1
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Abrego N, Furneaux B, Hardwick B, Somervuo P, Palorinne I, Aguilar-Trigueros CA, Andrew NR, Babiy UV, Bao T, Bazzano G, Bondarchuk SN, Bonebrake TC, Brennan GL, Bret-Harte S, Bässler C, Cagnolo L, Cameron EK, Chapurlat E, Creer S, D'Acqui LP, de Vere N, Desprez-Loustau ML, Dongmo MAK, Jacobsen IBD, Fisher BL, Flores de Jesus M, Gilbert GS, Griffith GW, Gritsuk AA, Gross A, Grudd H, Halme P, Hanna R, Hansen J, Hansen LH, Hegbe ADMT, Hill S, Hogg ID, Hultman J, Hyde KD, Hynson NA, Ivanova N, Karisto P, Kerdraon D, Knorre A, Krisai-Greilhuber I, Kurhinen J, Kuzmina M, Lecomte N, Lecomte E, Loaiza V, Lundin E, Meire A, Mešić A, Miettinen O, Monkhouse N, Mortimer P, Müller J, Nilsson RH, Nonti PYC, Nordén J, Nordén B, Norros V, Paz C, Pellikka P, Pereira D, Petch G, Pitkänen JM, Popa F, Potter C, Purhonen J, Pätsi S, Rafiq A, Raharinjanahary D, Rakos N, Rathnayaka AR, Raundrup K, Rebriev YA, Rikkinen J, Rogers HMK, Rogovsky A, Rozhkov Y, Runnel K, Saarto A, Savchenko A, Schlegel M, Schmidt NM, Seibold S, Skjøth C, Stengel E, Sutyrina SV, Syvänperä I, Tedersoo L, Timm J, Tipton L, Toju H, Uscka-Perzanowska M, van der Bank M, van der Bank FH, Vandenbrink B, Ventura S, Vignisson SR, Wang X, Weisser WW, Wijesinghe SN, Wright SJ, Yang C, Yorou NS, Young A, Yu DW, Zakharov EV, Hebert PDN, Roslin T, Ovaskainen O. Airborne DNA reveals predictable spatial and seasonal dynamics of fungi. Nature 2024; 631:835-842. [PMID: 38987593 PMCID: PMC11269176 DOI: 10.1038/s41586-024-07658-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Accepted: 06/04/2024] [Indexed: 07/12/2024]
Abstract
Fungi are among the most diverse and ecologically important kingdoms in life. However, the distributional ranges of fungi remain largely unknown as do the ecological mechanisms that shape their distributions1,2. To provide an integrated view of the spatial and seasonal dynamics of fungi, we implemented a globally distributed standardized aerial sampling of fungal spores3. The vast majority of operational taxonomic units were detected within only one climatic zone, and the spatiotemporal patterns of species richness and community composition were mostly explained by annual mean air temperature. Tropical regions hosted the highest fungal diversity except for lichenized, ericoid mycorrhizal and ectomycorrhizal fungi, which reached their peak diversity in temperate regions. The sensitivity in climatic responses was associated with phylogenetic relatedness, suggesting that large-scale distributions of some fungal groups are partially constrained by their ancestral niche. There was a strong phylogenetic signal in seasonal sensitivity, suggesting that some groups of fungi have retained their ancestral trait of sporulating for only a short period. Overall, our results show that the hyperdiverse kingdom of fungi follows globally highly predictable spatial and temporal dynamics, with seasonality in both species richness and community composition increasing with latitude. Our study reports patterns resembling those described for other major groups of organisms, thus making a major contribution to the long-standing debate on whether organisms with a microbial lifestyle follow the global biodiversity paradigms known for macroorganisms4,5.
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Affiliation(s)
- Nerea Abrego
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland.
- Department of Agricultural Sciences, University of Helsinki, Helsinki, Finland.
| | - Brendan Furneaux
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland
| | - Bess Hardwick
- Department of Agricultural Sciences, University of Helsinki, Helsinki, Finland
| | - Panu Somervuo
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Isabella Palorinne
- Department of Agricultural Sciences, University of Helsinki, Helsinki, Finland
| | | | - Nigel R Andrew
- Natural History Museum, University of New England, Armidale, New South Wales, Australia
- Faculty of Science and Engineering, Southern Cross University, Northern Rivers, New South Wales, Australia
| | | | - Tan Bao
- Department of Biological Sciences, MacEwan University, Edmonton, Alberta, Canada
| | - Gisela Bazzano
- Centro de Zoología Aplicada, Facultad de Ciencias Exactas Físicas y Naturales, Universidad Nacional de Córdoba, Córdoba, Argentina
| | - Svetlana N Bondarchuk
- Sikhote-Alin State Nature Biosphere Reserve named after K. G. Abramov, Terney, Russia
| | - Timothy C Bonebrake
- School of Biological Sciences, The University of Hong Kong, Hong Kong SAR, China
| | - Georgina L Brennan
- Institute of Marine Sciences, Consejo Superior de Investigaciones Científicas (CSIC), Passeig Marítim de la Barceloneta, Barcelona, Spain
| | | | - Claus Bässler
- Department of Conservation Biology, Institute for Ecology, Evolution and Diversity, Faculty of Biological Sciences, Goethe-University Frankfurt, Frankfurt am Main, Germany
- Bavarian Forest National Park, Grafenau, Germany
- Bayreuth Center of Ecology and Environmental Research (BayCEER), University of Bayreuth, Bayreuth, Germany
| | - Luciano Cagnolo
- Instituto Multidisciplinario de Biología Vegetal, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Córdoba, Argentina
| | - Erin K Cameron
- Department of Environmental Science, Saint Mary's University, Halifax, Nova Scotia, Canada
| | - Elodie Chapurlat
- Department of Ecology, Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden
| | - Simon Creer
- Molecular Ecology and Evolution at Bangor (MEEB), School of Biological Sciences, Bangor University, Bangor, Wales
| | - Luigi P D'Acqui
- Research Institute on Terrestrial Ecosystems - IRET, National Research Council - CNR and National Biodiversity Future Center, Palermo, Italy
| | - Natasha de Vere
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | | | - Michel A K Dongmo
- School of Biological Sciences, The University of Hong Kong, Hong Kong SAR, China
- International Institute of Tropical Agriculture (IITA), Yaoundé, Cameroon
| | | | - Brian L Fisher
- Department of Entomology, California Academy of Sciences, San Francisco, CA, USA
- Madagascar Biodiversity Center, Parc Botanique et Zoologique de Tsimbazaza, Antananarivo, Madagascar
| | | | - Gregory S Gilbert
- Department of Environmental Studies, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Gareth W Griffith
- Department of Life Sciences, Aberystwyth University, Aberystwyth, UK
| | - Anna A Gritsuk
- Sikhote-Alin State Nature Biosphere Reserve named after K. G. Abramov, Terney, Russia
| | - Andrin Gross
- Biodiversity and Conservation Biology Research Unit, SwissFungi Data Center, Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
| | - Håkan Grudd
- Swedish Polar Research Secretariat, Abisko Scientific Research Station, Abisko, Sweden
| | - Panu Halme
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland
| | - Rachid Hanna
- Center for Tropical Research, Congo Basin Institute, University of California Los Angeles, Los Angeles, CA, USA
| | - Jannik Hansen
- Department of Ecoscience, Aarhus University, Roskilde, Denmark
| | | | - Apollon D M T Hegbe
- Research Unit in Tropical Mycology and Plant-Soil Fungi Interactions, Faculty of Agronomy, University of Parakou, Parakou, Republic of Benin
| | - Sarah Hill
- Natural History Museum, University of New England, Armidale, New South Wales, Australia
| | - Ian D Hogg
- Canadian High Arctic Research Station, Polar Knowledge Canada, Cambridge Bay, Nunavut, Canada
- Department of Integrative Biology, College of Biological Science, University of Guelph, Guelph, Ontario, Canada
- School of Science, University of Waikato, Hamilton, New Zealand
| | - Jenni Hultman
- Department of Microbiology, University of Helsinki, Helsinki, Finland
- Natural Resources Institute Finland (Luke), Helsinki, Finland
| | - Kevin D Hyde
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, Thailand
| | - Nicole A Hynson
- Pacific Biosciences Research Center, University of Hawaii at Manoa, Honolulu, HI, USA
| | - Natalia Ivanova
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
- Nature Metrics North America Ltd., Guelph, Ontario, Canada
| | - Petteri Karisto
- Plant Pathology Group, Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland
- Plant Health, Natural Resources Institute Finland (Luke), Jokioinen, Finland
| | - Deirdre Kerdraon
- Department of Ecology, Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden
| | - Anastasia Knorre
- Science Department, National Park Krasnoyarsk Stolby, Krasnoyarsk, Russia
- Institute of Ecology and Geography, Siberian Federal University, Krasnoyarsk, Russia
| | | | - Juri Kurhinen
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Masha Kuzmina
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - Nicolas Lecomte
- Centre d'Études Nordiques and Canada Research Chair in Polar and Boreal Ecology, Department of Biology, Université de Moncton, Moncton, New Brunswick, Canada
| | - Erin Lecomte
- Centre d'Études Nordiques and Canada Research Chair in Polar and Boreal Ecology, Department of Biology, Université de Moncton, Moncton, New Brunswick, Canada
| | - Viviana Loaiza
- Department of Evolutionary Biology and Environmental Sciences, University of Zürich, Zurich, Switzerland
| | - Erik Lundin
- Swedish Polar Research Secretariat, Abisko Scientific Research Station, Abisko, Sweden
| | - Alexander Meire
- Swedish Polar Research Secretariat, Abisko Scientific Research Station, Abisko, Sweden
| | - Armin Mešić
- Laboratory for Biological Diversity, Rudjer Boskovic Institute, Zagreb, Croatia
| | - Otto Miettinen
- Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland
| | - Norman Monkhouse
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - Peter Mortimer
- Centre for Mountain Futures, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Jörg Müller
- Bavarian Forest National Park, Grafenau, Germany
- Department of Conservation Biology and Forest Ecology, Julius Maximilians University Würzburg, Rauhenebrach, Germany
| | - R Henrik Nilsson
- Department of Biological and Environmental Sciences, Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden
| | - Puani Yannick C Nonti
- Research Unit in Tropical Mycology and Plant-Soil Fungi Interactions, Faculty of Agronomy, University of Parakou, Parakou, Republic of Benin
| | - Jenni Nordén
- Norwegian Institute for Nature Research (NINA), Oslo, Norway
| | - Björn Nordén
- Norwegian Institute for Nature Research (NINA), Oslo, Norway
| | - Veera Norros
- Nature Solutions, Finnish Environment Institute (Syke), Helsinki, Finland
| | - Claudia Paz
- Department of Biodiversity, Institute of Biosciences, São Paulo State University, Rio Claro, Brazil
- Department of Entomology and Acarology, Laboratory of Pathology and Microbial Control, University of São Paulo, Piracicaba, Brazil
| | - Petri Pellikka
- Department of Geosciences and Geography, Faculty of Science, University of Helsinki, Helsinki, Finland
- State Key Laboratory for Information Engineering in Surveying, Mapping and Remote Sensing, Wuhan University, Wuhan, China
- Wangari Maathai Institute for Environmental and Peace Studies, University of Nairobi, Kangemi, Kenya
| | - Danilo Pereira
- Plant Pathology Group, Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland
- Laboratory of Biochemistry, Wageningen University, Wageningen, the Netherlands
| | - Geoff Petch
- School of Science and the Environment, University of Worcester, Worcester, UK
| | | | - Flavius Popa
- Department of Ecosystem Monitoring, Research & Conservation, Black Forest National Park, Bad Peterstal-Griesbach, Germany
| | - Caitlin Potter
- Department of Life Sciences, Aberystwyth University, Aberystwyth, UK
| | - Jenna Purhonen
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland
- School of Resource Wisdom, University of Jyväskylä, Jyväskylä, Finland
| | - Sanna Pätsi
- Biodiversity Unit, University of Turku, Turku, Finland
| | - Abdullah Rafiq
- Molecular Ecology and Evolution at Bangor (MEEB), School of Biological Sciences, Bangor University, Bangor, Wales
| | - Dimby Raharinjanahary
- Madagascar Biodiversity Center, Parc Botanique et Zoologique de Tsimbazaza, Antananarivo, Madagascar
| | - Niklas Rakos
- Swedish Polar Research Secretariat, Abisko Scientific Research Station, Abisko, Sweden
| | - Achala R Rathnayaka
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, Thailand
- School of Science, Mae Fah Luang University, Chiang Rai, Thailand
| | | | - Yury A Rebriev
- Southern Scientific Center of the Russian Academy of Sciences, Rostov-on-Don, Russia
| | - Jouko Rikkinen
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
- Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland
| | - Hanna M K Rogers
- Department of Ecology, Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden
| | - Andrey Rogovsky
- Science Department, National Park Krasnoyarsk Stolby, Krasnoyarsk, Russia
| | - Yuri Rozhkov
- State Nature Reserve Olekminsky, Olekminsk, Russia
| | - Kadri Runnel
- Mycology and Microbiology Center, University of Tartu, Tartu, Estonia
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Annika Saarto
- Biodiversity Unit, University of Turku, Turku, Finland
| | - Anton Savchenko
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Markus Schlegel
- Biodiversity and Conservation Biology Research Unit, SwissFungi Data Center, Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
| | - Niels Martin Schmidt
- Department of Ecoscience, Aarhus University, Roskilde, Denmark
- Arctic Research Center, Aarhus University, Roskilde, Denmark
| | - Sebastian Seibold
- Forest Zoology, TUD Dresden University of Technology, Berchtesgaden, Germany
- Terrestrial Ecology Research Group, Department of Life Science Systems, School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Carsten Skjøth
- School of Science and the Environment, University of Worcester, Worcester, UK
- Department of Environmental Science, Aarhus University, Roskilde, Denmark
| | - Elisa Stengel
- Field Station Fabrikschleichach, Department of Animal Ecology and Tropical Biology (Zoology III), Julius Maximilians University Würzburg, Rauhenebrach, Germany
| | - Svetlana V Sutyrina
- Sikhote-Alin State Nature Biosphere Reserve named after K. G. Abramov, Terney, Russia
| | - Ilkka Syvänperä
- Kevo Subarctic Research Institute, Biodiversity Unit, University of Turku, Utsjoki, Finland
| | - Leho Tedersoo
- Mycology and Microbiology Center, University of Tartu, Tartu, Estonia
- College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Jebidiah Timm
- Institute of Arctic Biology, University of Alaska, Fairbanks, AK, USA
| | - Laura Tipton
- School of Natural Science and Mathematics, Chaminade University of Honolulu, Honolulu, HI, USA
| | - Hirokazu Toju
- Laboratory of Ecosystems and Coevolution, Graduate School of Biostudies, Kyoto University, Kyoto, Japan
- Center for Living Systems Information Science (CeLiSIS), Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | | | - Michelle van der Bank
- African Centre for DNA Barcoding (ACDB), University of Johannesburg, Auckland Park, South Africa
| | - F Herman van der Bank
- African Centre for DNA Barcoding (ACDB), University of Johannesburg, Auckland Park, South Africa
| | - Bryan Vandenbrink
- Canadian High Arctic Research Station, Polar Knowledge Canada, Cambridge Bay, Nunavut, Canada
| | - Stefano Ventura
- Research Institute on Terrestrial Ecosystems - IRET, National Research Council - CNR and National Biodiversity Future Center, Palermo, Italy
| | | | - Xiaoyang Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Wolfgang W Weisser
- Terrestrial Ecology Research Group, Department of Life Science Systems, School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Subodini N Wijesinghe
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, Thailand
- School of Science, Mae Fah Luang University, Chiang Rai, Thailand
| | | | - Chunyan Yang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Nourou S Yorou
- Research Unit in Tropical Mycology and Plant-Soil Fungi Interactions, Faculty of Agronomy, University of Parakou, Parakou, Republic of Benin
| | - Amanda Young
- Institute of Arctic Biology, University of Alaska, Fairbanks, AK, USA
| | - Douglas W Yu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- School of Biological Sciences, University of East Anglia, Norwich, UK
- Yunnan Key Laboratory of Biodiversity and Ecological Security of Gaoligong Mountain, Kunming Institute of Zoology, Center of Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
| | - Evgeny V Zakharov
- Department of Integrative Biology, College of Biological Science, University of Guelph, Guelph, Ontario, Canada
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - Paul D N Hebert
- Department of Integrative Biology, College of Biological Science, University of Guelph, Guelph, Ontario, Canada
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - Tomas Roslin
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
- Department of Ecology, Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden
| | - Otso Ovaskainen
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
- Centre for Biodiversity Dynamics, Department of Biology, Norwegian University of Science and Technology, Trondheim, Norway
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Sanchez-Tello JD, Corrales A. Ectomycorrhizal fungal communities in natural and urban ecosystems: Quercus humboldtii as a study case in the tropical Andes. MYCORRHIZA 2024; 34:45-55. [PMID: 38483629 PMCID: PMC10998789 DOI: 10.1007/s00572-024-01140-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 02/22/2024] [Indexed: 04/07/2024]
Abstract
Worldwide urban landscapes are expanding because of the growing human population. Urban ecosystems serve as habitats to highly diverse communities. However, studies focusing on the diversity and structure of ectomycorrhizal communities are uncommon in this habitat. In Colombia, Quercus humboldtii Bonpl. is an ectomycorrhizal tree thriving in tropical montane forests hosting a high diversity of ectomycorrhizal fungi. Q. humboldtii is planted as an urban tree in Bogotá (Colombia). We studied how root-associated fungal communities of this tree change between natural and urban areas. Using Illumina sequencing, we amplified the ITS1 region and analyzed the resulting data using both OTUs and Amplicon Sequence Variants (ASVs) bioinformatics pipelines. The results obtained using both pipelines showed no substantial differences between OTUs and ASVs for the community patterns of root-associated fungi, and only differences in species richness were observed. We found no significant differences in the species richness between urban and rural sites based on Fisher's alpha or species-accumulation curves. However, we found significant differences in the community composition of fungi present in the roots of rural and urban trees with rural communities being dominated by Russula and Lactarius and urban communities by Scleroderma, Hydnangium, and Trechispora, suggesting a high impact of urban disturbances on ectomycorrhizal fungal communities. Our results highlight the importance of urban trees as reservoirs of fungal diversity and the potential impact of urban conditions on favoring fungal species adapted to more disturbed ecosystems.
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Affiliation(s)
- Juan David Sanchez-Tello
- Center for Research in Microbiology and Biotechnology-UR (CIMBIUR), Faculty of Natural Sciences, Universidad del Rosario, Bogotá, Colombia.
| | - Adriana Corrales
- Center for Research in Microbiology and Biotechnology-UR (CIMBIUR), Faculty of Natural Sciences, Universidad del Rosario, Bogotá, Colombia
- Society for the Protection of Underground Networks, SPUN, 3500 South DuPont Highway, Dover, DE, 19901, USA
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Piñuela Y, Alday JG, Oliach D, Castaño C, Büntgen U, Egli S, Martínez Peña F, Dashevskaya S, Colinas C, Peter M, Bonet JA. Habitat is more important than climate for structuring soil fungal communities associated in truffle sites. Fungal Biol 2024; 128:1724-1734. [PMID: 38575246 DOI: 10.1016/j.funbio.2024.02.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 02/09/2024] [Accepted: 02/23/2024] [Indexed: 04/06/2024]
Abstract
The ectomycorrhizal fungi Tuber melanosporum Vittad. and Tuber aestivum Vittad. produce highly valuable truffles, but little is known about the soil fungal communities associated with these truffle species in places where they co-occur. Here, we compared soil fungal communities present in wild and planted truffle sites, in which T. melanosporum and T. aestivum coexist, in Mediterranean and temperate regions over three sampling seasons spanning from 2018 to 2019. We showed that soil fungal community composition and ectomycorrhizal species composition are driven by habitat type rather than climate regions. Also, we observed the influence of soil pH, organic matter content and C:N ratio structuring total and ectomycorrhizal fungal assemblages. Soil fungal communities in wild sites revealed more compositional variability than those of plantations. Greater soil fungal diversity was found in temperate compared to Mediterranean sites when considering all fungal guilds. Ectomycorrhizal diversity was significantly higher in wild sites compared to plantations. Greater mould abundance at wild sites than those on plantation was observed while tree species and seasonal effects were not significant predictors in fungal community structure. Our results suggested a strong influence of both ecosystem age and management on the fungal taxa composition in truffle habitats.
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Affiliation(s)
- Yasmin Piñuela
- Department of Agricultural and Forest Sciences and Engineering, University of Lleida, Lleida, 25198, Spain; Forest Science and Technology Centre of Catalonia (CTFC), Crta. Sant Llorenç de Morunys km 2, 25280, Solsona, Spain; Swiss Federal Research Institute WSL, Birmensdorf, Switzerland.
| | - Josu G Alday
- Department of Agricultural and Forest Sciences and Engineering, University of Lleida, Lleida, 25198, Spain; Joint Research Unit CTFC - AGROTECNIO-CERCA, Av. Alcalde Rovira Roure 191, 25198, Lleida, Spain
| | - Daniel Oliach
- Forest Science and Technology Centre of Catalonia (CTFC), Crta. Sant Llorenç de Morunys km 2, 25280, Solsona, Spain
| | - Carles Castaño
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, SE-750 07, Sweden
| | - Ulf Büntgen
- Department of Geography, University of Cambridge, Cambridge, UK; Czech Globe Research Institute CAS and Masaryk University Brno, Brno, Czech Republic
| | - Simon Egli
- Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
| | - Fernando Martínez Peña
- Agrifood Research and Technology Centre of Aragon CITA, Montañana 930, E-50059, Zaragoza, Spain; European Mycological Institute EGTC-EMI, E-42003, Soria, Spain
| | - Svetlana Dashevskaya
- Department of Agricultural and Forest Sciences and Engineering, University of Lleida, Lleida, 25198, Spain
| | - Carlos Colinas
- Department of Agricultural and Forest Sciences and Engineering, University of Lleida, Lleida, 25198, Spain; Forest Science and Technology Centre of Catalonia (CTFC), Crta. Sant Llorenç de Morunys km 2, 25280, Solsona, Spain
| | - Martina Peter
- Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
| | - José Antonio Bonet
- Department of Agricultural and Forest Sciences and Engineering, University of Lleida, Lleida, 25198, Spain; Joint Research Unit CTFC - AGROTECNIO-CERCA, Av. Alcalde Rovira Roure 191, 25198, Lleida, Spain
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Olchowik J, Jankowski P, Suchocka M, Malewski T, Wiesiołek A, Hilszczańska D. The impact of anthropogenic transformation of urban soils on ectomycorrhizal fungal communities associated with silver birch (Betula pendula Roth.) growth in natural versus urban soils. Sci Rep 2023; 13:21268. [PMID: 38042912 PMCID: PMC10693619 DOI: 10.1038/s41598-023-48592-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 11/28/2023] [Indexed: 12/04/2023] Open
Abstract
Betula pendula Roth. is considered a pioneering plant species important for urban ecosystems. Based on the sequencing of fungal ITS, we characterized the ectomycorrhizal (ECM) communities of twenty silver birch trees growing in a contaminated, highly anthropo-pressured urban environment and in a natural reserve site. We analysed chemical properties of each tree soil samples, focusing on effects of anthropogenic transformation. Three effects of urbanization: high heavy metal content, increased salinity and soil alkalinity, were highly correlated. The examined trees were divided into two forest and two urban clusters according to the level of anthropogenic soil change. The effect of soil transformation on the ECM communities was studied, with the assumption that stronger urban transformation leads to lower ECM vitality and diversity. The results of the study did not confirm the above hypothesis. The ECM colonization was above 80% in all clusters, but the forest clusters had significantly higher share of vital non-ECM root tips than the urban ones. Eleven mycorrhizal fungal species were identified varying from seven to nine and with seven species observed in the most contaminated urban plot. However, the lowest Shannon species diversity index was found in the most natural forest cluster. In conclusion, our findings demonstrate no significant negative effect of the urban stresses on the ECM communities of silver birch suggesting that both forest and urban trees have the potential to generate a similar set of ECM taxa.
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Affiliation(s)
- Jacek Olchowik
- Department of Plant Protection, Institute of Horticultural Sciences, Warsaw University of Life Sciences-SGGW, Warsaw, Poland
| | - Paweł Jankowski
- Department of Computer Information Systems, Institute of Information Technology, Warsaw University of Life Sciences-SGGW, Warsaw, Poland.
| | - Marzena Suchocka
- Department of Landscape Architecture, Institute of Environmental Engineering, Warsaw University of Life Sciences-SGGW, Warsaw, Poland
| | - Tadeusz Malewski
- Department of Molecular and Biometric Techniques, Museum and Institute of Zoology, Polish Academy of Science, Warsaw, Poland
| | - Adam Wiesiołek
- Department of Plant Protection, Institute of Horticultural Sciences, Warsaw University of Life Sciences-SGGW, Warsaw, Poland
| | - Dorota Hilszczańska
- Department of Forest Ecology, Forest Research Institute, Sękocin Stary, Poland
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Xu D, Yu X, Chen J, Liu H, Zheng Y, Qu H, Bao Y. Microbial Assemblages Associated with the Soil-Root Continuum of an Endangered Plant, Helianthemum songaricum Schrenk. Microbiol Spectr 2023; 11:e0338922. [PMID: 37222598 PMCID: PMC10269481 DOI: 10.1128/spectrum.03389-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 04/22/2023] [Indexed: 05/25/2023] Open
Abstract
The microbial network of the soil-root continuum plays a key role in plant growth. To date, limited information is available about the microbial assemblages in the rhizosphere and endosphere of endangered plants. We suspect that unknown microorganisms in roots and soil play an important role in the survival strategies of endangered plants. To address this research gap, we investigated the diversity and composition of the microbial communities of the soil-root continuum of the endangered shrub Helianthemum songaricum and observed that the microbial communities and structures of the rhizosphere and endosphere samples were distinguishable. The dominant rhizosphere bacteria were Actinobacteria (36.98%) and Acidobacteria (18.15%), whereas most endophytes were Alphaproteobacteria (23.17%) as well as Actinobacteria (29.94%). The relative abundance of rhizosphere bacteria was higher than that in endosphere samples. Fungal rhizosphere and endophyte samples had approximately equal abundances of the Sordariomycetes (23%), while the Pezizomycetes were more abundant in the soil (31.95%) than in the roots (5.70%). The phylogenetic relationships of the abundances of microbes in root and soil samples also showed that the most abundant bacterial and fungal reads tended to be dominant in either the soil or root samples but not both. Additionally, Pearson correlation heatmap analysis showed that the diversity and composition of soil bacteria and fungi were closely related to pH, total nitrogen, total phosphorus, and organic matter, of which pH and organic matter were the main drivers. These results clarify the different patterns of microbial communities of the soil-root continuum, in support of the better conservation and utilization of endangered desert plants in Inner Mongolia. IMPORTANCE Microbial assemblages play significant roles in plant survival, health, and ecological services. The symbiosis between soil microorganisms and these plants and their interactions with soil factors are important features of the adaptation of desert plants to an arid and barren environment. Therefore, the profound study of the microbial diversity of rare desert plants can provide important data to support the protection and utilization of rare desert plants. Accordingly, in this study, high-throughput sequencing technology was applied to study the microbial diversity in plant roots and rhizosphere soils. We expect that research on the relationship between soil and root microbial diversity and the environment will improve the survival of endangered plants in this environment. In summary, this study is the first to study the microbial diversity and community structure of Helianthemum songaricum Schrenk and compare the diversity and composition of the root and soil microbiomes.
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Affiliation(s)
- Daolong Xu
- Inner Mongolia University, School of Life Sciences, Ministry of Education, Key Laboratory of Forage and Endemic Crop Biotechnology, Hohhot, People’s Republic of China
| | - Xiaowen Yu
- Inner Mongolia Autonomous Region Environmental Monitoring Station, Hohhot, People’s Republic of China
| | - Jin Chen
- National Engineering Laboratory of Crop Stress Resistance Breeding, Anhui Agricultural University, Hefei, People’s Republic of China
| | - Haijing Liu
- Inner Mongolia University, School of Life Sciences, Ministry of Education, Key Laboratory of Forage and Endemic Crop Biotechnology, Hohhot, People’s Republic of China
| | - Yaxin Zheng
- Inner Mongolia University, School of Life Sciences, Ministry of Education, Key Laboratory of Forage and Endemic Crop Biotechnology, Hohhot, People’s Republic of China
| | - Hanqing Qu
- Inner Mongolia University, School of Life Sciences, Ministry of Education, Key Laboratory of Forage and Endemic Crop Biotechnology, Hohhot, People’s Republic of China
| | - Yuying Bao
- Inner Mongolia University, School of Life Sciences, Ministry of Education, Key Laboratory of Forage and Endemic Crop Biotechnology, Hohhot, People’s Republic of China
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6
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Matsumura E, Morinaga K, Fukuda K. Host Specificity and Seasonal Variation in the Colonization of Tubakia sensu lato Associated with Evergreen Oak Species in Eastern Japan. MICROBIAL ECOLOGY 2022:10.1007/s00248-022-02067-9. [PMID: 35857039 DOI: 10.1007/s00248-022-02067-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 06/28/2022] [Indexed: 06/15/2023]
Abstract
Foliar fungal endophytes are ubiquitous and hyperdiverse, and tend to be host-specific among dominant forest tree species. The fungal genus Tubakia sensu lato is comprised of foliar pathogens and endophytes that exhibit host preference for Quercus and other Fagaceae species. To clarify interspecific differences in ecological characteristics among Tubakia species, we examined the endophyte communities of seven evergreen Quercus spp. at three sites in eastern Japan during summer and winter. Host tree species was the most significant factor affecting endophyte community composition. Tubakia species found at the study sites were divided into five specialists and three generalists according to their relative abundance in each host species and their host ranges. Specialists were dominant on their own host in summer, and their abundance declined in winter. To test the hypothesis that generalists are more widely adapted to their environment than specialists, we compared their spore germination rates at different temperatures. Spores of generalist Tubakia species were more tolerant of colder temperatures than were spores of specialist Tubakia species, supporting our hypothesis. Seasonal and site variations among Tubakia species were also consistent with our hypothesis. Host identity and ecology were significantly associated with endophyte community structure.
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Affiliation(s)
- Emi Matsumura
- Department of Natural Environmental Science, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwa-no-ha, Kashiwa, Chiba, 277-8563, Japan.
- Department of Forest Science, Graduate School of Agriculture and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan.
| | - Kenta Morinaga
- Department of Natural Environmental Science, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwa-no-ha, Kashiwa, Chiba, 277-8563, Japan
| | - Kenji Fukuda
- Department of Natural Environmental Science, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwa-no-ha, Kashiwa, Chiba, 277-8563, Japan
- Department of Forest Science, Graduate School of Agriculture and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
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7
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Imperato V, Portillo-Estrada M, Saran A, Thoonen A, Kowalkowski Ł, Gawronski SW, Rineau F, Vangronsveld J, Thijs S. Exploring the Diversity and Aromatic Hydrocarbon Degrading Potential of Epiphytic Fungi on Hornbeams from Chronically Polluted Areas. J Fungi (Basel) 2021; 7:jof7110972. [PMID: 34829258 PMCID: PMC8620586 DOI: 10.3390/jof7110972] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 11/04/2021] [Accepted: 11/10/2021] [Indexed: 01/12/2023] Open
Abstract
Plants can ‘catch’ and mitigate airborne pollutants and are assisted by fungi inhabiting their leaves. The structure and function of the fungal communities inhabiting the phyllosphere of hornbeam trees growing in two chronically polluted areas, the oilfield of Bóbrka and the city center of Warsaw, were compared to the ones growing in one nature reserve, the Białowieża National Park. Fungi were isolated and characterized both phylogenetically and functionally for their potential role in air pollution mitigation. Both culture-dependent (e.g., enzyme assays and tolerance tests) and culture-independent methods (e.g., ITS and shotgun sequencings) were used. Furthermore, the degradation potential of the fungi was assessed by gas chromatography mass spectrometry (GC-MS). Shotgun sequencing showed that the phyllosphere fungal communities were dominated by fungi belonging to the phylum Ascomycota. Aureobasidium was the only genus detected at the three locations with a relative abundance ≥1.0%. Among the cultivated epiphytic fungi from Bóbrka, Fusarium sporotrichioides AT11, Phoma herbarum AT15, and Lophiostoma sp. AT37 showed in vitro aromatic hydrocarbon degradation potential with laccase activities of 1.24, 3.62, and 7.2 μU L−1, respectively, and peroxidase enzymes with activities of 3.46, 2.28, and 7.49 μU L−1, respectively. Furthermore, Fusarium sporotrichioides AT11 and Phoma herbarum AT15 tolerated exposure to airborne naphthalene and benzene. Lophiostoma sp. AT37 was the most tolerant to exposure to these pollutants, in line with being the best potential aromatic hydrocarbon degrader isolated in this study.
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Affiliation(s)
- Valeria Imperato
- Department of Biology, Centre for Environmental Sciences, Hasselt University, BE3590 Diepenbeek, Belgium; (A.T.); (Ł.K.); (F.R.); (J.V.); (S.T.)
- Correspondence:
| | - Miguel Portillo-Estrada
- Plants and Ecosystems (PLECO), Department of Biology, University of Antwerp, BE2610 Wilrijk, Belgium;
| | - Anabel Saran
- AIC-CONICET, Scientific Research Agency, Santa Rosa 6360, La Pampa, Argentina;
| | - Anneleen Thoonen
- Department of Biology, Centre for Environmental Sciences, Hasselt University, BE3590 Diepenbeek, Belgium; (A.T.); (Ł.K.); (F.R.); (J.V.); (S.T.)
| | - Łukasz Kowalkowski
- Department of Biology, Centre for Environmental Sciences, Hasselt University, BE3590 Diepenbeek, Belgium; (A.T.); (Ł.K.); (F.R.); (J.V.); (S.T.)
- Faculty of Horticulture, Biotechnology and Landscape Architecture, Warsaw University of Life Sciences, 02-787 Warsaw, Poland;
| | - Stanislaw W. Gawronski
- Faculty of Horticulture, Biotechnology and Landscape Architecture, Warsaw University of Life Sciences, 02-787 Warsaw, Poland;
| | - Francois Rineau
- Department of Biology, Centre for Environmental Sciences, Hasselt University, BE3590 Diepenbeek, Belgium; (A.T.); (Ł.K.); (F.R.); (J.V.); (S.T.)
| | - Jaco Vangronsveld
- Department of Biology, Centre for Environmental Sciences, Hasselt University, BE3590 Diepenbeek, Belgium; (A.T.); (Ł.K.); (F.R.); (J.V.); (S.T.)
- Department of Plant Physiology and Biophysics, Faculty of Biology and Biotechnology, Maria Curie-Skłodowska University, 20-400 Lublin, Poland
| | - Sofie Thijs
- Department of Biology, Centre for Environmental Sciences, Hasselt University, BE3590 Diepenbeek, Belgium; (A.T.); (Ł.K.); (F.R.); (J.V.); (S.T.)
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8
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Current Insight into Culture-Dependent and Culture-Independent Methods in Discovering Ascomycetous Taxa. J Fungi (Basel) 2021; 7:jof7090703. [PMID: 34575741 PMCID: PMC8467358 DOI: 10.3390/jof7090703] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 08/22/2021] [Accepted: 08/23/2021] [Indexed: 01/08/2023] Open
Abstract
Culture techniques are vital in both traditional and modern fungal taxonomy. Establishing sexual-asexual links and synanamorphs, extracting DNA and secondary metabolites are mainly based on cultures. However, it is widely accepted that a large number of species are not sporulating in nature while others cannot be cultured. Recent ecological studies based on culture-independent methods revealed these unculturable taxa, i.e., dark taxa. Recent fungal diversity estimation studies suggested that environmental sequencing plays a vital role in discovering missing species. However, Sanger sequencing is still the main approach in determining DNA sequences in culturable species. In this paper, we summarize culture-based and culture-independent methods in the study of ascomycetous taxa. High-throughput sequencing of leaf endophytes, leaf litter fungi and fungi in aquatic environments is important to determine dark taxa. Nevertheless, currently, naming dark taxa is not recognized by the ICN, thus provisional naming of them is essential as suggested by several studies.
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9
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Bai XN, Hao H, Hu ZH, Leng PS. Ectomycorrhizal Inoculation Enhances the Salt Tolerance of Quercus mongolica Seedlings. PLANTS (BASEL, SWITZERLAND) 2021; 10:1790. [PMID: 34579323 PMCID: PMC8469051 DOI: 10.3390/plants10091790] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2021] [Revised: 08/20/2021] [Accepted: 08/25/2021] [Indexed: 05/14/2023]
Abstract
Salt stress harms the growth and development of plants, and the degree of soil salinization in North China is becoming increasingly severe. Ectomycorrhiza (ECM) is a symbiotic system formed by fungi and plants that can improve the growth and salt tolerance of plants. No studies to date have examined the salt tolerance of Quercus mongolica, a typical ectomycorrhizal tree species of temperate forests in the northern hemisphere. Here, we inoculated Q. mongolica with two ectomycorrhizal fungi (Gomphidius viscidus; Suillus luteus) under NaCl stress to characterize the effects of ECM. The results showed that the symbiotic relationship of Q. mongolica with G. viscidus was more stable than that with S. luteus. The cross-sectional area of roots increased after inoculation with the two types of ectomycorrhizal fungi. Compared with the control group, plant height, soluble sugar content, and soluble protein content of leaves were 1.62, 2.41, and 2.04 times higher in the G. viscidus group, respectively. Chlorophyll (Chl) content, stomatal conductance (Gs), and intracellular CO2 concentration (Ci) were significantly higher in Q. mongolica inoculated with ectomycorrhizal fungi than in the control, but differences in the net photosynthetic rate (Pn), transpiration rate (Tr), and photosystem II maximum photochemical efficiency (Fv/Fm) were lower. The relative conductivity of Q. mongolica inoculated with the two ectomycorrhizal fungi was consistently lower than that of non-mycorrhizal seedlings, with the effect of G. viscidus more pronounced than that of S. luteus. The malondialdehyde (MDA) content showed a similar pattern. Peroxidase (POD) and catylase (CAT) levels in mycorrhizal seedlings were generally higher than those of non-mycorrhizal seedlings under normal conditions, and were significantly higher than those of non-mycorrhizal seedlings on the 36th and 48th day after salt treatment, respectively. Overall, the results indicated that the salt tolerance of Q. mongolica seedlings was improved by ectomycorrhizal inoculation.
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Affiliation(s)
- Xiao-Ning Bai
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, College of Landscape Architecture, Beijing University of Agriculture, Beijing 102206, China; (X.-N.B.); (H.H.)
| | - Han Hao
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, College of Landscape Architecture, Beijing University of Agriculture, Beijing 102206, China; (X.-N.B.); (H.H.)
- China Meteorological Press, Beijing 100081, China
| | - Zeng-Hui Hu
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, College of Landscape Architecture, Beijing University of Agriculture, Beijing 102206, China; (X.-N.B.); (H.H.)
| | - Ping-Sheng Leng
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, College of Landscape Architecture, Beijing University of Agriculture, Beijing 102206, China; (X.-N.B.); (H.H.)
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10
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Tedersoo L, Anslan S, Bahram M, Drenkhan R, Pritsch K, Buegger F, Padari A, Hagh-Doust N, Mikryukov V, Gohar D, Amiri R, Hiiesalu I, Lutter R, Rosenvald R, Rähn E, Adamson K, Drenkhan T, Tullus H, Jürimaa K, Sibul I, Otsing E, Põlme S, Metslaid M, Loit K, Agan A, Puusepp R, Varik I, Kõljalg U, Abarenkov K. Regional-Scale In-Depth Analysis of Soil Fungal Diversity Reveals Strong pH and Plant Species Effects in Northern Europe. Front Microbiol 2020; 11:1953. [PMID: 33013735 PMCID: PMC7510051 DOI: 10.3389/fmicb.2020.01953] [Citation(s) in RCA: 73] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Accepted: 07/31/2020] [Indexed: 01/16/2023] Open
Abstract
Soil microbiome has a pivotal role in ecosystem functioning, yet little is known about its build-up from local to regional scales. In a multi-year regional-scale survey involving 1251 plots and long-read third-generation sequencing, we found that soil pH has the strongest effect on the diversity of fungi and its multiple taxonomic and functional groups. The pH effects were typically unimodal, usually both direct and indirect through tree species, soil nutrients or mold abundance. Individual tree species, particularly Pinus sylvestris, Picea abies, and Populus x wettsteinii, and overall ectomycorrhizal plant proportion had relatively stronger effects on the diversity of biotrophic fungi than saprotrophic fungi. We found strong temporal sampling and investigator biases for the abundance of molds, but generally all spatial, temporal and microclimatic effects were weak. Richness of fungi and several functional groups was highest in woodlands and around ruins of buildings but lowest in bogs, with marked group-specific trends. In contrast to our expectations, diversity of soil fungi tended to be higher in forest island habitats potentially due to the edge effect, but fungal richness declined with island distance and in response to forest fragmentation. Virgin forests supported somewhat higher fungal diversity than old non-pristine forests, but there were no differences in richness between natural and anthropogenic habitats such as parks and coppiced gardens. Diversity of most fungal groups suffered from management of seminatural woodlands and parks and thinning of forests, but especially for forests the results depended on fungal group and time since partial harvesting. We conclude that the positive effects of tree diversity on overall fungal richness represent a combined niche effect of soil properties and intimate associations.
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Affiliation(s)
- Leho Tedersoo
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Sten Anslan
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia.,Zoological Institute, Technische Universität Braunschweig, Brunswick, Germany
| | - Mohammad Bahram
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia.,Department of Ecology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Rein Drenkhan
- Institute of Forestry and Rural Engineering, Estonian University of Life Sciences, Tartu, Estonia
| | - Karin Pritsch
- Helmholtz Zentrum München - Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Neuherberg, Germany
| | - Franz Buegger
- Helmholtz Zentrum München - Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Neuherberg, Germany
| | - Allar Padari
- Institute of Forestry and Rural Engineering, Estonian University of Life Sciences, Tartu, Estonia
| | - Niloufar Hagh-Doust
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Vladimir Mikryukov
- Chair of Forest Management Planning and Wood Processing Technologies, Institute of Plant and Animal Ecology, Ural Branch, Russian Academy of Sciences, Yekaterinburg, Russia
| | - Daniyal Gohar
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Rasekh Amiri
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Indrek Hiiesalu
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Reimo Lutter
- Institute of Forestry and Rural Engineering, Estonian University of Life Sciences, Tartu, Estonia
| | - Raul Rosenvald
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Elisabeth Rähn
- Institute of Forestry and Rural Engineering, Estonian University of Life Sciences, Tartu, Estonia
| | - Kalev Adamson
- Institute of Forestry and Rural Engineering, Estonian University of Life Sciences, Tartu, Estonia
| | - Tiia Drenkhan
- Institute of Forestry and Rural Engineering, Estonian University of Life Sciences, Tartu, Estonia.,Forest Health and Biodiversity, Natural Resources Institute Finland (Luke), Helsinki, Finland
| | - Hardi Tullus
- Institute of Forestry and Rural Engineering, Estonian University of Life Sciences, Tartu, Estonia
| | - Katrin Jürimaa
- Institute of Forestry and Rural Engineering, Estonian University of Life Sciences, Tartu, Estonia
| | - Ivar Sibul
- Institute of Forestry and Rural Engineering, Estonian University of Life Sciences, Tartu, Estonia
| | - Eveli Otsing
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Sergei Põlme
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Marek Metslaid
- Institute of Forestry and Rural Engineering, Estonian University of Life Sciences, Tartu, Estonia
| | - Kaire Loit
- Chair of Plant Health, Estonian University of Life Sciences, Tartu, Estonia
| | - Ahto Agan
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Rasmus Puusepp
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Inge Varik
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Urmas Kõljalg
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia.,Natural History Museum and Botanical Garden, University of Tartu, Tartu, Estonia
| | - Kessy Abarenkov
- Natural History Museum and Botanical Garden, University of Tartu, Tartu, Estonia
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11
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Marjanović Ž, Nawaz A, Stevanović K, Saljnikov E, Maček I, Oehl F, Wubet T. Root-Associated Mycobiome Differentiate between Habitats Supporting Production of Different Truffle Species in Serbian Riparian Forests. Microorganisms 2020; 8:E1331. [PMID: 32878332 PMCID: PMC7563819 DOI: 10.3390/microorganisms8091331] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 08/24/2020] [Accepted: 08/29/2020] [Indexed: 11/17/2022] Open
Abstract
Balkan lowlands bordering with the Pannonia region are inhabited by diverse riparian forests that support production of different truffle species, predominantly the most prized white truffle of Piedmont (Tuber magnatum Pico), but also other commercial species (T.macrosporum Vitt., T. aestivum Vitt.). Surprisingly, little is known about the native root-associated mycobiome (RAM) of these lowland truffle-producing forests. Therefore, in this study we aim at exploring and comparing the RAMs of three different truffle-producing forests from Kolubara river plane in Serbia. Molecular methods based on next generation sequencing (NGS) were used to evaluate the diversity of root-associated fungal communities and to elucidate the influence of environmental factors on their differentiation. To our knowledge, this is the first study from such habitats with a particular focus on comparative analysis of the RAM in different truffle-producing habitats using a high-throughput sequencing approach. Our results indicated that the alpha diversity of investigated fungal communities was not significantly different between different truffle-producing forests and within a specific forest type, while the seasonal differences in the alpha diversity were only observed in the white truffle-producing forests. Taxonomic profiling at phylum level indicated the dominance of fungal OTUs belonging to phylum Ascomycota and Basidiomycota, with very minor presence of other phyla. Distinct community structures of root-associated mycobiomes were observed for white, mixed, and black truffle-producing forests. The core mycobiome analysis indicated a fair share of fungal genera present exclusively in white and black truffle-producing forest, while the core genera of mixed truffle-producing forests were shared with both white and black truffle-producing forests. The majority of detected fungal OTUs in all three forest types were symbiotrophs, with ectomycorrhizal fungi being a dominant functional guild. Apart from assumed vegetation factor, differentiation of fungal communities was driven by factors connected to the distance from the river and exposure to fluvial activities, soil age, structure, and pH. Overall, Pannonian riparian forests appear to host diverse root-associated fungal communities that are strongly shaped by variation in soil conditions.
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Affiliation(s)
- Žaklina Marjanović
- Institute for Multidisciplinary Research, Belgrade University, Kneza Višeslava 1, 11030 Belgrade, Serbia
| | - Ali Nawaz
- Helmholtz Centre for Environmental Research—UFZ, Department of Community Ecology, 06120 Halle (Saale), Germany;
| | - Katarina Stevanović
- Faculty of Biology, University of Belgrade, Studentski Trg 3, 11000 Belgrade, Serbia;
| | - Elmira Saljnikov
- Soil Science Institute, Teodora Drajzera 7, 11000 Belgrade, Serbia;
| | - Irena Maček
- Department of Agronomy, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, 1000 Ljubljana, Slovenia;
- Faculty of Mathematics, Natural Sciences and Information Technologies (FAMNIT), University of Primorska, Glagoljaška 8, 6000 Koper, Slovenia
| | - Fritz Oehl
- Agroscope, Competence Division for Plants and Plant Products, Ecotoxicology, Müller-Thurgau-Str. 29, 8820 Wädenswil, Switzerland;
| | - Tesfaye Wubet
- Helmholtz Centre for Environmental Research—UFZ, Department of Community Ecology, 06120 Halle (Saale), Germany;
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103 Leipzig, Germany
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12
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The Relationship between Fungal Diversity and Invasibility of a Foliar Niche-The Case of Ash Dieback. J Fungi (Basel) 2020; 6:jof6030150. [PMID: 32858843 PMCID: PMC7558441 DOI: 10.3390/jof6030150] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 08/19/2020] [Accepted: 08/24/2020] [Indexed: 12/30/2022] Open
Abstract
European ash (Fraxinus excelsior) is threatened by the invasive ascomycete Hymenoscyphus fraxineus originating from Asia. Ash leaf tissues serve as a route for shoot infection but also as a sporulation substrate for this pathogen. Knowledge of the leaf niche partitioning by indigenous fungi and H. fraxineus is needed to understand the fungal community receptiveness to the invasion. We subjected DNA extracted from unwashed and washed leaflets of healthy and diseased European ash to PacBio sequencing of the fungal ITS1-5.8S-ITS2 rDNA region. Leaflets from co-inhabiting rowan trees (Sorbus aucuparia) served as a reference. The overlap in leaflet mycobiomes between ash and rowan was remarkably high, but unlike in rowan, in ash leaflets the sequence read proportion, and the qPCR-based DNA amount estimates of H. fraxineus increased vigorously towards autumn, concomitant with a significant decline in overall fungal richness. The niche of ash and rowan leaves was dominated by epiphytic propagules (Vishniacozyma yeasts, the dimorphic fungus Aureobasidion pullulans and the dematiaceous hyphomycete Cladosporium ramotenellum and H. fraxineus), and endophytic thalli of biotrophs (Phyllactinia and Taphrina species), the indigenous necrotroph Venturia fraxini and H. fraxineus. Mycobiome comparison between healthy and symptomatic European ash leaflets revealed no significant differences in relative abundance of H. fraxineus, but A. pullulans was more prevalent in symptomatic trees. The impacts of host specificity, spatiotemporal niche partitioning, species carbon utilization profiles and life cycle traits are discussed to understand the ecological success of H. fraxineus in Europe. Further, the inherent limitations of different experimental approaches in the profiling of foliicolous fungi are addressed.
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13
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Větrovský T, Morais D, Kohout P, Lepinay C, Algora C, Awokunle Hollá S, Bahnmann BD, Bílohnědá K, Brabcová V, D'Alò F, Human ZR, Jomura M, Kolařík M, Kvasničková J, Lladó S, López-Mondéjar R, Martinović T, Mašínová T, Meszárošová L, Michalčíková L, Michalová T, Mundra S, Navrátilová D, Odriozola I, Piché-Choquette S, Štursová M, Švec K, Tláskal V, Urbanová M, Vlk L, Voříšková J, Žifčáková L, Baldrian P. GlobalFungi, a global database of fungal occurrences from high-throughput-sequencing metabarcoding studies. Sci Data 2020; 7:228. [PMID: 32661237 PMCID: PMC7359306 DOI: 10.1038/s41597-020-0567-7] [Citation(s) in RCA: 84] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 06/05/2020] [Indexed: 02/08/2023] Open
Abstract
Fungi are key players in vital ecosystem services, spanning carbon cycling, decomposition, symbiotic associations with cultivated and wild plants and pathogenicity. The high importance of fungi in ecosystem processes contrasts with the incompleteness of our understanding of the patterns of fungal biogeography and the environmental factors that drive those patterns. To reduce this gap of knowledge, we collected and validated data published on the composition of soil fungal communities in terrestrial environments including soil and plant-associated habitats and made them publicly accessible through a user interface at https://globalfungi.com . The GlobalFungi database contains over 600 million observations of fungal sequences across > 17 000 samples with geographical locations and additional metadata contained in 178 original studies with millions of unique nucleotide sequences (sequence variants) of the fungal internal transcribed spacers (ITS) 1 and 2 representing fungal species and genera. The study represents the most comprehensive atlas of global fungal distribution, and it is framed in such a way that third-party data addition is possible.
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Affiliation(s)
- Tomáš Větrovský
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Daniel Morais
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Petr Kohout
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Clémentine Lepinay
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Camelia Algora
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Sandra Awokunle Hollá
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Barbara Doreen Bahnmann
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Květa Bílohnědá
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Vendula Brabcová
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Federica D'Alò
- Laboratory of Systematic Botany and Mycology, University of Tuscia, Largo dell'Università snc, Viterbo, 01100, Italy
| | - Zander Rainier Human
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Mayuko Jomura
- Department of Forest Science and Resources, College of Bioresource Sciences, Nihon University, Fujisawa, Kanagawa, Japan
| | - Miroslav Kolařík
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Jana Kvasničková
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Salvador Lladó
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Rubén López-Mondéjar
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Tijana Martinović
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Tereza Mašínová
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Lenka Meszárošová
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Lenka Michalčíková
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Tereza Michalová
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Sunil Mundra
- Department of Biology, United Arab Emirates University, Al Ain, Abu Dhabi, United Arab Emirates
- Section for Genetics and Evolutionary Biology, University of Oslo, Blindernveien 31, 0316, Oslo, Norway
| | - Diana Navrátilová
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Iñaki Odriozola
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Sarah Piché-Choquette
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Martina Štursová
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Karel Švec
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Vojtěch Tláskal
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Michaela Urbanová
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Lukáš Vlk
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Jana Voříšková
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Lucia Žifčáková
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Petr Baldrian
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic.
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14
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Jia T, Guo T, Yao Y, Wang R, Chai B. Seasonal Microbial Community Characteristic and Its Driving Factors in a Copper Tailings Dam in the Chinese Loess Plateau. Front Microbiol 2020; 11:1574. [PMID: 32754138 PMCID: PMC7366875 DOI: 10.3389/fmicb.2020.01574] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 06/17/2020] [Indexed: 11/13/2022] Open
Abstract
A combined soil bacterial and fungal community survey was conducted for a copper tailings dam in the Chinese Loess Plateau. We investigated the seasonal differences in the composition and function of soil microbial community to examine the key environmental factors influencing soil microorganisms during restorative ecological processes. Significant seasonal differences were found in the community structure of both bacterial and fungal communities. Bacterial community abundance and fungal community (Shannon index) measurements were highest in summer. Soil nitrite nitrogen (NO2 --N) was the dominant factor influencing both bacterial and fungal communities. The bacterial community composition was significantly affected by NO2 --N and ammonium nitrogen (NH4 +-N) in spring, and fungal community structure was significantly affected by soil water content in autumn. Moreover, the fungal community exhibited significant functional feature differences among seasons, whereas bacterial community functional groups remained similar. This study aimed to clarify the adaptation response of microbes applying different approaches used in ecological restoration approaches specific to mining areas, and to identify the natural biofertility capacity of the microbial communities that colonize soil ecosystems.
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Affiliation(s)
- Tong Jia
- Shanxi Key Laboratory of Ecological Restoration on Loess Plateau, Institute of Loess Plateau, Shanxi University, Taiyuan, China
| | - Tingyan Guo
- Shanxi Key Laboratory of Ecological Restoration on Loess Plateau, Institute of Loess Plateau, Shanxi University, Taiyuan, China
| | - Yushan Yao
- Shanxi Key Laboratory of Ecological Restoration on Loess Plateau, Institute of Loess Plateau, Shanxi University, Taiyuan, China
| | - Ruihong Wang
- Shanxi Key Laboratory of Ecological Restoration on Loess Plateau, Institute of Loess Plateau, Shanxi University, Taiyuan, China
| | - Baofeng Chai
- Shanxi Key Laboratory of Ecological Restoration on Loess Plateau, Institute of Loess Plateau, Shanxi University, Taiyuan, China
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15
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Gupta S, Chaturvedi P, Kulkarni MG, Van Staden J. A critical review on exploiting the pharmaceutical potential of plant endophytic fungi. Biotechnol Adv 2020; 39:107462. [DOI: 10.1016/j.biotechadv.2019.107462] [Citation(s) in RCA: 94] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2019] [Revised: 09/22/2019] [Accepted: 10/22/2019] [Indexed: 02/08/2023]
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16
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Nilsson RH, Anslan S, Bahram M, Wurzbacher C, Baldrian P, Tedersoo L. Mycobiome diversity: high-throughput sequencing and identification of fungi. Nat Rev Microbiol 2020; 17:95-109. [PMID: 30442909 DOI: 10.1038/s41579-018-0116-y] [Citation(s) in RCA: 404] [Impact Index Per Article: 101.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Fungi are major ecological players in both terrestrial and aquatic environments by cycling organic matter and channelling nutrients across trophic levels. High-throughput sequencing (HTS) studies of fungal communities are redrawing the map of the fungal kingdom by hinting at its enormous - and largely uncharted - taxonomic and functional diversity. However, HTS approaches come with a range of pitfalls and potential biases, cautioning against unwary application and interpretation of HTS technologies and results. In this Review, we provide an overview and practical recommendations for aspects of HTS studies ranging from sampling and laboratory practices to data processing and analysis. We also discuss upcoming trends and techniques in the field and summarize recent and noteworthy results from HTS studies targeting fungal communities and guilds. Our Review highlights the need for reproducibility and public data availability in the study of fungal communities. If the associated challenges and conceptual barriers are overcome, HTS offers immense possibilities in mycology and elsewhere.
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Affiliation(s)
- R Henrik Nilsson
- Gothenburg Global Biodiversity Centre, Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden.
| | - Sten Anslan
- Zoological Institute, Braunschweig University of Technology, Braunschweig, Germany
| | - Mohammad Bahram
- Department of Ecology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Christian Wurzbacher
- Chair of Urban Water Systems Engineering, Technical University of Munich, Garching, Germany
| | - Petr Baldrian
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Praha, Czech Republic
| | - Leho Tedersoo
- Natural History Museum of Tartu University, Tartu, Estonia
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17
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Kim CS, Jo JW, Lee H, Kwag YN, Cho SE, Oh SH. Comparison of Soil Higher Fungal Communities between Dead and Living Abies koreana in Mt. Halla, the Republic of Korea. MYCOBIOLOGY 2020; 48:364-372. [PMID: 36860556 PMCID: PMC9969794 DOI: 10.1080/12298093.2020.1811193] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
To improve our understanding of the relationship between soil higher fungi (belonging to Ascomycota and Basidiomycota) and Abies koreana, we surveyed A. koreana soil fungal communities in a forest in Mt. Halla, Jeju Island, Korea by next-generation sequencing (Illumina Miseq). To confirm the soil higher fungal communities, we collected two types of soils from a defined plot: soils with dead (AKDTs) and living A. koreana (AKLTs), respectively. Soil fungi were classified into 2 phyla, 19 classes, 64 orders, 133 families, 195 genera, and 229 OTUs (895,705 sequence reads). Nonmetric multidimensional scaling (NMDS) showed significantly different soil higher fungal communities between AKDTs and AKLTs (p < .05). In addition, the saprophyte composition was significantly affected by A. koreana status (p < .05). The proportion of the mycorrhizal Clavulina spp. was different between soils with AKDTs and AKLTs, suggesting that Clavulina spp. may be a crucial soil fungal species influencing A. koreana. This study will lead to a better understanding of the ecological status of A. koreana in Mt. Halla. In addition, this study could be useful for the conservation and management of A. koreana habitats.
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Affiliation(s)
- Chang Sun Kim
- Forest Biodiversity Division, Korea National
Arboretum, Pocheon, Korea
- CONTACT Chang Sun Kim
| | - Jong Won Jo
- Forest Biodiversity Division, Korea National
Arboretum, Pocheon, Korea
| | - Hyen Lee
- Forest Biodiversity Division, Korea National
Arboretum, Pocheon, Korea
| | - Young-Nam Kwag
- Forest Biodiversity Division, Korea National
Arboretum, Pocheon, Korea
| | - Sung Eun Cho
- Forest Biodiversity Division, Korea National
Arboretum, Pocheon, Korea
| | - Seung Hwan Oh
- Forest Biodiversity Division, Korea National
Arboretum, Pocheon, Korea
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18
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Salwan R, Sharma A, Sharma V. Recent Advances in Molecular Approaches for Mining Potential Candidate Genes of Trichoderma for Biofuel. Fungal Biol 2020. [DOI: 10.1007/978-3-030-41870-0_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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19
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Contribution of root-associated microbial communities on soil quality of Oak and Pine forests in the Himalayan ecosystem. Trop Ecol 2019. [DOI: 10.1007/s42965-019-00031-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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20
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Boeraeve M, Honnay O, Jacquemyn H. Forest edge effects on the mycorrhizal communities of the dual-mycorrhizal tree species Alnus glutinosa (L.) Gaertn. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 666:703-712. [PMID: 30812005 DOI: 10.1016/j.scitotenv.2019.02.290] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Revised: 02/05/2019] [Accepted: 02/18/2019] [Indexed: 06/09/2023]
Abstract
Forest conversion into agricultural land has resulted in a continuous decline in forest cover and in a reduced size and increased edge-to-core ratio of the remaining fragments. Forest edges are more directly exposed to sunlight, wind and pollutants and the resulting changes in habitat quality might have a large impact on plant and animal communities. Few studies, however, have focused on forest edge effects on mycorrhizal fungus communities. Here, we used high-throughput sequencing to study how communities of arbuscular mycorrhizal (AMF) and ectomycorrhizal fungi (EcMF), present in both the roots of the dual mycorrhizal tree Alnus glutinosa and in the soil, changed with increasing distance from the forest edge within fragmented forests embedded in an intensively managed agricultural matrix. Overall, we found 158 AMF OTUs and 275 EcMF OTUs. Soil moisture content increased with increasing distance from the forest edge, whereas soil nitrate concentration increased with increasing distance in south-facing and decreased in north-facing edges. Distance to the forest edge had a significant effect on EcMF community composition that largely overlapped with the observed changes in soil variables, especially soil moisture content. Apart from this distance effect, there were also clear effects of edge orientation on mycorrhizal diversity and community composition. While AMF OTU richness was higher at south- than at north-facing edges, the opposite pattern was found for EcMF. Community composition of both mycorrhiza types also differed significantly between south- and north-facing edges. We conclude that altered environmental conditions at forest edges cause significant changes in mycorrhizal communities, which could subsequently affect ecosystem functioning.
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Affiliation(s)
- Margaux Boeraeve
- Department of Biology, Plant Conservation and Population Biology, KU Leuven, B-3001 Leuven, Belgium.
| | - Olivier Honnay
- Department of Biology, Plant Conservation and Population Biology, KU Leuven, B-3001 Leuven, Belgium
| | - Hans Jacquemyn
- Department of Biology, Plant Conservation and Population Biology, KU Leuven, B-3001 Leuven, Belgium
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21
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Murgia M, Fiamma M, Barac A, Deligios M, Mazzarello V, Paglietti B, Cappuccinelli P, Al‐Qahtani A, Squartini A, Rubino S, Al‐Ahdal MN. Biodiversity of fungi in hot desert sands. Microbiologyopen 2019; 8:e00595. [PMID: 29504263 PMCID: PMC6341031 DOI: 10.1002/mbo3.595] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Accepted: 01/08/2018] [Indexed: 11/09/2022] Open
Abstract
The fungal community of six sand samples from Saudi Arabia and Jordan deserts was characterized by culture-independent analysis via next generation sequencing of the 18S rRNA genes and by culture-dependent methods followed by sequencing of internal transcribed spacer (ITS) region. By 18S sequencing were identified from 163 to 507 OTUs per sample, with a percentage of fungi ranging from 3.5% to 82.7%. The identified fungal Phyla were Ascomycota, Basal fungi, and Basidiomycota and the most abundant detected classes were Dothideomycetes, Pezizomycetes, and Sordariomycetes. A total of 11 colonies of filamentous fungi were isolated and cultured from six samples, and the ITS sequencing pointed toward five different species of the class Sordariomycetes, belonging to genera Fusarium (F. redolens, F. solani, F. equiseti), Chaetomium (C. madrasense), and Albifimbria (A. terrestris). The results of this study show an unexpectedly large fungal biodiversity in the Middle East desert sand and their possible role and implications on human health.
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Affiliation(s)
- Manuela Murgia
- Department of Biomedical SciencesUniversity of SassariSassariItaly
| | - Maura Fiamma
- Department of Biomedical SciencesUniversity of SassariSassariItaly
| | - Aleksandra Barac
- Clinic for Infectious and Tropical DiseasesClinical Centre of SerbiaFaculty of MedicineUniversity of BelgradeBelgradeSerbia
| | - Massimo Deligios
- Department of Biomedical SciencesUniversity of SassariSassariItaly
| | | | - Bianca Paglietti
- Department of Biomedical SciencesUniversity of SassariSassariItaly
| | | | - Ahmed Al‐Qahtani
- Department of Infection and ImmunityKing Faisal Specialist Hospital and Research CentreRiyadhSaudi Arabia
| | - Andrea Squartini
- Department of Agronomy Animals, Food, Natural Resources and EnvironmentDAFNAEUniversity of PadovaPadovaItaly
| | - Salvatore Rubino
- Department of Biomedical SciencesUniversity of SassariSassariItaly
- Department of Infection and ImmunityKing Faisal Specialist Hospital and Research CentreRiyadhSaudi Arabia
| | - Mohammed N. Al‐Ahdal
- Department of Infection and ImmunityKing Faisal Specialist Hospital and Research CentreRiyadhSaudi Arabia
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22
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Castaño C, Lindahl BD, Alday JG, Hagenbo A, Martínez de Aragón J, Parladé J, Pera J, Bonet JA. Soil microclimate changes affect soil fungal communities in a Mediterranean pine forest. THE NEW PHYTOLOGIST 2018; 220:1211-1221. [PMID: 29757469 DOI: 10.1111/nph.15205] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Accepted: 03/30/2018] [Indexed: 06/08/2023]
Abstract
Soil microclimate is a potentially important regulator of the composition of plant-associated fungal communities in climates with significant drought periods. Here, we investigated the spatio-temporal dynamics of soil fungal communities in a Mediterranean Pinus pinaster forest in relation to soil moisture and temperature. Fungal communities in 336 soil samples collected monthly over 1 year from 28 long-term experimental plots were assessed by PacBio sequencing of ITS2 amplicons. Total fungal biomass was estimated by analysing ergosterol. Community changes were analysed in the context of functional traits. Soil fungal biomass was lowest during summer and late winter and highest during autumn, concurrent with a greater relative abundance of mycorrhizal species. Intra-annual spatio-temporal changes in community composition correlated significantly with soil moisture and temperature. Mycorrhizal fungi were less affected by summer drought than free-living fungi. In particular, mycorrhizal species of the short-distance exploration type increased in relative abundance under dry conditions, whereas species of the long-distance exploration type were more abundant under wetter conditions. Our observations demonstrate a potential for compositional and functional shifts in fungal communities in response to changing climatic conditions. Free-living fungi and mycorrhizal species with extensive mycelia may be negatively affected by increasing drought periods in Mediterranean forest ecosystems.
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Affiliation(s)
- Carles Castaño
- Forest Bioengineering Solutions S.A., Crta. de Sant Llorenç de Morunys Km. 2, E-25280, Solsona, Spain
- Departament de Producció Vegetal i Ciència Forestal, Universitat de Lleida-AGROTECNIO, Av. Rovira Roure, 191, E-25198, Lleida, Spain
| | - Björn D Lindahl
- Department of Soil and Environment, Swedish University of Agricultural Sciences, SE-75007, Uppsala, Sweden
| | - Josu G Alday
- Departament de Producció Vegetal i Ciència Forestal, Universitat de Lleida-AGROTECNIO, Av. Rovira Roure, 191, E-25198, Lleida, Spain
| | - Andreas Hagenbo
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, SE-75007, Uppsala, Sweden
| | - Juan Martínez de Aragón
- Forest Bioengineering Solutions S.A., Crta. de Sant Llorenç de Morunys Km. 2, E-25280, Solsona, Spain
- Centre Tecnològic Forestal de Catalunya, CTFC-CEMFOR, Ctra. de St. Llorenç de Morunys km 2, E-25280, Solsona, Spain
| | - Javier Parladé
- Centre de Cabrils, IRTA, Ctra. Cabrils Km. 2, E-08348, Cabrils, Barcelona, Spain
| | - Joan Pera
- Centre de Cabrils, IRTA, Ctra. Cabrils Km. 2, E-08348, Cabrils, Barcelona, Spain
| | - José Antonio Bonet
- Departament de Producció Vegetal i Ciència Forestal, Universitat de Lleida-AGROTECNIO, Av. Rovira Roure, 191, E-25198, Lleida, Spain
- Centre Tecnològic Forestal de Catalunya, CTFC-CEMFOR, Ctra. de St. Llorenç de Morunys km 2, E-25280, Solsona, Spain
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23
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Fungal communities in a Korean red pine stand, Gwangneung Forest, Korea. JOURNAL OF ASIA-PACIFIC BIODIVERSITY 2017. [DOI: 10.1016/j.japb.2017.08.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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24
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Huseyin CE, O'Toole PW, Cotter PD, Scanlan PD. Forgotten fungi-the gut mycobiome in human health and disease. FEMS Microbiol Rev 2017; 41:479-511. [PMID: 28430946 DOI: 10.1093/femsre/fuw047] [Citation(s) in RCA: 154] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Accepted: 01/04/2017] [Indexed: 12/11/2022] Open
Abstract
The human body is home to a complex and diverse microbial ecosystem that plays a central role in host health. This includes a diversity of fungal species that is collectively referred to as our 'mycobiome'. Although research into the mycobiome is still in its infancy, its potential role in human disease is increasingly recognised. Here we review the existing literature available on the human mycobiota with an emphasis on the gut mycobiome, including how fungi interact with the human host and other microbes. In doing so, we provide a comprehensive critique of the methodologies available to research the human mycobiota as well as highlighting the latest research findings from mycological surveys of different groups of interest including infants, obese and inflammatory bowel disease cohorts. This in turn provides new insights and directions for future studies in this burgeoning research area.
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Affiliation(s)
- Chloe E Huseyin
- Teagasc Food Research Centre, Moorepark, Fermoy, Cork P61 C996, Ireland.,APC Microbiome Institute, Biosciences Institute, University College Cork, Cork T12 YT20 Ireland.,School of Microbiology, University College Cork, Cork T12 YT20, Ireland
| | - Paul W O'Toole
- APC Microbiome Institute, Biosciences Institute, University College Cork, Cork T12 YT20 Ireland.,School of Microbiology, University College Cork, Cork T12 YT20, Ireland
| | - Paul D Cotter
- Teagasc Food Research Centre, Moorepark, Fermoy, Cork P61 C996, Ireland.,APC Microbiome Institute, Biosciences Institute, University College Cork, Cork T12 YT20 Ireland
| | - Pauline D Scanlan
- APC Microbiome Institute, Biosciences Institute, University College Cork, Cork T12 YT20 Ireland
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25
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Ectomycorrhizal Fungal Communities in Urban Parks Are Similar to Those in Natural Forests but Shaped by Vegetation and Park Age. Appl Environ Microbiol 2017; 83:AEM.01797-17. [PMID: 28970220 DOI: 10.1128/aem.01797-17] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Accepted: 09/21/2017] [Indexed: 12/31/2022] Open
Abstract
Ectomycorrhizal (ECM) fungi are important mutualists for the growth and health of most boreal trees. Forest age and its host species composition can impact the composition of ECM fungal communities. Although plentiful empirical data exist for forested environments, the effects of established vegetation and its successional trajectories on ECM fungi in urban greenspaces remain poorly understood. We analyzed ECM fungi in 5 control forests and 41 urban parks of two plant functional groups (conifer and broadleaf trees) and in three age categories (10, ∼50, and >100 years old) in southern Finland. Our results show that although ECM fungal richness was marginally greater in forests than in urban parks, urban parks still hosted rich and diverse ECM fungal communities. ECM fungal community composition differed between the two habitats but was driven by taxon rank order reordering, as key ECM fungal taxa remained largely the same. In parks, the ECM communities differed between conifer and broadleaf trees. The successional trajectories of ECM fungi, as inferred in relation to the time since park construction, differed among the conifers and broadleaf trees: the ECM fungal communities changed over time under the conifers, whereas communities under broadleaf trees provided no evidence for such age-related effects. Our data show that plant-ECM fungus interactions in urban parks, in spite of being constructed environments, are surprisingly similar in richness to those in natural forests. This suggests that the presence of host trees, rather than soil characteristics or even disturbance regime of the system, determine ECM fungal community structure and diversity.IMPORTANCE In urban environments, soil and trees improve environmental quality and provide essential ecosystem services. ECM fungi enhance plant growth and performance, increasing plant nutrient acquisition and protecting plants against toxic compounds. Recent evidence indicates that soil-inhabiting fungal communities, including ECM and saprotrophic fungi, in urban parks are affected by plant functional type and park age. However, ECM fungal diversity and its responses to urban stress, plant functional type, or park age remain unknown. The significance of our study is in identifying, in greater detail, the responses of ECM fungi in the rhizospheres of conifer and broadleaf trees in urban parks. This will greatly enhance our knowledge of ECM fungal communities under urban stresses, and the findings can be utilized by urban planners to improve urban ecosystem services.
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García-Guzmán OM, Garibay-Orijel R, Hernández E, Arellano-Torres E, Oyama K. Word-wide meta-analysis of Quercus forests ectomycorrhizal fungal diversity reveals southwestern Mexico as a hotspot. MYCORRHIZA 2017; 27:811-822. [PMID: 28819747 DOI: 10.1007/s00572-017-0793-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Accepted: 07/31/2017] [Indexed: 06/07/2023]
Abstract
Quercus is the most diverse genus of ectomycorrhizal (ECM) host plants; it is distributed in the Northern and Southern Hemispheres, from temperate to tropical regions. However, their ECM communities have been scarcely studied in comparison to those of conifers. The objectives of this study were to determine the richness of ECM fungi associated with oak forests in the Cuitzeo basin in southwestern Mexico; and to determine the level of richness, potential endemism and species similarity among ECM fungal communities associated with natural oak forests worldwide through a meta-analysis. The ITS DNA sequences of ECM root tips from 14 studies were included in the meta-analysis. In total, 1065 species of ECM fungi have been documented worldwide; however, 812 species have been only found at one site. Oak forests in Europe contain 416 species, Mexico 307, USA 285, and China 151. Species with wider distributions are Sebacinaceae sp. SH197130, Amanita subjunquillea, Cenococcum geophilum, Cortinarius decipiens, Russula hortensis, R. risigallina, R. subrubescens, Sebacinaceae sp. SH214607, Tomentella ferruginea, and T. lapida. The meta-analysis revealed (1) that Mexico is not only a hotspot for oak species but also for their ECM mycobionts. (2) There is a particularly high diversity of ECM Pezizales in oak seasonal forests from western USA to southwestern Mexico. (3) The oak forests in southwestern Mexico have the largest number of potential endemic species. (4) Globally, there is a high turnover of ECM fungal species associated with oaks, which indicates high levels of alpha and beta diversity in these communities.
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Affiliation(s)
- Olimpia Mariana García-Guzmán
- Instituto de Biología, Universidad Nacional Autónoma de México (UNAM), Tercer Circuito s/n, Ciudad Universitaria. Delegación Coyoacán, C.P. 04510, Mexico City, Mexico
- Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Roberto Garibay-Orijel
- Instituto de Biología, Universidad Nacional Autónoma de México (UNAM), Tercer Circuito s/n, Ciudad Universitaria. Delegación Coyoacán, C.P. 04510, Mexico City, Mexico.
| | - Edith Hernández
- Instituto de Biología, Universidad Nacional Autónoma de México (UNAM), Tercer Circuito s/n, Ciudad Universitaria. Delegación Coyoacán, C.P. 04510, Mexico City, Mexico
| | - Elsa Arellano-Torres
- Departamento de Ecología y Recursos Naturales. Facultad de Ciencias, Universidad Nacional Autónoma de México, Circuito Exterior s/n, Ciudad. Universitaria. Delegación Coyoacán, C.P. 04510, Mexico City, Mexico
| | - Ken Oyama
- Escuela Nacional de Estudios Superiores Unidad Morelia, Universidad Nacional Autónoma de México, Antigua carretera a Pátzcuaro No. 8701, Expropiación Petrolera INDECO, Mexico City, Michoacán, Mexico
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Khan AL, Asaf S, Al-Rawahi A, Lee IJ, Al-Harrasi A. Rhizospheric microbial communities associated with wild and cultivated frankincense producing Boswellia sacra tree. PLoS One 2017; 12:e0186939. [PMID: 29053752 PMCID: PMC5650177 DOI: 10.1371/journal.pone.0186939] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Accepted: 10/10/2017] [Indexed: 12/14/2022] Open
Abstract
Boswellia sacra, a frankincense producing endemic tree, has been well known for its cultural, religious and economic values. However, the tree has been least explored for the associated microsymbiota in the rhizosphere. The current study elucidates the fungal and bacterial communities of the rhizospheric regions of the wild and cultivated B. sacra tree populations through next generation sequencing. The sequence analysis showed the existence of 1006±8.9 and 60.6±3.1 operational taxonomic unit (OTUs) for bacterial and fungal communities respectively. In fungal communities, five major phyla were found with significantly higher abundance of Ascomycota (60.3%) in wild population and Basidiomycota (52%) in cultivated tree rhizospheres. Among bacterial communities, 31 major phyla were found, with significant distribution of Actinobacteria in wild tree rhizospheres, whereas Proteobacteria and Acidobacteria were highly abundant in cultivated trees. The diversity and abundance of microbiome varied significantly depending upon soil characteristics of the three different populations. In addition, significantly higher glucosidases, cellulases and indole-3-acetic acid were found in cultivated tree’s rhizospheres as compared to wild tree populations. for these plants to survive the harsh arid-land environmental conditions. The current study is a first comprehensive work and advances our knowledge about the core fungal and bacterial microbial microbiome associated with this economically important tree.
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Affiliation(s)
- Abdul Latif Khan
- UoN Chair of Oman’s Medicinal Plants and Marine Natural Products, University of Nizwa, Nizwa, Oman
| | - Sajjad Asaf
- School of Applied Biosciences, Kyungpook National University, Daegu, Republic of Korea
| | - Ahmed Al-Rawahi
- UoN Chair of Oman’s Medicinal Plants and Marine Natural Products, University of Nizwa, Nizwa, Oman
| | - In-Jung Lee
- School of Applied Biosciences, Kyungpook National University, Daegu, Republic of Korea
| | - Ahmed Al-Harrasi
- UoN Chair of Oman’s Medicinal Plants and Marine Natural Products, University of Nizwa, Nizwa, Oman
- * E-mail:
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Moussa TAA, Al-Zahrani HS, Almaghrabi OA, Abdelmoneim TS, Fuller MP. Comparative metagenomics approaches to characterize the soil fungal communities of western coastal region, Saudi Arabia. PLoS One 2017; 12:e0185096. [PMID: 28934322 PMCID: PMC5608318 DOI: 10.1371/journal.pone.0185096] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Accepted: 09/06/2017] [Indexed: 11/26/2022] Open
Abstract
A total of 145007 reads were obtained from pyrosequencing for all the 4 samples. The total count ranged from 11,301,014 (Mecca old road) to 23,503,512 bp (Thuwal). A total of 460 fungal species belonging to 133 genera, 58 families, 33 orders, 13 classes and 4 phyla was identified across the four sites. The most abundant phylum at all four sites was Ascomycota followed by Basidiomycota. Four phyla (Ascomycota—99.31%, Basidiomycota—0.59%, Chytridiomycota—0.04%, Glomeromycota—0.03%) were detected in Khulais. Except for Glomeromycota, all phyla were detected at Mecca old road (Ascomycota—74.26%, Basidiomycota—25.71%, Chytridiomycota—0.01%) and Thuwal (Ascomycota—99.59%, Basidiomycota—0.40%, Chytridiomycota—0.002%); while only Ascomycota—90.98% and Basidiomycota—9.01% were detected in Asfan road. At the class level, Sordariomycetes was predominantly observed at Asfan road—59.88%, Khulais—68.26% and Thuwal—94.84%; while Pezizomycetes was dominant at Mecca old road—56.01%, was absent at Asfan road. Agaricomycetes was present only at Mecca old road—25.73%; while Tremellomycetes—5.77%, Malasseizomycetes—2.13% and Microbotryomycetes—1.10% were found only at Asfan road. The phylogenetic trees revealed that clear genus level differences are visible across all the four sites, with an overall predominance of Thielavia followed by Madurella, Aspergillus, and Gelasinospora. Chaetomium sp., Aspergillus caespitosus and Aspergillus sp. were found in moderate (Mecca old road and Thuwal) to abundant (Asfan road and Khulais) quantities. Thielavia sp., Thielavia hyalocarpa and Madurella sp. are found in moderate quantities at Khulais and Mecca old road, while in abundant levels at Asfan road and Thuwal. Fusarium equisati and F. oxysporum were detected at Thuwal and Khulais. Sordaria araneosa was present at Khulais, while Malasseiza globosa species was detected in moderate quantities across all sites except Khulais.
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Affiliation(s)
- Tarek A A Moussa
- Biological Sciences Department, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
- Biological Sciences Department, Faculty of Science, University of Jeddah, Jeddah, Saudi Arabia
- Botany and Microbiology Department, Faculty of Science, Cairo University, Giza, Egypt
| | - Hassan S Al-Zahrani
- Biological Sciences Department, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Omar A Almaghrabi
- Biological Sciences Department, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
- Biological Sciences Department, Faculty of Science, University of Jeddah, Jeddah, Saudi Arabia
| | - Tamer S Abdelmoneim
- Biological Sciences Department, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
- Biological Sciences Department, Faculty of Science, University of Jeddah, Jeddah, Saudi Arabia
- Department of Agricultural Botany, Faculty of Agriculture, Suez Canal University, Ismailia, Egypt
| | - Michael P Fuller
- School of Biological Science, Faculty of Science and Engineering, Plymouth University, Plymouth, United Kingdom
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Žifčáková L, Větrovský T, Lombard V, Henrissat B, Howe A, Baldrian P. Feed in summer, rest in winter: microbial carbon utilization in forest topsoil. MICROBIOME 2017; 5:122. [PMID: 28923122 PMCID: PMC5604414 DOI: 10.1186/s40168-017-0340-0] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Accepted: 09/12/2017] [Indexed: 05/21/2023]
Abstract
BACKGROUND Evergreen coniferous forests contain high stocks of organic matter. Significant carbon transformations occur in litter and soil of these ecosystems, making them important for the global carbon cycle. Due to seasonal allocation of photosynthates to roots, carbon availability changes seasonally in the topsoil. The aim of this paper was to describe the seasonal differences in C source utilization and the involvement of various members of soil microbiome in this process. RESULTS Here, we show that microorganisms in topsoil encode a diverse set of carbohydrate-active enzymes, including glycoside hydrolases and auxiliary enzymes. While the transcription of genes encoding enzymes degrading reserve compounds, such as starch or trehalose, was high in soil in winter, summer was characterized by high transcription of ligninolytic and cellulolytic enzymes produced mainly by fungi. Fungi strongly dominated the transcription in litter and an equal contribution of bacteria and fungi was found in soil. The turnover of fungal biomass appeared to be faster in summer than in winter, due to high activity of enzymes targeting its degradation, indicating fast growth in both litter and soil. In each enzyme family, hundreds to thousands of genes were typically transcribed simultaneously. CONCLUSIONS Seasonal differences in the transcription of glycoside hydrolases and auxiliary enzyme genes are more pronounced in soil than in litter. Our results suggest that mainly fungi are involved in decomposition of recalcitrant biopolymers in summer, while bacteria replace them in this role in winter. Transcripts of genes encoding enzymes targeting plant biomass biopolymers, reserve compounds and fungal cell walls were especially abundant in the coniferous forest topsoil.
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Affiliation(s)
- Lucia Žifčáková
- Institute of Microbiology of the CAS, Vídeňská 1083, 14220 Praha 4, Czech Republic
- Faculty of Science, Charles University, Albertov 6, 128 43 Praha 2, Czech Republic
| | - Tomáš Větrovský
- Institute of Microbiology of the CAS, Vídeňská 1083, 14220 Praha 4, Czech Republic
| | - Vincent Lombard
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille Université, Marseille, France
- INRA, USC 1408 AFMB, Marseille, France
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille Université, Marseille, France
- INRA, USC 1408 AFMB, Marseille, France
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | | | - Petr Baldrian
- Institute of Microbiology of the CAS, Vídeňská 1083, 14220 Praha 4, Czech Republic
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Wang X, Liu J, Long D, Han Q, Huang J. The ectomycorrhizal fungal communities associated with Quercus liaotungensis in different habitats across northern China. MYCORRHIZA 2017; 27:441-449. [PMID: 28120112 DOI: 10.1007/s00572-017-0762-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Accepted: 01/06/2017] [Indexed: 06/06/2023]
Abstract
Quercus liaotungensis is a major tree species in deciduous broad-leaved forests in northern China. In this study, we investigated ectomycorrhizal (ECM) communities associated with Q. liaotungensis from five typical habitats across northern China. We used internal transcribed spacer-polymerase chain reaction and DNA sequencing to identify ECM fungi, and we detected 220 operational taxonomic units. In general, at the regional scale, the dominant ECM lineages were /tomentella-thelephora, /cenococcum, /russula-lactarius, and /inocybe. Analysis of variance demonstrated significant differences in alpha diversity among these ECM communities, and the ECM fungal richness was positively correlated with elevation and soil organic matter. Analysis of similarity and a nonmetric multidimensional scaling analysis revealed that there were significant differences in community composition, and the geographical distance was correlated with the ECM fungal communities. Among the environmental factors we studied, soil parameters and climate factors were the primary direct driving factors of the ECM fungal communities. Our study primarily advances our understanding of environmental factors affecting ECM fungal communities at regional scale.
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Affiliation(s)
- Xiaobing Wang
- College of Forestry, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Jianjun Liu
- College of Landscape Architecture and Arts, Northwest A&F University, Yangling, Shaanxi, 712100, China.
- Ningxia Helan Mountain Forest Ecosystem Orientational Research Station, Yinchuan, Ningxia, 750000, China.
| | - Dongfeng Long
- College of Forestry, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Qisheng Han
- College of Forestry, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Jian Huang
- College of Forestry, Northwest A&F University, Yangling, Shaanxi, 712100, China.
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31
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Hui N, Jumpponen A, Francini G, Kotze DJ, Liu X, Romantschuk M, Strömmer R, Setälä H. Soil microbial communities are shaped by vegetation type and park age in cities under cold climate. Environ Microbiol 2017; 19:1281-1295. [DOI: 10.1111/1462-2920.13660] [Citation(s) in RCA: 88] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Revised: 12/22/2016] [Accepted: 12/28/2016] [Indexed: 02/02/2023]
Affiliation(s)
- Nan Hui
- Department of Environmental Sciences; University of Helsinki, Niemenkatu 73; Lahti 15140 Finland
| | - Ari Jumpponen
- Division of Biology; Kansas State University; Manhattan KS 66506 USA
| | - Gaia Francini
- Department of Environmental Sciences; University of Helsinki, Niemenkatu 73; Lahti 15140 Finland
| | - D. Johan Kotze
- Department of Environmental Sciences; University of Helsinki, Niemenkatu 73; Lahti 15140 Finland
| | - Xinxin Liu
- Department of Environmental Sciences; University of Helsinki, Niemenkatu 73; Lahti 15140 Finland
| | - Martin Romantschuk
- Department of Environmental Sciences; University of Helsinki, Niemenkatu 73; Lahti 15140 Finland
- Institute of Environmental Sciences; Kazan Federal University; Kazan 420008 Russia
| | - Rauni Strömmer
- Department of Environmental Sciences; University of Helsinki, Niemenkatu 73; Lahti 15140 Finland
| | - Heikki Setälä
- Department of Environmental Sciences; University of Helsinki, Niemenkatu 73; Lahti 15140 Finland
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32
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Jumpponen A, Jones KL, Blair J. Vertical distribution of fungal communities in tallgrass prairie soil. Mycologia 2017; 102:1027-41. [DOI: 10.3852/09-316] [Citation(s) in RCA: 97] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Ari Jumpponen
- Division of Biology and Ecological Genomics Institute, Kansas State University, Manhattan, Kansas 66506
| | - Kenneth L. Jones
- Ecological Genomics Institute, Kansas State University, Manhattan, Kansas 66506, and, Environmental Health Sciences and Georgia Genomics Facility, University of Georgia, Athens, Georgia 30602
| | - John Blair
- Division of Biology, Kansas State University, Manhattan, Kansas 66506
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Davey ML, Skogen MJ, Heegaard E, Halvorsen R, Kauserud H, Ohlson M. Host and tissue variations overshadow the response of boreal moss-associated fungal communities to increased nitrogen load. Mol Ecol 2017; 26:571-588. [DOI: 10.1111/mec.13938] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Revised: 09/28/2016] [Accepted: 09/30/2016] [Indexed: 11/28/2022]
Affiliation(s)
- Marie L. Davey
- Department of Ecology and Natural Resource Management; Norwegian University of Life Sciences; PO Box 5003 NO-1432 Ås Norway
- Section for Genetics and Evolutionary Biology; Department of Biosciences; University of Oslo; PO Box 1066 Blindern NO-0316 Oslo Norway
| | - Marte J. Skogen
- Department of Ecology and Natural Resource Management; Norwegian University of Life Sciences; PO Box 5003 NO-1432 Ås Norway
| | - Einar Heegaard
- Norwegian Forest and Landscape Institute; Fanaflaten 4 NO-5244 Fana Norway
| | - Rune Halvorsen
- Department of Botany; Natural History Museum; University of Oslo; PO Box 1172 Blindern NO-0318 Oslo Norway
| | - Håvard Kauserud
- Section for Genetics and Evolutionary Biology; Department of Biosciences; University of Oslo; PO Box 1066 Blindern NO-0316 Oslo Norway
| | - Mikael Ohlson
- Department of Ecology and Natural Resource Management; Norwegian University of Life Sciences; PO Box 5003 NO-1432 Ås Norway
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Influences of host plant identity and disturbance on spatial structure and community composition of ectomycorrhizal fungi in a northern Mississippi uplands ecosystem. FUNGAL ECOL 2016. [DOI: 10.1016/j.funeco.2016.08.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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35
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Morrison EW, Frey SD, Sadowsky JJ, van Diepen LT, Thomas WK, Pringle A. Chronic nitrogen additions fundamentally restructure the soil fungal community in a temperate forest. FUNGAL ECOL 2016. [DOI: 10.1016/j.funeco.2016.05.011] [Citation(s) in RCA: 82] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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36
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Nguyen D, Boberg J, Ihrmark K, Stenström E, Stenlid J. Do foliar fungal communities of Norway spruce shift along a tree species diversity gradient in mature European forests? FUNGAL ECOL 2016. [DOI: 10.1016/j.funeco.2016.07.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Ramanjaneyulu G, Rajasekhar Reddy B. Optimization of Xylanase Production through Response Surface Methodology by Fusarium sp. BVKT R2 Isolated from Forest Soil and Its Application in Saccharification. Front Microbiol 2016; 7:1450. [PMID: 27713726 PMCID: PMC5032753 DOI: 10.3389/fmicb.2016.01450] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2016] [Accepted: 08/30/2016] [Indexed: 11/13/2022] Open
Abstract
Xylanses are hydrolytic enzymes with wide applications in several industries like biofuels, paper and pulp, deinking, food, and feed. The present study was aimed at hitting at high yield xylanase producing fungi from natural resources. Two highest xylanase producing fungal isolates-Q12 and L1 were picked from collection of 450 fungal cultures for the utilization of xylan. These fungal isolates-Q12 and L1 were identified basing on ITS gene sequencing analysis as Fusarium sp. BVKT R2 (KT119615) and Fusarium strain BRR R6 (KT119619), respectively with construction of phylogenetic trees. Fusarium sp. BVKT R2 was further optimized for maximum xylanase production and the interaction effects between variables on production of xylanase were studied through response surface methodology. The optimal conditions for maximal production of xylanase were sorbitol 1.5%, yeast extract 1.5%, pH of 5.0, Temperature of 32.5°C, and agitation of 175 rpm. Under optimal conditions, the yields of xylanase production by Fusarium sp. BVKT R2 was as high as 4560 U/ml in SmF. Incubation of different lignocellulosic biomasses with crude enzyme of Fusarium sp. BVKT R2 at 37°C for 72 h could achieve about 45% saccharification. The results suggest that Fusarium sp. BVKT R2 has potential applications in saccharification process of biomass.
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Affiliation(s)
- Golla Ramanjaneyulu
- Department of Microbiology, Sri Krishnadevaraya UniversityAnantapuramu, India
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38
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Santalahti M, Sun H, Jumpponen A, Pennanen T, Heinonsalo J. Vertical and seasonal dynamics of fungal communities in boreal Scots pine forest soil. FEMS Microbiol Ecol 2016; 92:fiw170. [DOI: 10.1093/femsec/fiw170] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/05/2016] [Indexed: 11/14/2022] Open
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Setälä HM, Francini G, Allen JA, Hui N, Jumpponen A, Kotze DJ. Vegetation Type and Age Drive Changes in Soil Properties, Nitrogen, and Carbon Sequestration in Urban Parks under Cold Climate. Front Ecol Evol 2016. [DOI: 10.3389/fevo.2016.00093] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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40
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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
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41
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Martinová V, van Geel M, Lievens B, Honnay O. Strong differences in Quercus robur-associated ectomycorrhizal fungal communities along a forest-city soil sealing gradient. FUNGAL ECOL 2016. [DOI: 10.1016/j.funeco.2015.12.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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42
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Barnes CJ, van der Gast CJ, Burns CA, McNamara NP, Bending GD. Temporally Variable Geographical Distance Effects Contribute to the Assembly of Root-Associated Fungal Communities. Front Microbiol 2016; 7:195. [PMID: 26941720 PMCID: PMC4766365 DOI: 10.3389/fmicb.2016.00195] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2015] [Accepted: 12/05/2015] [Indexed: 11/16/2022] Open
Abstract
Root-associated fungi are key contributors to ecosystem functioning, however, the factors which determine community assembly are still relatively poorly understood. This study simultaneously quantified the roles of geographical distance, environmental heterogeneity and time in determining root-associated fungal community composition at the local scale within a short rotation coppice (SRC) willow plantation. Culture independent molecular analyses of the root-associated fungal community suggested a strong but temporally variable effect of geographical distance among fungal communities in terms of composition at the local geographical level. Whilst these distance effects were most prevalent on October communities, soil pH had an effect on structuring of the communities throughout the sampling period. Given the temporal variation in the effects of geographical distance and the environment for shaping root-associated fungal communities, there is clearly need for a temporal component to sampling strategies in future investigations of fungal ecology.
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Affiliation(s)
- Christopher J. Barnes
- School of Life Sciences, Gibbet Hill Campus, University of WarwickCoventry, UK
- Section of Evolutionary Genomics, National History Museum of Denmark, University of CopenhagenCopenhagen, Denmark
| | | | - Caitlin A. Burns
- School of Life Sciences, Gibbet Hill Campus, University of WarwickCoventry, UK
| | - Niall P. McNamara
- Natural Environment Research Council Centre for Ecology and Hydrology – Lancaster Environment CentreLancaster, UK
| | - Gary D. Bending
- School of Life Sciences, Gibbet Hill Campus, University of WarwickCoventry, UK
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Kim CS, Nam JW, Jo JW, Kim SY, Han JG, Hyun MW, Sung GH, Han SK. Studies on seasonal dynamics of soil-higher fungal communities in Mongolian oak-dominant Gwangneung forest in Korea. J Microbiol 2016; 54:14-22. [PMID: 26727897 DOI: 10.1007/s12275-016-5521-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Accepted: 11/16/2015] [Indexed: 10/22/2022]
Abstract
We surveyed macrofungi biweekly at defined plots from April to December in 2014, in the Mongolian oak-dominant forest, Gwangneung Forest, Pochen-si, Korea, and analyzed a soilhigher fungal diversity during four seasons (represented by April, August, October, and December). Based on morphological observation of collected specimens, the collected macrofungi were classified into 2 phyla 3 classes 7 orders, 14 families, 21 genera, and 33 species (36 specimens). DNA-based community analyses indicated that soil-higher fungi were classified into 2 phyla, 18 classes, 49 orders, 101 families, and 155 genera (83,360 sequence reads), defined herein as 155 genus-level operational taxonomic units (GOTUs). In the present study, we evaluated and discussed the fungal diversity in seasonal dynamics and soil layers based on collected macrofungi and pyrosequencing data while considering environmental parameters (pH, exchangeable K, T-P, NH 4 (+) , NO 3 (-) , OM, WR, TOC, and T-N). Moreover, principal components analysis (PCA) showed distinct clusters of the GOTU assemblage associated with the seasons.
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Affiliation(s)
- Chang Sun Kim
- Forest Biodiversity Division, Korea National Arboretum, Pocheon, 487-820, Republic of Korea
| | - Jong Woo Nam
- Forest Biodiversity Division, Korea National Arboretum, Pocheon, 487-820, Republic of Korea
| | - Jong Won Jo
- Forest Biodiversity Division, Korea National Arboretum, Pocheon, 487-820, Republic of Korea
| | - Sang-Yong Kim
- Forest Biodiversity Division, Korea National Arboretum, Pocheon, 487-820, Republic of Korea
| | - Jae-Gu Han
- Mushroom Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Eumseong, 369-873, Republic of Korea
| | - Min Woo Hyun
- Mushroom Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Eumseong, 369-873, Republic of Korea
| | - Gi-Ho Sung
- Institute for Bio-medical Convergence, International St. Mary's Hospital and College of Medicine, Catholic Kwandong University, Incheon, 404-834, Republic of Korea.
| | - Sang-Kuk Han
- Forest Biodiversity Division, Korea National Arboretum, Pocheon, 487-820, Republic of Korea.
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Kaul S, Sharma T, K. Dhar M. "Omics" Tools for Better Understanding the Plant-Endophyte Interactions. FRONTIERS IN PLANT SCIENCE 2016; 7:955. [PMID: 27446181 PMCID: PMC4925718 DOI: 10.3389/fpls.2016.00955] [Citation(s) in RCA: 112] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2015] [Accepted: 06/15/2016] [Indexed: 05/20/2023]
Abstract
Endophytes, which mostly include bacteria, fungi and actinomycetes, are the endosymbionts that reside asymptomatically in plants for at least a part of their life cycle. They have emerged as a valuable source of novel metabolites, industrially important enzymes and as stress relievers of host plant, but still many aspects of endophytic biology are unknown. Functions of individual endophytes are the result of their continuous and complex interactions with the host plant as well as other members of the host microbiome. Understanding plant microbiomes as a system allows analysis and integration of these complex interactions. Modern genomic studies involving metaomics and comparative studies can prove to be helpful in unraveling the gray areas of endophytism. A deeper knowledge of the mechanism of host infestation and role of endophytes could be exploited to improve the agricultural management in terms of plant growth promotion, biocontrol and bioremediation. Genome sequencing, comparative genomics, microarray, next gen sequencing, metagenomics, metatranscriptomics are some of the techniques that are being used or can be used to unravel plant-endophyte relationship. The modern techniques and approaches need to be explored to study endophytes and their putative role in host plant ecology. This review highlights "omics" tools that can be explored for understanding the role of endophytes in the plant microbiome.
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Ectomycorrhizal fungal communities in Nothofagus nervosa ( Raulí ): A comparison between domesticated and naturally established specimens in a native forest of Patagonia, Argentina. FUNGAL ECOL 2015. [DOI: 10.1016/j.funeco.2015.05.011] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Runnel K, Tamm H, Lõhmus A. Surveying wood-inhabiting fungi: Most molecularly detected polypore species form fruit-bodies within short distances. FUNGAL ECOL 2015. [DOI: 10.1016/j.funeco.2015.08.008] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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Hayward J, Horton TR, Nuñez MA. Ectomycorrhizal fungal communities coinvading with Pinaceae host plants in Argentina: Gringos bajo el bosque. THE NEW PHYTOLOGIST 2015; 208:497-506. [PMID: 25963605 DOI: 10.1111/nph.13453] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Accepted: 04/07/2015] [Indexed: 06/04/2023]
Abstract
Coinvasive ectomycorrhizal (ECM) fungi allow Pinaceae species to invade regions otherwise lacking compatible symbionts, but ECM fungal communities permitting Pinaceae invasions are poorly understood. In the context of Pinaceae invasions on Isla Victoria, Nahuel Huapi National Park, Argentina, we asked: what ECM fungi are coinvading with Pinaceae hosts on Isla Victoria; are some ECM fungal species or genera more prone to invade than others; and are all ECM fungal species that associate with Northern Hemisphere hosts also nonnative, or are some native fungi compatible with nonnative plants? We sampled ECMs from 226 Pinaceae host plant individuals, both planted individuals and recruits, growing inside and invading from plantations. We used molecular techniques to examine ECM fungal communities associating with these trees. A distinctive subset of the ECM fungal community predominated far from plantations, indicating differences between highly invasive and less invasive ECM fungi. Some fungal invaders reported here have been detected in other locations around the world, suggesting strong invasion potential. Fungi that were frequently detected far from plantations are often found in early-successional sites in the native range, while fungi identified as late-successional species in the native range are rarely found far from plantations, suggesting a means for predicting potential fungal coinvaders.
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Affiliation(s)
- Jeremy Hayward
- Department of Environmental and Forest Biology, State University of New York College of Environmental Science and Forestry, Syracuse, NY, USA
| | - Thomas R Horton
- Department of Environmental and Forest Biology, State University of New York College of Environmental Science and Forestry, Syracuse, NY, USA
| | - Martin A Nuñez
- Laboratorio Ecotono, INIBIOMA, CONICET, Universidad Nacional del Comahue, Bariloche, Argentina
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Rincón A, Santamaría-Pérez B, Rabasa SG, Coince A, Marçais B, Buée M. Compartmentalized and contrasted response of ectomycorrhizal and soil fungal communities of Scots pine forests along elevation gradients in France and Spain. Environ Microbiol 2015; 17:3009-24. [DOI: 10.1111/1462-2920.12894] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Revised: 04/29/2015] [Accepted: 04/30/2015] [Indexed: 11/28/2022]
Affiliation(s)
- Ana Rincón
- Instituto de Ciencias Agrarias, ICA; CSIC; Serrano 115bis 28006 Madrid Spain
| | | | - Sonia G. Rabasa
- Museo Nacional de Ciencias Naturales, MNCN; CSIC; Serrano 115bis 28006 Madrid Spain
| | - Aurore Coince
- UMR1136 INRA Nancy - Université de Lorraine; Interactions Arbres-Microorganismes; Lab of Excellence ARBRE; INRA; 54280 Champenoux France
| | - Benoit Marçais
- UMR1136 INRA Nancy - Université de Lorraine; Interactions Arbres-Microorganismes; Lab of Excellence ARBRE; INRA; 54280 Champenoux France
| | - Marc Buée
- UMR1136 INRA Nancy - Université de Lorraine; Interactions Arbres-Microorganismes; Lab of Excellence ARBRE; INRA; 54280 Champenoux France
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Yamashita S, Masuya H, Abe S, Masaki T, Okabe K. Relationship between the decomposition process of coarse woody debris and fungal community structure as detected by high-throughput sequencing in a deciduous broad-leaved forest in Japan. PLoS One 2015; 10:e0131510. [PMID: 26110605 PMCID: PMC4481346 DOI: 10.1371/journal.pone.0131510] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2015] [Accepted: 06/03/2015] [Indexed: 11/18/2022] Open
Abstract
We examined the relationship between the community structure of wood-decaying fungi, detected by high-throughput sequencing, and the decomposition rate using 13 years of data from a forest dynamics plot. For molecular analysis and wood density measurements, drill dust samples were collected from logs and stumps of Fagus and Quercus in the plot. Regression using a negative exponential model between wood density and time since death revealed that the decomposition rate of Fagus was greater than that of Quercus. The residual between the expected value obtained from the regression curve and the observed wood density was used as a decomposition rate index. Principal component analysis showed that the fungal community compositions of both Fagus and Quercus changed with time since death. Principal component analysis axis scores were used as an index of fungal community composition. A structural equation model for each wood genus was used to assess the effect of fungal community structure traits on the decomposition rate and how the fungal community structure was determined by the traits of coarse woody debris. Results of the structural equation model suggested that the decomposition rate of Fagus was affected by two fungal community composition components: one that was affected by time since death and another that was not affected by the traits of coarse woody debris. In contrast, the decomposition rate of Quercus was not affected by coarse woody debris traits or fungal community structure. These findings suggest that, in the case of Fagus coarse woody debris, the fungal community structure is related to the decomposition process of its host substrate. Because fungal community structure is affected partly by the decay stage and wood density of its substrate, these factors influence each other. Further research on interactive effects is needed to improve our understanding of the relationship between fungal community structure and the woody debris decomposition process.
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Affiliation(s)
- Satoshi Yamashita
- Forestry and Forest Products Research Institute, Tsukuba, Ibaraki, Japan
- * E-mail:
| | - Hayato Masuya
- Tohoku Research Center, Forestry and Forest Products Research Institute, Morioka, Iwate, Japan
| | - Shin Abe
- Forestry and Forest Products Research Institute, Tsukuba, Ibaraki, Japan
| | - Takashi Masaki
- Forestry and Forest Products Research Institute, Tsukuba, Ibaraki, Japan
| | - Kimiko Okabe
- Forestry and Forest Products Research Institute, Tsukuba, Ibaraki, Japan
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