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Bosch J, Dobbler PT, Větrovský T, Tláskal V, Baldrian P, Brabcová V. Decomposition of Fomes fomentatius fruiting bodies - transition of healthy living fungus into a decayed bacteria-rich habitat is primarily driven by Arthropoda. FEMS Microbiol Ecol 2024; 100:fiae044. [PMID: 38640440 PMCID: PMC11030162 DOI: 10.1093/femsec/fiae044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 03/06/2024] [Accepted: 03/28/2024] [Indexed: 04/21/2024] Open
Abstract
Fomes fomentarius is a widespread, wood-rotting fungus of temperate, broadleaved forests. Although the fruiting bodies of F. fomentarius persist for multiple years, little is known about its associated microbiome or how these recalcitrant structures are ultimately decomposed. Here we used metagenomics and metatranscriptomics to analyse the microbial community associated with healthy living and decomposing F. fomentarius fruiting bodies to assess the functional potential of the fruiting body-associated microbiome and to determine the main players involved in fruiting body decomposition. F. fomentarius sequences in the metagenomes were replaced by bacterial sequences as the fruiting body decomposed. Most CAZymes expressed in decomposing fruiting bodies targeted components of the fungal cell wall with almost all chitin-targeting sequences, plus a high proportion of beta-glucan-targeting sequences, belonging to Arthropoda. We suggest that decomposing fruiting bodies of F. fomentarius represent a habitat rich in bacteria, while its decomposition is primarily driven by Arthropoda. Decomposing fruiting bodies thus represent a specific habitat supporting both microorganisms and microfauna.
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Affiliation(s)
- Jason Bosch
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, 142 00 Prague, Czechia
| | - Priscila Thiago Dobbler
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, 142 00 Prague, Czechia
| | - Tomáš Větrovský
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, 142 00 Prague, Czechia
| | - Vojtěch Tláskal
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, 142 00 Prague, Czechia
| | - Petr Baldrian
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, 142 00 Prague, Czechia
| | - Vendula Brabcová
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, 142 00 Prague, Czechia
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Větrovský T, Kolaříková Z, Lepinay C, Awokunle Hollá S, Davison J, Fleyberková A, Gromyko A, Jelínková B, Kolařík M, Krüger M, Lejsková R, Michalčíková L, Michalová T, Moora M, Moravcová A, Moulíková Š, Odriozola I, Öpik M, Pappová M, Piché-Choquette S, Skřivánek J, Vlk L, Zobel M, Baldrian P, Kohout P. GlobalAMFungi: a global database of arbuscular mycorrhizal fungal occurrences from high-throughput sequencing metabarcoding studies. New Phytol 2023; 240:2151-2163. [PMID: 37781910 DOI: 10.1111/nph.19283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 09/04/2023] [Indexed: 10/03/2023]
Abstract
Arbuscular mycorrhizal (AM) fungi are crucial mutualistic symbionts of the majority of plant species, with essential roles in plant nutrient uptake and stress mitigation. The importance of AM fungi in ecosystems contrasts with our limited understanding of the patterns of AM fungal biogeography and the environmental factors that drive those patterns. This article presents a release of a newly developed global AM fungal dataset (GlobalAMFungi database, https://globalamfungi.com) that aims to reduce this knowledge gap. It contains almost 50 million observations of Glomeromycotinian AM fungal amplicon DNA sequences across almost 8500 samples with geographical locations and additional metadata obtained from 100 original studies. The GlobalAMFungi database is built on sequencing data originating from AM fungal taxon barcoding regions in: i) the small subunit rRNA (SSU) gene; ii) the internal transcribed spacer 2 (ITS2) region; and iii) the large subunit rRNA (LSU) gene. The GlobalAMFungi database is an open source and open access initiative that compiles the most comprehensive atlas of AM fungal distribution. It is designed as a permanent effort that will be continuously updated by its creators and through the collaboration of the scientific community. This study also documented applicability of the dataset to better understand ecology of AM fungal taxa.
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Affiliation(s)
- Tomáš Větrovský
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 142 20, Prague, Czechia
| | - Zuzana Kolaříková
- Institute of Botany of the Czech Academy of Sciences, Zámek 1, 252 43, Průhonice, Czechia
| | - Clémentine Lepinay
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 142 20, Prague, Czechia
| | - Sandra Awokunle Hollá
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 142 20, Prague, Czechia
| | - John Davison
- Institute of Ecology and Earth Sciences, University of Tartu, J. Liivi St 2, 504 09, Tartu, Estonia
| | - Anna Fleyberková
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 142 20, Prague, Czechia
| | - Anastasiia Gromyko
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 142 20, Prague, Czechia
| | - Barbora Jelínková
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 142 20, Prague, Czechia
| | - Miroslav Kolařík
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 142 20, Prague, Czechia
| | - Manuela Krüger
- Institute of Botany of the Czech Academy of Sciences, Zámek 1, 252 43, Průhonice, Czechia
| | - Renata Lejsková
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 142 20, Prague, Czechia
| | - Lenka Michalčíková
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 142 20, Prague, Czechia
| | - Tereza Michalová
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 142 20, Prague, Czechia
| | - Mari Moora
- Institute of Ecology and Earth Sciences, University of Tartu, J. Liivi St 2, 504 09, Tartu, Estonia
| | - Andrea Moravcová
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 142 20, Prague, Czechia
- Faculty of Science, Charles University, Albertov 6, 128 43, Prague, Czechia
| | - Štěpánka Moulíková
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 142 20, Prague, Czechia
| | - Iñaki Odriozola
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 142 20, Prague, Czechia
| | - Maarja Öpik
- Institute of Ecology and Earth Sciences, University of Tartu, J. Liivi St 2, 504 09, Tartu, Estonia
| | - Monika Pappová
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 142 20, Prague, Czechia
| | - Sarah Piché-Choquette
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 142 20, Prague, Czechia
| | - Jakub Skřivánek
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 142 20, Prague, Czechia
- Faculty of Science, Charles University, Albertov 6, 128 43, Prague, Czechia
| | - Lukáš Vlk
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 142 20, Prague, Czechia
| | - Martin Zobel
- Institute of Ecology and Earth Sciences, University of Tartu, J. Liivi St 2, 504 09, Tartu, Estonia
| | - Petr Baldrian
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 142 20, Prague, Czechia
| | - Petr Kohout
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 142 20, Prague, Czechia
- Faculty of Science, Charles University, Albertov 6, 128 43, Prague, Czechia
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Maleček J, Omcirk D, Skálová K, Pádecký J, Janikov MT, Obrtel M, Jonáš M, Kolář D, Michalička V, Sýkora K, Vágner M, Přívětivý L, Větrovský T, Bendová Z, Třebický V, Tufano JJ. Effects of 36 hours of sleep deprivation on military-related tasks: Can ammonium inhalants maintain performance? PLoS One 2023; 18:e0293804. [PMID: 37967128 PMCID: PMC10651003 DOI: 10.1371/journal.pone.0293804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 10/12/2023] [Indexed: 11/17/2023] Open
Abstract
INTRODUCTION A lack of sleep can pose a risk during military operations due to the associated decreases in physical and cognitive performance. However, fast-acting ergogenic aids, such as ammonia inhalants (AI), may temporarily mitigate those adverse effects of total sleep deprivation (TSD). Therefore, the present study aimed to investigate the acute effect of AI on cognitive and physical performance throughout 36 hours of TSD in military personnel. METHODS Eighteen male military cadets (24.1 ± 3.0 y; 79.3 ± 8.3 kg) performed 5 identical testing sessions during 36 hours of TSD (after 0 [0], 12 [-12], 24 [-24], and 36 [-36] hours of TSD), and after 8 [+8] hours of recovery sleep. During each testing session, the following assessments were conducted: Epworth sleepiness scale (ESS), simple reaction time (SRT), shooting accuracy (SA), rifle disassembling and reassembling (DAS), and countermovement jump height (JH). Heart rate (HR) was continuously monitored during the SA task, and a rating of perceived exertion (RPE) was obtained during the JH task. At each time point, tests were performed twice, either with AI or without AI as control (CON), in a counterbalanced order. RESULTS There was faster SRT (1.6%; p < 0.01) without increasing the number of errors, higher JH (1.5%; p < 0.01), lower RPE (9.4%; p < 0.001), and higher HR (5.0%; p < 0.001) after using AI compared to CON regardless of TSD. However, neither SA nor DAS were affected by AI or TSD (p > 0.05). Independent of AI, the SRT was slower (3.2-9.3%; p < 0.001) in the mornings (-24, +8) than in the evening (-12), JH was higher (3.0-4.7%, p < 0.001) in the evenings (-12, -36) than in the mornings (0, -24, +8), and RPE was higher (20.0-40.1%; p < 0.001) in the sleep-deprived morning (-24) than all other timepoints (0, -12, -36, +8). Furthermore, higher ESS (59.5-193.4%; p < 0.001) was reported at -24 and -36 than the rest of the time points (0, -12, and + 8). CONCLUSION Although there were detrimental effects of TSD, the usage of AI did not reduce those adverse effects. However, regardless of TSD, AI did result in a short-term increase in HR, improved SRT without affecting the number of errors, and improved JH while concurrently decreasing the RPE. No changes, yet, were observed in SA and DAS. These results suggest that AI could potentially be useful in some military scenarios, regardless of sleep deprivation.
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Affiliation(s)
- Jan Maleček
- Faculty of Physical Education and Sport, Charles University, Prague, Czech Republic
| | - Dan Omcirk
- Faculty of Physical Education and Sport, Charles University, Prague, Czech Republic
| | - Kateřina Skálová
- National Institute of Mental Health, Klecany, Czech Republic
- Faculty of Science, Charles University, Prague, Czech Republic
| | - Jan Pádecký
- Faculty of Physical Education and Sport, Charles University, Prague, Czech Republic
| | - Martin Tino Janikov
- Faculty of Physical Education and Sport, Charles University, Prague, Czech Republic
| | - Michael Obrtel
- Faculty of Physical Education and Sport, Charles University, Prague, Czech Republic
| | - Michal Jonáš
- Faculty of Physical Education and Sport, Charles University, Prague, Czech Republic
| | - David Kolář
- National Institute of Mental Health, Klecany, Czech Republic
| | - Vladimír Michalička
- Faculty of Physical Education and Sport, Charles University, Prague, Czech Republic
| | - Karel Sýkora
- Faculty of Physical Education and Sport, Charles University, Prague, Czech Republic
| | - Michal Vágner
- Faculty of Physical Education and Sport, Charles University, Prague, Czech Republic
| | - Lubomír Přívětivý
- Faculty of Physical Education and Sport, Charles University, Prague, Czech Republic
| | - Tomáš Větrovský
- Faculty of Physical Education and Sport, Charles University, Prague, Czech Republic
| | - Zdeňka Bendová
- National Institute of Mental Health, Klecany, Czech Republic
- Faculty of Science, Charles University, Prague, Czech Republic
| | - Vít Třebický
- Faculty of Physical Education and Sport, Charles University, Prague, Czech Republic
| | - James J. Tufano
- Faculty of Physical Education and Sport, Charles University, Prague, Czech Republic
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Vohník M, Bruzone MC, Knoblochová T, Fernández NV, Kolaříková Z, Větrovský T, Fontenla SB. Exploring structural and molecular diversity of Ericaceae hair root mycobionts: a comparison between Northern Bohemia and Argentine Patagonia. Mycorrhiza 2023; 33:425-447. [PMID: 37792114 DOI: 10.1007/s00572-023-01125-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 08/29/2023] [Indexed: 10/05/2023]
Abstract
Core Ericaceae produce delicate hair roots with inflated rhizodermal cells that host plethora of fungal symbionts. These poorly known mycobionts include various endophytes, parasites, saprobes, and the ericoid mycorrhizal (ErM) fungi (ErMF) that form the ErM symbiosis crucial for the fitness of their hosts. Using microscopy and high-throughput sequencing, we investigated their structural and molecular diversity in 14 different host × site combinations in Northern Bohemia (Central Europe) and Argentine Patagonia (South America). While we found typical ericoid mycorrhiza in all combinations, we did not detect ectomycorrhiza and arbuscular mycorrhiza. Superficial mantles of various thickness formed by non-clamped hyphae were observed in all combinations except Calluna vulgaris from N. Bohemia. Some samples contained frequent intercellular hyphae while others possessed previously unreported intracellular haustoria-like structures linked with intracellular hyphal coils. The 711 detected fungal OTU were dominated by Ascomycota (563) and Basidiomycota (119), followed by four other phyla. Ascomycetes comprised Helotiales (255), Pleosporales (53), Chaetothyriales (42), and other 19 orders, while basidiomycetes Sebacinales (42), Agaricales (28), Auriculariales (7), and other 14 orders. While many dominant OTU from both hemispheres lacked close relatives in reference databases, many were very similar to identical to unnamed sequences from around the world. On the other hand, several significant ericaceous mycobionts were absent in our dataset, incl. Cairneyella, Gamarada, Kurtia, Lachnum, and Leohumicola. Most of the detected OTU could not be reliably linked to a particular trophic mode, and only two could be reliably assigned to the archetypal ErMF Hyaloscypha hepaticicola. Probable ErMF comprised Hyaloscypha variabilis and Oidiodendron maius, both detected only in N. Bohemia. Possible ErMF comprised sebacinoid fungi and several unnamed members of Hyaloscypha s. str. While H. hepaticicola was dominant only in C. vulgaris, this model ErM host lacked O. maius and sebacinoid mycobionts. Hyaloscypha hepaticicola was absent in two and very rare in six combinations from Patagonia. Nine OTU represented dark septate endophytes from the Phialocephala fortinii s. lat.-Acephala applanata species complex, including the most abundant OTU (the only detected in all combinations). Statistical analyses revealed marked differences between N. Bohemia and Patagonia, but also within Patagonia, due to the unique community detected in a Valdivian temperate rainforest. Our results show that the ericaceous hair roots may host diverse mycobionts with mostly unknown functions and indicate that many novel ErMF lineages await discovery. Transhemispheric differences (thousands of km) in their communities may be evenly matched by local differences (scales of km, m, and less).
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Affiliation(s)
- Martin Vohník
- Department of Mycorrhizal Symbioses, Institute of Botany, Czech Academy of Sciences, Průhonice, Czechia.
| | - M Clara Bruzone
- Laboratorio de Microbiología Aplicada y Biotecnología, Centro Regional Universitario Bariloche, IPATEC (Universidad Nacional del Comahue-CONICET), San Carlos de Bariloche, Río Negro, Argentina
| | - Tereza Knoblochová
- Department of Mycorrhizal Symbioses, Institute of Botany, Czech Academy of Sciences, Průhonice, Czechia
| | - Natalia V Fernández
- Laboratorio de Microbiología Aplicada y Biotecnología, Centro Regional Universitario Bariloche, IPATEC (Universidad Nacional del Comahue-CONICET), San Carlos de Bariloche, Río Negro, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Zuzana Kolaříková
- Department of Mycorrhizal Symbioses, Institute of Botany, Czech Academy of Sciences, Průhonice, Czechia
| | - Tomáš Větrovský
- Laboratory of Environmental Microbiology, Institute of Microbiology, Czech Academy of Sciences, Prague, Czechia
| | - Sonia B Fontenla
- Laboratorio de Microbiología Aplicada y Biotecnología, Centro Regional Universitario Bariloche, IPATEC (Universidad Nacional del Comahue-CONICET), San Carlos de Bariloche, Río Negro, Argentina
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Le AV, Větrovský T, Barucic D, Saraiva JP, Dobbler PT, Kohout P, Pospíšek M, da Rocha UN, Kléma J, Baldrian P. Improved recovery and annotation of genes in metagenomes through the prediction of fungal introns. Mol Ecol Resour 2023; 23:1800-1811. [PMID: 37561110 DOI: 10.1111/1755-0998.13852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 06/27/2023] [Accepted: 07/31/2023] [Indexed: 08/11/2023]
Abstract
Metagenomics provides a tool to assess the functional potential of environmental and host-associated microbiomes based on the analysis of environmental DNA: assembly, gene prediction and annotation. While gene prediction is straightforward for most bacterial and archaeal taxa, it has limited applicability in the majority of eukaryotic organisms, including fungi that contain introns in gene coding sequences. As a consequence, eukaryotic genes are underrepresented in metagenomics datasets and our understanding of the contribution of fungi and other eukaryotes to microbiome functioning is limited. Here, we developed a machine intelligence-based algorithm that predicts fungal introns in environmental DNA with reasonable precision and used it to improve the annotation of environmental metagenomes. Intron removal increased the number of predicted genes by up to 9.1% and improved the annotation of several others. The proportion of newly predicted genes increased with the share of eukaryotic genes in the metagenome and-within fungal taxa-increased with the number of introns per gene. Our approach provides a tool named SVMmycointron for improved metagenome annotation, especially of microbiomes with a high proportion of eukaryotes. The scripts described in the paper are made publicly available and can be readily utilized by microbiome researchers analysing metagenomics data.
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Affiliation(s)
- Anh Vu Le
- Department of Computer Science, Czech Technical University in Prague, Praha, Czech Republic
| | - Tomáš Větrovský
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Praha, Czech Republic
| | - Denis Barucic
- Department of Computer Science, Czech Technical University in Prague, Praha, Czech Republic
| | - Joao Pedro Saraiva
- Department of Environmental Microbiology, UFZ-Helmholtz Centre for Environmental Research, Leipzig, Germany
| | - Priscila Thiago Dobbler
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Praha, Czech Republic
| | - Petr Kohout
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Praha, Czech Republic
| | - Martin Pospíšek
- Department of Genetics and Microbiology, Charles University, Praha, Czech Republic
| | - Ulisses Nunes da Rocha
- Department of Environmental Microbiology, UFZ-Helmholtz Centre for Environmental Research, Leipzig, Germany
| | - Jiří Kléma
- Department of Computer Science, Czech Technical University in Prague, Praha, Czech Republic
| | - Petr Baldrian
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Praha, Czech Republic
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Aguilar-Trigueros CA, Krah FS, Cornwell WK, Zanne AE, Abrego N, Anderson IC, Andrew CJ, Baldrian P, Bässler C, Bissett A, Chaudhary VB, Chen B, Chen Y, Delgado-Baquerizo M, Deveautour C, Egidi E, Flores-Moreno H, Golan J, Heilmann-Clausen J, Hempel S, Hu Y, Kauserud H, Kivlin SN, Kohout P, Lammel DR, Maestre FT, Pringle A, Purhonen J, Singh BK, Veresoglou SD, Větrovský T, Zhang H, Rillig MC, Powell JR. Symbiotic status alters fungal eco-evolutionary offspring trajectories. Ecol Lett 2023; 26:1523-1534. [PMID: 37330626 DOI: 10.1111/ele.14271] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 05/21/2023] [Accepted: 05/23/2023] [Indexed: 06/19/2023]
Abstract
Despite host-fungal symbiotic interactions being ubiquitous in all ecosystems, understanding how symbiosis has shaped the ecology and evolution of fungal spores that are involved in dispersal and colonization of their hosts has been ignored in life-history studies. We assembled a spore morphology database covering over 26,000 species of free-living to symbiotic fungi of plants, insects and humans and found more than eight orders of variation in spore size. Evolutionary transitions in symbiotic status correlated with shifts in spore size, but the strength of this effect varied widely among phyla. Symbiotic status explained more variation than climatic variables in the current distribution of spore sizes of plant-associated fungi at a global scale while the dispersal potential of their spores is more restricted compared to free-living fungi. Our work advances life-history theory by highlighting how the interaction between symbiosis and offspring morphology shapes the reproductive and dispersal strategies among living forms.
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Affiliation(s)
- Carlos A Aguilar-Trigueros
- Institute of Biology, Freie Universität Berlin, Berlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin, Germany
- Department of Biological and Environmental Science, University of Jyväskylä, Jyvaskyla, Finland
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, New South Wales, Australia
| | - Franz-Sebastian Krah
- Faculty of Biological Sciences, Department of Conservation Biology, Institute for Ecology, Evolution and Diversity, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - William K Cornwell
- Evolution & Ecology Research Center, School of Biological, Earth, and Environmental Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Amy E Zanne
- Department of Biology, University of Miami, Coral Gables, Florida, USA
| | - Nerea Abrego
- Department of Biological and Environmental Science, University of Jyväskylä, Jyvaskyla, Finland
- Department of Agricultural Sciences, University of Helsinki, Helsinki, Finland
| | - Ian C Anderson
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, New South Wales, Australia
| | - Carrie J Andrew
- Biology Department, Oberlin College & Conservatory, Oberlin, Ohio, USA
| | - Petr Baldrian
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Praha 4, Czech Republic
| | - Claus Bässler
- Faculty of Biological Sciences, Department of Conservation Biology, Institute for Ecology, Evolution and Diversity, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Andrew Bissett
- Oceans and Atmosphere, CSIRO, Hobart, Tasmania, Australia
| | - V Bala Chaudhary
- Department of Environmental Studies, Dartmouth College, Hanover, New Hampshire, USA
| | - Baodong Chen
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Yongliang Chen
- College of Resources and Environmental Sciences, China Agricultural University, Beijing, People's Republic of China
| | - Manuel Delgado-Baquerizo
- Laboratorio de Biodiversidad y Funcionamiento Ecosistémico. Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS), CSIC, Sevilla, Spain
- Unidad Asociada CSIC-UPO (BioFun). Universidad Pablo de Olavide, Sevilla, Spain
| | - Coline Deveautour
- AGHYLE Research Unit, Institut Polytechnique UniLaSalle, Mont-Saint-Aignan, France
| | - Eleonora Egidi
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, New South Wales, Australia
| | | | - Jacob Golan
- Departments of Botany and Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Jacob Heilmann-Clausen
- Center for Macroecology, Evolution and Climate, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Stefan Hempel
- Institute of Biology, Freie Universität Berlin, Berlin, Germany
| | - Yajun Hu
- Key Laboratory of Agro-ecological Processes in Subtropical Region & Changsha Research Station for Agricultural and Environmental Monitoring, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Hunan, China
| | - Håvard Kauserud
- Evogene, Department of Biosciences, University of Oslo, Oslo, Norway
| | - Stephanie N Kivlin
- Department of Ecology and Evolution, University of Tennessee, Knoxville, Tennessee, USA
| | - Petr Kohout
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Praha 4, Czech Republic
| | - Daniel R Lammel
- Institute of Biology, Freie Universität Berlin, Berlin, Germany
| | - Fernando T Maestre
- Instituto Multidisciplinar para el Estudio del Medio "Ramon Margalef", Universidad de Alicante, Carretera de San Vicente del Raspeig s/n, Alicante, Spain
- Departamento de Ecología, Universidad de Alicante, Carretera de San Vicente del Raspeig s/n, Alicante, Spain
| | - Anne Pringle
- Departments of Botany and Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Jenna Purhonen
- Department of Biological and Environmental Science, University of Jyväskylä, Jyvaskyla, Finland
- Department of Music, Art and Culture Studies, University of Jyväskylä, Jyvaskyla, Finland
- School of Resource Wisdom, University of Jyväskylä, Jyvaskyla, Finland
| | - Brajesh K Singh
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, New South Wales, Australia
- Global Centre for Land Based Innovation, Western Sydney University, Penrith, New South Wales, Australia
| | | | - Tomáš Větrovský
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Praha 4, Czech Republic
| | - Haiyang Zhang
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, New South Wales, Australia
- College of Life Sciences, Hebei University, Baoding, China
| | - Matthias C Rillig
- Institute of Biology, Freie Universität Berlin, Berlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin, Germany
| | - Jeff R Powell
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, New South Wales, Australia
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Hakimzadeh A, Asbun AA, Albanese D, Bernard M, Buchner D, Callahan B, Caporaso JG, Curd E, Djemiel C, Durling MB, Elbrecht V, Gold Z, Gweon HS, Hajibabaei M, Hildebrand F, Mikryukov V, Normandeau E, Özkurt E, Palmer JM, Pascal G, Porter TM, Straub D, Vasar M, Větrovský T, Zafeiropoulos H, Anslan S. A pile of pipelines: An overview of the bioinformatics software for metabarcoding data analyses. Mol Ecol Resour 2023:10.1111/1755-0998.13847. [PMID: 37548515 PMCID: PMC10847385 DOI: 10.1111/1755-0998.13847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 06/05/2023] [Accepted: 07/06/2023] [Indexed: 08/08/2023]
Abstract
Environmental DNA (eDNA) metabarcoding has gained growing attention as a strategy for monitoring biodiversity in ecology. However, taxa identifications produced through metabarcoding require sophisticated processing of high-throughput sequencing data from taxonomically informative DNA barcodes. Various sets of universal and taxon-specific primers have been developed, extending the usability of metabarcoding across archaea, bacteria and eukaryotes. Accordingly, a multitude of metabarcoding data analysis tools and pipelines have also been developed. Often, several developed workflows are designed to process the same amplicon sequencing data, making it somewhat puzzling to choose one among the plethora of existing pipelines. However, each pipeline has its own specific philosophy, strengths and limitations, which should be considered depending on the aims of any specific study, as well as the bioinformatics expertise of the user. In this review, we outline the input data requirements, supported operating systems and particular attributes of thirty-two amplicon processing pipelines with the goal of helping users to select a pipeline for their metabarcoding projects.
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Affiliation(s)
- Ali Hakimzadeh
- Institute of Ecology and Earth Sciences, University of Tartu, Estonia
| | - Alejandro Abdala Asbun
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, Texel, Netherlands
| | - Davide Albanese
- Unit of Computational Biology, Research and Innovation Centre, Fondazione Edmund Mach, Italy
| | - Maria Bernard
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350, Jouy-en-Josas, France
- INRAE, SIGENAE, 78350, Jouy-en-Josas, France
| | - Dominik Buchner
- Aquatic Ecosystem Research, University of Duisburg-Essen, Universitätsstraße 5, 45141 Essen, Germany
| | - Benjamin Callahan
- Department of Population Health and Pathobiology, College of Veterinary Medicine and Bioinformatics Research Center, North Carolina State University, Raleigh, North Carolina, USA
| | - J. Gregory Caporaso
- Center for Applied Microbiome Science, Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | - Emily Curd
- Vermont Biomedical Research Network, University of Vermont, Burlington, VT, USA
| | - Christophe Djemiel
- Agroécologie, INRAE, Institut Agro, Univ. Bourgogne Franche-Comté, F-21000 Dijon, France
| | - Mikael B. Durling
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Box 7026, 75007 Uppsala, Sweden
| | - Vasco Elbrecht
- Aquatic Ecosystem Research, University of Duisburg-Essen, Universitaetsstrasse 5, 45141, Essen, Germany
| | - Zachary Gold
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Hyun S. Gweon
- UK Centre for Ecology & Hydrology, Wallingford, Oxfordshire, OX10 8BB, UK
- School of Biological Sciences, University of Reading, Reading, RG6 6EX, UK
| | - Mehrdad Hajibabaei
- Department of Integrative Biology and Centre for Biodiversity Genomics, University of Guelph, Canada
| | - Falk Hildebrand
- Gut Microbes & Health, Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk, NR4 7UQ, UK
- Earlham Institute, Norwich Research Park, Norwich, Norfolk, NR4 7UZ, UK
| | | | - Eric Normandeau
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, QC, Canada
| | - Ezgi Özkurt
- Gut Microbes & Health, Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk, NR4 7UQ, UK
- Earlham Institute, Norwich Research Park, Norwich, Norfolk, NR4 7UZ, UK
| | - Jonathan M. Palmer
- Center for Forest Mycology Research, Northern Research Station, US Forest Service, Madison, WI USA (current address: Genencor Technology Center, IFF, Palo Alto, CA USA)
| | - Géraldine Pascal
- GenPhySE, Université de Toulouse, INRAE, ENVT, F-31326, Castanet Tolosan, France
| | - Teresita M. Porter
- Department of Integrative Biology and Centre for Biodiversity Genomics, University of Guelph, Canada
| | - Daniel Straub
- Quantitative Biology Center (QBiC), University of Tübingen, Tübingen D-72076, Germany
| | - Martti Vasar
- Institute of Ecology and Earth Sciences, University of Tartu, Estonia
| | - Tomáš Větrovský
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220 Praha 4, Czech Republic
| | - Haris Zafeiropoulos
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Molecular Bacteriology, 3000 Leuven, Belgium
| | - Sten Anslan
- Institute of Ecology and Earth Sciences, University of Tartu, Estonia
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Chakraborty A, Šobotník J, Votýpková K, Hradecký J, Stiblik P, Synek J, Bourguignon T, Baldrian P, Engel MS, Novotný V, Odriozola I, Větrovský T. Impact of Wood Age on Termite Microbial Assemblages. Appl Environ Microbiol 2023; 89:e0036123. [PMID: 37067424 PMCID: PMC10231148 DOI: 10.1128/aem.00361-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 03/25/2023] [Indexed: 04/18/2023] Open
Abstract
The decomposition of wood and detritus is challenging to most macroscopic organisms due to the recalcitrant nature of lignocellulose. Moreover, woody plants often protect themselves by synthesizing toxic or nocent compounds which infuse their tissues. Termites are essential wood decomposers in warmer terrestrial ecosystems and, as such, they have to cope with high concentrations of plant toxins in wood. In this paper, we evaluated the influence of wood age on the gut microbial (bacterial and fungal) communities associated with the termites Reticulitermes flavipes (Rhinotermitidae) (Kollar, 1837) and Microcerotermes biroi (Termitidae) (Desneux, 1905). We confirmed that the secondary metabolite concentration decreased with wood age. We identified a core microbial consortium maintained in the gut of R. flavipes and M. biroi and found that its diversity and composition were not altered by the wood age. Therefore, the concentration of secondary metabolites had no effect on the termite gut microbiome. We also found that both termite feeding activities and wood age affect the wood microbiome. Whether the increasing relative abundance of microbes with termite activities is beneficial to the termites is unknown and remains to be investigated. IMPORTANCE Termites can feed on wood thanks to their association with their gut microbes. However, the current understanding of termites as holobiont is limited. To our knowledge, no studies comprehensively reveal the influence of wood age on the termite-associated microbial assemblage. The wood of many tree species contains high concentrations of plant toxins that can vary with their age and may influence microbes. Here, we studied the impact of Norway spruce wood of varying ages and terpene concentrations on the microbial communities associated with the termites Reticulitermes flavipes (Rhinotermitidae) and Microcerotermes biroi (Termitidae). We performed a bacterial 16S rRNA and fungal ITS2 metabarcoding study to reveal the microbial communities associated with R. flavipes and M. biroi and their impact on shaping the wood microbiome. We noted that a stable core microbiome in the termites was unaltered by the feeding substrate, while termite activities influenced the wood microbiome, suggesting that plant secondary metabolites have negligible effects on the termite gut microbiome. Hence, our study shed new insights into the termite-associated microbial assemblage under the influence of varying amounts of terpene content in wood and provides a groundwork for future investigations for developing symbiont-mediated termite control measures.
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Affiliation(s)
- Amrita Chakraborty
- EVA 4.0 Unit, Faculty of Forestry and Wood Sciences, Czech University of Life Sciences, Prague, Czech Republic
| | - Jan Šobotník
- Faculty of Tropical AgriSciences, Czech University of Life Sciences, Prague, Czech Republic
| | - Kateřina Votýpková
- EVA 4.0 Unit, Faculty of Forestry and Wood Sciences, Czech University of Life Sciences, Prague, Czech Republic
| | - Jaromír Hradecký
- Faculty of Forestry and Wood Sciences, Czech University of Life Sciences, Prague, Czech Republic
| | - Petr Stiblik
- EVA 4.0 Unit, Faculty of Forestry and Wood Sciences, Czech University of Life Sciences, Prague, Czech Republic
| | - Jiří Synek
- EVA 4.0 Unit, Faculty of Forestry and Wood Sciences, Czech University of Life Sciences, Prague, Czech Republic
| | - Thomas Bourguignon
- Faculty of Tropical AgriSciences, Czech University of Life Sciences, Prague, Czech Republic
- Okinawa Institute of Science & Technology Graduate University, Okinawa, Japan
| | - Petr Baldrian
- Institute of Microbiology, Czech Academy of Sciences, Prague, Czech Republic
| | - Michael S. Engel
- American Museum of Natural History, New York, New York, USA
- Division of Entomology, Natural History Museum, University of Kansas, Lawrence, Kansas, USA
- Department of Ecology & Evolutionary Biology, University of Kansas, Lawrence, Kansas, USA
| | - Vojtěch Novotný
- Faculty of Science, University of South Bohemia, Ceske Budejovice, Czech Republic
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, Ceske Budejovice, Czech Republic
| | - Iñaki Odriozola
- Institute of Microbiology, Czech Academy of Sciences, Prague, Czech Republic
| | - Tomáš Větrovský
- EVA 4.0 Unit, Faculty of Forestry and Wood Sciences, Czech University of Life Sciences, Prague, Czech Republic
- Institute of Microbiology, Czech Academy of Sciences, Prague, Czech Republic
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9
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Švarcová M, Větrovský T, Kolařík M, Hubka V. Defining the relationship between phylogeny, clinical manifestation and phenotype for Trichophyton mentagrophytes/interdigitale complex; a literature review and taxonomic recommendations. Med Mycol 2023; 61:7127701. [PMID: 37070928 PMCID: PMC10148955 DOI: 10.1093/mmy/myad042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 04/06/2023] [Accepted: 04/14/2023] [Indexed: 04/19/2023] Open
Abstract
This study looked for correlations between molecular identification, clinical manifestation and morphology for Trichophyton interdigitale and T. mentagrophytes. For this purpose, a total of 110 isolates were obtained from Czech patients with various clinical manifestations of dermatophytosis. Phenotypic characters were analysed, and the strains were characterized using multilocus sequence typing. Among the 12 measured/scored phenotypic features, statistically significant differences between species were found only in growth rates at 37°C and in the production of spiral hyphae. Correlations were found between T. interdigitale and higher age of patients and between clinical manifestations such as tinea pedis or onychomychosis. In addition, the T. interdigitale lineage consisted exclusively of isolates with MAT1-2-1 mating type gene idiomorphs. The MLST approach showed that ITS genotyping of T. mentagrophytes isolates has limited practical benefits because of extensive gene flow between sublineages. Based on our results and previous studies, there are few taxonomic arguments for preserving both species names. The species show a lack of monophyly and unique morphology. On the other hand, some genotypes are associated with predominant clinical manifestations and sources of infections, which keep those names alive. This practice is questionable because the use of both names confuses identification, leading to difficulty in comparing epidemiological studies. The current identification method using ITS genotyping is ambiguous for some isolates and is not user-friendly. Additionally, identification tools such as MALDI-TOF MS fail to distinguish these species. To avoid further confusion and simplify identification in practice, we recommend using the name T. mentagrophytes for the entire complex. When clear differentiation of populations corresponding to T. interdigitale and T. indotineae is possible based on molecular data, we recommend optionally using a variety rank: T. mentagrophytes var. interdigitale and T. mentagrophytes var. indotineae.
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Affiliation(s)
- Michaela Švarcová
- Department of Botany, Faculty of Science, Charles University, Prague, Czech Republic
| | - Tomáš Větrovský
- Laboratory of Environmental Microbiology, Institute of Microbiology, Czech Academy of Sciences, Prague, Czech Republic
| | - Miroslav Kolařík
- Department of Botany, Faculty of Science, Charles University, Prague, Czech Republic
- Laboratory of Fungal Genetics and Metabolism, Institute of Microbiology, Czech Academy of Sciences, Prague, Czech Republic
| | - Vit Hubka
- Department of Botany, Faculty of Science, Charles University, Prague, Czech Republic
- Laboratory of Fungal Genetics and Metabolism, Institute of Microbiology, Czech Academy of Sciences, Prague, Czech Republic
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10
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Baldrian P, Bell-Dereske L, Lepinay C, Větrovský T, Kohout P. Fungal communities in soils under global change. Stud Mycol 2022; 103:1-24. [PMID: 36760734 PMCID: PMC9886077 DOI: 10.3114/sim.2022.103.01] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 09/16/2022] [Indexed: 11/07/2022] Open
Abstract
Soil fungi play indispensable roles in all ecosystems including the recycling of organic matter and interactions with plants, both as symbionts and pathogens. Past observations and experimental manipulations indicate that projected global change effects, including the increase of CO2 concentration, temperature, change of precipitation and nitrogen (N) deposition, affect fungal species and communities in soils. Although the observed effects depend on the size and duration of change and reflect local conditions, increased N deposition seems to have the most profound effect on fungal communities. The plant-mutualistic fungal guilds - ectomycorrhizal fungi and arbuscular mycorrhizal fungi - appear to be especially responsive to global change factors with N deposition and warming seemingly having the strongest adverse effects. While global change effects on fungal biodiversity seem to be limited, multiple studies demonstrate increases in abundance and dispersal of plant pathogenic fungi. Additionally, ecosystems weakened by global change-induced phenomena, such as drought, are more vulnerable to pathogen outbreaks. The shift from mutualistic fungi to plant pathogens is likely the largest potential threat for the future functioning of natural and managed ecosystems. However, our ability to predict global change effects on fungi is still insufficient and requires further experimental work and long-term observations. Citation: Baldrian P, Bell-Dereske L, Lepinay C, Větrovský T, Kohout P (2022). Fungal communities in soils under global change. Studies in Mycology 103: 1-24. doi: 10.3114/sim.2022.103.01.
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Affiliation(s)
- P. Baldrian
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeòská 1083, 142 20 Prague, Czech Republic,*Corresponding author: Petr Baldrian,
| | - L. Bell-Dereske
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeòská 1083, 142 20 Prague, Czech Republic
| | - C. Lepinay
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeòská 1083, 142 20 Prague, Czech Republic
| | - T. Větrovský
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeòská 1083, 142 20 Prague, Czech Republic
| | - P. Kohout
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeòská 1083, 142 20 Prague, Czech Republic
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11
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D'Alò F, Baldrian P, Odriozola I, Morais D, Větrovský T, Zucconi L, Ripa C, Cannone N, Malfasi F, Onofri S. Composition and functioning of the soil microbiome in the highest altitudes of the Italian Alps and potential effects of climate change. FEMS Microbiol Ecol 2022; 98:6541846. [PMID: 35238906 DOI: 10.1093/femsec/fiac025] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 02/04/2022] [Accepted: 03/01/2022] [Indexed: 11/14/2022] Open
Abstract
As the European Alps are experiencing a strong climate warming; this study analyzed the soil microbiome at different altitudes and among different vegetation types at the Stelvio Pass (Italian Alps), aiming to i) characterize the composition and functional potential of the microbiome of soils and their gene expression during the peak vegetative stage; ii) explore the potential short-term (using open top chambers) and long-term (space-for-time substitutions) effects of increasing temperature on the alpine soil microbiome. We found that the functional potential of the soil microbiome and its expression differed among vegetation types. Microbial α-diversity increased along the altitudinal gradient. At lower altitude, shrubland had the highest proportion of fungi, which was correlated with higher amounts of CAZymes, specific for degrading fungal biomass and recalcitrant plant biopolymers. Subalpine upward vegetation shift could lead a possible loss of species of alpine soils. Shrub encroachment may accelerate higher recalcitrant C decomposition and reduce total ecosystem C storage, increasing the efflux of CO2 to the atmosphere with a positive feedback to warming. Five years of warming had no effect on the composition and functioning of microbial communities, indicating that longer-term warming experiments are needed to investigate the effects of temperature increases on the soil microbiome.
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Affiliation(s)
- Federica D'Alò
- Department of Ecological and Biological Sciences, University of Tuscia, Largo dell'Università, 01100 Viterbo, Italy
| | - Petr Baldrian
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220 Praha 4, Czech Republic
| | - Iñaki Odriozola
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220 Praha 4, Czech Republic
| | - Daniel Morais
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220 Praha 4, Czech Republic
| | - Tomáš Větrovský
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220 Praha 4, Czech Republic
| | - Laura Zucconi
- Department of Ecological and Biological Sciences, University of Tuscia, Largo dell'Università, 01100 Viterbo, Italy
| | - Caterina Ripa
- Department of Ecological and Biological Sciences, University of Tuscia, Largo dell'Università, 01100 Viterbo, Italy
| | - Nicoletta Cannone
- Department of Science and High Technology, Insubria University, Via Valleggio, 11, 21100 Como (CO), Italy
| | - Francesco Malfasi
- Department of Science and High Technology, Insubria University, Via Valleggio, 11, 21100 Como (CO), Italy
| | - Silvano Onofri
- Department of Ecological and Biological Sciences, University of Tuscia, Largo dell'Università, 01100 Viterbo, Italy
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12
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Martinović T, Odriozola I, Mašínová T, Doreen Bahnmann B, Kohout P, Sedlák P, Merunková K, Větrovský T, Tomšovský M, Ovaskainen O, Baldrian P. Temporal turnover of the soil microbiome composition is guild-specific. Ecol Lett 2021; 24:2726-2738. [PMID: 34595822 DOI: 10.1111/ele.13896] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 09/10/2021] [Indexed: 01/06/2023]
Abstract
Although spatial and temporal variation are both important components structuring microbial communities, the exact quantification of temporal turnover rates of fungi and bacteria has not been performed to date. In this study, we utilised repeated resampling of bacterial and fungal communities at specific locations across multiple years to describe their patterns and rates of temporal turnover. Our results show that microbial communities undergo temporal change at a rate of 0.010-0.025 per year (in units of Sorensen similarity), and the change in soil is slightly faster in fungi than in bacteria, with bacterial communities changing more rapidly in litter than soil. Importantly, temporal development differs across fungal guilds and bacterial phyla with different ecologies. While some microbial guilds show consistent responses across regional locations, others show site-specific development with weak general patterns. These results indicate that guild-level resolution is important for understanding microbial community assembly, dynamics and responses to environmental factors.
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Affiliation(s)
- Tijana Martinović
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská, Czech Republic
| | - Iñaki Odriozola
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská, Czech Republic
| | - Tereza Mašínová
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská, Czech Republic
| | - Barbara Doreen Bahnmann
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská, Czech Republic
| | - Petr Kohout
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská, Czech Republic.,Department of Experimental Plant Biology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Petr Sedlák
- Faculty of Forestry and Wood Technology, Mendel University in Brno, Brno, Czech Republic
| | - Kristina Merunková
- Department of Botany and Zoology, Masaryk University, Brno, Czech Republic
| | - Tomáš Větrovský
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská, Czech Republic
| | - Michal Tomšovský
- Faculty of Forestry and Wood Technology, Mendel University in Brno, Brno, Czech Republic
| | - Otso Ovaskainen
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland.,Organismal and Evolutionary Biology Research Programme, University of Helsinki, Helsinki, Finland.,Department of Biology, Centre for Biodiversity Dynamics, Norwegian University of Science and Technology, Trondheim, Norway
| | - Petr Baldrian
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská, Czech Republic
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14
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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. Author Correction: GlobalFungi, a global database of fungal occurrences from high-throughput-sequencing metabarcoding studies. Sci Data 2020; 7:308. [PMID: 32934218 PMCID: PMC7493946 DOI: 10.1038/s41597-020-00647-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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15
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Větrovský T, Soukup P, Stiblik P, Votýpková K, Chakraborty A, Larrañaga IO, Sillam-Dussès D, Lo N, Bourguignon T, Baldrian P, Šobotník J, Kolařík M. Termites host specific fungal communities that differ from those in their ambient environments. FUNGAL ECOL 2020. [DOI: 10.1016/j.funeco.2020.100991] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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16
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Čmoková A, Kolařík M, Dobiáš R, Hoyer LL, Janouškovcová H, Kano R, Kuklová I, Lysková P, Machová L, Maier T, Mallátová N, Man M, Mencl K, Nenoff P, Peano A, Prausová H, Stubbe D, Uhrlaß S, Větrovský T, Wiegand C, Hubka V. Resolving the taxonomy of emerging zoonotic pathogens in the Trichophyton benhamiae complex. FUNGAL DIVERS 2020. [DOI: 10.1007/s13225-020-00465-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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17
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Vlk L, Tedersoo L, Antl T, Větrovský T, Abarenkov K, Pergl J, Albrechtová J, Vosátka M, Baldrian P, Pyšek P, Kohout P. Alien ectomycorrhizal plants differ in their ability to interact with co-introduced and native ectomycorrhizal fungi in novel sites. ISME J 2020; 14:2336-2346. [PMID: 32499492 PMCID: PMC7608243 DOI: 10.1038/s41396-020-0692-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 05/07/2020] [Accepted: 05/27/2020] [Indexed: 11/29/2022]
Abstract
Alien plants represent a potential threat to environment and society. Understanding the process of alien plants naturalization is therefore of primary importance. In alien plants, successful establishment can be constrained by the absence of suitable fungal partners. Here, we used 42 independent datasets of ectomycorrhizal fungal (EcMF) communities associated with alien Pinaceae and Eucalyptus spp., as the most commonly introduced tree species worldwide, to explore the strategies these plant groups utilize to establish symbioses with EcMF in the areas of introduction. We have also determined the differences in composition of EcMF communities associated with alien ectomycorrhizal plants in different regions. While alien Pinaceae introduced to new regions rely upon association with co-introduced EcMF, alien Eucalyptus often form novel interactions with EcMF species native to the region where the plant was introduced. The region of origin primarily determines species composition of EcMF communities associated with alien Pinaceae in new areas, which may largely affect invasion potential of the alien plants. Our study shows that alien ectomycorrhizal plants largely differ in their ability to interact with co-introduced and native ectomycorrhizal fungi in sites of introduction, which may potentially affect their invasive potential.
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Affiliation(s)
- Lukáš Vlk
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, CZ-142 20, Prague, Czech Republic
- Institute of Botany of the Czech Academy of Sciences, Zámek 1, CZ-252 43, Průhonice, Czech Republic
- Faculty of Science, Charles University, Viničná 7, CZ-128 44, Prague, Czech Republic
| | - Leho Tedersoo
- Natural History Museum, University of Tartu, 14a Ravila, 50411, Tartu, Estonia
- Department of Biology, King Saud University, Riyadh, 11451, Saudi Arabia
| | - Tomáš Antl
- Institute of Botany of the Czech Academy of Sciences, Zámek 1, CZ-252 43, Průhonice, Czech Republic
- Faculty of Science, Charles University, Viničná 7, CZ-128 44, Prague, Czech Republic
| | - Tomáš Větrovský
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, CZ-142 20, Prague, Czech Republic
| | - Kessy Abarenkov
- Natural History Museum, University of Tartu, 14a Ravila, 50411, Tartu, Estonia
| | - Jan Pergl
- Institute of Botany of the Czech Academy of Sciences, Zámek 1, CZ-252 43, Průhonice, Czech Republic
| | - Jana Albrechtová
- Faculty of Science, Charles University, Viničná 7, CZ-128 44, Prague, Czech Republic
| | - Miroslav Vosátka
- Institute of Botany of the Czech Academy of Sciences, Zámek 1, CZ-252 43, Průhonice, Czech Republic
- Faculty of Science, Charles University, Viničná 7, CZ-128 44, Prague, Czech Republic
| | - Petr Baldrian
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, CZ-142 20, Prague, Czech Republic
| | - Petr Pyšek
- Institute of Botany of the Czech Academy of Sciences, Zámek 1, CZ-252 43, Průhonice, Czech Republic
- Faculty of Science, Charles University, Viničná 7, CZ-128 44, Prague, Czech Republic
- Department of Botany and Zoology, Stellenbosch University, Matieland, 7602, South Africa
| | - Petr Kohout
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, CZ-142 20, Prague, Czech Republic.
- Institute of Botany of the Czech Academy of Sciences, Zámek 1, CZ-252 43, Průhonice, Czech Republic.
- Faculty of Science, Charles University, Viničná 7, CZ-128 44, Prague, Czech Republic.
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Vlk L, Tedersoo L, Antl T, Větrovský T, Abarenkov K, Pergl J, Albrechtová J, Vosátka M, Baldrian P, Pyšek P, Kohout P. Early successional ectomycorrhizal fungi are more likely to naturalize outside their native range than other ectomycorrhizal fungi. New Phytol 2020; 227:1289-1293. [PMID: 32215923 DOI: 10.1111/nph.16557] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 03/13/2020] [Indexed: 06/10/2023]
Affiliation(s)
- Lukáš Vlk
- Institute of Microbiology, Czech Academy of Sciences, Vídeňská 1083, CZ-142 20, Prague, Czech Republic
- Institute of Botany, Czech Academy of Sciences, Zámek 1, CZ-252 43, Průhonice, Czech Republic
- Faculty of Science, Charles University, Viničná 7, CZ-128 44, Prague, Czech Republic
| | - Leho Tedersoo
- Natural History Museum, University of Tartu, 14a Ravila, 50411, Tartu, Estonia
- Institute of Ecology and Earth Science, University of Tartu, 14a Ravila, 50411, Tartu, Estonia
| | - Tomáš Antl
- Institute of Botany, Czech Academy of Sciences, Zámek 1, CZ-252 43, Průhonice, Czech Republic
- Faculty of Science, Charles University, Viničná 7, CZ-128 44, Prague, Czech Republic
| | - Tomáš Větrovský
- Institute of Microbiology, Czech Academy of Sciences, Vídeňská 1083, CZ-142 20, Prague, Czech Republic
| | - Kessy Abarenkov
- Institute of Ecology and Earth Science, University of Tartu, 14a Ravila, 50411, Tartu, Estonia
| | - Jan Pergl
- Institute of Botany, Czech Academy of Sciences, Zámek 1, CZ-252 43, Průhonice, Czech Republic
| | - Jana Albrechtová
- Faculty of Science, Charles University, Viničná 7, CZ-128 44, Prague, Czech Republic
| | - Miroslav Vosátka
- Institute of Botany, Czech Academy of Sciences, Zámek 1, CZ-252 43, Průhonice, Czech Republic
- Faculty of Science, Charles University, Viničná 7, CZ-128 44, Prague, Czech Republic
| | - Petr Baldrian
- Institute of Microbiology, Czech Academy of Sciences, Vídeňská 1083, CZ-142 20, Prague, Czech Republic
| | - Petr Pyšek
- Institute of Botany, Czech Academy of Sciences, Zámek 1, CZ-252 43, Průhonice, Czech Republic
- Faculty of Science, Charles University, Viničná 7, CZ-128 44, Prague, Czech Republic
- Centre for Invasion Biology, Department of Botany and Zoology, Stellenbosch University, Matieland, South Africa
| | - Petr Kohout
- Institute of Microbiology, Czech Academy of Sciences, Vídeňská 1083, CZ-142 20, Prague, Czech Republic
- Institute of Botany, Czech Academy of Sciences, Zámek 1, CZ-252 43, Průhonice, Czech Republic
- Faculty of Science, Charles University, Viničná 7, CZ-128 44, Prague, Czech Republic
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19
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Starke R, Morais D, Větrovský T, López Mondéjar R, Baldrian P, Brabcová V. Feeding on fungi: genomic and proteomic analysis of the enzymatic machinery of bacteria decomposing fungal biomass. Environ Microbiol 2020; 22:4604-4619. [PMID: 32743948 DOI: 10.1111/1462-2920.15183] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 07/21/2020] [Accepted: 07/31/2020] [Indexed: 11/29/2022]
Abstract
Dead fungal biomass is an abundant source of nutrition in both litter and soil of temperate forests largely decomposed by bacteria. Here, we have examined the utilization of dead fungal biomass by the five dominant bacteria isolated from the in situ decomposition of fungal mycelia using a multiOMIC approach. The genomes of the isolates encoded a broad suite of carbohydrate-active enzymes, peptidases and transporters. In the extracellular proteome, only Ewingella americana expressed chitinases while the two Pseudomonas isolates attacked chitin by lytic chitin monooxygenase, deacetylation and deamination. Variovorax sp. expressed enzymes acting on the side-chains of various glucans and the chitin backbone. Surprisingly, despite its genomic potential, Pedobacter sp. did not produce extracellular proteins to decompose fungal mycelia but presumably feeds on simple substrates. The ecological roles of the five individual strains exhibited complementary features for a fast and efficient decomposition of dead fungal biomass by the entire bacterial community.
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Affiliation(s)
- Robert Starke
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220 Praha 4, Czech Republic
| | - Daniel Morais
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220 Praha 4, Czech Republic
| | - Tomáš Větrovský
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220 Praha 4, Czech Republic
| | - Ruben López Mondéjar
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220 Praha 4, Czech Republic
| | - Petr Baldrian
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220 Praha 4, Czech Republic
| | - Vendula Brabcová
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220 Praha 4, Czech Republic
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20
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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: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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21
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Větrovský T, Kohout P, Kopecký M, Machac A, Man M, Bahnmann BD, Brabcová V, Choi J, Meszárošová L, Human ZR, Lepinay C, Lladó S, López-Mondéjar R, Martinović T, Mašínová T, Morais D, Navrátilová D, Odriozola I, Štursová M, Švec K, Tláskal V, Urbanová M, Wan J, Žifčáková L, Howe A, Ladau J, Peay KG, Storch D, Wild J, Baldrian P. A meta-analysis of global fungal distribution reveals climate-driven patterns. Nat Commun 2019; 10:5142. [PMID: 31723140 PMCID: PMC6853883 DOI: 10.1038/s41467-019-13164-8] [Citation(s) in RCA: 147] [Impact Index Per Article: 29.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Accepted: 10/23/2019] [Indexed: 02/06/2023] Open
Abstract
The evolutionary and environmental factors that shape fungal biogeography are incompletely understood. Here, we assemble a large dataset consisting of previously generated mycobiome data linked to specific geographical locations across the world. We use this dataset to describe the distribution of fungal taxa and to look for correlations with different environmental factors such as climate, soil and vegetation variables. Our meta-study identifies climate as an important driver of different aspects of fungal biogeography, including the global distribution of common fungi as well as the composition and diversity of fungal communities. In our analysis, fungal diversity is concentrated at high latitudes, in contrast with the opposite pattern previously shown for plants and other organisms. Mycorrhizal fungi appear to have narrower climatic tolerances than pathogenic fungi. We speculate that climate change could affect ecosystem functioning because of the narrow climatic tolerances of key fungal taxa. The authors assemble and analyse previously generated mycobiome data linked to geographical locations across the world. They describe the distribution of fungal taxa and show that climate is an important driver of fungal biogeography and that fungal diversity appears to be concentrated at high latitudes.
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Affiliation(s)
- Tomáš Větrovský
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Petr Kohout
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic.,Faculty of Science, Charles University, Albertov 6, 12844, Praha 2, Czech Republic
| | - Martin Kopecký
- Institute of Botany of the Czech Academy of Sciences, Zámek 1, 25243, Průhonice, Czech Republic.,Faculty of Forestry and Wood Sciences, Czech University of Life Sciences Prague, Kamýcká 129, 16521, Praha 6, Czech Republic
| | - Antonin Machac
- Faculty of Science, Charles University, Albertov 6, 12844, Praha 2, Czech Republic.,Center for Theoretical Study, Charles University and the Czech Academy of Sciences, Jilská 1, 11000, Praha 1, Czech Republic.,Center for Macroecology, Evolution and Climate, Natural History Museum of Denmark, University of Copenhagen, DK-2100, Copenhagen, Denmark.,Biodiversity Research Centre, University of British Columbia, 2212 Main Mall, Vancouver, V6T 1Z4, Canada
| | - Matěj Man
- Institute of Botany of the Czech Academy of Sciences, Zámek 1, 25243, Průhonice, Czech Republic
| | - Barbara Doreen Bahnmann
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Vendula Brabcová
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Jinlyung Choi
- Department of Agricultural and Biosystems Engineering, Iowa State University, 1201 Sukup Hall, Ames, IA, 50011, USA
| | - Lenka Meszárošová
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Zander Rainier Human
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Clémentine Lepinay
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Salvador Lladó
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Rubén López-Mondéjar
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Tijana Martinović
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Tereza Mašínová
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Daniel Morais
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Diana Navrátilová
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Iñaki Odriozola
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Martina Štursová
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Karel Švec
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Vojtěch Tláskal
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Michaela Urbanová
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Joe Wan
- Department of Biology, Stanford University, Stanford, CA, 94305, USA
| | - Lucia Žifčáková
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Adina Howe
- Department of Agricultural and Biosystems Engineering, Iowa State University, 1201 Sukup Hall, Ames, IA, 50011, USA
| | - Joshua Ladau
- Gladstone Institutes, San Francisco, CA, 94158, USA
| | | | - David Storch
- Center for Theoretical Study, Charles University and the Czech Academy of Sciences, Jilská 1, 11000, Praha 1, Czech Republic.,Center for Macroecology, Evolution and Climate, Natural History Museum of Denmark, University of Copenhagen, DK-2100, Copenhagen, Denmark
| | - Jan Wild
- Institute of Botany of the Czech Academy of Sciences, Zámek 1, 25243, Průhonice, Czech Republic
| | - Petr Baldrian
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic.
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22
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Houfani AA, Větrovský T, Navarrete OU, Štursová M, Tláskal V, Beiko RG, Boucherba N, Baldrian P, Benallaoua S, Jorquera MA. Cellulase-Hemicellulase Activities and Bacterial Community Composition of Different Soils from Algerian Ecosystems. Microb Ecol 2019; 77:713-725. [PMID: 30209585 DOI: 10.1007/s00248-018-1251-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Accepted: 08/29/2018] [Indexed: 06/08/2023]
Abstract
Soil microorganisms are important mediators of carbon cycling in nature. Although cellulose- and hemicellulose-degrading bacteria have been isolated from Algerian ecosystems, the information on the composition of soil bacterial communities and thus the potential of their members to decompose plant residues is still limited. The objective of the present study was to describe and compare the bacterial community composition in Algerian soils (crop, forest, garden, and desert) and the activity of cellulose- and hemicellulose-degrading enzymes. Bacterial communities were characterized by high-throughput 16S amplicon sequencing followed by the in silico prediction of their functional potential. The highest lignocellulolytic activity was recorded in forest and garden soils whereas activities in the agricultural and desert soils were typically low. The bacterial phyla Proteobacteria (in particular classes α-proteobacteria, δ-proteobacteria, and γ-proteobacteria), Firmicutes, and Actinobacteria dominated in all soils. Forest and garden soils exhibited higher diversity than agricultural and desert soils. Endocellulase activity was elevated in forest and garden soils. In silico analysis predicted higher share of genes assigned to general metabolism in forest and garden soils compared with agricultural and arid soils, particularly in carbohydrate metabolism. The highest potential of lignocellulose decomposition was predicted for forest soils, which is in agreement with the highest activity of corresponding enzymes.
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Affiliation(s)
- Aicha Asma Houfani
- Laboratoire de Microbiologie Appliquée (LMA), Département de Microbiologie, Faculté des Sciences de la Nature et de la Vie, Université de Bejaia, 06000, Bejaia, Algérie
- Laboratory of Environmental Microbiology, Institute of Microbiology of the CAS, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Tomáš Větrovský
- Laboratory of Environmental Microbiology, Institute of Microbiology of the CAS, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Oscar U Navarrete
- Laboratorio de Ecología Microbiana Aplicada, Departmento de Ciencias Químicas y Recursos Naturales, Universidad de La Frontera, Ave. Franciosco Salazar, 01145, Temuco, Chile
- Scientific and Biotechnological Bioresource Nucleus, Universidad de La Frontera, Ave. Franciosco Salazar, 01145, Temuco, Chile
| | - Martina Štursová
- Laboratory of Environmental Microbiology, Institute of Microbiology of the CAS, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Vojtěch Tláskal
- Laboratory of Environmental Microbiology, Institute of Microbiology of the CAS, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Robert G Beiko
- Faculty of Computer Science, Dalhousie University, 6050 University Avenue, Halifax, NS, B3H 4R2, Canada
| | - Nawel Boucherba
- Laboratoire de Microbiologie Appliquée (LMA), Département de Microbiologie, Faculté des Sciences de la Nature et de la Vie, Université de Bejaia, 06000, Bejaia, Algérie
| | - Petr Baldrian
- Laboratory of Environmental Microbiology, Institute of Microbiology of the CAS, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Said Benallaoua
- Laboratoire de Microbiologie Appliquée (LMA), Département de Microbiologie, Faculté des Sciences de la Nature et de la Vie, Université de Bejaia, 06000, Bejaia, Algérie
| | - Milko A Jorquera
- Laboratorio de Ecología Microbiana Aplicada, Departmento de Ciencias Químicas y Recursos Naturales, Universidad de La Frontera, Ave. Franciosco Salazar, 01145, Temuco, Chile.
- Scientific and Biotechnological Bioresource Nucleus, Universidad de La Frontera, Ave. Franciosco Salazar, 01145, Temuco, Chile.
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23
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Martins C, Varela A, Leclercq CC, Núñez O, Větrovský T, Renaut J, Baldrian P, Silva Pereira C. Specialisation events of fungal metacommunities exposed to a persistent organic pollutant are suggestive of augmented pathogenic potential. Microbiome 2018; 6:208. [PMID: 30466483 PMCID: PMC6251201 DOI: 10.1186/s40168-018-0589-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Accepted: 11/02/2018] [Indexed: 05/31/2023]
Abstract
BACKGROUND The impacts of man-made chemicals, in particular of persistent organic pollutants, are multifactorial as they may affect the integrity of ecosystems, alter biodiversity and have undesirable effects on many organisms. We have previously demonstrated that the belowground mycobiota of forest soils acts as a buffer against the biocide pollutant pentachlorophenol. However, the trade-offs made by mycobiota to mitigate this pollutant remain cryptic. RESULTS Herein, we demonstrate using a culture-dependent approach that exposure to pentachlorophenol led to alterations in the composition and functioning of the metacommunity, many of which were not fully alleviated when most of the biocide was degraded. Proteomic and physiological analyses showed that the carbon and nitrogen metabolisms were particularly affected. This dysregulation is possibly linked to the higher pathogenic potential of the metacommunity following exposure to the biocide, supported by the secretion of proteins related to pathogenicity and reduced susceptibility to a fungicide. Our findings provide additional evidence for the silent risks of environmental pollution, particularly as it may favour the development of pathogenic trade-offs in fungi, which may impose serious threats to animals and plant hosts.
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Affiliation(s)
- Celso Martins
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), Av. da República, 2780-157, Oeiras, Portugal
| | - Adélia Varela
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), Av. da República, 2780-157, Oeiras, Portugal
- Instituto Nacional Investigação Agrária e Veterinária, Av. da República, 2780-157, Oeiras, Portugal
| | - Céline C Leclercq
- Integrative biology platform, Environmental Research and Technology Platform, Luxembourg Institute of Science and Technology, Belvaux, Luxembourg
| | - Oscar Núñez
- Department of Chemical Engineering and Analytical Chemistry, University of Barcelona, Martí i Franquès 1-11, 08028, Barcelona, Spain
- Serra Hunter Fellow, Generalitat de Catalunya, Barcelona, Spain
| | - Tomáš Větrovský
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, 14220, Prague 4, Czech Republic
| | - Jenny Renaut
- Integrative biology platform, Environmental Research and Technology Platform, Luxembourg Institute of Science and Technology, Belvaux, Luxembourg
| | - Petr Baldrian
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, 14220, Prague 4, Czech Republic
| | - Cristina Silva Pereira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), Av. da República, 2780-157, Oeiras, Portugal.
- Institute of Biomedical & Environmental Health Research, School of Science & Sport, University of the West of Scotland, Paisley Campus, PA1 2BE, Paisley, UK.
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Lladó Fernández S, Větrovský T, Baldrian P. The concept of operational taxonomic units revisited: genomes of bacteria that are regarded as closely related are often highly dissimilar. Folia Microbiol (Praha) 2018; 64:19-23. [DOI: 10.1007/s12223-018-0627-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 06/12/2018] [Indexed: 02/07/2023]
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25
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Saati-Santamaría Z, López-Mondéjar R, Jiménez-Gómez A, Díez-Méndez A, Větrovský T, Igual JM, Velázquez E, Kolarik M, Rivas R, García-Fraile P. Discovery of Phloeophagus Beetles as a Source of Pseudomonas Strains That Produce Potentially New Bioactive Substances and Description of Pseudomonas bohemica sp. nov. Front Microbiol 2018; 9:913. [PMID: 29867824 PMCID: PMC5953339 DOI: 10.3389/fmicb.2018.00913] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Accepted: 04/20/2018] [Indexed: 12/21/2022] Open
Abstract
Antimicrobial resistance is a worldwide problem that threatens the effectiveness of treatments for microbial infection. Consequently, it is essential to study unexplored niches that can serve for the isolation of new microbial strains able to produce antimicrobial compounds to develop new drugs. Bark beetles live in phloem of host trees and establish symbioses with microorganisms that provide them with nutrients. In addition, some of their associated bacteria play a role in the beetle protection by producing substances that inhibit antagonists. In this study the capacity of several bacterial strains, isolated from the bark beetles Ips acuminatus, Pityophthorus pityographus Cryphalus piceae, and Pityogenes bidentatus, to produce antimicrobial compounds was analyzed. Several isolates exhibited the capacity to inhibit Gram-positive and Gram-negative bacteria, as well as fungi. The genome sequence analysis of three Pseudomonas isolates predicted the presence of several gene clusters implicated in the production of already described antimicrobials and moreover, the low similarity of some of these clusters with those previously described, suggests that they encode new undescribed substances, which may be useful for developing new antimicrobial agents. Moreover, these bacteria appear to have genetic machinery for producing antitumoral and antiviral substances. Finally, the strain IA19T showed to represent a new species of the genus Pseudomonas. The 16S rRNA gene sequence analysis showed that its most closely related species include Pseudomonas lutea, Pseudomonas graminis, Pseudomonas abietaniphila and Pseudomonas alkylphenolica, with 98.6, 98.5 98.4, and 98.4% identity, respectively. MLSA of the housekeeping genes gyrB, rpoB, and rpoD confirmed that strain IA19T clearly separates from its closest related species. Average nucleotide identity between strains IA19T and P. abietaniphila ATCC 700689T, P. graminis DSM 11363T, P. alkylphenolica KL28T and P. lutea DSM 17257T were 85.3, 80.2, 79.0, and 72.1%, respectively. Growth occurs at 4-37°C and pH 6.5-8. Optimal growth occurs at 28°C, pH 7-8 and up to 2.5% NaCl. Respiratory ubiquinones are Q9 (97%) and Q8 (3%). C16:0 and in summed feature 3 are the main fatty acids. Based on genotypic, phenotypic and chemotaxonomic characteristics, the description of Pseudomonas bohemica sp. nov. has been proposed. The type strain is IA19T (=CECT 9403T = LMG 30182T).
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Affiliation(s)
- Zaki Saati-Santamaría
- Microbiology and Genetics Department, University of Salamanca, Salamanca, Spain.,Spanish-Portuguese Institute for Agricultural Research (CIALE), Salamanca, Spain
| | | | - Alejandro Jiménez-Gómez
- Microbiology and Genetics Department, University of Salamanca, Salamanca, Spain.,Spanish-Portuguese Institute for Agricultural Research (CIALE), Salamanca, Spain
| | - Alexandra Díez-Méndez
- Microbiology and Genetics Department, University of Salamanca, Salamanca, Spain.,Spanish-Portuguese Institute for Agricultural Research (CIALE), Salamanca, Spain
| | - Tomáš Větrovský
- Institute of Microbiology of the Czech Academy of Sciences, Vestec, Czechia
| | - José M Igual
- Institute of Natural Resources and Agrobiology of Salamanca, IRNASA-CSIC, Salamanca, Spain.,Associated R&D Unit, USAL-CSIC (IRNASA), Salamanca, Spain
| | - Encarna Velázquez
- Microbiology and Genetics Department, University of Salamanca, Salamanca, Spain.,Spanish-Portuguese Institute for Agricultural Research (CIALE), Salamanca, Spain.,Associated R&D Unit, USAL-CSIC (IRNASA), Salamanca, Spain
| | - Miroslav Kolarik
- Institute of Microbiology of the Czech Academy of Sciences, Vestec, Czechia
| | - Raúl Rivas
- Microbiology and Genetics Department, University of Salamanca, Salamanca, Spain.,Spanish-Portuguese Institute for Agricultural Research (CIALE), Salamanca, Spain.,Associated R&D Unit, USAL-CSIC (IRNASA), Salamanca, Spain
| | - Paula García-Fraile
- Microbiology and Genetics Department, University of Salamanca, Salamanca, Spain.,Spanish-Portuguese Institute for Agricultural Research (CIALE), Salamanca, Spain.,Institute of Microbiology of the Czech Academy of Sciences, Vestec, Czechia
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Bastida F, Torres IF, Andrés-Abellán M, Baldrian P, López-Mondéjar R, Větrovský T, Richnow HH, Starke R, Ondoño S, García C, López-Serrano FR, Jehmlich N. Differential sensitivity of total and active soil microbial communities to drought and forest management. Glob Chang Biol 2017; 23:4185-4203. [PMID: 28614633 DOI: 10.1111/gcb.13790] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Accepted: 05/30/2017] [Indexed: 05/25/2023]
Abstract
Climate change will affect semiarid ecosystems through severe droughts that increase the competition for resources in plant and microbial communities. In these habitats, adaptations to climate change may consist of thinning-that reduces competition for resources through a decrease in tree density and the promotion of plant survival. We deciphered the functional and phylogenetic responses of the microbial community to 6 years of drought induced by rainfall exclusion and how forest management affects its resistance to drought, in a semiarid forest ecosystem dominated by Pinus halepensis Mill. A multiOMIC approach was applied to reveal novel, community-based strategies in the face of climate change. The diversity and the composition of the total and active soil microbiome were evaluated by 16S rRNA gene (bacteria) and ITS (fungal) sequencing, and by metaproteomics. The microbial biomass was analyzed by phospholipid fatty acids (PLFAs), and the microbially mediated ecosystem multifunctionality was studied by the integration of soil enzyme activities related to the cycles of C, N, and P. The microbial biomass and ecosystem multifunctionality decreased in drought-plots, as a consequence of the lower soil moisture and poorer plant development, but this decrease was more notable in unthinned plots. The structure and diversity of the total bacterial community was unaffected by drought at phylum and order level, but did so at genus level, and was influenced by seasonality. However, the total fungal community and the active microbial community were more sensitive to drought and were related to ecosystem multifunctionality. Thinning in plots without drought increased the active diversity while the total diversity was not affected. Thinning promoted the resistance of ecosystem multifunctionality to drought through changes in the active microbial community. The integration of total and active microbiome analyses avoids misinterpretations of the links between the soil microbial community and climate change.
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Affiliation(s)
- Felipe Bastida
- Department of Soil and Water Conservation, CEBAS-CSIC, Murcia, Spain
| | - Irene F Torres
- Department of Soil and Water Conservation, CEBAS-CSIC, Murcia, Spain
| | - Manuela Andrés-Abellán
- Department of Science and Agroforestry Technology and Genetics, Higher Technical School of Agricultural and Forestry Engineering, University of Castilla-La Mancha, Albacete, Spain
| | - Petr Baldrian
- Laboratory of Environmental Microbiology, Institute of Microbiology of the CAS, Praha 4, Czech Republic
| | - Rubén López-Mondéjar
- Laboratory of Environmental Microbiology, Institute of Microbiology of the CAS, Praha 4, Czech Republic
| | - Tomáš Větrovský
- Laboratory of Environmental Microbiology, Institute of Microbiology of the CAS, Praha 4, Czech Republic
| | - Hans H Richnow
- Department of Isotope Biogeochemistry, Helmholtz-Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Robert Starke
- Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Sara Ondoño
- Department of Soil and Water Conservation, CEBAS-CSIC, Murcia, Spain
| | - Carlos García
- Department of Soil and Water Conservation, CEBAS-CSIC, Murcia, Spain
| | - Francisco R López-Serrano
- Department of Science and Agroforestry Technology and Genetics, Higher Technical School of Agricultural and Forestry Engineering, University of Castilla-La Mancha, Albacete, Spain
| | - Nico Jehmlich
- Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research - UFZ, Leipzig, Germany
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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: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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Navrátilová D, Větrovský T, Baldrian P. Spatial heterogeneity of cellulolytic activity and fungal communities within individual decomposing Quercus petraea leaves. FUNGAL ECOL 2017. [DOI: 10.1016/j.funeco.2016.08.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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Mašínová T, Bahnmann BD, Větrovský T, Tomšovský M, Merunková K, Baldrian P. Drivers of yeast community composition in the litter and soil of a temperate forest. FEMS Microbiol Ecol 2016; 93:fiw223. [PMID: 27789535 DOI: 10.1093/femsec/fiw223] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 04/08/2016] [Accepted: 10/26/2016] [Indexed: 01/09/2023] Open
Abstract
Fungi represent a group of soil microorganisms fulfilling important ecological functions. Although several studies have shown that yeasts represent a significant proportion of fungal communities, our current knowledge is based mainly on cultivation experiments. In this study, we used amplicon sequencing of environmental DNA to describe the composition of yeast communities in European temperate forest and to identify the potential biotic and abiotic drivers of community assembly. Based on the analysis of ITS2 PCR amplicons, yeasts represented a substantial proportion of fungal communities ranging from 0.4 to 14.3% of fungal sequences in soil and 0.2 to 9.9% in litter. The species richness at individual sites was 28 ± 9 in soil and 31 ± 11 in litter. The basidiomycetous yeasts dominated over ascomycetous ones. In litter, yeast communities differed significantly among beech-, oak- and spruce-dominated stands. Drivers of community assembly are probably more complex in soils and comprise the effects of environmental conditions and vegetation.
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Affiliation(s)
- Tereza Mašínová
- Laboratory of Environmental Microbiology, Institute of Microbiology of the CAS, Vídeňská 1083, 14220 Praha 4, Czech Republic
| | - Barbara Doreen Bahnmann
- Laboratory of Environmental Microbiology, Institute of Microbiology of the CAS, Vídeňská 1083, 14220 Praha 4, Czech Republic
| | - Tomáš Větrovský
- Laboratory of Environmental Microbiology, Institute of Microbiology of the CAS, Vídeňská 1083, 14220 Praha 4, Czech Republic
| | - Michal Tomšovský
- Faculty of Forestry and Wood Technology, Mendel University in Brno, Zemědělská 3, 613 00 Brno, Czech Republic
| | - Kristina Merunková
- Department of Botany and Zoology, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic
| | - Petr Baldrian
- Laboratory of Environmental Microbiology, Institute of Microbiology of the CAS, Vídeňská 1083, 14220 Praha 4, Czech Republic
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30
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López-Mondéjar R, Zühlke D, Větrovský T, Becher D, Riedel K, Baldrian P. Decoding the complete arsenal for cellulose and hemicellulose deconstruction in the highly efficient cellulose decomposer Paenibacillus O199. Biotechnol Biofuels 2016; 9:104. [PMID: 27186238 PMCID: PMC4867992 DOI: 10.1186/s13068-016-0518-x] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Accepted: 05/04/2016] [Indexed: 05/11/2023]
Abstract
BACKGROUND The search for new enzymes and microbial strains to degrade plant biomass is one of the most important strategies for improving the conversion processes in the production of environment-friendly chemicals and biofuels. In this study, we report a new Paenibacillus isolate, O199, which showed the highest efficiency for cellulose deconstruction in a screen of environmental isolates. Here, we provide a detailed description of the complex multi-component O199 enzymatic system involved in the degradation of lignocellulose. RESULTS We examined the genome and the proteome of O199 grown on complex lignocellulose (wheat straw) and on microcrystalline cellulose. The genome contained 476 genes with domains assigned to carbohydrate-active enzyme (CAZyme) families, including 100 genes coding for glycosyl hydrolases (GHs) putatively involved in cellulose and hemicellulose degradation. Moreover, 31 % of these CAZymes were expressed on cellulose and 29 % on wheat straw. Proteomic analyses also revealed a complex and complete set of enzymes for deconstruction of cellulose (at least 22 proteins, including 4 endocellulases, 2 exocellulases, 2 cellobiohydrolases and 2 β-glucosidases) and hemicellulose (at least 28 proteins, including 5 endoxylanases, 1 β-xylosidase, 2 xyloglucanases, 2 endomannanases, 2 licheninases and 1 endo-β-1,3(4)-glucanase). Most of these proteins were secreted extracellularly and had numerous carbohydrate-binding domains (CBMs). In addition, O199 also secreted a high number of substrate-binding proteins (SBPs), including at least 42 proteins binding carbohydrates. Interestingly, both plant lignocellulose and crystalline cellulose triggered the production of a wide array of hydrolytic proteins, including cellulases, hemicellulases, and other GHs. CONCLUSIONS Our data provide an in-depth analysis of the complex and complete set of enzymes and accessory non-catalytic proteins-GHs, CBMs, transporters, and SBPs-implicated in the high cellulolytic capacity shown by this bacterial strain. The large diversity of hydrolytic enzymes and the extracellular secretion of most of them supports the use of Paenibacillus O199 as a candidate for second-generation technologies using paper or lignocellulosic agricultural wastes.
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Affiliation(s)
- Rubén López-Mondéjar
- />Laboratory of Environmental Microbiology, Institute of Microbiology of the CAS, v. v. i., Průmyslová 595, 252 42 Vestec, Czech Republic
| | - Daniela Zühlke
- />Institute of Microbiology, Ernst-Moritz-Arndt-University of Greifswald, Friedrich-Ludwig-Jahnstrasse 15, 17487 Greifswald, Germany
| | - Tomáš Větrovský
- />Laboratory of Environmental Microbiology, Institute of Microbiology of the CAS, v. v. i., Průmyslová 595, 252 42 Vestec, Czech Republic
| | - Dörte Becher
- />Institute of Microbiology, Ernst-Moritz-Arndt-University of Greifswald, Friedrich-Ludwig-Jahnstrasse 15, 17487 Greifswald, Germany
| | - Katharina Riedel
- />Institute of Microbiology, Ernst-Moritz-Arndt-University of Greifswald, Friedrich-Ludwig-Jahnstrasse 15, 17487 Greifswald, Germany
| | - Petr Baldrian
- />Laboratory of Environmental Microbiology, Institute of Microbiology of the CAS, v. v. i., Průmyslová 595, 252 42 Vestec, Czech Republic
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Stella T, Covino S, Burianová E, Filipová A, Křesinová Z, Voříšková J, Větrovský T, Baldrian P, Cajthaml T. Chemical and microbiological characterization of an aged PCB-contaminated soil. Sci Total Environ 2015; 533:177-186. [PMID: 26156136 DOI: 10.1016/j.scitotenv.2015.06.019] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Revised: 06/03/2015] [Accepted: 06/03/2015] [Indexed: 06/04/2023]
Abstract
This study was aimed at complex characterization of three soil samples (bulk soil, topsoil and rhizosphere soil) from a site historically contaminated with polychlorinated biphenyls (PCB). The bulk soil was the most highly contaminated, with a PCB concentration of 705.95 mg kg(-1), while the rhizosphere soil was the least contaminated (169.36 mg kg(-1)). PCB degradation intermediates, namely chlorobenzoic acids (CBAs), were detected in all the soil samples, suggesting the occurrence of microbial transformation processes over time. The higher content of organic carbon in the topsoil and rhizosphere soil than in the bulk soil could be linked to the reduced bioaccessibility (bioavailability) of these chlorinated pollutants. However, different proportions of the PCB congener contents and different bioaccessibility of the PCB homologues indicate microbial biotransformation of the compounds. The higher content of organic carbon probably also promoted the growth of microorganisms, as revealed by phospholipid fatty acid (PFLA) quantification. Tag-encoded pyrosequencing analysis showed that the bacterial community structure was significantly similar among the three soils and was predominated by Proteobacteria (44-48%) in all cases. Moreover, analysis at lower taxonomic levels pointed to the presence of genera (Sphingomonas, Bulkholderia, Arthrobacter, Bacillus) including members with reported PCB removal abilities. The fungal community was mostly represented by Basidiomycota and Ascomycota, which accounted for >80% of all the sequences detected in the three soils. Fungal taxa with biodegradation potential (Paxillus, Cryptococcus, Phoma, Mortierella) were also found. These results highlight the potential of the indigenous consortia present at the site as a starting point for PCB bioremediation processes.
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Affiliation(s)
- T Stella
- Institute of Microbiology, Academy of Sciences of the Czech Republic v.v.i., Vídeňská 1083, CZ-142 20 Prague 4, Czech Republic; Department for Innovation in Biological, Agro-food and Forest Systems (DIBAF), University of Tuscia, Via S. Camillo De Lellis, 01100 Viterbo, Italy; Institute for Environmental Studies, Faculty of Science, Charles University in Prague, Benátská 2, CZ-128 01 Prague 2, Czech Republic
| | - S Covino
- Institute of Microbiology, Academy of Sciences of the Czech Republic v.v.i., Vídeňská 1083, CZ-142 20 Prague 4, Czech Republic
| | - E Burianová
- Institute of Microbiology, Academy of Sciences of the Czech Republic v.v.i., Vídeňská 1083, CZ-142 20 Prague 4, Czech Republic
| | - A Filipová
- Institute of Microbiology, Academy of Sciences of the Czech Republic v.v.i., Vídeňská 1083, CZ-142 20 Prague 4, Czech Republic
| | - Z Křesinová
- Institute of Microbiology, Academy of Sciences of the Czech Republic v.v.i., Vídeňská 1083, CZ-142 20 Prague 4, Czech Republic
| | - J Voříšková
- Institute of Microbiology, Academy of Sciences of the Czech Republic v.v.i., Vídeňská 1083, CZ-142 20 Prague 4, Czech Republic
| | - T Větrovský
- Institute of Microbiology, Academy of Sciences of the Czech Republic v.v.i., Vídeňská 1083, CZ-142 20 Prague 4, Czech Republic
| | - P Baldrian
- Institute of Microbiology, Academy of Sciences of the Czech Republic v.v.i., Vídeňská 1083, CZ-142 20 Prague 4, Czech Republic
| | - T Cajthaml
- Institute of Microbiology, Academy of Sciences of the Czech Republic v.v.i., Vídeňská 1083, CZ-142 20 Prague 4, Czech Republic; Institute for Environmental Studies, Faculty of Science, Charles University in Prague, Benátská 2, CZ-128 01 Prague 2, Czech Republic.
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Žifčáková L, Větrovský T, Howe A, Baldrian P. Microbial activity in forest soil reflects the changes in ecosystem properties between summer and winter. Environ Microbiol 2015; 18:288-301. [DOI: 10.1111/1462-2920.13026] [Citation(s) in RCA: 250] [Impact Index Per Article: 27.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2015] [Revised: 08/13/2015] [Accepted: 08/13/2015] [Indexed: 11/26/2022]
Affiliation(s)
- Lucia Žifčáková
- Laboratory of Environmental Microbiology; Institute of Microbiology of the ASCR; v.v.i., Vídeňská 1083 Praha 4 14220 Czech Republic
| | - Tomáš Větrovský
- Laboratory of Environmental Microbiology; Institute of Microbiology of the ASCR; v.v.i., Vídeňská 1083 Praha 4 14220 Czech Republic
| | - Adina Howe
- Department of Agricultural and Biosystems Engineering; Iowa State University; Ames IA 50011 USA
| | - Petr Baldrian
- Laboratory of Environmental Microbiology; Institute of Microbiology of the ASCR; v.v.i., Vídeňská 1083 Praha 4 14220 Czech Republic
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Větrovský T, Kolařík M, Žifčáková L, Zelenka T, Baldrian P. Therpb2gene represents a viable alternative molecular marker for the analysis of environmental fungal communities. Mol Ecol Resour 2015; 16:388-401. [DOI: 10.1111/1755-0998.12456] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2014] [Revised: 07/28/2015] [Accepted: 08/14/2015] [Indexed: 01/27/2023]
Affiliation(s)
- Tomáš Větrovský
- Institute of Microbiology of the ASCR, v.v.i.; Vídeňská 1083 14220 Praha 4 Czech Republic
| | - Miroslav Kolařík
- Institute of Microbiology of the ASCR, v.v.i.; Vídeňská 1083 14220 Praha 4 Czech Republic
| | - Lucia Žifčáková
- Institute of Microbiology of the ASCR, v.v.i.; Vídeňská 1083 14220 Praha 4 Czech Republic
| | - Tomáš Zelenka
- Institute of Microbiology of the ASCR, v.v.i.; Vídeňská 1083 14220 Praha 4 Czech Republic
| | - Petr Baldrian
- Institute of Microbiology of the ASCR, v.v.i.; Vídeňská 1083 14220 Praha 4 Czech Republic
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Lukešová T, Kohout P, Větrovský T, Vohník M. The potential of Dark Septate Endophytes to form root symbioses with ectomycorrhizal and ericoid mycorrhizal middle European forest plants. PLoS One 2015; 10:e0124752. [PMID: 25905493 PMCID: PMC4408093 DOI: 10.1371/journal.pone.0124752] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2014] [Accepted: 03/08/2015] [Indexed: 11/19/2022] Open
Abstract
The unresolved ecophysiological significance of Dark Septate Endophytes (DSE) may be in part due to existence of morphologically indistinguishable cryptic species in the most common Phialocephala fortinii s. l.--Acephala applanata species complex (PAC). We inoculated three middle European forest plants (European blueberry, Norway spruce and silver birch) with 16 strains of eight PAC cryptic species and other DSE and ectomycorrhizal/ericoid mycorrhizal fungi and focused on intraradical structures possibly representing interfaces for plant-fungus nutrient transfer and on host growth response. The PAC species Acephala applanata simultaneously formed structures resembling ericoid mycorrhiza (ErM) and DSE microsclerotia in blueberry. A. macrosclerotiorum, a close relative to PAC, formed ectomycorrhizae with spruce but not with birch, and structures resembling ErM in blueberry. Phialocephala glacialis, another close relative to PAC, formed structures resembling ErM in blueberry. In blueberry, six PAC strains significantly decreased dry shoot biomass compared to ErM control. In birch, one A. macrosclerotiorum strain increased root biomass and the other shoot biomass in comparison with non-inoculated control. The dual mycorrhizal ability of A. macrosclerotiorum suggested that it may form mycorrhizal links between Ericaceae and Pinaceae. However, we were unable to detect this species in Ericaceae roots growing in a forest with presence of A. macrosclerotiorum ectomycorrhizae. Nevertheless, the diversity of Ericaceae mycobionts was high (380 OTUs) with individual sites often dominated by hitherto unreported helotialean and chaetothyrialean/verrucarialean species; in contrast, typical ErM fungi were either absent or low in abundance. Some DSE apparently have a potential to form mycorrhizae with typical middle European forest plants. However, except A. applanata, the tested representatives of all hitherto described PAC cryptic species formed typical DSE colonization without specific structures necessary for mycorrhizal nutrient transport. A. macrosclerotiorum forms ectomycorrhiza with conifers but not with broadleaves and probably does not form common mycorrhizal networks between conifers with Ericaceae.
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Affiliation(s)
- Tereza Lukešová
- Department of Plant Experimental Biology, Faculty of Science, Charles University in Prague, Prague, Czech Republic
- Department of Mycorrhizal Symbioses, Institute of Botany ASCR, Průhonice, Czech Republic
| | - Petr Kohout
- Department of Plant Experimental Biology, Faculty of Science, Charles University in Prague, Prague, Czech Republic
- Department of Mycorrhizal Symbioses, Institute of Botany ASCR, Průhonice, Czech Republic
- Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Tomáš Větrovský
- Laboratory of Environmental Microbiology, Institute of Microbiology ASCR, Prague, Czech Republic
| | - Martin Vohník
- Department of Plant Experimental Biology, Faculty of Science, Charles University in Prague, Prague, Czech Republic
- Department of Mycorrhizal Symbioses, Institute of Botany ASCR, Průhonice, Czech Republic
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Větrovský T, Steffen KT, Baldrian P. Potential of cometabolic transformation of polysaccharides and lignin in lignocellulose by soil Actinobacteria. PLoS One 2014; 9:e89108. [PMID: 24551229 PMCID: PMC3923840 DOI: 10.1371/journal.pone.0089108] [Citation(s) in RCA: 87] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2013] [Accepted: 01/18/2014] [Indexed: 11/25/2022] Open
Abstract
While it is known that several Actinobacteria produce enzymes that decompose polysaccharides or phenolic compounds in dead plant biomass, the occurrence of these traits in the environment remains largely unclear. The aim of this work was to screen isolated actinobacterial strains to explore their ability to produce extracellular enzymes that participate in the degradation of polysaccharides and their ability to cometabolically transform phenolic compounds of various complexities. Actinobacterial strains were isolated from meadow and forest soils and screened for their ability to grow on lignocellulose. The potential to transform 14C-labelled phenolic substrates (dehydrogenation polymer (DHP), lignin and catechol) and to produce a range of extracellular, hydrolytic enzymes was investigated in three strains of Streptomyces spp. that possessed high lignocellulose degrading activity. Isolated strains showed high variation in their ability to produce cellulose- and hemicellulose-degrading enzymes and were able to mineralise up to 1.1% and to solubilise up to 4% of poplar lignin and to mineralise up to 11.4% and to solubilise up to 64% of catechol, while only minimal mineralisation of DHP was observed. The results confirm the potential importance of Actinobacteria in lignocellulose degradation, although it is likely that the decomposition of biopolymers is limited to strains that represent only a minor portion of the entire community, while the range of simple, carbon-containing compounds that serve as sources for actinobacterial growth is relatively wide.
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Affiliation(s)
- Tomáš Větrovský
- Laboratory of Environmental Microbiology, Institute of Microbiology of the ASCR, v.v.i., Praha, Czech Republic
| | - Kari Timo Steffen
- Department of Applied Chemistry and Microbiology, University of Helsinki, Helsinki, Finland
| | - Petr Baldrian
- Laboratory of Environmental Microbiology, Institute of Microbiology of the ASCR, v.v.i., Praha, Czech Republic
- * E-mail:
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Větrovský T, Baldrian P. The variability of the 16S rRNA gene in bacterial genomes and its consequences for bacterial community analyses. PLoS One 2013; 8:e57923. [PMID: 23460914 PMCID: PMC3583900 DOI: 10.1371/journal.pone.0057923] [Citation(s) in RCA: 632] [Impact Index Per Article: 57.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2012] [Accepted: 01/28/2013] [Indexed: 11/19/2022] Open
Abstract
16S ribosomal RNA currently represents the most important target of study in bacterial ecology. Its use for the description of bacterial diversity is, however, limited by the presence of variable copy numbers in bacterial genomes and sequence variation within closely related taxa or within a genome. Here we use the information from sequenced bacterial genomes to explore the variability of 16S rRNA sequences and copy numbers at various taxonomic levels and apply it to estimate bacterial genome and DNA abundances. In total, 7,081 16S rRNA sequences were in silico extracted from 1,690 available bacterial genomes (1-15 per genome). While there are several phyla containing low 16S rRNA copy numbers, in certain taxa, e.g., the Firmicutes and Gammaproteobacteria, the variation is large. Genome sizes are more conserved at all tested taxonomic levels than 16S rRNA copy numbers. Only a minority of bacterial genomes harbors identical 16S rRNA gene copies, and sequence diversity increases with increasing copy numbers. While certain taxa harbor dissimilar 16S rRNA genes, others contain sequences common to multiple species. Sequence identity clusters (often termed operational taxonomic units) thus provide an imperfect representation of bacterial taxa of a certain phylogenetic rank. We have demonstrated that the information on 16S rRNA copy numbers and genome sizes of genome-sequenced bacteria may be used as an estimate for the closest related taxon in an environmental dataset to calculate alternative estimates of the relative abundance of individual bacterial taxa in environmental samples. Using an example from forest soil, this procedure would increase the abundance estimates of Acidobacteria and decrease these of Firmicutes. Using the currently available information, alternative estimates of bacterial community composition may be obtained in this way if the variation of 16S rRNA copy numbers among bacteria is considered.
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Affiliation(s)
- Tomáš Větrovský
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Academy of Sciences of the Czech Republic, Praha, Czech Republic
| | - Petr Baldrian
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Academy of Sciences of the Czech Republic, Praha, Czech Republic
- * E-mail:
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Baldrian P, Větrovský T, Cajthaml T, Dobiášová P, Petránková M, Šnajdr J, Eichlerová I. Estimation of fungal biomass in forest litter and soil. FUNGAL ECOL 2013. [DOI: 10.1016/j.funeco.2012.10.002] [Citation(s) in RCA: 124] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Větrovský T, Baldrian P, Gabriel J. Extracellular enzymes of the white-rot fungus Fomes fomentarius and purification of 1,4-β-glucosidase. Appl Biochem Biotechnol 2012; 169:100-9. [PMID: 23149715 DOI: 10.1007/s12010-012-9952-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2012] [Accepted: 10/31/2012] [Indexed: 01/24/2023]
Abstract
Production of the lignocellulose-degrading enzymes endo-1,4-β-glucanase, 1,4-β-glucosidase, cellobiohydrolase, endo-1,4-β-xylanase, 1,4-β-xylosidase, Mn peroxidase, and laccase was characterized in a common wood-rotting fungus Fomes fomentarius, a species able to efficiently decompose dead wood, and compared to the production in eight other fungal species. The main aim of this study was to characterize the 1,4-β-glucosidase produced by F. fomentarius that was produced in high quantities in liquid stationary culture (25.9 U ml(-1)), at least threefold compared to other saprotrophic basidiomycetes, such as Rhodocollybia butyracea, Hypholoma fasciculare, Irpex lacteus, Fomitopsis pinicola, Pleurotus ostreatus, Piptoporus betulinus, and Gymnopus sp. (between 0.7 and 7.9 U ml(-1)). The 1,4-β-glucosidase enzyme was purified to electrophoretic homogeneity by both anion-exchange and size-exclusion chromatography. A single 1,4-β-glucosidase was found to have an apparent molecular mass of 58 kDa and a pI of 6.7. The enzyme exhibited high thermotolerance with an optimum temperature of 60 °C. Maximal activity was found in the pH range of 4.5-5.0, and K (M) and V (max) values were 62 μM and 15.8 μmol min(-1) l(-1), respectively, when p-nitrophenylglucoside was used as a substrate. The enzyme was competitively inhibited by glucose with a K (i) of 3.37 mM. The enzyme also acted on p-nitrophenylxyloside, p-nitrophenylcellobioside, p-nitrophenylgalactoside, and p-nitrophenylmannoside with optimal pH values of 6.0, 3.5, 5.0, and 4.0-6.0, respectively. The combination of relatively low molecular mass and low K (M) value make the 1,4-β-glucosidase a promising enzyme for biotechnological applications.
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Affiliation(s)
- Tomáš Větrovský
- Laboratory of Environmental Microbiology, Institute of Microbiology of the ASCR, v.v.i., Vídeňská 1083, 14220 Praha 4, Czech Republic
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Baldrian P, Kolařík M, Stursová M, Kopecký J, Valášková V, Větrovský T, Zifčáková L, Snajdr J, Rídl J, Vlček C, Voříšková J. Active and total microbial communities in forest soil are largely different and highly stratified during decomposition. ISME J 2012; 6:248-58. [PMID: 21776033 PMCID: PMC3260513 DOI: 10.1038/ismej.2011.95] [Citation(s) in RCA: 421] [Impact Index Per Article: 35.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2011] [Revised: 06/16/2011] [Accepted: 06/20/2011] [Indexed: 11/09/2022]
Abstract
Soils of coniferous forest ecosystems are important for the global carbon cycle, and the identification of active microbial decomposers is essential for understanding organic matter transformation in these ecosystems. By the independent analysis of DNA and RNA, whole communities of bacteria and fungi and its active members were compared in topsoil of a Picea abies forest during a period of organic matter decomposition. Fungi quantitatively dominate the microbial community in the litter horizon, while the organic horizon shows comparable amount of fungal and bacterial biomasses. Active microbial populations obtained by RNA analysis exhibit similar diversity as DNA-derived populations, but significantly differ in the composition of microbial taxa. Several highly active taxa, especially fungal ones, show low abundance or even absence in the DNA pool. Bacteria and especially fungi are often distinctly associated with a particular soil horizon. Fungal communities are less even than bacterial ones and show higher relative abundances of dominant species. While dominant bacterial species are distributed across the studied ecosystem, distribution of dominant fungi is often spatially restricted as they are only recovered at some locations. The sequences of cbhI gene encoding for cellobiohydrolase (exocellulase), an essential enzyme for cellulose decomposition, were compared in soil metagenome and metatranscriptome and assigned to their producers. Litter horizon exhibits higher diversity and higher proportion of expressed sequences than organic horizon. Cellulose decomposition is mediated by highly diverse fungal populations largely distinct between soil horizons. The results indicate that low-abundance species make an important contribution to decomposition processes in soils.
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Affiliation(s)
- Petr Baldrian
- Laboratory of Environmental Microbiology, Institute of Microbiology of the ASCR, v.v.i., Vídeňská, Praha, Czech Republic.
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Snajdr J, Dobiášová P, Větrovský T, Valášková V, Alawi A, Boddy L, Baldrian P. Saprotrophic basidiomycete mycelia and their interspecific interactions affect the spatial distribution of extracellular enzymes in soil. FEMS Microbiol Ecol 2011; 78:80-90. [PMID: 21539585 DOI: 10.1111/j.1574-6941.2011.01123.x] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
Abstract
Saprotrophic cord-forming basidiomycetes are important decomposers of lignocellulosic substrates in soil. The production of extracellular hydrolytic enzymes was studied during the growth of two saprotrophic basidiomycetes, Hypholoma fasciculare and Phanerochaete velutina, across the surface of nonsterile soil microcosms, along with the effects of these basidiomycetes on fungi and bacteria within the soil. Higher activities of α-glucosidase, β-glucosidase, cellobiohydrolase, β-xylosidase, phosphomonoesterase and phosphodiesterase, but not of arylsulphatase, were recorded beneath the mycelia. Despite the fact that H. fasciculare, with exploitative hyphal growth, produced much denser hyphal cover on the soil surface than P. velutina, with explorative growth, both fungi produced similar amounts of extracellular enzymes. In the areas where the mycelia of H. fasciculare and P. velutina interacted, the activities of N-acetylglucosaminidase, α-glucosidase and phosphomonoesterase, the enzymes potentially involved in hyphal cell wall damage, and the utilization of compounds released from damaged hyphae of interacting fungi, were particularly increased. No significant differences in fungal biomass were observed between basidiomycete-colonized and noncolonized soil, but bacterial biomass was reduced in soil with H. fasciculare. The increases in the activities of β-xylosidase, β-glucosidase, phosphomonoesterase and cellobiohydrolase with increasing fungal:bacterial biomass ratio indicate the positive effects of fungal enzymes on nutrient release and bacterial abundance, which is reflected in the positive correlation of bacterial and fungal biomass content.
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Affiliation(s)
- Jaroslav Snajdr
- Laboratory of Environmental Microbiology, Institute of Microbiology of the ASCR, Prague, Czech Republic
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