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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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Liu J, Zhang T, Piché-Choquette S, Wang G, Li J. Microplastic Pollution in China, an Invisible Threat Exacerbated by Food Delivery Services. Bull Environ Contam Toxicol 2021; 107:778-785. [PMID: 33078289 DOI: 10.1007/s00128-020-03018-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [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: 06/15/2020] [Accepted: 10/06/2020] [Indexed: 06/11/2023]
Abstract
With the rapid development and democratization of the internet and smart phone industry, online food delivery services have become increasingly popular all over the globe, namely in China. One of the unfortunate drawbacks of these delivery services is that they mainly use single-use plastics as food packaging, therefore generating large amounts of disposable food containers to meet demand. Such plastic containers reach the end of their service life after a single meal, and are then discarded as plastic waste. The sheer amount of plastic food containers discarded in this manner exacerbates various environmental issues, including one that is invisible to the naked eye: microplastic pollution. This minireview summarizes the history of food delivery services in China, from orders made face-to-face to digital orders, as well as the consequences introduced by the tremendous amounts of plastic waste generated by the food delivery services. Microplastic pollution could be mitigated to a certain extent by improving the classification, handling and management of single-use plastic containers in China. Furthermore, additional studies focusing on microplastic pollution caused by food delivery services are needed, especially as the use of these services is on the rise worldwide.
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Affiliation(s)
- Jun Liu
- Civil Engineering, Tongji Zhejiang College, Jiaxing, 314051, China
| | - Ting Zhang
- Civil Engineering, Tongji Zhejiang College, Jiaxing, 314051, China
| | - Sarah Piché-Choquette
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Guofang Wang
- Civil Engineering, Tongji Zhejiang College, Jiaxing, 314051, China
| | - Jun Li
- College of Environment, Zhejiang University of Technology, Hangzhou, 310014, China.
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Tiwari B, Sellamuthu B, Piché-Choquette S, Drogui P, Tyagi RD, Vaudreuil MA, Sauvé S, Buelna G, Dubé R. Acclimatization of microbial community of submerged membrane bioreactor treating hospital wastewater. Bioresour Technol 2021; 319:124223. [PMID: 33254452 DOI: 10.1016/j.biortech.2020.124223] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [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: 07/16/2020] [Revised: 09/30/2020] [Accepted: 10/02/2020] [Indexed: 06/12/2023]
Abstract
This study was performed to understand the dynamics of the microbial community of submerged membrane bioreactor during the acclimatization process to treat the hospital wastewater. In this regard, three acclimatization phases were examined using a mixture of synthetic wastewater (SWW) and real hospital wastewater (HWW) in the following proportions; In Phase 1: 75:25 v/v (SWW: HWW); Phase 2: 50:50 v/v (SWW: HWW); and Phase 3: 25:75 v/v (SWW: HWW) of wastewater. The microbial community was analyzed using Illumina high throughput sequencing to identify the bacterial and micro-eukaryotes community in SMBR. The acclimatization study clearly demonstrated that shift in microbial community composition with time. The dominance of pathogenic and degrading bacterial communities such as Mycobacterium, Pseudomonas, and Zoogloea was observed at the phase 3 of acclimatization. This study witnessed the major shift in the micro-eukaryotes community, and the proliferation of fungi Basidiomycota was observed in phase 3 of acclimatization.
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Affiliation(s)
| | - Balasubramanian Sellamuthu
- Département de radiologie, radio-oncologie et médecine nucléaire, Centre Hospitalier de l'Université de Montréal, H2X 0A9 Montréal, QC, Canada
| | | | - Patrick Drogui
- INRS-Eau, Terre et Environnement, G1K9A9 Quebec, QC, Canada
| | | | | | - Sébastien Sauvé
- Department of Chemistry, Université de Montréal, Montreal, QC, Canada
| | - Gerardo Buelna
- Investissement Québec - CRIQ, 333, rue Franquet, Quebec, QC G1P 4C7, Canada
| | - Rino Dubé
- Investissement Québec - CRIQ, 333, rue Franquet, Quebec, QC G1P 4C7, Canada
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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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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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Saavedra-Lavoie J, de la Porte A, Piché-Choquette S, Guertin C, Constant P. Biological H 2 and CO oxidation activities are sensitive to compositional change of soil microbial communities. Can J Microbiol 2020; 66:263-273. [PMID: 31999470 DOI: 10.1139/cjm-2019-0412] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Trace gas uptake by microorganisms controls the oxidative capacity of the troposphere, but little is known about how this important function is affected by changes in soil microbial diversity. This article bridges that knowledge gap by examining the response of the microbial community-level physiological profiles (CLPPs), carbon dioxide (CO2) production, and molecular hydrogen (H2) and carbon monoxide (CO) oxidation activities to manipulation of microbial diversity in soil microcosms. Microbial diversity was manipulated by mixing nonsterile and sterile soil with and without the addition of antibiotics. Nonsterile soil without antibiotics was used as a reference. Species composition changed significantly in soil microcosms as a result of dilution and antibiotic treatments, but there was no difference in species richness, according to PCR amplicon sequencing of the bacterial 16S rRNA gene. The CLPP was 15% higher in all dilution and antibiotic treatments than in reference microcosms, but the dilution treatment had no effect on CO2 production. Soil microcosms with dilution treatments had 58%-98% less H2 oxidation and 54%-99% lower CO oxidation, relative to reference microcosms, but did not differ among the antibiotic treatments. These results indicate that H2 and CO oxidation activities respond to compositional changes of microbial community in soil.
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Affiliation(s)
- Julien Saavedra-Lavoie
- Institut national de la recherche scientifique, Centre Armand Frappier Santé Biotechnologie, 531 boulevard des Prairies, Laval, QC H7V 1B7, Canada.,Institut national de la recherche scientifique, Centre Armand Frappier Santé Biotechnologie, 531 boulevard des Prairies, Laval, QC H7V 1B7, Canada
| | - Anne de la Porte
- Institut national de la recherche scientifique, Centre Armand Frappier Santé Biotechnologie, 531 boulevard des Prairies, Laval, QC H7V 1B7, Canada.,Institut national de la recherche scientifique, Centre Armand Frappier Santé Biotechnologie, 531 boulevard des Prairies, Laval, QC H7V 1B7, Canada
| | - Sarah Piché-Choquette
- Institut national de la recherche scientifique, Centre Armand Frappier Santé Biotechnologie, 531 boulevard des Prairies, Laval, QC H7V 1B7, Canada.,Institut national de la recherche scientifique, Centre Armand Frappier Santé Biotechnologie, 531 boulevard des Prairies, Laval, QC H7V 1B7, Canada
| | - Claude Guertin
- Institut national de la recherche scientifique, Centre Armand Frappier Santé Biotechnologie, 531 boulevard des Prairies, Laval, QC H7V 1B7, Canada.,Institut national de la recherche scientifique, Centre Armand Frappier Santé Biotechnologie, 531 boulevard des Prairies, Laval, QC H7V 1B7, Canada
| | - Philippe Constant
- Institut national de la recherche scientifique, Centre Armand Frappier Santé Biotechnologie, 531 boulevard des Prairies, Laval, QC H7V 1B7, Canada.,Institut national de la recherche scientifique, Centre Armand Frappier Santé Biotechnologie, 531 boulevard des Prairies, Laval, QC H7V 1B7, Canada
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Tiwari B, Sellamuthu B, Piché-Choquette S, Drogui P, Tyagi RD, Vaudreuil MA, Sauvé S, Buelna G, Dubé R. The bacterial community structure of submerged membrane bioreactor treating synthetic hospital wastewater. Bioresour Technol 2019; 286:121362. [PMID: 31054410 DOI: 10.1016/j.biortech.2019.121362] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [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: 01/17/2019] [Revised: 04/16/2019] [Accepted: 04/17/2019] [Indexed: 06/09/2023]
Abstract
The pharmaceuticals are biologically active compounds used to prevent and treat diseases. These pharmaceutical compounds were not fully metabolized by the human body and thus excreted out in the wastewater stream. Thus, the study on the treatment of synthetic hospital wastewater containing pharmaceuticals (ibuprofen, carbamazepine, estradiol and venlafaxine) was conducted to understand the variation of the bacterial community in a submerged membrane bioreactor (SMBR) at varying hydraulic retention time (HRT) of 6, 12 and 18 h. The variation in bacterial community dynamics of SMBR was studied using high throughput sequencing. The removal of pharmaceuticals was uniform at varying HRT. The removal of both ibuprofen and estradiol was accounted for 90%, whereas a lower removal of venlafaxine (<10%) and carbamazepine (>5%) in SMBR was observed. The addition of pharmaceuticals alters the bacterial community structure and result in increased abundance of bacteria (e.g., Flavobacterium, Pedobacter, and Methylibium) reported to degrade toxic pollutant.
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Affiliation(s)
| | - Balasubramanian Sellamuthu
- Département de radiologie, radio-oncologie et médecine nucléaire, Centre Hospitalier de l'Université de Montréal, H2X 0A9 Montréal, QC, Canada
| | | | - Patrick Drogui
- INRS-Eau, Terre et Environnement, G1K9A9 Quebec, QC, Canada
| | | | | | - Sébastien Sauvé
- Department of Chemistry, Université de Montréal, Montreal, QC, Canada
| | - G Buelna
- Centre de Recherche Industrielle du Québec (CRIQ), Quebec, QC, Canada
| | - R Dubé
- Centre de Recherche Industrielle du Québec (CRIQ), Quebec, QC, Canada
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Abstract
The atmosphere of the early Earth is hypothesized to have been rich in reducing gases such as hydrogen (H2). H2 has been proposed as the first electron donor leading to ATP synthesis due to its ubiquity throughout the biosphere as well as its ability to easily diffuse through microbial cells and its low activation energy requirement. Even today, hydrogenase enzymes enabling the production and oxidation of H2 are found in thousands of genomes spanning the three domains of life across aquatic, terrestrial, and even host-associated ecosystems. Even though H2 has already been proposed as a universal growth and maintenance energy source, its potential contribution as a driver of biogeochemical cycles has received little attention. Here, we bridge this knowledge gap by providing an overview of the classification, distribution, and physiological role of hydrogenases. Distribution of these enzymes in various microbial functional groups and recent experimental evidence are finally integrated to support the hypothesis that H2-oxidizing microbes are keystone species driving C cycling along O2 concentration gradients found in H2-rich soil ecosystems. In conclusion, we suggest focusing on the metabolic flexibility of H2-oxidizing microbes by combining community-level and individual-level approaches aiming to decipher the impact of H2 on C cycling and the C-cycling potential of H2-oxidizing microbes, via both culture-dependent and culture-independent methods, to give us more insight into the role of H2 as a driver of biogeochemical processes.
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Piché-Choquette S, Tremblay J, Tringe SG, Constant P. H2-saturation of high affinity H2-oxidizing bacteria alters the ecological niche of soil microorganisms unevenly among taxonomic groups. PeerJ 2016; 4:e1782. [PMID: 26989620 PMCID: PMC4793312 DOI: 10.7717/peerj.1782] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [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: 01/13/2016] [Accepted: 02/17/2016] [Indexed: 02/01/2023] Open
Abstract
Soil microbial communities are continuously exposed to H2 diffusing into the soil from the atmosphere. N2-fixing nodules represent a peculiar microniche in soil where H2 can reach concentrations up to 20,000 fold higher than in the global atmosphere (0.530 ppmv). In this study, we investigated the impact of H2 exposure on soil bacterial community structure using dynamic microcosm chambers simulating soil H2 exposure from the atmosphere and N2-fixing nodules. Biphasic kinetic parameters governing H2 oxidation activity in soil changed drastically upon elevated H2 exposure, corresponding to a slight but significant decay of high affinity H2-oxidizing bacteria population, accompanied by an enrichment or activation of microorganisms displaying low-affinity for H2. In contrast to previous studies that unveiled limited response by a few species, the relative abundance of 958 bacterial ribotypes distributed among various taxonomic groups, rather than a few distinct taxa, was influenced by H2 exposure. Furthermore, correlation networks showed important alterations of ribotype covariation in response to H2 exposure, suggesting that H2 affects microbe-microbe interactions in soil. Taken together, our results demonstrate that H2-rich environments exert a direct influence on soil H2-oxidizing bacteria in addition to indirect effects on other members of the bacterial communities.
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Affiliation(s)
| | - Julien Tremblay
- Biomonitoring, National Research Council Canada , Montreal, Quebec , Canada
| | - Susannah G Tringe
- DOE Joint Genome Institute , Walnut Creek, California , United States of America
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