi and nitrogen-fixing actinobacteria associated with alders, and compared their communities in Corsica and on the European continent. Nodules and root tips were sampled on the three alder species present in Corsica and continental France and Italy. Phylogenies based on internal transcribed spacer (ITS) and a multilocus sequence analysis approach were used to characterize fungal and Frankia species, respectively. Patterns of diversity, endemism and specialization were compared between hosts and regions for each symbiont community. In Corsica, communities were not generally richer than on the mainland. The species richness per site depended mainly on host identity: Alnus glutinosa and Alnus cordata hosted richer Frankia and EM communities, respectively. Half of the Frankia species were endemic to Corsica against only 4% of EM species. Corsica is not a hotspot of diversity for all alder symbionts but sustains an increased frequency of poor-dispersers such as hypogeous fungi. Generalist EM fungi and host-dependent profusely sporulating (Sp+) Frankia were abundantly associated with Corsican A. cordata, a pattern related to a more thermophilic and xerophylic climate and to the co-occurrence with other host trees.
Collapse
Affiliation(s)
- Adrien C Pozzi
- Laboratoire d'Ecologie Microbienne, UMR5557, CNRS, INRA, VetAgro Sup, UCBL, Université de Lyon, Villeurbanne, 69622, France
- Biométrie et Biologie Evolutive, UMR5558, CNRS, INRIA, VetAgro Sup, HCL, UCBL, Université de Lyon, Villeurbanne, 69622, France
| | - Mélanie Roy
- Laboratoire Evolution et Diversité Biologique, UMR5174, Université Paul Sabatier - CNRS, 118 route de Narbonne, Toulouse Cedex, F-31062, France
| | - Mélissande Nagati
- Laboratoire Evolution et Diversité Biologique, UMR5174, Université Paul Sabatier - CNRS, 118 route de Narbonne, Toulouse Cedex, F-31062, France
| | - Guillaume Schwob
- Laboratoire d'Ecologie Microbienne, UMR5557, CNRS, INRA, VetAgro Sup, UCBL, Université de Lyon, Villeurbanne, 69622, France
| | - Sophie Manzi
- Laboratoire Evolution et Diversité Biologique, UMR5174, Université Paul Sabatier - CNRS, 118 route de Narbonne, Toulouse Cedex, F-31062, France
| | - Monique Gardes
- Laboratoire Evolution et Diversité Biologique, UMR5174, Université Paul Sabatier - CNRS, 118 route de Narbonne, Toulouse Cedex, F-31062, France
| | - Pierre-Arthur Moreau
- Laboratoire IMPECS EA 4483, Fac. Pharma. Lille, Université de Lille, Lille, F-59000, France
| | - Maria P Fernandez
- Laboratoire d'Ecologie Microbienne, UMR5557, CNRS, INRA, VetAgro Sup, UCBL, Université de Lyon, Villeurbanne, 69622, France
| |
Collapse
|
116
|
Davison J, Moora M, Öpik M, Ainsaar L, Ducousso M, Hiiesalu I, Jairus T, Johnson N, Jourand P, Kalamees R, Koorem K, Meyer JY, Püssa K, Reier Ü, Pärtel M, Semchenko M, Traveset A, Vasar M, Zobel M. Microbial island biogeography: isolation shapes the life history characteristics but not diversity of root-symbiotic fungal communities. ISME JOURNAL 2018; 12:2211-2224. [PMID: 29884829 DOI: 10.1038/s41396-018-0196-8] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Revised: 03/07/2018] [Accepted: 03/29/2018] [Indexed: 11/09/2022]
Abstract
Island biogeography theory is one of the most influential paradigms in ecology. That island characteristics, including remoteness, can profoundly modulate biological diversity has been borne out by studies of animals and plants. By contrast, the processes influencing microbial diversity in island systems remain largely undetermined. We sequenced arbuscular mycorrhizal (AM) fungal DNA from plant roots collected on 13 islands worldwide and compared AM fungal diversity on islands with existing data from mainland sites. AM fungal communities on islands (even those >6000 km from the closest mainland) comprised few endemic taxa and were as diverse as mainland communities. Thus, in contrast to patterns recorded among macro-organisms, efficient dispersal appears to outweigh the effects of taxogenesis and extinction in regulating AM fungal diversity on islands. Nonetheless, AM fungal communities on more distant islands comprised a higher proportion of previously cultured and large-spored taxa, indicating that dispersal may be human-mediated or require tolerance of significant environmental stress, such as exposure to sunlight or high salinity. The processes driving large-scale patterns of microbial diversity are a key consideration for attempts to conserve and restore functioning ecosystems in this era of rapid global change.
Collapse
Affiliation(s)
- John Davison
- Institute of Ecology and Earth Sciences, University of Tartu, Lai 40, Tartu, 51005, Estonia.
| | - Mari Moora
- Institute of Ecology and Earth Sciences, University of Tartu, Lai 40, Tartu, 51005, Estonia
| | - Maarja Öpik
- Institute of Ecology and Earth Sciences, University of Tartu, Lai 40, Tartu, 51005, Estonia
| | - Leho Ainsaar
- Institute of Ecology and Earth Sciences, University of Tartu, Lai 40, Tartu, 51005, Estonia
| | - Marc Ducousso
- CIRAD UMR082 LSTM, 34398, Montpellier Cedex 5, France
| | - Inga Hiiesalu
- Institute of Ecology and Earth Sciences, University of Tartu, Lai 40, Tartu, 51005, Estonia
| | - Teele Jairus
- Institute of Ecology and Earth Sciences, University of Tartu, Lai 40, Tartu, 51005, Estonia
| | - Nancy Johnson
- Department of Biological Sciences, School of Earth and Sustainability, Northern Arizona University, Flagstaff, AZ, 86011-5694, USA
| | | | - Rein Kalamees
- Institute of Ecology and Earth Sciences, University of Tartu, Lai 40, Tartu, 51005, Estonia
| | - Kadri Koorem
- Institute of Ecology and Earth Sciences, University of Tartu, Lai 40, Tartu, 51005, Estonia
| | - Jean-Yves Meyer
- Délégation à la Recherche de la Polynésie française, Bâtiment du Gouvernement, Avenue Pouvanaa a Oopa, B.P. 20981, 98713, Papeete, Tahiti, French Polynesia
| | - Kersti Püssa
- Institute of Ecology and Earth Sciences, University of Tartu, Lai 40, Tartu, 51005, Estonia
| | - Ülle Reier
- Institute of Ecology and Earth Sciences, University of Tartu, Lai 40, Tartu, 51005, Estonia
| | - Meelis Pärtel
- Institute of Ecology and Earth Sciences, University of Tartu, Lai 40, Tartu, 51005, Estonia
| | - Marina Semchenko
- School of Earth and Environmental Sciences, University of Manchester, Oxford Road, Manchester, M13 9PL, UK
| | - Anna Traveset
- Global Change Research Group, Mediterranean Institute of Advanced Studies, CSIC-UIB, Miquel Marqués 21, Esporles, 07190, Mallorca, Spain
| | - Martti Vasar
- Institute of Ecology and Earth Sciences, University of Tartu, Lai 40, Tartu, 51005, Estonia
| | - Martin Zobel
- Institute of Ecology and Earth Sciences, University of Tartu, Lai 40, Tartu, 51005, Estonia
| |
Collapse
|
117
|
Smith GR, Steidinger BS, Bruns TD, Peay KG. Competition-colonization tradeoffs structure fungal diversity. THE ISME JOURNAL 2018; 12:1758-1767. [PMID: 29491493 PMCID: PMC6018791 DOI: 10.1038/s41396-018-0086-0] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Revised: 01/28/2018] [Accepted: 02/07/2018] [Indexed: 01/13/2023]
Abstract
Findings of immense microbial diversity are at odds with observed functional redundancy, as competitive exclusion should hinder coexistence. Tradeoffs between dispersal and competitive ability could resolve this contradiction, but the extent to which they influence microbial community assembly is unclear. Because fungi influence the biogeochemical cycles upon which life on earth depends, understanding the mechanisms that maintain the richness of their communities is critically important. Here, we focus on ectomycorrhizal fungi, which are microbial plant mutualists that significantly affect global carbon dynamics and the ecology of host plants. Synthesizing theory with a decade of empirical research at our study site, we show that competition-colonization tradeoffs structure diversity in situ and that models calibrated only with empirically derived competition-colonization tradeoffs can accurately predict species-area relationships in this group of key eukaryotic microbes. These findings provide evidence that competition-colonization tradeoffs can sustain the landscape-scale diversity of microbes that compete for a single limiting resource.
Collapse
Affiliation(s)
- Gabriel R Smith
- Department of Biology, Stanford University, Stanford, CA, 94305, USA.
| | | | - Thomas D Bruns
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA
| | - Kabir G Peay
- Department of Biology, Stanford University, Stanford, CA, 94305, USA.
| |
Collapse
|
118
|
Zeng Q, Rodrigo A. Neutral models of short-term microbiome dynamics with host subpopulation structure and migration limitation. MICROBIOME 2018; 6:80. [PMID: 29703247 PMCID: PMC5921780 DOI: 10.1186/s40168-018-0464-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Accepted: 04/19/2018] [Indexed: 05/10/2023]
Abstract
BACKGROUND Most empirical studies tend to focus on microbiome dynamics within hosts or microbiome compositional differences between hosts over short periods. However, there is still a dearth of formal models that allow us to investigate the observed short-term dynamics of microbiomes under a unified ecological and evolutionary framework. In our previous study, we developed a computational agent-based neutral framework that simulates microbiome dynamics spanning many host generations with the added dimension of a genealogy of hosts. Although this long-term framework revealed interesting microbial diversity patterns under a simple but plausible evolutionary process and provided a platform for future elaboration of more complex systems, it does not allow us to explore microbiome dynamics within a single host generation. METHODS In this paper, we developed a computational, agent-based, forward-time framework of microbiome dynamics within a single host generation. As we have done under our neutral long-term models, we incorporate neutral processes of environmental microbiome assembly and microbe acquisition from parents and environment. We also incorporate a Moran genealogical model of hosts, so that the dynamics of microbiome evolution can be studied within a single host generation. Furthermore, we allow host subpopulation structure and host migration to affect microbiome recruitment. RESULTS We show that microbiome diversity within hosts increases monotonically with increases in environmental contribution, while microbiome diversity between hosts increases with increasing parental inheritance. Host population division and dispersal limitation under high host contribution further shaped the patterns by elevating microbiome differences between hosts and depressing microbial diversity within hosts. Microbiome diversity within the whole population showed strong temporal stability regardless of the modes of microbiome acquisition and subpopulation structures. CONCLUSIONS We present a computational framework that integrates various processes including host genealogy, microbe recruitment, and host dispersal limitation acting on the short-term dynamics of microbiomes. Our framework demonstrates that the neutral dynamics of microbiomes within a population of hosts is strongly influenced by transmission mode and shared environment.
Collapse
Affiliation(s)
- Qinglong Zeng
- Department of Biology, Duke University, Durham, NC USA
- Research School of Biology, The Australian National University, Canberra, ACT Australia
| | - Allen Rodrigo
- Research School of Biology, The Australian National University, Canberra, ACT Australia
| |
Collapse
|
119
|
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: 516] [Impact Index Per Article: 86.0] [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.
Collapse
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.
| |
Collapse
|
120
|
Spiesman BJ, Stapper AP, Inouye BD. Patch size, isolation, and matrix effects on biodiversity and ecosystem functioning in a landscape microcosm. Ecosphere 2018. [DOI: 10.1002/ecs2.2173] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Affiliation(s)
- Brian J. Spiesman
- Department of Biological Science Florida State University Tallahassee Florida 32306 USA
| | - Andres P. Stapper
- Department of Otolaryngology Stanford University Stanford California 94304 USA
| | - Brian D. Inouye
- Department of Biological Science Florida State University Tallahassee Florida 32306 USA
| |
Collapse
|
121
|
Abstract
Dispersal is a fundamental biological process, operating at multiple temporal and spatial scales. Despite an increasing understanding of fungal biodiversity, most research on fungal dispersal focuses on only a small fraction of species. Thus, any discussion of the dispersal dynamics of fungi as a whole is problematic. While abundant morphological and biogeographic data are available for hundreds of species, researchers have yet to integrate this information into a unifying paradigm of fungal dispersal, especially in the context of long-distance dispersal (LDD). Fungal LDD is mediated by multiple vectors, including meteorological phenomena (e.g., wind and precipitation), plants (e.g., seeds and senesced leaves), animals (e.g., fur, feathers, and gut microbiomes), and in many cases humans. In addition, fungal LDD is shaped by both physical constraints on travel and the ability of spores to survive harsh environments. Finally, fungal LDD is commonly measured in different ways, including by direct capture of spores, genetic comparisons of disconnected populations, and statistical modeling and simulations of dispersal data. To unify perspectives on fungal LDD, we propose a synthetic three-part definition that includes (i) an identification of the source population and a measure of the concentration of source inoculum and (ii) a measured and/or modeled dispersal kernel. With this information, LDD is defined as (iii) the distance found within the dispersal kernel beyond which only 1% of spores travel.
Collapse
|
122
|
Tian J, Zhu D, Wang J, Wu B, Hussain M, Liu X. Environmental factors driving fungal distribution in freshwater lake sediments across the Headwater Region of the Yellow River, China. Sci Rep 2018; 8:3768. [PMID: 29491438 PMCID: PMC5830880 DOI: 10.1038/s41598-018-21995-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Accepted: 02/14/2018] [Indexed: 11/29/2022] Open
Abstract
Dispersal limitation and environmental filtering are two primary processes involved in shaping microbial community structure. The pristine environmental and geographical relatively isolation of small lakes distributed in the Headwater Region of Yellow River (HRYR) offer a unique opportunity to test the relative roles of these two processes on fungal communities. Here, we investigated the fungal community in sediment samples from 10 lakes located in the HRYR using high-throughput sequencing. The results showed that the fungal community was dominated by Sordariomycetes, Leotiomycetes, Dothideomycetes, Pezizomycetes and Agaricomycetes. The results revealed that altitude, mean annual temperature, C/N ration, dissolve organic carbon and total nitrogen were the best predictors for shaping fungal community structure in these lakes. Significant spatial and environmental distance decay relationships in the fungal community were detected. The partial Mantel test indicated that the fungal community structure was significantly correlated with environmental distance but not with geographic distance. Overall, environmental filtering plays a more important role than dispersal limitation in fungal community structure at a local scale in such an pristine and isolated region.
Collapse
Affiliation(s)
- Jianqing Tian
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Dan Zhu
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
- Zoige Peatland and Global Change Research Station, Chinese Academy of Sciences, Hongyuan, 624400, China
| | - Jinzhi Wang
- Beijing Key Laboratory of Wetland Services and Restoration, Institute of Wetland Research, Chinese Academy of Forestry, Beijing, 100091, China
| | - Bing Wu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Muzammil Hussain
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xingzhong Liu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.
| |
Collapse
|
123
|
Variations in bacterial and archaeal communities along depth profiles of Alaskan soil cores. Sci Rep 2018; 8:504. [PMID: 29323168 PMCID: PMC5765012 DOI: 10.1038/s41598-017-18777-x] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Accepted: 12/12/2017] [Indexed: 12/20/2022] Open
Abstract
Understating the microbial communities and ecological processes that influence their structure in permafrost soils is crucial for predicting the consequences of climate change. In this study we investigated the bacterial and archaeal communities along depth profiles of four soil cores collected across Alaska. The bacterial and archaeal diversity (amplicon sequencing) overall decreased along the soil depth but the depth-wise pattern of their abundances (qPCR) varied by sites. The community structure of bacteria and archaea displayed site-specific pattern, with a greater role of soil geochemical characteristics rather than soil depth. In particular, we found significant positive correlations between methane trapped in cores and relative abundance of methanogenic archaeal genera, indicating a strong association between microbial activity and methane production in subsurface soils. We observed that bacterial phylogenetic community assembly tended to be more clustered in surface soils than in deeper soils. Analyses of phylogenetic community turnover among depth profiles across cores indicated that the relative influence of deterministic and stochastic processes was mainly determined by soil properties rather than depth. Overall, our findings emphasize that the vertical distributions of bacterial and archaeal communities in permafrost soils are to a large extent determined by the variation in site-specific soil properties.
Collapse
|
124
|
Miura T, Sánchez R, Castañeda LE, Godoy K, Barbosa O. Is microbial terroir related to geographic distance between vineyards? ENVIRONMENTAL MICROBIOLOGY REPORTS 2017; 9:742-749. [PMID: 28892290 DOI: 10.1111/1758-2229.12589] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Accepted: 08/28/2017] [Indexed: 05/20/2023]
Abstract
While there are substantial studies suggesting that characteristics of wine are related to regional microbial community composition (microbial terroir), there has been little discussion about what factors affect variation in regional microbial community composition. In this study, we compared the microbial community composition of leaves and berries of a grape variety (Carmenere) from six different Chilean vineyards within 35 km of each other. In order to determine relationships between spatial proximity and microbial compositional dissimilarity, we sequenced amplicons of the internal transcribed spacer (ITS) region for fungi and 16S rRNA gene for bacteria. Results showed that both the fungal and the bacterial community compositions of the studied vineyards differed, but this difference was much clearer in fungi than in bacteria. In addition, while bacterial community dissimilarity was not correlated with geographic distance, the leaf and berry fungal community dissimilarities between locations increased with geographic distance. This indicates that spatial processes play an important role in structuring the biogeographic pattern of grape-associated fungal communities at local scales, which might in turn contribute to the local identity of wine.
Collapse
Affiliation(s)
- Toshiko Miura
- Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
- Instituto de Ecología & Biodiversidad (IEB-Chile), Casilla 653, Santiago, Chile
| | - Roland Sánchez
- Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
- Instituto de Ecología & Biodiversidad (IEB-Chile), Casilla 653, Santiago, Chile
| | - Luis E Castañeda
- Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
- Millennium Nucleus Center in Molecular Ecology and Evolutionary Applications in the Agroecosystems, Universidad de Talca, Talca, Chile
| | - Karina Godoy
- Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
- Instituto de Ecología & Biodiversidad (IEB-Chile), Casilla 653, Santiago, Chile
| | - Olga Barbosa
- Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
- Instituto de Ecología & Biodiversidad (IEB-Chile), Casilla 653, Santiago, Chile
| |
Collapse
|
125
|
Glassman SI, Wang IJ, Bruns TD. Environmental filtering by
pH
and soil nutrients drives community assembly in fungi at fine spatial scales. Mol Ecol 2017; 26:6960-6973. [DOI: 10.1111/mec.14414] [Citation(s) in RCA: 151] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Revised: 10/17/2017] [Accepted: 10/25/2017] [Indexed: 12/15/2022]
Affiliation(s)
- Sydney I. Glassman
- Department of Environmental Science Policy and Management University of California, Berkeley CA USA
- Department of Ecology and Evolutionary Biology University of California, Irvine CA USA
- Department of Plant & Microbial Biology University of California Berkeley CA USA
| | - Ian J. Wang
- Department of Environmental Science Policy and Management University of California, Berkeley CA USA
| | - Thomas D. Bruns
- Department of Environmental Science Policy and Management University of California, Berkeley CA USA
- Department of Plant & Microbial Biology University of California Berkeley CA USA
| |
Collapse
|
126
|
Luria CM, Amaral-Zettler LA, Ducklow HW, Repeta DJ, Rhyne AL, Rich JJ. Seasonal Shifts in Bacterial Community Responses to Phytoplankton-Derived Dissolved Organic Matter in the Western Antarctic Peninsula. Front Microbiol 2017; 8:2117. [PMID: 29163409 PMCID: PMC5675858 DOI: 10.3389/fmicb.2017.02117] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Accepted: 10/17/2017] [Indexed: 11/13/2022] Open
Abstract
Bacterial consumption of dissolved organic matter (DOM) drives much of the movement of carbon through the oceanic food web and the global carbon cycle. Understanding complex interactions between bacteria and marine DOM remains an important challenge. We tested the hypothesis that bacterial growth and community succession would respond differently to DOM additions due to seasonal changes in phytoplankton abundance in the environment. Four mesocosm experiments were conducted that spanned the spring transitional period (August-December 2013) in surface waters of the Western Antarctic Peninsula (WAP). Each mesocosm consisted of nearshore surface seawater (50 L) incubated in the laboratory for 10 days. The addition of DOM, in the form of cell-free exudates extracted from Thalassiosira weissflogii diatom cultures led to changes in bacterial abundance, production, and community composition. The timing of each mesocosm experiment (i.e., late winter vs. late spring) influenced the magnitude and direction of bacterial changes. For example, the same DOM treatment applied at different times during the season resulted in different levels of bacterial production and different bacterial community composition. There was a mid-season shift from Collwelliaceae to Polaribacter having the greatest relative abundance after incubation. This shift corresponded to a modest but significant increase in the initial relative abundance of Polaribacter in the nearshore seawater used to set up experiments. This finding supports a new hypothesis that starting community composition, through priority effects, influenced the trajectory of community succession in response to DOM addition. As strong inter-annual variability and long-term climate change may shift the timing of WAP phytoplankton blooms, and the corresponding production of DOM exudates, this study suggests a mechanism by which different seasonal successional patterns in bacterial communities could occur.
Collapse
Affiliation(s)
- Catherine M. Luria
- Department of Ecology and Evolutionary Biology, Brown University, Providence, RI, United States
| | - Linda A. Amaral-Zettler
- Marine Biological Laboratory, Josephine Bay Paul Center, Woods Hole, MA, United States
- Department of Earth, Environmental and Planetary Sciences, Brown University, Providence, RI, United States
- NIOZ Royal Netherlands Institute for Sea Research, Utrecht University, Den Burg, Netherlands
| | - Hugh W. Ducklow
- Lamont-Doherty Earth Observatory, Columbia University, Palisades, NY, United States
| | - Daniel J. Repeta
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, United States
| | - Andrew L. Rhyne
- Department of Biology, Marine Biology, and Environmental Science, Roger Williams University, Bristol, RI, United States
| | - Jeremy J. Rich
- School of Marine Sciences, Darling Marine Center, University of Maine, Walpole, ME, United States
| |
Collapse
|
127
|
Caiafa M, Gómez-Hernández M, Williams-Linera G, Ramírez-Cruz V. Functional diversity of macromycete communities along an environmental gradient in a Mexican seasonally dry tropical forest. FUNGAL ECOL 2017. [DOI: 10.1016/j.funeco.2017.04.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
|
128
|
Tian J, Qiao Y, Wu B, Chen H, Li W, Jiang N, Zhang X, Liu X. Ecological Succession Pattern of Fungal Community in Soil along a Retreating Glacier. Front Microbiol 2017; 8:1028. [PMID: 28649234 PMCID: PMC5465267 DOI: 10.3389/fmicb.2017.01028] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Accepted: 05/22/2017] [Indexed: 01/12/2023] Open
Abstract
Accelerated by global climate changing, retreating glaciers leave behind soil chronosequences of primary succession. Current knowledge of primary succession is mainly from studies of vegetation dynamics, whereas information about belowground microbes remains unclear. Here, we combined shifts in community assembly processes with microbial primary succession to better understand mechanisms governing the stochastic/deterministic balance. We investigated fungal succession and community assembly via high-throughput sequencing along a well-established glacier forefront chronosequence that spans 2-188 years of deglaciation. Shannon diversity and evenness peaked at a distance of 370 m and declined afterwards. The response of fungal diversity to distance varied in different phyla. Basidiomycota Shannon diversity significantly decreased with distance, while the pattern of Rozellomycota Shannon diversity was unimodal. Abundance of most frequencies OTU2 (Cryptococcus terricola) increased with successional distance, whereas that of OTU65 (Tolypocladium tundrense) decreased. Based on null deviation analyses, composition of the fungal community was initially governed by deterministic processes strongly but later less deterministic processes. Our results revealed that distance, altitude, soil microbial biomass carbon, soil microbial biomass nitrogen and [Formula: see text]-N significantly correlated with fungal community composition along the chronosequence. These results suggest that the drivers of fungal community are dynamics in a glacier chronosequence, that may relate to fungal ecophysiological traits and adaptation in an evolving ecosystem. The information will provide understanding the mechanistic underpinnings of microbial community assembly during ecosystem succession under different scales and scenario.
Collapse
Affiliation(s)
- Jianqing Tian
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of SciencesBeijing, China
| | - Yuchen Qiao
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of SciencesBeijing, China
- Beijing Radiation Centre, Beijing Academy of Science and TechnologyBeijing, China
| | - Bing Wu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of SciencesBeijing, China
| | - Huai Chen
- Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization and Ecological Restoration Biodiversity Conservation, Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of SciencesChengdu, China
- Zoige Peatland and Global Change Research Station, Chengdu Institute of Biology, Chinese Academy of SciencesHongyuan, China
| | - Wei Li
- School of Ecology and Environmental Science, Yunnan UniversityKunming, China
| | - Na Jiang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of SciencesBeijing, China
| | - Xiaoling Zhang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of SciencesBeijing, China
| | - Xingzhong Liu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of SciencesBeijing, China
| |
Collapse
|
129
|
Nuske S, Vernes K, May T, Claridge A, Congdon B, Krockenberger A, Abell S. Redundancy among mammalian fungal dispersers and the importance of declining specialists. FUNGAL ECOL 2017. [DOI: 10.1016/j.funeco.2017.02.005] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
|
130
|
|
131
|
Shanmugam SG, Magbanua ZV, Williams MA, Jangid K, Whitman WB, Peterson DG, Kingery WL. Bacterial Diversity Patterns Differ in Soils Developing in Sub-tropical and Cool-Temperate Ecosystems. MICROBIAL ECOLOGY 2017; 73:556-569. [PMID: 27889811 DOI: 10.1007/s00248-016-0884-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Accepted: 10/24/2016] [Indexed: 06/06/2023]
Abstract
Microbial diversity patterns have been surveyed in many different soils and ecosystems, but we are unaware of studies comparing similar soils developing from similar parent materials in contrasting climates. In 2008, developmental chronosequences with ages ranging from 105 to 500,000 years across Georgia (GA) and Michigan (MI) were studied to investigate how bacterial community composition and diversity change as a result of local environmental gradients that develop during pedogenesis. Geographic factors were studied between and within locations spanning two scales: (1) regionally between 0.1 and 50 and (2) ∼1700 km apart. The diversity was surveyed using high-throughput pyrosequencing, and variance partitioning was used to describe the effects of spatial, environmental, and spatio-environmental factors on bacterial community composition. At the local scale, variation in bacterial communities was most closely related to environmental factors (rM = 0.59, p = 0.0001). There were differences in bacterial communities between the two locations, indicating spatial biogeography. Estimates of bacterial diversity were much greater in MI (numbers of OTU, ACE, and Chao1) and remained 2-3× greater in MI than GA after removing the effect of soil properties. The large differences in diversity between geographically separated bacterial communities in different climates need further investigation. It is not known if the rare members of the community, which contributed to greater bacterial diversity in GA relative to MI, play an important role in ecosystem function but has been hypothesized to play a role in ecosystem resiliency, resistance, and stability. Further research on the link between bacterial diversity and spatial variability related to climate needs further investigation.
Collapse
Affiliation(s)
- Shankar G Shanmugam
- Department of Plant and Soil Sciences, Mississippi State University, 117 Dorman Hall, Mississippi State, MS, 39762, USA.
- Institute for Genomics, Biocomputing & Biotechnology, Mississippi State University, Mississippi State, MS, 39762, USA.
| | - Zenaida V Magbanua
- Department of Plant and Soil Sciences, Mississippi State University, 117 Dorman Hall, Mississippi State, MS, 39762, USA
- Institute for Genomics, Biocomputing & Biotechnology, Mississippi State University, Mississippi State, MS, 39762, USA
| | - Mark A Williams
- College of Agriculture and Life Sciences, Virginia Polytechnic and State University, Horticulture, 301 Latham Hall, Blacksburg, VA, 24060, USA
| | - Kamlesh Jangid
- Microbial Culture Collection, National Centre for Cell Science, Pune, 411007, Maharashtra, India
| | - William B Whitman
- Department of Microbiology, University of Georgia, 527 Biological Sciences, Athens, GA, 30602, USA
| | - Daniel G Peterson
- Department of Plant and Soil Sciences, Mississippi State University, 117 Dorman Hall, Mississippi State, MS, 39762, USA
- Institute for Genomics, Biocomputing & Biotechnology, Mississippi State University, Mississippi State, MS, 39762, USA
| | - William L Kingery
- Department of Plant and Soil Sciences, Mississippi State University, 117 Dorman Hall, Mississippi State, MS, 39762, USA
| |
Collapse
|
132
|
Habitat-specific patterns and drivers of bacterial β-diversity in China's drylands. ISME JOURNAL 2017; 11:1345-1358. [PMID: 28282041 DOI: 10.1038/ismej.2017.11] [Citation(s) in RCA: 154] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Revised: 12/19/2016] [Accepted: 01/13/2017] [Indexed: 11/08/2022]
Abstract
The existence of biogeographic patterns among most free-living microbial taxa has been well established, yet little is known about the underlying mechanisms that shape these patterns. Here, we examined soil bacterial β-diversity across different habitats in the drylands of northern China. We evaluated the relative importance of environmental factors versus geographic distance to a distance-decay relationship, which would be explained by the relative effect of basic ecological processes recognized as drivers of diversity patterns in macrobial theoretical models such as selection and dispersal. Although the similarity of bacterial communities significantly declined with increasing geographic distance, the distance-decay slope and the relative importance of factors driving distance-decay patterns varied across different habitats. A strong distance-decay relationship was observed in the alpine grassland, where the community similarity was influenced only by the environmental factors. In contrast, geographic distance was solely responsible for community similarity in the desert. Even the average compositional similarity among locations in the desert was distinctly lower compared with those in other habitats. We found no evidence that dispersal limitation strongly influenced the β-diversity of bacterial communities in the desert grassland and typical grassland. Together, our results provide robust evidence of habitat specificity for microbial diversity patterns and their underlying drivers. Our findings suggest that microorganisms also have multiple drivers of diversity patterns and some of which may be parallel to some fundamental processes for explaining biodiversity patterns in macroorganisms.
Collapse
|
133
|
Wilson AW, Hosaka K, Mueller GM. Evolution of ectomycorrhizas as a driver of diversification and biogeographic patterns in the model mycorrhizal mushroom genus Laccaria. THE NEW PHYTOLOGIST 2017; 213:1862-1873. [PMID: 28164331 PMCID: PMC5324586 DOI: 10.1111/nph.14270] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Accepted: 09/15/2016] [Indexed: 05/03/2023]
Abstract
A systematic and evolutionary ecology study of the model ectomycorrhizal (ECM) genus Laccaria was performed using herbarium material and field collections from over 30 countries covering its known geographic range. A four-gene (nrITS, 28S, RPB2, EF1α) nucleotide sequence dataset consisting of 232 Laccaria specimens was analyzed phylogenetically. The resulting Global Laccaria dataset was used for molecular dating and estimating diversification rates in the genus. Stable isotope analysis of carbon and nitrogen was used to evaluate the origin of Laccaria's ECM ecology. In all, 116 Laccaria molecular species were identified, resulting in a near 50% increase in its known diversity, including the new species described herein: Laccaria ambigua. Molecular dating indicates that the most recent common ancestor to Laccaria existed in the early Paleocene (56-66 million yr ago), probably in Australasia. At this time, Laccaria split into two lineages: one represented by the new species L. ambigua, and the other reflecting a large shift in diversification that resulted in the remainder of Laccaria. L. ambigua shows a different isotopic profile than all other Laccaria species. Isotopes and diversification results suggest that the evolution of the ECM ecology was a key innovation in the evolution of Laccaria. Diversification shifts associated with Laccaria's dispersal to the northern hemisphere are attributed to adaptations to new ecological niches.
Collapse
Affiliation(s)
- Andrew W. Wilson
- Chicago Botanic GardenPlant Science and Conservation1000 Lake Cook RoadGlencoeIL60022USA
- Sam Mitchel Herbarium of FungiDenver Botanic Gardens909 York StreetDenverCO80206USA
| | - Kentaro Hosaka
- Department of BotanyNational Museum of Nature and ScienceTsukubaIbaraki305‐0005Japan
| | - Gregory M. Mueller
- Chicago Botanic GardenPlant Science and Conservation1000 Lake Cook RoadGlencoeIL60022USA
| |
Collapse
|
134
|
Gao C, Shi NN, Chen L, Ji NN, Wu BW, Wang YL, Xu Y, Zheng Y, Mi XC, Ma KP, Guo LD. Relationships between soil fungal and woody plant assemblages differ between ridge and valley habitats in a subtropical mountain forest. THE NEW PHYTOLOGIST 2017; 213:1874-1885. [PMID: 28164340 DOI: 10.1111/nph.14287] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2016] [Accepted: 09/26/2016] [Indexed: 06/06/2023]
Abstract
Elucidating interactions of above-ground and below-ground communities in different habitat types is essential for understanding biodiversity maintenance and ecosystem functioning. Using 454 pyrosequencing of ITS2 sequences we examined the relationship between subtropical mountain forest soil fungal communities, abiotic conditions, and plant communities using correlation and partial models. Ridge and valley habitats with differing fungal communities were delineated. Total, saprotrophic and pathogenic fungal richness were significantly correlated with plant species richness and/or soil nutrients and moisture in the ridge habitat, but with habitat convexity or basal area of Castanopsis eyrei in the valley habitat. Ectomycorrhizal (EM) fungal richness was significantly correlated with basal area of C. eyrei and total EM plants in the ridge and valley habitats, respectively. Total, saprotrophic, pathogenic and EM fungal compositions were significantly correlated with plant species composition and geographic distance in the ridge habitat, but with various combinations of plant species composition, plant species richness, soil C : N ratio and pH or no variables in the valley habitat. Our findings suggest that mechanisms influencing soil fungal diversity and community composition differ between ridge and valley habitats, and relationships between fungal and woody plant assemblages depend on habitat types in the subtropical forest ecosystem.
Collapse
Affiliation(s)
- Cheng Gao
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Nan-Nan Shi
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Liang Chen
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Niu-Niu Ji
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Bin-Wei Wu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yong-Long Wang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ying Xu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yong Zheng
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xiang-Cheng Mi
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Ke-Ping Ma
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Liang-Dong Guo
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| |
Collapse
|
135
|
Glassman SI, Lubetkin KC, Chung JA, Bruns TD. The theory of island biogeography applies to ectomycorrhizal fungi in subalpine tree “islands” at a fine scale. Ecosphere 2017. [DOI: 10.1002/ecs2.1677] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Affiliation(s)
- Sydney I. Glassman
- Department of Ecology and Evolutionary Biology University of California Irvine California 92697 USA
- Department of Plant & Microbial Biology University of California Berkeley California 94720 USA
| | | | - Judy A. Chung
- Department of Plant & Microbial Biology University of California Berkeley California 94720 USA
| | - Thomas D. Bruns
- Department of Plant & Microbial Biology University of California Berkeley California 94720 USA
| |
Collapse
|
136
|
Rosenthal LM, Larsson KH, Branco S, Chung JA, Glassman SI, Liao HL, Peay KG, Smith DP, Talbot JM, Taylor JW, Vellinga EC, Vilgalys R, Bruns TD. Survey of corticioid fungi in North American pinaceous forests reveals hyperdiversity, underpopulated sequence databases, and species that are potentially ectomycorrhizal. Mycologia 2017; 109:115-127. [DOI: 10.1080/00275514.2017.1281677] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Lisa M. Rosenthal
- Department of Plant Pathology, University of California Davis, Davis, California 95818
| | | | - Sara Branco
- Ecologie, Systematique et Evolution, Université Paris Sud, CNRS, AgroParisTech, Université Paris-Saclay, 91405 Orsay, France
| | - Judy A. Chung
- Department of Environmental Science Policy and Management, University of California Berkeley, Berkeley, California 94720
| | - Sydney I. Glassman
- Department of Environmental Science Policy and Management, University of California Berkeley, Berkeley, California 94720
| | - Hui-Ling Liao
- Department of Biology, Duke University, Durham, North Carolina 27708
| | - Kabir G. Peay
- Department of Biology, Stanford University, Stanford, California 94305
| | - Dylan P. Smith
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, California 94720
| | | | - John W. Taylor
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, California 94720
| | - Else C. Vellinga
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, California 94720
| | - Rytas Vilgalys
- Department of Biology, Duke University, Durham, North Carolina 27708
| | - Thomas D. Bruns
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, California 94720
| |
Collapse
|
137
|
Galante TE, Horton TR, Swaney DP. 95% of basidiospores fall within 1 m of the cap: a field-and modeling-based study. Mycologia 2017; 103:1175-83. [PMID: 21700637 DOI: 10.3852/10-388] [Citation(s) in RCA: 82] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Tera E. Galante
- Department of Forest and Wildlife Ecology, University of Wisconsin at Madison, 120 Russell Labs, 1630 Linden Drive, Madison, Wisconsin 53706-1520
| | - Thomas R. Horton
- Department of Environmental Forest Biology, SUNY-ESF, 350 Illick Hall, 1 Forestry Drive, Syracuse, New York 13210
| | - Dennis P. Swaney
- Department of Ecology and Evolutionary Biology, E309b Corson Hall, Cornell University, Ithaca, New York 14853
| |
Collapse
|
138
|
Overview of Phylogenetic Approaches to Mycorrhizal Biogeography, Diversity and Evolution. BIOGEOGRAPHY OF MYCORRHIZAL SYMBIOSIS 2017. [DOI: 10.1007/978-3-319-56363-3_1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
|
139
|
Environmental and Geographical Factors Structure Soil Microbial Diversity in New Caledonian Ultramafic Substrates: A Metagenomic Approach. PLoS One 2016. [PMID: 27907121 DOI: 10.1371/journal.pone.0167405,] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Soil microorganisms play key roles in ecosystem functioning and are known to be influenced by biotic and abiotic factors, such as plant cover or edaphic parameters. New Caledonia, a biodiversity hotspot located in the southwest Pacific, is one-third covered by ultramafic substrates. These types of soils are notably characterised by low nutrient content and high heavy metal concentrations. Ultramafic outcrops harbour diverse vegetation types and remarkable plant diversity. In this study, we aimed to assess soil bacterial and fungal diversity in New Caledonian ultramafic substrates and to determine whether floristic composition, edaphic parameters and geographical factors affect this microbial diversity. Therefore, four plant formation types at two distinct sites were studied. These formations represent different stages in a potential chronosequence. Soil cores, according to a given sampling procedure, were collected to assess microbial diversity using a metagenomic approach, and to characterise the physico-chemical parameters. A botanical inventory was also performed. Our results indicated that microbial richness, composition and abundance were linked to the plant cover type and the dominant plant species. Furthermore, a large proportion of Ascomycota phylum (fungi), mostly in non-rainforest formations, and Planctomycetes phylum (bacteria) in all formations were observed. Interestingly, such patterns could be indicators of past disturbances that occurred on different time scales. Furthermore, the bacteria and fungi were influenced by diverse edaphic parameters as well as by the interplay between these two soil communities. Another striking finding was the existence of a site effect. Differences in microbial communities between geographical locations may be explained by dispersal limitation in the context of the biogeographical island theory. In conclusion, each plant formation at each site possesses is own microbial community resulting from multiple interactions between abiotic and biotic factors.
Collapse
|
140
|
Gourmelon V, Maggia L, Powell JR, Gigante S, Hortal S, Gueunier C, Letellier K, Carriconde F. Environmental and Geographical Factors Structure Soil Microbial Diversity in New Caledonian Ultramafic Substrates: A Metagenomic Approach. PLoS One 2016; 11:e0167405. [PMID: 27907121 PMCID: PMC5131939 DOI: 10.1371/journal.pone.0167405] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Accepted: 11/14/2016] [Indexed: 11/30/2022] Open
Abstract
Soil microorganisms play key roles in ecosystem functioning and are known to be influenced by biotic and abiotic factors, such as plant cover or edaphic parameters. New Caledonia, a biodiversity hotspot located in the southwest Pacific, is one-third covered by ultramafic substrates. These types of soils are notably characterised by low nutrient content and high heavy metal concentrations. Ultramafic outcrops harbour diverse vegetation types and remarkable plant diversity. In this study, we aimed to assess soil bacterial and fungal diversity in New Caledonian ultramafic substrates and to determine whether floristic composition, edaphic parameters and geographical factors affect this microbial diversity. Therefore, four plant formation types at two distinct sites were studied. These formations represent different stages in a potential chronosequence. Soil cores, according to a given sampling procedure, were collected to assess microbial diversity using a metagenomic approach, and to characterise the physico-chemical parameters. A botanical inventory was also performed. Our results indicated that microbial richness, composition and abundance were linked to the plant cover type and the dominant plant species. Furthermore, a large proportion of Ascomycota phylum (fungi), mostly in non-rainforest formations, and Planctomycetes phylum (bacteria) in all formations were observed. Interestingly, such patterns could be indicators of past disturbances that occurred on different time scales. Furthermore, the bacteria and fungi were influenced by diverse edaphic parameters as well as by the interplay between these two soil communities. Another striking finding was the existence of a site effect. Differences in microbial communities between geographical locations may be explained by dispersal limitation in the context of the biogeographical island theory. In conclusion, each plant formation at each site possesses is own microbial community resulting from multiple interactions between abiotic and biotic factors.
Collapse
Affiliation(s)
- Véronique Gourmelon
- Institut Agronomique néo-Calédonien (IAC), Axe 2 "Diversités biologique et fonctionnelle des écosystèmes terrestres", Nouméa, New Caledonia
| | - Laurent Maggia
- Institut Agronomique néo-Calédonien (IAC), Axe 2 "Diversités biologique et fonctionnelle des écosystèmes terrestres", Nouméa, New Caledonia.,CIRAD, UMR AGAP, Nouméa, New Caledonia
| | - Jeff R Powell
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, New South Wales, Australia
| | - Sarah Gigante
- Institut Agronomique néo-Calédonien (IAC), Axe 2 "Diversités biologique et fonctionnelle des écosystèmes terrestres", Nouméa, New Caledonia
| | - Sara Hortal
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, New South Wales, Australia
| | - Claire Gueunier
- Société Le Nickel (SLN) - Groupe ERAMET, Département Environnement, Nouméa, New Caledonia
| | - Kelly Letellier
- Institut Agronomique néo-Calédonien (IAC), Axe 2 "Diversités biologique et fonctionnelle des écosystèmes terrestres", Nouméa, New Caledonia
| | - Fabian Carriconde
- Institut Agronomique néo-Calédonien (IAC), Axe 2 "Diversités biologique et fonctionnelle des écosystèmes terrestres", Nouméa, New Caledonia
| |
Collapse
|
141
|
Tipton AG, Miller‐Struttmann NE, Galen C. Finding partners in a habitat mosaic: Patch history and size mediate host colonization by arbuscular mycorrhizal fungi. Ecosphere 2016. [DOI: 10.1002/ecs2.1570] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
- Alice G. Tipton
- Division of Biological Sciences University of Missouri 105 Tucker Hall Columbia Missouri 65211 USA
- Kansas Biological Survey University of Kansas 2101 Constant Avenue Lawrence Kansas 66047 USA
| | - Nicole E. Miller‐Struttmann
- Division of Biological Sciences University of Missouri 105 Tucker Hall Columbia Missouri 65211 USA
- Biological Sciences Department Webster University Webster Hall Rm 13, 470 East Lockwood Avenue St. Louis Missouri 63119 USA
| | - Candace Galen
- Division of Biological Sciences University of Missouri 105 Tucker Hall Columbia Missouri 65211 USA
| |
Collapse
|
142
|
Fort T, Robin C, Capdevielle X, Delière L, Vacher C. Foliar fungal communities strongly differ between habitat patches in a landscape mosaic. PeerJ 2016; 4:e2656. [PMID: 27833817 PMCID: PMC5101609 DOI: 10.7717/peerj.2656] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Accepted: 10/05/2016] [Indexed: 11/28/2022] Open
Abstract
Background Dispersal events between habitat patches in a landscape mosaic can structure ecological communities and influence the functioning of agrosystems. Here we investigated whether short-distance dispersal events between vineyard and forest patches shape foliar fungal communities. We hypothesized that these communities homogenize between habitats over the course of the growing season, particularly along habitat edges, because of aerial dispersal of spores. Methods We monitored the richness and composition of foliar and airborne fungal communities over the season, along transects perpendicular to edges between vineyard and forest patches, using Illumina sequencing of the Internal Transcribed Spacer 2 (ITS2) region. Results In contrast to our expectation, foliar fungal communities in vineyards and forest patches increasingly differentiate over the growing season, even along habitat edges. Moreover, the richness of foliar fungal communities in grapevine drastically decreased over the growing season, in contrast to that of forest trees. The composition of airborne communities did not differ between habitats. The composition of oak foliar fungal communities change between forest edge and centre. Discussion These results suggest that dispersal events between habitat patches are not major drivers of foliar fungal communities at the landscape scale. Selective pressures exerted in each habitat by the host plant, the microclimate and the agricultural practices play a greater role, and might account for the differentiation of foliar fugal communities between habitats.
Collapse
Affiliation(s)
- Thomas Fort
- BIOGECO, UMR 1202, INRA, Université de Bordeaux , Cestas , France
| | - Cécile Robin
- BIOGECO, UMR 1202, INRA, Université de Bordeaux , Cestas , France
| | | | - Laurent Delière
- SAVE, UMR 1065, INRA, ISVV, Université de Bordeaux , Villenave d'Ornon , France
| | - Corinne Vacher
- BIOGECO, UMR 1202, INRA, Université de Bordeaux , Pessac , France
| |
Collapse
|
143
|
Peay KG. The Mutualistic Niche: Mycorrhizal Symbiosis and Community Dynamics. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2016. [DOI: 10.1146/annurev-ecolsys-121415-032100] [Citation(s) in RCA: 83] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The niche is generally viewed in terms of species' intrinsic physiological potential and limitations due to competition. Although DNA sequencing has revealed the ubiquity of beneficial microbial symbioses, the role of mutualisms in shaping species niches is not broadly recognized. In this review, I use a widespread terrestrial mutualism, the ectomycorrhizal symbiosis, to help develop the mutualistic niche concept. Using contemporary niche theory, I show how mycorrhizal symbioses expand environmental ranges (requirement niche) and influence resource use (impact niche) for both plants and fungi. Simple niche models for competition between resource specialists and generalists also predict a range of ecological phenomena, from unexpected monodominance by some tropical trees to the functional biogeography of mycorrhizal symbiosis. A niche-based view of mutualism may also help explain stability of mutualisms even in the absence of clear benefits. The niche is a central concept in ecology, and better integration of mutualism will more accurately reflect the positive interactions experienced by nearly all species.
Collapse
Affiliation(s)
- Kabir G. Peay
- Department of Biology, Stanford University, Stanford, California 94122
| |
Collapse
|
144
|
Vannette RL, Leopold DR, Fukami T. Forest area and connectivity influence root‐associated fungal communities in a fragmented landscape. Ecology 2016; 97:2374-2383. [DOI: 10.1002/ecy.1472] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Revised: 03/14/2016] [Accepted: 03/25/2016] [Indexed: 11/05/2022]
Affiliation(s)
| | - Devin R. Leopold
- Department of Biology Stanford University Stanford California 94305 USA
| | - Tadashi Fukami
- Department of Biology Stanford University Stanford California 94305 USA
| |
Collapse
|
145
|
Effects of dispersal and selection on stochastic assembly in microbial communities. ISME JOURNAL 2016; 11:176-185. [PMID: 27494293 DOI: 10.1038/ismej.2016.96] [Citation(s) in RCA: 186] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Revised: 06/02/2016] [Accepted: 06/07/2016] [Indexed: 11/08/2022]
Abstract
Stochastic processes can play an important role in microbial community assembly. Dispersal limitation is one process that can increase stochasticity and obscure relationships between environmental variables and microbial community composition, but the relationship between dispersal, selection and stochasticity has not been described in a comprehensive way. We examine how dispersal and its interactions with drift and selection alter the consistency with which microbial communities assemble using a realistic, individual-based model of microbial decomposers. Communities were assembled under different environmental conditions and dispersal rates in repeated simulations, and we examined the compositional difference among replicate communities colonizing the same type of leaf litter ('within-group distance'), as well as between-group deterministic selection. Dispersal rates below 25% turnover per year resulted in high within-group distance among communities and no significant environmental effects. As dispersal limitation was alleviated, both within- and between-group distance decreased, but despite this homogenization, deterministic environmental effects remained significant. In addition to direct effects of dispersal rate, stochasticity of community composition was influenced by an interaction between dispersal and selection strength. Specifically, communities experiencing stronger selection (less favorable litter chemistries) were more stochastic, possibly because lower biomass and richness intensified drift or priority effects. Overall, we show that dispersal rate can significantly alter patterns of community composition. Partitioning the effects of dispersal, selection and drift based on static patterns of microbial composition will be difficult, if not impossible. Experiments will be required to tease apart these complex interactions between assembly processes shaping microbial communities.
Collapse
|
146
|
Jackson D, Zemenick AT, Malloure B, Quandt CA, James TY. Fine-scale spatial genetic structure of a fungal parasite of coffee scale insects. J Invertebr Pathol 2016; 139:34-41. [PMID: 27449676 DOI: 10.1016/j.jip.2016.07.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2016] [Revised: 07/12/2016] [Accepted: 07/18/2016] [Indexed: 01/21/2023]
Abstract
The entomopathogenic fungus Lecanicillium lecanii persists in a highly dynamic network of habitat patches (i.e., a metapopulation) formed by its primary host, the green coffee scale Coccus viridis. Lecanicillium lecanii is an important biological control of both C. viridis and the coffee rust, Hemileia vastatrix. Successfully managing this biocontrol agent will depend on an increased understanding of the characteristics of its dispersal, as migration between occupied and unoccupied patches is essential for the persistence of this metapopulation. In the present study, we employ a population genetics approach, and show that in our study system, a coffee farm in the Soconusco region of southern Mexico, L. lecanii is characterized by clear spatial genetic structure among plots within the farm but a lack of apparent structure at smaller scales. This is consistent with dispersal dominated by highly localized transport, such as by insects or rain splash, and less dependence on longer distance dispersal such as wind transport. The study site was dominated by a few multi-locus microsatellite genotypes, and their identities and large-scale locations persist across both study years, suggesting that local epizootics (outbreaks) are initiated each wet season by residual propagules from the previous wet season, and not by long-distance transport of propagules from other sites. The index of association, a measure of linkage disequilibrium, indicates that epizootics are primarily driven by asexual, clonal reproduction, which is consistent with the apparent lack of a teleomorph in the study site and the presence of only a single mating type across the site (MAT-1-2-1). Although the same predominant clonal genotypes were found across years, a drastic difference in genotypic diversity was witnessed across two sites between the two years, suggesting that interclonal selection was occurring. In light of the dispersal limitation of L. lecanii, spatial structure may be an essential axis of management to ensure the persistence of L. lecanii and preserve the ecosystem services provided by this versatile biocontrol agent in this and similar coffee farms.
Collapse
Affiliation(s)
- Doug Jackson
- Department of Ecology and Evolutionary Biology, University of Michigan, 2019 Kraus Nat. Sci. Bldg., 830 North University, Ann Arbor, MI 48109, USA.
| | - Ash T Zemenick
- Department of Ecology and Evolutionary Biology, University of Michigan, 2019 Kraus Nat. Sci. Bldg., 830 North University, Ann Arbor, MI 48109, USA
| | - Brian Malloure
- Department of Ecology and Evolutionary Biology, University of Michigan, 2019 Kraus Nat. Sci. Bldg., 830 North University, Ann Arbor, MI 48109, USA
| | - C Alisha Quandt
- Department of Ecology and Evolutionary Biology, University of Michigan, 2019 Kraus Nat. Sci. Bldg., 830 North University, Ann Arbor, MI 48109, USA
| | - Timothy Y James
- Department of Ecology and Evolutionary Biology, University of Michigan, 2019 Kraus Nat. Sci. Bldg., 830 North University, Ann Arbor, MI 48109, USA
| |
Collapse
|
147
|
Bauman D, Raspé O, Meerts P, Degreef J, Ilunga Muledi J, Drouet T. Multiscale assemblage of an ectomycorrhizal fungal community: the influence of host functional traits and soil properties in a 10-ha miombo forest. FEMS Microbiol Ecol 2016; 92:fiw151. [PMID: 27402715 DOI: 10.1093/femsec/fiw151] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/04/2016] [Indexed: 11/14/2022] Open
Abstract
Ectomycorrhizal fungi (EMF) are highly diversified and dominant in a number of forest ecosystems. Nevertheless, their scales of spatial distribution and the underlying ecological processes remain poorly understood. Although most EMF are considered to be generalists regarding host identity, a preference toward functional strategies of host trees has never been tested. Here, the EMF community was characterised by DNA sequencing in a 10-ha tropical dry season forest-referred to as miombo-an understudied ecosystem from a mycorrhizal perspective. We used 36 soil parameters and 21 host functional traits (FTs) as candidate explanatory variables in spatial constrained ordinations for explaining the EMF community assemblage. Results highlighted that the community variability was explained by host FTs related to the 'leaf economics spectrum' (adjusted R(2) = 11%; SLA, leaf area, foliar Mg content), and by soil parameters (adjusted R(2) = 17%), notably total forms of micronutrients or correlated available elements (Al, N, K, P). Both FTs and soil generated patterns in the community at scales ranging from 75 to 375 m. Our results indicate that soil is more important than previously thought for EMF in miombo woodlands, and show that FTs of host species can be better predictors of symbiont distribution than taxonomical identity.
Collapse
Affiliation(s)
- David Bauman
- Laboratoire d'Écologie Végétale et Biogéochimie, Université Libre de Bruxelles, 50 av. F. D. Roosevelt, CP 244, 1050 Brussels, Belgium
| | - Olivier Raspé
- Department of Bryophyta and Thallophyta, Botanic Garden Meise, 38 Nieuwlaan, B-1860 Meise, Belgium Fédération Wallonie-Bruxelles, Direction Générale de l'Enseignement non obligatoire et de la Recherche scientifique, Rue A. Lavallée 1, 1080 Brussels, Belgium
| | - Pierre Meerts
- Laboratoire d'Écologie Végétale et Biogéochimie, Université Libre de Bruxelles, 50 av. F. D. Roosevelt, CP 244, 1050 Brussels, Belgium
| | - Jérôme Degreef
- Department of Bryophyta and Thallophyta, Botanic Garden Meise, 38 Nieuwlaan, B-1860 Meise, Belgium Fédération Wallonie-Bruxelles, Direction Générale de l'Enseignement non obligatoire et de la Recherche scientifique, Rue A. Lavallée 1, 1080 Brussels, Belgium
| | - Jonathan Ilunga Muledi
- Faculté des Sciences agronomiques, Université de Lubumbashi, Route Kasapa, BP 1825 Lubumbashi, The Democratic Republic of the Congo
| | - Thomas Drouet
- Laboratoire d'Écologie Végétale et Biogéochimie, Université Libre de Bruxelles, 50 av. F. D. Roosevelt, CP 244, 1050 Brussels, Belgium
| |
Collapse
|
148
|
Lankau RA, Keymer DP. Ectomycorrhizal fungal richness declines towards the host species’ range edge. Mol Ecol 2016; 25:3224-41. [DOI: 10.1111/mec.13628] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Accepted: 03/15/2016] [Indexed: 01/01/2023]
Affiliation(s)
- Richard A. Lankau
- Department of Plant Biology University of Georgia Athens GA 30606 USA
| | - Daniel P. Keymer
- Department of Plant Biology University of Georgia Athens GA 30606 USA
| |
Collapse
|
149
|
Microbial interactions lead to rapid micro-scale successions on model marine particles. Nat Commun 2016; 7:11965. [PMID: 27311813 PMCID: PMC4915023 DOI: 10.1038/ncomms11965] [Citation(s) in RCA: 241] [Impact Index Per Article: 30.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Accepted: 05/16/2016] [Indexed: 01/24/2023] Open
Abstract
In the ocean, organic particles harbour diverse bacterial communities, which collectively digest and recycle essential nutrients. Traits like motility and exo-enzyme production allow individual taxa to colonize and exploit particle resources, but it remains unclear how community dynamics emerge from these individual traits. Here we track the taxon and trait dynamics of bacteria attached to model marine particles and demonstrate that particle-attached communities undergo rapid, reproducible successions driven by ecological interactions. Motile, particle-degrading taxa are selected for during early successional stages. However, this selective pressure is later relaxed when secondary consumers invade, which are unable to use the particle resource but, instead, rely on carbon from primary degraders. This creates a trophic chain that shifts community metabolism away from the particle substrate. These results suggest that primary successions may shape particle-attached bacterial communities in the ocean and that rapid community-wide metabolic shifts could limit rates of marine particle degradation. Particles of organic matter in the ocean harbour microbial communities that digest and recycle essential nutrients. Here, Datta et al. use model marine particles to show that the attached bacterial communities undergo rapid, reproducible successions driven by ecological interactions.
Collapse
|
150
|
Bödeker ITM, Lindahl BD, Olson Å, Clemmensen KE. Mycorrhizal and saprotrophic fungal guilds compete for the same organic substrates but affect decomposition differently. Funct Ecol 2016. [DOI: 10.1111/1365-2435.12677] [Citation(s) in RCA: 134] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Affiliation(s)
- Inga T. M. Bödeker
- Department of Forest Mycology and Plant Pathology Swedish University of Agricultural Sciences Uppsala BioCenter Box 7026 SE‐750 07 Uppsala Sweden
- Southern Swedish Forest Research Centre Swedish University of Agricultural Sciences Box 49 SE‐230 53 Alnarp Sweden
| | - Björn D. Lindahl
- Department of Soil and Environment Swedish University of Agricultural Sciences Box 7014 SE‐750 07 Uppsala Sweden
| | - Åke Olson
- Department of Forest Mycology and Plant Pathology Swedish University of Agricultural Sciences Uppsala BioCenter Box 7026 SE‐750 07 Uppsala Sweden
| | - Karina E. Clemmensen
- Department of Forest Mycology and Plant Pathology Swedish University of Agricultural Sciences Uppsala BioCenter Box 7026 SE‐750 07 Uppsala Sweden
| |
Collapse
|