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Gu Y, Li Z, Lei P, Wang R, Xu H, Friman VP. Phylogenetic distance-decay patterns are not explained by local community assembly processes in freshwater lake microbial communities. Environ Microbiol 2023; 25:1940-1954. [PMID: 37254577 DOI: 10.1111/1462-2920.16437] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 05/23/2023] [Indexed: 06/01/2023]
Abstract
While water and sediment microbial communities exhibit pronounced spatio-temporal patterns in freshwater lakes, the underlying drivers are yet poorly understood. Here, we evaluated the importance of spatial and temporal variation in abiotic environmental factors for bacterial and microeukaryotic community assembly and distance-decay relationships in water and sediment niches in Hongze Lake. By sampling across the whole lake during both Autumn and Spring sampling time points, we show that only bacterial sediment communities were governed by deterministic community assembly processes due to abiotic environmental drivers. Nevertheless, consistent distance-decay relationships were found with both bacterial and microeukaryotic communities, which were relatively stable with both sampling time points. Our results suggest that spatio-temporal variation in environmental factors was important in explaining mainly bacterial community assembly in the sediment, possibly due lesser disturbance. However, clear distance-decay patterns emerged also when the community assembly was stochastic. Together, these results suggest that abiotic environmental factors do not clearly drive the spatial structuring of lake microbial communities, highlighting the need to understand the role of other potential drivers, such as spatial heterogeneity and biotic species interactions.
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Affiliation(s)
- Yian Gu
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing, China
- Jiangsu Key Laboratory for Eco-Agricultural Biotechnology around Hongze Lake, Huaiyin Normal University, China
| | - Zhidan Li
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China
| | - Peng Lei
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing, China
| | - Rui Wang
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing, China
| | - Hong Xu
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing, China
| | - Ville-Petri Friman
- Department of Microbiology, University of Helsinki, Helsinki, Finland
- Department of Biology, University of York, York, UK
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2
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Current Insight into Traditional and Modern Methods in Fungal Diversity Estimates. J Fungi (Basel) 2022; 8:jof8030226. [PMID: 35330228 PMCID: PMC8955040 DOI: 10.3390/jof8030226] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Revised: 02/19/2022] [Accepted: 02/20/2022] [Indexed: 12/04/2022] Open
Abstract
Fungi are an important and diverse component in various ecosystems. The methods to identify different fungi are an important step in any mycological study. Classical methods of fungal identification, which rely mainly on morphological characteristics and modern use of DNA based molecular techniques, have proven to be very helpful to explore their taxonomic identity. In the present compilation, we provide detailed information on estimates of fungi provided by different mycologistsover time. Along with this, a comprehensive analysis of the importance of classical and molecular methods is also presented. In orderto understand the utility of genus and species specific markers in fungal identification, a polyphasic approach to investigate various fungi is also presented in this paper. An account of the study of various fungi based on culture-based and cultureindependent methods is also provided here to understand the development and significance of both approaches. The available information on classical and modern methods compiled in this study revealed that the DNA based molecular studies are still scant, and more studies are required to achieve the accurate estimation of fungi present on earth.
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Réblová M, Kolařík M, Nekvindová J, Réblová K, Sklenář F, Miller AN, Hernández-Restrepo M. Phylogenetic Reassessment, Taxonomy, and Biogeography of Codinaea and Similar Fungi. J Fungi (Basel) 2021; 7:1097. [PMID: 34947079 PMCID: PMC8704094 DOI: 10.3390/jof7121097] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 12/14/2021] [Accepted: 12/15/2021] [Indexed: 12/18/2022] Open
Abstract
The genus Codinaea is a phialidic, dematiaceous hyphomycete known for its intriguing morphology and turbulent taxonomic history. This polyphasic study represents a new, comprehensive view on the taxonomy, systematics, and biogeography of Codinaea and its relatives. Phylogenetic analyses of three nuclear loci confirmed that Codinaea is polyphyletic. The generic concept was emended; it includes four morphotypes that contribute to its morphological complexity. Ancestral inference showed that the evolution of some traits is correlated and that these traits previously used to delimit taxa at the generic level occur in species that were shown to be congeneric. Five lineages of Codinaea-like fungi were recognized and introduced as new genera: Codinaeella, Nimesporella, Stilbochaeta, Tainosphaeriella, and Xyladelphia. Dual DNA barcoding facilitated identification at the species level. Codinaea and its segregates thrive on decaying plants, rarely occurring as endophytes or plant pathogens. Environmental ITS sequences indicate that they are common in bulk soil. The geographic distribution found using GlobalFungi database was consistent with known data. Most species are distributed in either the Holarctic realm or tropical geographic regions. The ancestral climatic zone was temperate, followed by transitions to the tropics; these fungi evolved primarily in Eurasia and Americas, with subsequent transitions to Africa and Australasia.
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Affiliation(s)
- Martina Réblová
- Department of Taxonomy, Institute of Botany, The Czech Academy of Sciences, 252 43 Průhonice, Czech Republic; (K.R.); (F.S.)
| | - Miroslav Kolařík
- Laboratory of Fungal Genetics and Metabolism, Institute of Microbiology, The Czech Academy of Sciences, 142 20 Prague, Czech Republic;
| | - Jana Nekvindová
- Department of Clinical Biochemistry and Diagnostics, University Hospital Hradec Králové, 500 05 Hradec Králové, Czech Republic;
| | - Kamila Réblová
- Department of Taxonomy, Institute of Botany, The Czech Academy of Sciences, 252 43 Průhonice, Czech Republic; (K.R.); (F.S.)
- CEITEC—Central European Institute of Technology, Masaryk University, 625 00 Brno, Czech Republic
| | - František Sklenář
- Department of Taxonomy, Institute of Botany, The Czech Academy of Sciences, 252 43 Průhonice, Czech Republic; (K.R.); (F.S.)
- Laboratory of Fungal Genetics and Metabolism, Institute of Microbiology, The Czech Academy of Sciences, 142 20 Prague, Czech Republic;
| | - Andrew N. Miller
- Illinois Natural History Survey, University of Illinois Urbana-Champaign, Champaign, IL 61820, USA;
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Laking AE, Li Z, Goossens E, Miñarro M, Beukema W, Lens L, Bonte D, Verheyen K, Pasmans F, Martel A. Salamander loss alters litter decomposition dynamics. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 776:145994. [PMID: 33647642 DOI: 10.1016/j.scitotenv.2021.145994] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 02/08/2021] [Accepted: 02/14/2021] [Indexed: 06/12/2023]
Abstract
Biodiversity loss affects ecosystem functioning. Top down effects of amphibian declines on the trophic food web of the forest floor are poorly understood. Here we quantify and explain the effects of disease-driven loss of salamanders on the dynamics of forest leaf litter. Using paired mesocosms, within a Belgian forest, we tested the effect of fire salamander (Salamandra salamandra) presence on the trophic cascade that results in the decomposition rate of good quality (maple - Acer pseudoplatanus) and poorer quality (oak - Quercus robur) leaf litter, over an 18 month period. The presence of salamanders reduced decomposition rate of Quercus litter up to 20%. This was associated with a significantly higher predation rate on detritivores, which altered the functional composition of the invertebrate community. Functional composition analysis of the litter microbiome showed less bacteria associated with leaf litter degradation on the Quercus litter in the presence of salamanders. Salamanders thus influence ecosystem functions through trophic cascades and promote the retention of the leaf litter fraction in poorer quality litter.
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Affiliation(s)
- Alexandra E Laking
- Wildlife Health Ghent, Department of Pathology, Bacteriology and Poultry Diseases, Ghent University Salisburylaan 133, 9820 Merelbeke, Belgium.
| | - Zhimin Li
- Wildlife Health Ghent, Department of Pathology, Bacteriology and Poultry Diseases, Ghent University Salisburylaan 133, 9820 Merelbeke, Belgium
| | - Evy Goossens
- Department of Pathology, Bacteriology and Poultry Diseases, Ghent University Salisburylaan 133, 9820 Merelbeke, Belgium
| | - Marta Miñarro
- Museo Nacional de Ciencias Naturales (MNCN-CSIC), c/ José Gutiérrez Abascal 2, 28006 Madrid, Spain
| | - Wouter Beukema
- Wildlife Health Ghent, Department of Pathology, Bacteriology and Poultry Diseases, Ghent University Salisburylaan 133, 9820 Merelbeke, Belgium
| | - Luc Lens
- Terrestrial Ecology Unit, Department of Biology, Ghent University, K.L. Ledeganckstraat 35, 9000 Gent, Belgium
| | - Dries Bonte
- Terrestrial Ecology Unit, Department of Biology, Ghent University, K.L. Ledeganckstraat 35, 9000 Gent, Belgium
| | - Kris Verheyen
- Forest & Nature Lab, Department of Environment, Ghent University, Geraardsbergsesteenweg 267, BE-9090 Gontrode (Melle), Belgium
| | - Frank Pasmans
- Wildlife Health Ghent, Department of Pathology, Bacteriology and Poultry Diseases, Ghent University Salisburylaan 133, 9820 Merelbeke, Belgium
| | - An Martel
- Wildlife Health Ghent, Department of Pathology, Bacteriology and Poultry Diseases, Ghent University Salisburylaan 133, 9820 Merelbeke, Belgium
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The Effects of Climate on the Hypogean Migration of Cave Salamanders, Eurycea lucifuga (Rafinesque, 1822). J HERPETOL 2021. [DOI: 10.1670/19-092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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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: 72] [Impact Index Per Article: 18.0] [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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Non-target Effects of Naphthalene on the Soil Microbial Biomass and Bacterial Communities in the Subalpine Forests of Western China. Sci Rep 2019; 9:9811. [PMID: 31285516 PMCID: PMC6614484 DOI: 10.1038/s41598-019-46394-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 06/28/2019] [Indexed: 11/08/2022] Open
Abstract
Naphthalene is a biocide of soil fauna, particularly of soil arthropods, that has been widely applied to test the functional roles of soil fauna in soil processes. However, whether the use of naphthalene to expel soil fauna has a non-target effect on soil bacteria in subalpine forests remains unclear. We conducted a naphthalene treatment experiment to explore the effects of naphthalene on the soil bacterial community in subalpine forest soil. The results suggested that naphthalene treatment (at 100 g.m-2 per month) significantly increased the abundances of total bacterial, gram-positive bacterial and gram-negative bacterial phospholipid fatty acids (PLFA) and did not change the microbial biomass carbon (MBC), microbial biomass nitrogen (MBN) or MBC/MBN ratio. Moreover, a total of 1038 operational taxonomic units (OTUs) were detected by Illumina MiSeq sequencing analysis. Proteobacteria, Actinobacteria, and Acidobacteria Chloroflexi were the dominant phyla, and Bradyrhizobium was the most abundant genus. The naphthalene treatment did not affect soil bacterial diversity or community structure. Overall, these results demonstrated that the naphthalene treatment had non-target effects on the active bacterial community abundance but not the soil bacterial community structure. Thus, the non-target effects of naphthalene treatment should be considered before using it to expel soil fauna.
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Walker DM, Murray CM, Talbert D, Tinker P, Graham SP, Crowther TW. A salamander's top down effect on fungal communities in a detritivore ecosystem. FEMS Microbiol Ecol 2018; 94:5104376. [DOI: 10.1093/femsec/fiy168] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Accepted: 08/17/2018] [Indexed: 12/17/2022] Open
Affiliation(s)
- Donald M Walker
- Middle Tennessee State University, Toxicology and Disease Group, Biology Department, PO Box 60, Murfreesboro, TN, USA
| | | | - Doug Talbert
- Tennessee Technological University, Department of Computer Science, Cookeville, TN, USA
| | - Paul Tinker
- Tennessee Technological University, Department of Computer Science, Cookeville, TN, USA
| | - Sean P Graham
- Sul Ross University, Department of Biology, Alpine, TX, USA
| | - Thomas W Crowther
- Institute of Integrative Biology, Department of Environmental Systems Science, ETH Zurich, Univeritätstrasse 16, 8092 Zürich, Switzerland
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