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Wang M, Mara P, Burgaud G, Edgcomb V, Long X, Yang H, Cai L, Li W. Metatranscriptomics and metabarcoding reveal spatiotemporal shifts in fungal communities and their activities in Chinese coastal waters. Mol Ecol 2023; 32:2750-2765. [PMID: 36852430 DOI: 10.1111/mec.16905] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 02/22/2023] [Accepted: 02/24/2023] [Indexed: 03/01/2023]
Abstract
Fungal communities are diverse and abundant in coastal waters, yet, their ecological roles and adaptations remain largely unknown. To address these gaps, ITS2 metabarcoding and metatranscriptomic analyses were used to capture the whole suite of fungal diversity and their metabolic potential in water column and sediments in the Yellow Sea during August and October 2019. ITS2 metabarcoding described successfully the abundance of Dikarya during August and October at the different examined habitats, but strongly underrepresented or failed to identify other fungal taxa, including zoosporic and early-diverging lineages, that were abundant in the mycobiome as uncovered by metatranscriptomes. Metatranscriptomics also revealed enriched expression of genes annotated to zoosporic fungi (e.g., chytrids) mainly in the surface water column in October. This enriched expression was correlated with the two-fold increase in chlorophyll-a intensity attributed to phytoplanktonic species which are known to be parasitized by chytrids. The concurrent high expression of genes related to calcium signalling and GTPase activity suggested that these metabolic traits facilitate the parasitic lifestyle of chytrids. Similarly, elevated expression of phagosome genes annotated to Rozellomycota, an early-diverging fungal phylum not fully detected with ITS2 metabarcoding, suggested that this taxon utilizes a suite of feeding modes, including phagotrophy in this coastal setting. Our data highlight the necessity of using combined approaches to accurately describe the community structure of coastal mycobiome. We also provide in-depth insights into the fungal ecological roles in coastal waters, and report potential metabolic mechanisms utilized by fungi to cope with environmental stresses that occur during distinct seasonal months in coastal ecosystems.
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Affiliation(s)
- Mengmeng Wang
- College of Science, Shantou University, Shantou, China.,State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Paraskevi Mara
- Department of Geology and Geophysics, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, USA
| | - Gaëtan Burgaud
- University of Brest, INRAE, Laboratoire Universitaire de Biodiversité et Écologie Microbienne, Plouzané, France
| | - Virginia Edgcomb
- Department of Geology and Geophysics, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, USA
| | - Xuedan Long
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Haiping Yang
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Lei Cai
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Wei Li
- College of Science, Shantou University, Shantou, China
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Keuschnig C, Martins JMF, Navel A, Simonet P, Larose C. Micro-fractionation shows microbial community changes in soil particles below 20 μm. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.1091773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
IntroductionMicro-scale analysis of microbes in soil is essential to the overall understanding of microbial organization, interactions, and ecosystem functioning. Soil fractionation according to its aggregated structure has been used to access microbial habitats. While bacterial communities have been extensively described, little is known about the fungal communities at scales relevant to microbial interactions.MethodsWe applied a gentle soil fractionation method to preserve stable aggregated structures within the range of micro-aggregates and studied fungal and bacterial communities as well as nitrogen cycling potentials in the pristine Rothamsted Park Grass soil (bulk soil) as well as in its particle size fractions (PSFs; >250 μm, 250–63 μm, 63–20 μm, 20–2 μm, <2 μm, and supernatant).ResultsOverall bacterial and fungal community structures changed in PSFs below 20 μm. The relative abundance of Basidiomycota decreased with decreasing particle size over the entire measure range, while Ascomycota showed an increase and Mucoromycota became more prominent in particles below 20 μm. Bacterial diversity was found highest in the < 2 μm fraction, but only a few taxa were washed-off during the procedure and found in supernatant samples. These taxa have been associated with exopolysaccharide production and biofilm formation (e.g., Pseudomonas, Massilia, Mucilaginibacter, Edaphobaculum, Duganella, Janthinobacterium, and Variovorax). The potential for nitrogen reduction was found elevated in bigger aggregates.DiscussionThe observed changes below 20 μm particle are in line with scales where microbes operate and interact, highlighting the potential to focus on little researched sub-fractions of micro-aggregates. The applied method shows potential for use in studies focusing on the role of microbial biofilms in soil and might also be adapted to research various other soil microbial functions. Technical advances in combination with micro-sampling methods in soil promise valuable output in soil studies when particles below 20 μm are included.
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Hanrahan-Tan DG, Henderson L, Kertesz MA, Lilje O. The Effects of Nitrogen and Phosphorus on Colony Growth and Zoospore Characteristics of Soil Chytridiomycota. J Fungi (Basel) 2022; 8:jof8040341. [PMID: 35448572 PMCID: PMC9024642 DOI: 10.3390/jof8040341] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 03/21/2022] [Accepted: 03/21/2022] [Indexed: 01/03/2023] Open
Abstract
The Chytridiomycota phylum contributes to nutrient cycling and the flow of energy between trophic levels in terrestrial and aquatic ecosystems yet remains poorly described or absent from publications discussing fungal communities in these environments. This study contributes to the understanding of three species of soil chytrids in vitro—Gaertneriomyces semiglobifer, Spizellomyces sp. and Rhizophlyctis rosea—in the presence of elevated concentrations of nitrogen and phosphorus and with different sources of nitrogen. Colony growth was measured after 4 weeks as dry weight and total protein. To determine the impacts on zoospore reproduction, motility, lipid content, and attachment to organic substrates, 4- and 8-week incubation times were investigated. Whilst all isolates were able to assimilate ammonium as a sole source of nitrogen, nitrate was less preferred or even unsuitable as a nutrient source for G. semiglobifer and R. rosea, respectively. Increasing phosphate concentrations led to diverse responses between isolates. Zoospore production was also variable between isolates, and the parameters for zoospore motility appeared only to be influenced by the phosphate concentration for Spizellomyces sp. and R. rosea. Attachment rates increased for G. semiglobifer in the absence of an inorganic nitrogen source. These findings highlight variability between the adaptive responses utilised by chytrids to persist in a range of environments and provide new techniques to study soil chytrid biomass and zoospore motility by total protein quantification and fluorescent imaging respectively.
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Affiliation(s)
- Deirdre G. Hanrahan-Tan
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2006, Australia;
- Correspondence: (D.G.H.-T.); (O.L.)
| | - Linda Henderson
- Department of Planning and Environment, Locked Bag 5022, Parramatta, NSW 2124, Australia;
| | - Michael A. Kertesz
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2006, Australia;
| | - Osu Lilje
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2006, Australia;
- Correspondence: (D.G.H.-T.); (O.L.)
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Blaalid R, Khomich M. Current knowledge of Chytridiomycota diversity in Northern Europe and future research needs. FUNGAL BIOL REV 2021. [DOI: 10.1016/j.fbr.2021.03.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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5
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What has happened to the “aquatic phycomycetes” (sensu Sparrow)? Part II: Shared properties of zoosporic true fungi and fungus-like microorganisms. FUNGAL BIOL REV 2018. [DOI: 10.1016/j.fbr.2017.09.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Berbee ML, James TY, Strullu-Derrien C. Early Diverging Fungi: Diversity and Impact at the Dawn of Terrestrial Life. Annu Rev Microbiol 2017; 71:41-60. [DOI: 10.1146/annurev-micro-030117-020324] [Citation(s) in RCA: 120] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Mary L. Berbee
- Department of Botany, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Timothy Y. James
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan 48109
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Jordan HR, Tomberlin JK. Abiotic and Biotic Factors Regulating Inter-Kingdom Engagement between Insects and Microbe Activity on Vertebrate Remains. INSECTS 2017; 8:E54. [PMID: 28538664 PMCID: PMC5492068 DOI: 10.3390/insects8020054] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Revised: 05/10/2017] [Accepted: 05/18/2017] [Indexed: 11/17/2022]
Abstract
Abstract: A number of abiotic and biotic factors are known to regulate arthropod attraction, colonization, and utilization of decomposing vertebrate remains. Such information is critical when assessing arthropod evidence associated with said remains in terms of forensic relevance. Interactions are not limited to just between the resource and arthropods. There is another biotic factor that has been historically overlooked; however, with the advent of high-throughput sequencing, and other molecular techniques, the curtain has been pulled back to reveal a microscopic world that is playing a major role with regards to carrion decomposition patterns in association with arthropods. The objective of this publication is to review many of these factors and draw attention to their impact on microbial, specifically bacteria, activity associated with these remains as it is our contention that microbes serve as a primary mechanism regulating associated arthropod behavior.
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Affiliation(s)
- Heather R Jordan
- Department of Biological Sciences, Mississippi State University, Starkville, MS 39705, USA.
| | - Jeffery K Tomberlin
- Department of Entomology, Texas A&M University, College Station, TX 77843, USA.
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Davis WJ, Letcher PM, Powell MJ. Borealophlyctis nickersoniae, a new species in Rhizophlyctidales. Mycologia 2016; 108:744-52. [PMID: 27582566 DOI: 10.3852/15-205] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Accepted: 01/13/2016] [Indexed: 11/10/2022]
Abstract
Zoospore ultrastructural characters combined with molecular phylogenetic hypotheses have been used to revise the taxonomy of zoosporic true fungi. An example is the reclassification of Rhizophlyctis rosea-like fungal strains into four new families and three new genera within the order Rhizophlyctidales. One genus was Borealophlyctis, which included a Canadian isolate, DAOMC 229843. A recent survey of chytrid diversity in Alabama (USA) yielded additional strains (WJD 170, WJD 171) in the Borealophlyctis lineage. With light and transmission-electron microscopy we examined strains DAOMC 229843, WJD 170 and WJD 171. We also analyzed partial nuc 28S rDNA D1-D3 domains (28S) and nuc rDNA region encompassing the internal transcribed spacers 1 and 2 and 5.8S (ITS) sequences to determine the phylogenetic placement of the strains within Rhizophlyctidales. Based on molecular divergence and morphological differences from the type Borealophlyctis paxensis, we recognize DAOMC 229843, WJD 170 and WJD 171 as representatives of the new species Borealophlyctis nickersoniae.
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Affiliation(s)
- William J Davis
- Department of Biological Sciences, University of Alabama, Tuscaloosa, Alabama 35487
| | - Peter M Letcher
- Department of Biological Sciences, University of Alabama, Tuscaloosa, Alabama 35487
| | - Martha J Powell
- Department of Biological Sciences, University of Alabama, Tuscaloosa, Alabama 35487
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Sturrock CJ, Woodhall J, Brown M, Walker C, Mooney SJ, Ray RV. Effects of damping-off caused by Rhizoctonia solani anastomosis group 2-1 on roots of wheat and oil seed rape quantified using X-ray Computed Tomography and real-time PCR. FRONTIERS IN PLANT SCIENCE 2015; 6:461. [PMID: 26157449 PMCID: PMC4478850 DOI: 10.3389/fpls.2015.00461] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Accepted: 06/10/2015] [Indexed: 05/02/2023]
Abstract
Rhizoctonia solani is a plant pathogenic fungus that causes significant establishment and yield losses to several important food crops globally. This is the first application of high resolution X-ray micro Computed Tomography (X-ray μCT) and real-time PCR to study host-pathogen interactions in situ and elucidate the mechanism of Rhizoctonia damping-off disease over a 6-day period caused by R. solani, anastomosis group (AG) 2-1 in wheat (Triticum aestivum cv. Gallant) and oil seed rape (OSR, Brassica napus cv. Marinka). Temporal, non-destructive analysis of root system architectures was performed using RooTrak and validated by the destructive method of root washing. Disease was assessed visually and related to pathogen DNA quantification in soil using real-time PCR. R. solani AG2-1 at similar initial DNA concentrations in soil was capable of causing significant damage to the developing root systems of both wheat and OSR. Disease caused reductions in primary root number, root volume, root surface area, and convex hull which were affected less in the monocotyledonous host. Wheat was more tolerant to the pathogen, exhibited fewer symptoms and developed more complex root systems. In contrast, R. solani caused earlier damage and maceration of the taproot of the dicot, OSR. Disease severity was related to pathogen DNA accumulation in soil only for OSR, however, reductions in root traits were significantly associated with both disease and pathogen DNA. The method offers the first steps in advancing current understanding of soil-borne pathogen behavior in situ at the pore scale, which may lead to the development of mitigation measures to combat disease influence in the field.
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Affiliation(s)
- Craig J. Sturrock
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, LoughboroughUK
| | | | - Matthew Brown
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, LoughboroughUK
| | - Catherine Walker
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, LoughboroughUK
| | - Sacha J. Mooney
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, LoughboroughUK
| | - Rumiana V. Ray
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, LoughboroughUK
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Henderson L, Pilgaard B, Gleason FH, Lilje O. Copper (II) lead (II), and zinc (II) reduce growth and zoospore release in four zoosporic true fungi from soils of NSW, Australia. Fungal Biol 2015; 119:648-55. [PMID: 26058540 DOI: 10.1016/j.funbio.2015.04.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2015] [Revised: 03/31/2015] [Accepted: 04/02/2015] [Indexed: 10/23/2022]
Abstract
This study examined the responses of a group of four zoosporic true fungi isolated from soils in NSW Australia, to concentrations of toxic metals in the laboratory that may be found in polluted soils. All isolates showed greatest sensitivity to Cu and least sensitivity to Pb. All isolates showed significant reduction in growth at 60 ppm (0.94 mmol m(-3)) for Cu, while three declined significantly at 60 ppm (0.92 mmol m(-3)) Zn. The growth of two isolates declined significantly at 100 ppm (0.48 mmol m(-3)) Pb and one at 200 ppm (0.96 mmol m(-3)) Pb. The rate of production of zoospores for all isolates was reduced when sporangia were grown in solid PYG media with 60 ppm Cu. Three isolates significantly declined in production at 60 ppm Zn and three at 100 ppm Pb. All isolates recovered growth after incubation in solid media with 60 ppm Zn or 100 ppm Pb. Two isolates did not recover growth after incubation in 60 ppm Cu. If these metals cause similar effects in the field, Cu, Pb, and Zn contamination of NSW soils is likely to reduce biomass of zoosporic true fungi. Loss of the fungi may reduce the rate of mineralisation of soil organic matter.
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Affiliation(s)
- Linda Henderson
- School of Biological Sciences, Macleay Building A12, University of Sydney, New South Wales 2006, Australia.
| | - Bo Pilgaard
- Section for Sustainable Biotechnology, Aalborg University, Copenhagen, Denmark
| | - Frank H Gleason
- School of Biological Sciences, Macleay Building A12, University of Sydney, New South Wales 2006, Australia
| | - Osu Lilje
- School of Biological Sciences, Macleay Building A12, University of Sydney, New South Wales 2006, Australia
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Gerphagnon M, Macarthur DJ, Latour D, Gachon CMM, Van Ogtrop F, Gleason FH, Sime-Ngando T. Microbial players involved in the decline of filamentous and colonial cyanobacterial blooms with a focus on fungal parasitism. Environ Microbiol 2015; 17:2573-87. [DOI: 10.1111/1462-2920.12860] [Citation(s) in RCA: 81] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Revised: 03/01/2015] [Accepted: 03/05/2015] [Indexed: 11/28/2022]
Affiliation(s)
- Mélanie Gerphagnon
- LMGE; Laboratoire Microorganismes: Génome et Environnement; UMR CNRS 6023; Clermont Université; Université Blaise Pascal; BP 80026 Aubière CEDEX 63171 France
- Culture Collection for Algae and Protozoa; Scottish Marine Institute; Scottish Association for Marine Science; Oban PA37 1QA UK
| | | | - Delphine Latour
- LMGE; Laboratoire Microorganismes: Génome et Environnement; UMR CNRS 6023; Clermont Université; Université Blaise Pascal; BP 80026 Aubière CEDEX 63171 France
| | - Claire M. M. Gachon
- Culture Collection for Algae and Protozoa; Scottish Marine Institute; Scottish Association for Marine Science; Oban PA37 1QA UK
| | - Floris Van Ogtrop
- School of Biological Sciences; University of Sydney; Sydney Australia
| | - Frank H. Gleason
- School of Biological Sciences; University of Sydney; Sydney Australia
| | - Télesphore Sime-Ngando
- LMGE; Laboratoire Microorganismes: Génome et Environnement; UMR CNRS 6023; Clermont Université; Université Blaise Pascal; BP 80026 Aubière CEDEX 63171 France
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Gleason FH, Jephcott TG, Küpper FC, Gerphagnon M, Sime-Ngando T, Karpov SA, Guillou L, van Ogtrop FF. Potential roles for recently discovered chytrid parasites in the dynamics of harmful algal blooms. FUNGAL BIOL REV 2015. [DOI: 10.1016/j.fbr.2015.03.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Guo X, Zhang Q, Zhang X, Zhang J, Gong J. Marine fungal communities in water and surface sediment of a sea cucumber farming system: habitat-differentiated distribution and nutrients driving succession. FUNGAL ECOL 2015. [DOI: 10.1016/j.funeco.2014.12.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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Gleason FH, Lilje O, Marano AV, Sime-Ngando T, Sullivan BK, Kirchmair M, Neuhauser S. Ecological functions of zoosporic hyperparasites. Front Microbiol 2014; 5:244. [PMID: 24904557 PMCID: PMC4035849 DOI: 10.3389/fmicb.2014.00244] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2014] [Accepted: 05/05/2014] [Indexed: 11/13/2022] Open
Abstract
Zoosporic parasites have received increased attention during the last years, but it is still largely unnoted that these parasites can themselves be infected by hyperparasites. Some members of the Chytridiomycota, Blastocladiomycota, Cryptomycota, Hyphochytriomycota, Labyrinthulomycota, Oomycota, and Phytomyxea are hyperparasites of zoosporic hosts. Because of sometimes complex tripartite interactions between hyperparasite, their parasite-host, and the primary host, hyperparasites can be difficult to detect and monitor. Some of these hyperparasites use similar mechanisms as their parasite-hosts to find and infect their target and to access food resources. The life cycle of zoosporic hyperparasites is usually shorter than the life cycle of their hosts, so hyperparasites may accelerate the turnaround times of nutrients within the ecosystem. Hyperparasites may increase the complexity of food webs and play significant roles in regulating population sizes and population dynamics of their hosts. We suggest that hyperparasites lengthen food chains but can also play a role in conducting or suppressing diseases of animals, plants, or algae. Hyperparasites can significantly impact ecosystems in various ways, therefore it is important to increase our understanding about these cryptic and diverse organisms.
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Affiliation(s)
- Frank H Gleason
- School of Biological Sciences A12, University of Sydney Sydney, NSW, Australia
| | - Osu Lilje
- School of Biological Sciences A12, University of Sydney Sydney, NSW, Australia
| | - Agostina V Marano
- Núcleo de Pesquisa em Micologia, Instituto de Botânica São Paulo, Brazil
| | - Télesphore Sime-Ngando
- Laboratoire Microorganismes: Génome and Environnement, Université Blaise Pascal, Clermont-Ferrand II Aubière, France
| | | | - Martin Kirchmair
- Institute of Microbiology, Leopold Franzens University Innsbruck Innsbruck, Austria
| | - Sigrid Neuhauser
- Institute of Microbiology, Leopold Franzens University Innsbruck Innsbruck, Austria ; Microbial Diversity and Genomics, Department of Life Sciences, Natural History Museum London, UK
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van der Wal A, Geydan TD, Kuyper TW, de Boer W. A thready affair: linking fungal diversity and community dynamics to terrestrial decomposition processes. FEMS Microbiol Rev 2013; 37:477-94. [DOI: 10.1111/1574-6976.12001] [Citation(s) in RCA: 223] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2012] [Revised: 08/02/2012] [Accepted: 08/21/2012] [Indexed: 12/24/2022] Open
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