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Tecon R, Or D. Biophysical processes supporting the diversity of microbial life in soil. FEMS Microbiol Rev 2017; 41:599-623. [PMID: 28961933 PMCID: PMC5812502 DOI: 10.1093/femsre/fux039] [Citation(s) in RCA: 136] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Accepted: 07/10/2017] [Indexed: 12/13/2022] Open
Abstract
Soil, the living terrestrial skin of the Earth, plays a central role in supporting life and is home to an unimaginable diversity of microorganisms. This review explores key drivers for microbial life in soils under different climates and land-use practices at scales ranging from soil pores to landscapes. We delineate special features of soil as a microbial habitat (focusing on bacteria) and the consequences for microbial communities. This review covers recent modeling advances that link soil physical processes with microbial life (termed biophysical processes). Readers are introduced to concepts governing water organization in soil pores and associated transport properties and microbial dispersion ranges often determined by the spatial organization of a highly dynamic soil aqueous phase. The narrow hydrological windows of wetting and aqueous phase connectedness are crucial for resource distribution and longer range transport of microorganisms. Feedbacks between microbial activity and their immediate environment are responsible for emergence and stabilization of soil structure-the scaffolding for soil ecological functioning. We synthesize insights from historical and contemporary studies to provide an outlook for the challenges and opportunities for developing a quantitative ecological framework to delineate and predict the microbial component of soil functioning.
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Affiliation(s)
- Robin Tecon
- Soil and Terrestrial Environmental Physics, Department of Environmental Systems Science, ETH Zürich, Universitätstrasse 16, 8092 Zürich, Switzerland
| | - Dani Or
- Soil and Terrestrial Environmental Physics, Department of Environmental Systems Science, ETH Zürich, Universitätstrasse 16, 8092 Zürich, Switzerland
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52
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Schwob G, Roy M, Manzi S, Pommier T, Fernandez MP. Green alder (
Alnus viridis
) encroachment shapes microbial communities in subalpine soils and impacts its bacterial or fungal symbionts differently. Environ Microbiol 2017; 19:3235-3250. [DOI: 10.1111/1462-2920.13818] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Revised: 06/01/2017] [Accepted: 06/06/2017] [Indexed: 12/13/2022]
Affiliation(s)
- G. Schwob
- CNRS, UMR 5557, INRA, UMR 1418, Laboratoire d'Ecologie MicrobienneUniversité de Lyon, Université Lyon143, Boulevard du 11 novembre 1918Villeurbanne Cedex 69622 France
| | - M. Roy
- Laboratoire Evolution et Diversité BiologiqueUMR 5174 UPS CNRS ENFA IRDToulouse France
| | - S. Manzi
- Laboratoire Evolution et Diversité BiologiqueUMR 5174 UPS CNRS ENFA IRDToulouse France
| | - T. Pommier
- CNRS, UMR 5557, INRA, UMR 1418, Laboratoire d'Ecologie MicrobienneUniversité de Lyon, Université Lyon143, Boulevard du 11 novembre 1918Villeurbanne Cedex 69622 France
| | - M. P. Fernandez
- CNRS, UMR 5557, INRA, UMR 1418, Laboratoire d'Ecologie MicrobienneUniversité de Lyon, Université Lyon143, Boulevard du 11 novembre 1918Villeurbanne Cedex 69622 France
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53
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Han Q, Huang J, Long D, Wang X, Liu J. Diversity and community structure of ectomycorrhizal fungi associated with Larix chinensis across the alpine treeline ecotone of Taibai Mountain. MYCORRHIZA 2017; 27:487-497. [PMID: 28280941 DOI: 10.1007/s00572-017-0766-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Accepted: 02/16/2017] [Indexed: 06/06/2023]
Abstract
Alpine treeline ecotones represent ecosystems that are vulnerable to climate change. We investigated the ectomycorrhizal (ECM) community, which has potential to stabilize alpine ecosystems. ECM communities associated with Larix chinensis were studied in four zones along a natural ecotone from a mixed forest stand over pure forest stands, the timberline, and eventually, the treeline (3050-3450 m) in Tabai Mountain, China. Sixty operational taxonomic units (OTUs) of ECM fungi were identified by sequencing the rDNA internal transcribed spacer of ECM tips. The richness of ECM species increased with elevation. The soil C/N ratio was the most important factor explaining ECM species richness. The treeline zone harbored some unique ECM fungi whereas no unique genera were observed in the timberline and pure forest zone. Elevation and topography were equally important factors influencing ECM communities in the alpine region. We suggest that a higher diversity of the ECM fungal community associated with L. chinensis in the treeline zone could result from niche differentiation.
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Affiliation(s)
- Qisheng Han
- College of Forestry, Northwest A&F University, Yangling, 712100, China
| | - Jian Huang
- College of Forestry, Northwest A&F University, Yangling, 712100, China.
| | - Dongfeng Long
- College of Forestry, Northwest A&F University, Yangling, 712100, China
| | - Xiaobing Wang
- College of Forestry, Northwest A&F University, Yangling, 712100, China
| | - Jianjun Liu
- College of Landscape Architecture and Arts, Northwest A&F University, Yangling, 712100, China.
- Ningxia Helan Mountain Forest Ecosystem Orientational Research Station, Yinchuan, 750000, China.
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54
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Should Environmental Filtering be Abandoned? Trends Ecol Evol 2017; 32:429-437. [DOI: 10.1016/j.tree.2017.03.004] [Citation(s) in RCA: 388] [Impact Index Per Article: 55.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Revised: 03/07/2017] [Accepted: 03/08/2017] [Indexed: 11/23/2022]
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Abstract
Fungi represent a large proportion of the genetic diversity on Earth and fungal activity influences the structure of plant and animal communities, as well as rates of ecosystem processes. Large-scale DNA-sequencing datasets are beginning to reveal the dimensions of fungal biodiversity, which seem to be fundamentally different to bacteria, plants and animals. In this Review, we describe the patterns of fungal biodiversity that have been revealed by molecular-based studies. Furthermore, we consider the evidence that supports the roles of different candidate drivers of fungal diversity at a range of spatial scales, as well as the role of dispersal limitation in maintaining regional endemism and influencing local community assembly. Finally, we discuss the ecological mechanisms that are likely to be responsible for the high heterogeneity that is observed in fungal communities at local scales.
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Affiliation(s)
- Kabir G Peay
- Department of Biology, Stanford University, Stanford, California 94305, USA
| | - Peter G Kennedy
- Department of Plant Biology, University of Minnesota.,Department of Ecology, Evolution and Behavior, University of Minnesota, St. Paul, Minnesota 55108, USA
| | - Jennifer M Talbot
- Department of Biology, Boston University, Boston, Massachusetts 02215, USA
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56
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Mamet SD, Lamb EG, Piper CL, Winsley T, Siciliano SD. Archaea and bacteria mediate the effects of native species root loss on fungi during plant invasion. THE ISME JOURNAL 2017; 11:1261-1275. [PMID: 28140393 PMCID: PMC5437935 DOI: 10.1038/ismej.2016.205] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Revised: 11/16/2016] [Accepted: 12/15/2016] [Indexed: 01/21/2023]
Abstract
Although invasive plants can drive ecosystem change, little is known about the directional nature of belowground interactions between invasive plants, native roots, bacteria, archaea and fungi. We used detailed bioinformatics and a recently developed root assay on soils collected in fescue grassland along a gradient of smooth brome (Bromus inermis Leyss) invasion to examine the links between smooth brome shoot litter and root, archaea, bacteria and fungal communities. We examined (1) aboveground versus belowground influences of smooth brome on soil microbial communities, (2) the importance of direct versus microbe-mediated impacts of plants on soil fungal communities, and (3) the web of roots, shoots, archaea, bacteria and fungi interactions across the A and B soil horizons in invaded and non-invaded sites. Archaea and bacteria influenced fungal composition, but not vice versa, as indicated by redundancy analyses. Co-inertia analyses suggested that bacterial-fungal variance was driven primarily by 12 bacterial operational taxonomic units (OTUs). Brome increased bacterial diversity via smooth brome litter in the A horizon and roots in the B horizon, which then reduced fungal diversity. Archaea increased abundance of several bacterial OTUs, and the key bacterial OTUs mediated changes in the fungi's response to invasion. Overall, native root diversity loss and bacterial mediation were more important drivers of fungal composition than were the direct effects of increases in smooth brome. Critically, native plant species displacement and root loss appeared to be the most important driver of fungal composition during invasion. This causal web likely gives rise to the plant-fungi feedbacks, which are an essential factor determining plant diversity in invaded grassland ecosystems.
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Affiliation(s)
- Steven D Mamet
- Department of Soil Science, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Eric G Lamb
- Department of Plant Science, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Candace L Piper
- Department of Plant Science, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Tristrom Winsley
- Department of Soil Science, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Steven D Siciliano
- Department of Soil Science, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
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57
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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.
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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
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58
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Casazza G, Lumini E, Ercole E, Dovana F, Guerrina M, Arnulfo A, Minuto L, Fusconi A, Mucciarelli M. The abundance and diversity of arbuscular mycorrhizal fungi are linked to the soil chemistry of screes and to slope in the Alpic paleo-endemic Berardia subacaulis. PLoS One 2017; 12:e0171866. [PMID: 28192471 PMCID: PMC5305098 DOI: 10.1371/journal.pone.0171866] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Accepted: 01/26/2017] [Indexed: 01/12/2023] Open
Abstract
Berardia subacaulis Vill. is a monospecific genus that is endemic to the South-western Alps, where it grows on alpine screes, which are extreme habitats characterized by soil disturbance and limiting growth conditions. Root colonization by arbuscular mycorrhizal fungi (AMF) is presumably of great importance in these environments, because of its positive effect on plant nutrition and stress tolerance, as well as on structuring the soil. However, there is currently a lack of information on this topic. In this paper, we tested which soil characteristics and biotic factors could contribute to determining the abundance and community composition of AMF in the roots of B. subacaulis, which had previously been found to be mycorrhizal. For such a reason, the influence of soil properties and environmental factors on AMF abundance and community composition in the roots of B. subacaulis, sampled on three different scree slopes, were analysed through microscopic and molecular analysis. The results have shown that the AMF community of Berardia roots was dominated by Glomeraceae, and included a core of AMF taxa, common to all three scree slopes. The vegetation coverage and dark septate endophytes were not related to the AMF colonization percentage and plant community did not influence the root AMF composition. The abundance of AMF in the roots was related to some chemical (available extractable calcium and potassium) and physical (cation exchange capacity, electrical conductivity and field capacity) properties of the soil, thus suggesting an effect of AMF on improving the soil quality. The non-metric multidimensional scaling (NMDS) ordination of the AMF community composition showed that the diversity of AMF in the various sites was influenced not only by the soil quality, but also by the slope. Therefore, the slope-induced physical disturbance of alpine screes may contribute to the selection of disturbance-tolerant AMF taxa, which in turn may lead to different plant-fungus assemblages.
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Affiliation(s)
| | - Erica Lumini
- Istituto per la Protezione Sostenibile delle Piante–CNR, Viale P.A. Mattioli 25, TORINO, Italy
| | - Enrico Ercole
- Dipartimento di Scienze della Vita e Biologia dei Sistemi, Università di Torino, Viale P.A. Mattioli 25, TORINO, Italy
| | - Francesco Dovana
- Dipartimento di Scienze della Vita e Biologia dei Sistemi, Università di Torino, Viale P.A. Mattioli 25, TORINO, Italy
| | - Maria Guerrina
- Università di Genova, DISTAV, Corso Europa 26, GENOVA, Italy
| | - Annamaria Arnulfo
- Dipartimento di Scienze della Vita e Biologia dei Sistemi, Università di Torino, Viale P.A. Mattioli 25, TORINO, Italy
| | - Luigi Minuto
- Università di Genova, DISTAV, Corso Europa 26, GENOVA, Italy
| | - Anna Fusconi
- Dipartimento di Scienze della Vita e Biologia dei Sistemi, Università di Torino, Viale P.A. Mattioli 25, TORINO, Italy
| | - Marco Mucciarelli
- Dipartimento di Scienze della Vita e Biologia dei Sistemi, Università di Torino, Viale P.A. Mattioli 25, TORINO, Italy
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59
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da Silva IR, da Silva DKA, de Souza FA, Oehl F, Maia LC. Changes in arbuscular mycorrhizal fungal communities along a river delta island in northeastern Brazil. ACTA OECOLOGICA 2017. [DOI: 10.1016/j.actao.2016.12.011] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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60
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LeBlanc N, Kinkel L, Kistler HC. Plant diversity and plant identity influence Fusarium communities in soil. Mycologia 2017; 109:128-139. [PMID: 28402790 DOI: 10.1080/00275514.2017.1281697] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Fusarium communities play important functional roles in soil and in plants as pathogens, endophytes, and saprotrophs. This study tests how rhizosphere Fusarium communities may vary with plant species, changes in the diversity of the surrounding plant community, and soil physiochemical characteristics. Fusarium communities in soil associated with the roots of two perennial prairie plant species maintained as monocultures or growing within polyculture plant communities were characterized using targeted metagenomics. Amplicon libraries targeting the RPB2 locus were generated from rhizosphere soil DNAs and sequenced using pyrosequencing. Sequences were clustered into operational taxonomic units (OTUs) and assigned a taxonomy using the Evolutionary Placement Algorithm. Fusarium community composition was differentiated between monoculture and polyculture plant communities, and by plant species in monoculture, but not in polyculture. Taxonomic classification of the Fusarium OTUs showed a predominance of F. tricinctum and F. oxysporum as well of the presence of a clade previously only found in the Southern Hemisphere. Total Fusarium richness was not affected by changes in plant community richness or correlated with soil physiochemical characteristics. However, OTU richness within two predominant phylogenetic lineages within the genus was positively or negatively correlated with soil physiochemical characteristics among samples within each lineage. This work shows that plant species, plant community richness, and soil physiochemical characteristics may all influence the composition and richness of Fusarium communities in soil.
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Affiliation(s)
- Nicholas LeBlanc
- a Department of Plant Pathology , University of Minnesota , St. Paul , Minnesota 55108
| | - Linda Kinkel
- a Department of Plant Pathology , University of Minnesota , St. Paul , Minnesota 55108
| | - H Corby Kistler
- a Department of Plant Pathology , University of Minnesota , St. Paul , Minnesota 55108.,b United States Department of Agriculture, Agricultural Research Service Cereal Disease Laboratory , University of Minnesota , St. Paul , Minnesota 55108
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61
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Sanders IR, Rodriguez A. Aligning molecular studies of mycorrhizal fungal diversity with ecologically important levels of diversity in ecosystems. THE ISME JOURNAL 2016; 10:2780-2786. [PMID: 27128992 PMCID: PMC5148194 DOI: 10.1038/ismej.2016.73] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Revised: 03/10/2016] [Accepted: 03/23/2016] [Indexed: 02/02/2023]
Abstract
Arbuscular mycorrhizal fungi (AMF) occur in the roots of most plants and are an ecologically important component of the soil microbiome. Richness of AMF taxa is a strong driver of plant diversity and productivity, thus providing a rationale for characterizing AMF diversity in natural ecosystems. Consequently, a large number of molecular studies on AMF community composition are currently underway. Most published studies, at best, only address species or genera-level resolution. However, several experimental studies indicate that variation in plant performance is large among plants colonised by different individuals of one AMF species. Thus, there is a potential disparity between how molecular community ecologists are currently describing AMF diversity and the level of AMF diversity that may actually be ecologically relevant. We propose a strategy to find many polymorphic loci that can define within-species genetic variability within AMF, or at any level of resolution desired within the Glomermycota. We propose that allele diversity at the intraspecific level could then be measured for target AMF groups, or at other levels of resolution, in environmental DNA samples. Combining the use of such markers with experimental studies on AMF diversity would help to elucidate the most important level(s) of AMF diversity in plant communities. Our goal is to encourage ecologists who are trying to explain how mycorrhizal fungal communities are structured to take an approach that could also yield meaningful information that is relevant to the diversity, functioning and productivity of ecosystems.
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Affiliation(s)
- Ian R Sanders
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Alia Rodriguez
- Biology Department, Faculty of Science, National University of Colombia, Ciudad Universitaria, Bogotá, Colombia
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62
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Xu T, Veresoglou SD, Chen Y, Rillig MC, Xiang D, Ondřej D, Hao Z, Liu L, Deng Y, Hu Y, Chen W, Wang J, He J, Chen B. Plant community, geographic distance and abiotic factors play different roles in predicting AMF biogeography at the regional scale in northern China. ENVIRONMENTAL MICROBIOLOGY REPORTS 2016; 8:1048-1057. [PMID: 27718332 DOI: 10.1111/1758-2229.12485] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Arbuscular mycorrhizal fungi (AMF) are ubiquitous mutualists of terrestrial plants and play key roles in regulating various ecosystem processes, but little is known about AMF biogeography at regional scale. This study aims at exploring the key predictors of AMF communities across a 5000-km transect in northern China. We determined the soil AMF species richness and community composition at 47 sites representative of four vegetation types (meadow steppe, typical steppe, desert steppe and desert) and related them to plant community characteristics, abiotic factors and geographic distance. The results showed that soil pH was the strongest predictor of AMF richness and phylogenetic diversity. However, abiotic factors only have a low predictive effect on AMF community composition or phylogenetic patterns. By contrast, we found a significant relationship between community composition of AMF and plants, which was a surprising result given the extent of heterogeneity in the plant community across this transect. Moreover, the geographic distance predominantly explained the AMF phylogenetic structure, implying that history evolutionary may play a role in shaping AMF biogeographic patterns. This study highlighted the different roles of main factors in predicting AMF biogeography, and bridge landscape-scale studies to more recent global-scale efforts.
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Affiliation(s)
- Tianle Xu
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- Collage of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Stavros D Veresoglou
- Freie Universität Berlin-Institut für Biologie, Dahlem Center of Plant Sciences, Plant Ecology, Berlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin, Germany (BIBB)
| | - Yongliang Chen
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany Chinese Academy of Sciences, Beijing, China
| | - Matthias C Rillig
- Freie Universität Berlin-Institut für Biologie, Dahlem Center of Plant Sciences, Plant Ecology, Berlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin, Germany (BIBB)
| | - Dan Xiang
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- College of Resources and Environment, Qingdao Agricultural University, Qingdao, China
| | - Daniel Ondřej
- Department of Mycorrhizal Symbioses, Institute of Botany Academy of Sciences of the Czech Republic, Průhonice, Czech Republic
| | - Zhipeng Hao
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Lei Liu
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Ye Deng
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Yajun Hu
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- Key laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture Chinese Academy of Sciences, Changsha, China
| | - Weiping Chen
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Juntao Wang
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Jizheng He
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Baodong Chen
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
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63
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Yashiro E, Pinto-Figueroa E, Buri A, Spangenberg JE, Adatte T, Niculita-Hirzel H, Guisan A, van der Meer JR. Local Environmental Factors Drive Divergent Grassland Soil Bacterial Communities in the Western Swiss Alps. Appl Environ Microbiol 2016; 82:6303-6316. [PMID: 27542929 DOI: 10.1128/aem.01170-16.editor] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Accepted: 07/28/2016] [Indexed: 05/22/2023] Open
Abstract
UNLABELLED Mountain ecosystems are characterized by a diverse range of climatic and topographic conditions over short distances and are known to shelter a high biodiversity. Despite important progress, still little is known on bacterial diversity in mountain areas. Here, we investigated soil bacterial biogeography at more than 100 sampling sites randomly stratified across a 700-km2 area with 2,200-m elevation gradient in the western Swiss Alps. Bacterial grassland communities were highly diverse, with 12,741 total operational taxonomic units (OTUs) across 100 sites and an average of 2,918 OTUs per site. Bacterial community structure was correlated with local climatic, topographic, and soil physicochemical parameters with high statistical significance. We found pH (correlated with % CaO and % mineral carbon), hydrogen index (correlated with bulk gravimetric water content), and annual average number of frost days during the growing season to be among the groups of the most important environmental drivers of bacterial community structure. In contrast, bacterial community structure was only weakly stratified as a function of elevation. Contrasting patterns were discovered for individual bacterial taxa. Acidobacteria responded both positively and negatively to pH extremes. Various families within the Bacteroidetes responded to available phosphorus levels. Different verrucomicrobial groups responded to electrical conductivity, total organic carbon, water content, and mineral carbon contents. Alpine grassland bacterial communities are thus highly diverse, which is likely due to the large variety of different environmental conditions. These results shed new light on the biodiversity of mountain ecosystems, which were already identified as potentially fragile to anthropogenic influences and climate change. IMPORTANCE This article addresses the question of how microbial communities in alpine regions are dependent on local climatic and soil physicochemical variables. We benefit from a unique 700-km2 study region in the western Swiss Alps region, which has been exhaustively studied for macro-organismal and fungal ecology, and for topoclimatic modeling of future ecological trends, but without taking into account soil bacterial diversity. Here, we present an in-depth biogeographical characterization of the bacterial community diversity in this alpine region across 100 randomly stratified sites, using 56 environmental variables. Our exhaustive sampling ensured the detection of ecological trends with high statistical robustness. Our data both confirm previously observed general trends and show many new detailed trends for a wide range of bacterial taxonomic groups and environmental parameters.
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Affiliation(s)
- Erika Yashiro
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Eric Pinto-Figueroa
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Aline Buri
- Institute of Earth Surface Dynamics, University of Lausanne, Lausanne, Switzerland
| | - Jorge E Spangenberg
- Institute of Earth Surface Dynamics, University of Lausanne, Lausanne, Switzerland
| | - Thierry Adatte
- Institute of Earth Sciences, University of Lausanne, Lausanne, Switzerland
| | - Hélène Niculita-Hirzel
- Institute for Work and Health, University of Lausanne and Geneva, Epalinges-Lausanne, Switzerland
| | - Antoine Guisan
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland Institute of Earth Surface Dynamics, University of Lausanne, Lausanne, Switzerland
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Local Environmental Factors Drive Divergent Grassland Soil Bacterial Communities in the Western Swiss Alps. Appl Environ Microbiol 2016; 82:6303-6316. [PMID: 27542929 DOI: 10.1128/aem.01170-16] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Accepted: 07/28/2016] [Indexed: 02/01/2023] Open
Abstract
Mountain ecosystems are characterized by a diverse range of climatic and topographic conditions over short distances and are known to shelter a high biodiversity. Despite important progress, still little is known on bacterial diversity in mountain areas. Here, we investigated soil bacterial biogeography at more than 100 sampling sites randomly stratified across a 700-km2 area with 2,200-m elevation gradient in the western Swiss Alps. Bacterial grassland communities were highly diverse, with 12,741 total operational taxonomic units (OTUs) across 100 sites and an average of 2,918 OTUs per site. Bacterial community structure was correlated with local climatic, topographic, and soil physicochemical parameters with high statistical significance. We found pH (correlated with % CaO and % mineral carbon), hydrogen index (correlated with bulk gravimetric water content), and annual average number of frost days during the growing season to be among the groups of the most important environmental drivers of bacterial community structure. In contrast, bacterial community structure was only weakly stratified as a function of elevation. Contrasting patterns were discovered for individual bacterial taxa. Acidobacteria responded both positively and negatively to pH extremes. Various families within the Bacteroidetes responded to available phosphorus levels. Different verrucomicrobial groups responded to electrical conductivity, total organic carbon, water content, and mineral carbon contents. Alpine grassland bacterial communities are thus highly diverse, which is likely due to the large variety of different environmental conditions. These results shed new light on the biodiversity of mountain ecosystems, which were already identified as potentially fragile to anthropogenic influences and climate change. IMPORTANCE This article addresses the question of how microbial communities in alpine regions are dependent on local climatic and soil physicochemical variables. We benefit from a unique 700-km2 study region in the western Swiss Alps region, which has been exhaustively studied for macro-organismal and fungal ecology, and for topoclimatic modeling of future ecological trends, but without taking into account soil bacterial diversity. Here, we present an in-depth biogeographical characterization of the bacterial community diversity in this alpine region across 100 randomly stratified sites, using 56 environmental variables. Our exhaustive sampling ensured the detection of ecological trends with high statistical robustness. Our data both confirm previously observed general trends and show many new detailed trends for a wide range of bacterial taxonomic groups and environmental parameters.
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Nguyen NH, Williams LJ, Vincent JB, Stefanski A, Cavender-Bares J, Messier C, Paquette A, Gravel D, Reich PB, Kennedy PG. Ectomycorrhizal fungal diversity and saprotrophic fungal diversity are linked to different tree community attributes in a field-based tree experiment. Mol Ecol 2016; 25:4032-46. [DOI: 10.1111/mec.13719] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Revised: 05/23/2016] [Accepted: 05/26/2016] [Indexed: 12/31/2022]
Affiliation(s)
- Nhu H. Nguyen
- Department of Plant Biology; University of Minnesota; St. Paul MN USA
| | - Laura J. Williams
- Department of Ecology, Evolution and Behavior; University of Minnesota; St. Paul MN USA
| | - John B. Vincent
- Department of Plant Biology; University of Minnesota; St. Paul MN USA
| | - Artur Stefanski
- Department of Forest Resources; University of Minnesota; St. Paul MN USA
| | | | - Christian Messier
- Department of Biological Sciences; University of Quebec; Montreal QC Canada
| | - Alain Paquette
- Department of Biological Sciences; University of Quebec; Montreal QC Canada
| | - Dominique Gravel
- Department of Biology; University of Sherbrooke; Sherbrooke QC Canada
| | - Peter B. Reich
- Department of Forest Resources; University of Minnesota; St. Paul MN USA
| | - Peter G. Kennedy
- Department of Plant Biology; University of Minnesota; St. Paul MN USA
- Department of Ecology, Evolution and Behavior; University of Minnesota; St. Paul MN USA
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Soil pH, total phosphorus, climate and distance are the major factors influencing microbial activity at a regional spatial scale. Sci Rep 2016; 6:25815. [PMID: 27170469 PMCID: PMC4864422 DOI: 10.1038/srep25815] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Accepted: 04/18/2016] [Indexed: 11/08/2022] Open
Abstract
Considering the extensive functional redundancy in microbial communities and great difficulty in elucidating it based on taxonomic structure, studies on the biogeography of soil microbial activity at large spatial scale are as important as microbial community structure. Eighty-four soil samples were collected across a region from south to north China (about 1,000 km) to address the questions if microbial activity displays biogeographic patterns and what are driving forces. These samples represented different soil types, land use and climate. Redundancy analysis and nonmetric multidimensional scaling clearly revealed that soil microbial activities showed distinct differentiation at different sites over a regional spatial scale, which were strongly affected by soil pH, total P, rainfall, temperature, soil type and location. In addition, microbial community structure was greatly influenced by rainfall, location, temperature, soil pH and soil type and was correlated with microbial activity to some extent. Our results suggest that microbial activities display a clear geographic pattern that is greatly altered by geographic distance and reflected by climate, soil pH and total P over large spatial scales. There are common (distance, climate, pH and soil type) but differentiated aspects (TP, SOC and N) in the biogeography of soil microbial community structure and activity.
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67
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Looby CI, Maltz MR, Treseder KK. Belowground responses to elevation in a changing cloud forest. Ecol Evol 2016; 6:1996-2009. [PMID: 27066220 PMCID: PMC4767876 DOI: 10.1002/ece3.2025] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Revised: 01/08/2016] [Accepted: 01/23/2016] [Indexed: 12/27/2022] Open
Abstract
Few studies have investigated how soil fungal communities respond to elevation, especially within TMCF (tropical montane cloud forests). We used an elevation gradient in a TMCF in Costa Rica to determine how soil properties, processes, and community composition of fungi change in response to elevation and across seasons. As elevation increased, soil temperature and soil pH decreased, while soil moisture and soil C:N ratios increased with elevation. Responses of these properties varied seasonally. Fungal abundance increased with elevation during wet and dry seasons. Fungal community composition shifted in response to elevation, and to a lesser extent by season. These shifts were accompanied by varying responses of important fungal functional groups during the wet season and the relative abundance of certain fungal phyla. We suggest that elevation and the responses of certain fungal functional groups may be structuring fungal communities along this elevation gradient. TMCF are ecosystems that are rapidly changing due to climate change. Our study suggests that these changes may affect how fungal communities are structured.
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Affiliation(s)
- Caitlin I. Looby
- Department of Ecology and Evolutionary BiologyUniversity of CaliforniaIrvineCalifornia92697
| | - Mia R. Maltz
- Department of Ecology and Evolutionary BiologyUniversity of CaliforniaIrvineCalifornia92697
| | - Kathleen K. Treseder
- Department of Ecology and Evolutionary BiologyUniversity of CaliforniaIrvineCalifornia92697
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Zhang Y, Ni J, Tang F, Pei K, Luo Y, Jiang L, Sun L, Liang Y. Root-associated fungi of Vaccinium carlesii in subtropical forests of China: intra- and inter-annual variability and impacts of human disturbances. Sci Rep 2016; 6:22399. [PMID: 26928608 PMCID: PMC4772160 DOI: 10.1038/srep22399] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Accepted: 02/15/2016] [Indexed: 11/09/2022] Open
Abstract
Ericoid mycorrhiza (ERM) are expected to facilitate establishment of ericaceous plants in harsh habitats. However, diversity and driving factors of the root-associated fungi of ericaceous plants are poorly understood. In this study, hair-root samples of Vaccinium carlesii were taken from four forest types: old growth forests (OGF), secondary forests with once or twice cutting (SEC I and SEC II), and Cunninghamia lanceolata plantation (PLF). Fungal communities were determined using high-throughput sequencing, and impacts of human disturbances and the intra- and inter-annual variability of root-associated fungal community were evaluated. Diverse fungal taxa were observed and our results showed that (1) Intra- and inter-annual changes in root-associated fungal community were found, and the Basidiomycota to Ascomycota ratio was related to mean temperature of the sampling month; (2) Human disturbances significantly affected structure of root-associated fungal community of V. carlesii, and two secondary forest types were similar in root-associated fungal community and were closer to that of the old growth forest; (3) Plant community composition, edaphic parameters, and geographic factors significantly affected root-associated fungal communities of V. carlesii. These results may be helpful in better understanding the maintenance mechanisms of fungal diversity associated with hair roots of ERM plants under human disturbances.
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Affiliation(s)
- Yanhua Zhang
- College of Life Sciences, Shaoxing University, Shaoxing, China
| | - Jian Ni
- College of Life Sciences, Shaoxing University, Shaoxing, China
| | - Fangping Tang
- College of Life Sciences, Shaoxing University, Shaoxing, China
| | - Kequan Pei
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Yiqi Luo
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK 73019, USA
| | - Lifen Jiang
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK 73019, USA
| | - Lifu Sun
- College of Life Sciences, Shaoxing University, Shaoxing, China
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK 73019, USA
| | - Yu Liang
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, China
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Tedersoo L, Bahram M, Cajthaml T, Põlme S, Hiiesalu I, Anslan S, Harend H, Buegger F, Pritsch K, Koricheva J, Abarenkov K. Tree diversity and species identity effects on soil fungi, protists and animals are context dependent. THE ISME JOURNAL 2016; 10:346-62. [PMID: 26172210 PMCID: PMC4737927 DOI: 10.1038/ismej.2015.116] [Citation(s) in RCA: 152] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Revised: 06/01/2015] [Accepted: 06/04/2015] [Indexed: 11/08/2022]
Abstract
Plant species richness and the presence of certain influential species (sampling effect) drive the stability and functionality of ecosystems as well as primary production and biomass of consumers. However, little is known about these floristic effects on richness and community composition of soil biota in forest habitats owing to methodological constraints. We developed a DNA metabarcoding approach to identify the major eukaryote groups directly from soil with roughly species-level resolution. Using this method, we examined the effects of tree diversity and individual tree species on soil microbial biomass and taxonomic richness of soil biota in two experimental study systems in Finland and Estonia and accounted for edaphic variables and spatial autocorrelation. Our analyses revealed that the effects of tree diversity and individual species on soil biota are largely context dependent. Multiple regression and structural equation modelling suggested that biomass, soil pH, nutrients and tree species directly affect richness of different taxonomic groups. The community composition of most soil organisms was strongly correlated due to similar response to environmental predictors rather than causal relationships. On a local scale, soil resources and tree species have stronger effect on diversity of soil biota than tree species richness per se.
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Affiliation(s)
- Leho Tedersoo
- Natural History Museum, University of Tartu, Tartu, Estonia
| | - Mohammad Bahram
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Tomáš Cajthaml
- Institute of Microbiology AS CR, Prague, Czech Republic
- Institute for Environmental Studies, Faculty of Science, Charles University in Prague, Prague, Czech Republic
| | - Sergei Põlme
- Natural History Museum, University of Tartu, Tartu, Estonia
| | - Indrek Hiiesalu
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Sten Anslan
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Helery Harend
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | | | | | - Julia Koricheva
- School of Biological Sciences, Royal Holloway University of London, Surrey, UK
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Airborne and Grain Dust Fungal Community Compositions Are Shaped Regionally by Plant Genotypes and Farming Practices. Appl Environ Microbiol 2016; 82:2121-2131. [PMID: 26826229 DOI: 10.1128/aem.03336-15] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Accepted: 01/22/2016] [Indexed: 12/26/2022] Open
Abstract
Chronic exposure to airborne fungi has been associated with different respiratory symptoms and pathologies in occupational populations, such as grain workers. However, the homogeneity in the fungal species composition of these bioaerosols on a large geographical scale and the different drivers that shape these fungal communities remain unclear. In this study, the diversity of fungi in grain dust and in the aerosols released during harvesting was determined across 96 sites at a geographical scale of 560 km(2) along an elevation gradient of 500 m by tag-encoded 454 pyrosequencing of the internal transcribed spacer (ITS) sequences. Associations between the structure of fungal communities in the grain dust and different abiotic (farming system, soil characteristics, and geographic and climatic parameters) and biotic (wheat cultivar and previous crop culture) factors were explored. These analyses revealed a strong relationship between the airborne and grain dust fungal communities and showed the presence of allergenic and mycotoxigenic species in most samples, which highlights the potential contribution of these fungal species to work-related respiratory symptoms of grain workers. The farming system was the major driver of the alpha and beta phylogenetic diversity values of fungal communities. In addition, elevation and soil CaCO3 concentrations shaped the alpha diversity, whereas wheat cultivar, cropping history, and the number of freezing days per year shaped the taxonomic beta diversity of these communities.
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Wang SK, Zuo XA, Zhao XY, Li YQ, Zhou X, Lv P, Luo YQ, Yun JY. Responses of soil fungal community to the sandy grassland restoration in Horqin Sandy Land, northern China. ENVIRONMENTAL MONITORING AND ASSESSMENT 2016; 188:21. [PMID: 26661957 DOI: 10.1007/s10661-015-5031-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2015] [Accepted: 12/02/2015] [Indexed: 06/05/2023]
Abstract
Sandy grassland restoration is a vital process including re-structure of soils, restoration of vegetation, and soil functioning in arid and semi-arid regions. Soil fungal community is a complex and critical component of soil functioning and ecological balance due to its roles in organic matter decomposition and nutrient cycling following sandy grassland restoration. In this study, soil fungal community and its relationship with environmental factors were examined along a habitat gradient of sandy grassland restoration: mobile dunes (MD), semi-fixed dunes (SFD), fixed dunes (FD), and grassland (G). It was found that species abundance, richness, and diversity of fungal community increased along with the sandy grassland restoration. The sequences analysis suggested that most of the fungal species (68.4 %) belonged to the phylum of Ascomycota. The three predominant fungal species were Pleospora herbarum, Wickerhamomyces anomalus, and Deconica Montana, accounting for more than one fourth of all the 38 species. Geranomyces variabilis was the subdominant species in MD, Pseudogymnoascus destructans and Mortierella alpine were the subdominant species in SFD, and P. destructans and Fungi incertae sedis were the dominant species in FD and G. The result from redundancy analysis (RDA) and stepwise regression analysis indicated that the vegetation characteristics and soil properties explain a significant proportion of the variation in the fungal community, and aboveground biomass and C:N ratio are the key factors to determine soil fungal community composition during sandy grassland restoration. It was suggested that the restoration of sandy grassland combined with vegetation and soil properties improved the soil fungal diversity. Also, the dominant species was found to be alternative following the restoration of sandy grassland ecosystems.
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Affiliation(s)
- Shao-Kun Wang
- Naiman Desertification Research Station, Cold and Arid Regions Environmental and Engineering Research Institute (CAREERI), Chinese Academy of Sciences (CAS), 320# Donggang West Road, Lanzhou, 730000, China.
- Laboratory of Stress Ecophysiology and Biotechnology (LSEB), CAREERI, CAS, Lanzhou, 730000, China.
| | - Xiao-An Zuo
- Naiman Desertification Research Station, Cold and Arid Regions Environmental and Engineering Research Institute (CAREERI), Chinese Academy of Sciences (CAS), 320# Donggang West Road, Lanzhou, 730000, China
- Laboratory of Stress Ecophysiology and Biotechnology (LSEB), CAREERI, CAS, Lanzhou, 730000, China
| | - Xue-Yong Zhao
- Naiman Desertification Research Station, Cold and Arid Regions Environmental and Engineering Research Institute (CAREERI), Chinese Academy of Sciences (CAS), 320# Donggang West Road, Lanzhou, 730000, China
- Laboratory of Stress Ecophysiology and Biotechnology (LSEB), CAREERI, CAS, Lanzhou, 730000, China
| | - Yu-Qiang Li
- Naiman Desertification Research Station, Cold and Arid Regions Environmental and Engineering Research Institute (CAREERI), Chinese Academy of Sciences (CAS), 320# Donggang West Road, Lanzhou, 730000, China
- Laboratory of Stress Ecophysiology and Biotechnology (LSEB), CAREERI, CAS, Lanzhou, 730000, China
| | - Xin Zhou
- Naiman Desertification Research Station, Cold and Arid Regions Environmental and Engineering Research Institute (CAREERI), Chinese Academy of Sciences (CAS), 320# Donggang West Road, Lanzhou, 730000, China
| | - Peng Lv
- Naiman Desertification Research Station, Cold and Arid Regions Environmental and Engineering Research Institute (CAREERI), Chinese Academy of Sciences (CAS), 320# Donggang West Road, Lanzhou, 730000, China
| | - Yong-Qing Luo
- Naiman Desertification Research Station, Cold and Arid Regions Environmental and Engineering Research Institute (CAREERI), Chinese Academy of Sciences (CAS), 320# Donggang West Road, Lanzhou, 730000, China
| | - Jian-Ying Yun
- Naiman Desertification Research Station, Cold and Arid Regions Environmental and Engineering Research Institute (CAREERI), Chinese Academy of Sciences (CAS), 320# Donggang West Road, Lanzhou, 730000, China
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72
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Rodolfi M, Longa CMO, Pertot I, Tosi S, Savino E, Guglielminetti M, Altobelli E, Del Frate G, Picco AM. Fungal biodiversity in the periglacial soil of Dosdè Glacier (Valtellina, Northern Italy). J Basic Microbiol 2015; 56:263-74. [PMID: 26575579 DOI: 10.1002/jobm.201500392] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Accepted: 10/18/2015] [Indexed: 11/09/2022]
Abstract
Periglacial areas are one of the least studied habitats on Earth, especially in terms of their fungal communities. In this work, both molecular and culture-dependent methods have been used to analyse the microfungi in soils sampled on the front of the East Dosdè Glacier (Valtellina, Northern Italy). Although this survey revealed a community that was rich in fungal species, a distinct group of psychrophilic microfungi has not been detected. Most of the isolated microfungi were mesophiles, which are well adapted to the sensitive climatic changes that occur in this alpine environment. A discrepancy in the results that were obtained by means of the two diagnostic approaches suggests that the used molecular methods cannot entirely replace traditional culture-dependent methods, and vice versa.
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Affiliation(s)
- Marinella Rodolfi
- Dipartimento di Scienze della Terra e dell'Ambiente, Università degli Studi di Pavia, Pavia, Italy
| | - Claudia Maria Oliveira Longa
- Dipartimento Agroecosistemi Sostenibile e Biorisorse, Fondazione Edmund Mach, Centro Ricerca e Innovazione, San Michele all'Adige (TN), Italy
| | - Ilaria Pertot
- Dipartimento Agroecosistemi Sostenibile e Biorisorse, Fondazione Edmund Mach, Centro Ricerca e Innovazione, San Michele all'Adige (TN), Italy
| | - Solveig Tosi
- Dipartimento di Scienze della Terra e dell'Ambiente, Università degli Studi di Pavia, Pavia, Italy
| | - Elena Savino
- Dipartimento di Scienze della Terra e dell'Ambiente, Università degli Studi di Pavia, Pavia, Italy
| | - Maria Guglielminetti
- Dipartimento di Scienze della Terra e dell'Ambiente, Università degli Studi di Pavia, Pavia, Italy
| | - Elisa Altobelli
- Dipartimento di Scienze della Terra e dell'Ambiente, Università degli Studi di Pavia, Pavia, Italy
| | - Giuseppe Del Frate
- Dipartimento di Scienze della Terra e dell'Ambiente, Università degli Studi di Pavia, Pavia, Italy
| | - Anna Maria Picco
- Dipartimento di Scienze della Terra e dell'Ambiente, Università degli Studi di Pavia, Pavia, Italy
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Jumpponen A, Brown SP, Trappe JM, Cázares E, Strömmer R. Analyses of Sporocarps, Morphotyped Ectomycorrhizae, Environmental ITS and LSU Sequences Identify Common Genera that Occur at a Periglacial Site. J Fungi (Basel) 2015; 1:76-93. [PMID: 29376900 PMCID: PMC5770010 DOI: 10.3390/jof1010076] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2015] [Accepted: 05/18/2015] [Indexed: 11/17/2022] Open
Abstract
Periglacial substrates exposed by retreating glaciers represent extreme and sensitive environments defined by a variety of abiotic stressors that challenge organismal establishment and survival. The simple communities often residing at these sites enable their analyses in depth. We utilized existing data and mined published sporocarp, morphotyped ectomycorrhizae (ECM), as well as environmental sequence data of internal transcribed spacer (ITS) and large subunit (LSU) regions of the ribosomal RNA gene to identify taxa that occur at a glacier forefront in the North Cascades Mountains in Washington State in the USA. The discrete data types consistently identified several common and widely distributed genera, perhaps best exemplified by Inocybe and Laccaria. Although we expected low diversity and richness, our environmental sequence data included 37 ITS and 26 LSU operational taxonomic units (OTUs) that likely form ECM. While environmental surveys of metabarcode markers detected large numbers of targeted ECM taxa, both the fruiting body and the morphotype datasets included genera that were undetected in either of the metabarcode datasets. These included hypogeous (Hymenogaster) and epigeous (Lactarius) taxa, some of which may produce large sporocarps but may possess small and/or spatially patchy genets. We highlight the importance of combining various data types to provide a comprehensive view of a fungal community, even in an environment assumed to host communities of low species richness and diversity.
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Affiliation(s)
- Ari Jumpponen
- Division of Biology, Kansas State University, Manhattan, KS 66506, USA.
- Ecological Genomics Institute, Kansas State University, Manhattan, KS 66506, USA.
| | - Shawn P Brown
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
| | - James M Trappe
- Department of Forest Ecosystems and Environment, Oregon State University, Corvallis, OR 97331, USA.
- U.S. Forest Service, Forestry Sciences Laboratory, 3200 Jefferson Way, Corvallis, OR 97331, USA.
| | - Efrén Cázares
- Department of Forest Ecosystems and Environment, Oregon State University, Corvallis, OR 97331, USA.
| | - Rauni Strömmer
- Department of Environmental Sciences, University of Helsinki, Lahti, FIN15140, Finland.
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