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Joublin-Delavat A, Touahri K, Crétin P, Morot A, Rodrigues S, Jesus B, Trigodet F, Delavat F. Genetic and physiological insights into the diazotrophic activity of a non-cyanobacterial marine diazotroph. Environ Microbiol 2022; 24:6510-6523. [PMID: 36302093 PMCID: PMC10099842 DOI: 10.1111/1462-2920.16261] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Accepted: 10/21/2022] [Indexed: 01/12/2023]
Abstract
Nitrogen (N2 ) fixation, or diazotrophy, supports a large part of primary production in oceans. Culture-independent approaches highlighted the presence in abundance of marine non-cyanobacterial diazotrophs (NCD), but their ecophysiology remains elusive, mostly because of the low number of isolated NCD and because of the lack of available genetic tools for these isolates. Here, a dual genetic and functional approach allowed unveiling the ecophysiology of a marine NCD affiliated to the species Vibrio diazotrophicus. Physiological characterization of the first marine NCD mutant obtained so far was performed using a soft-gellan assay, demonstrating that a ΔnifH mutant is not able to grow in nitrogen-free media. Furthermore, we demonstrated that V. diazotrophicus produces a thick biofilm under diazotrophic conditions, suggesting biofilm production as an adaptive response of this NCD to cope with the inhibition of nitrogen fixation by molecular oxygen. Finally, the genomic signature of V. diazotrophicus is essentially absent from metagenomic data of Tara Ocean expeditions, despite having been isolated from various marine environments. We think that the genetically tractable V. diazotrophicus strain used in this study may serve as an ideal model to study the ecophysiology of these overlooked procaryotic group.
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Affiliation(s)
| | - Katia Touahri
- Nantes Université, CNRS, US2B, UMR6286, Nantes, France.,Laboratoire Chimie et Biochimie de Molécules Bioactives, Université de Strasbourg/CNRS, UMR7177, Strasbourg, France
| | | | - Amandine Morot
- Univ Brest, CNRS, IRD, Ifremer, LEMAR, Plouzané, France.,Université de Bretagne-Sud, UR3884, LBCM, IUEM, Lorient, France
| | | | - Bruno Jesus
- Nantes Université, RSBE2 ISOMer, UR2160, Nantes, France
| | - Florian Trigodet
- Department of Medicine, The University of Chicago, Chicago, Illinois, USA
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2
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Mieszkin S, Pouder E, Uroz S, Simon-Colin C, Alain K. Acidisoma silvae sp. nov. and Acidisomacellulosilytica sp. nov., Two Acidophilic Bacteria Isolated from Decaying Wood, Hydrolyzing Cellulose and Producing Poly-3-hydroxybutyrate. Microorganisms 2021; 9:microorganisms9102053. [PMID: 34683374 PMCID: PMC8537097 DOI: 10.3390/microorganisms9102053] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 09/17/2021] [Accepted: 09/25/2021] [Indexed: 12/02/2022] Open
Abstract
Two novel strains, HW T2.11T and HW T5.17T, were isolated from decaying wood (forest of Champenoux, France). Study of the 16S rRNA sequence similarity indicated that the novel strains belong to the genus Acidisoma. The sequence similarity of the 16S rRNA gene of HW T2.11T with the corresponding sequences of A. tundrae and A. sibiricum was 97.30% and 97.25%, while for HW T5.17T it was 96.85% and 97.14%, respectively. The DNA G+C contents of the strains were 62.32–62.50%. Cells were Gram-negative coccobacilli that had intracellular storage granules (poly-3-hydroxybutyrate (P3HB)) that confer resistance to environmental stress conditions. They were mesophilic and acidophilic organisms growing at 8–25 °C, at a pH of 2.0–6.5, and were capable of using a wide range of organic compounds and complex biopolymers such as starch, fucoidan, laminarin, pectin and cellulose, the latter two being involved in wood composition. The major cellular fatty acid was cyclo C19:0ω8c and the major quinone was Q-10. Overall, genome relatedness indices between genomes of strains HW T2.11T and HW T5.17T (Orthologous Average Nucleotide Identity (OrthoANI) value = 83.73% and digital DNA-DNA hybridization score = 27.5%) confirmed that they belonged to two different species. Genetic predictions indicate that the cyclopropane fatty acid (CFA) pathway is present, conferring acid-resistance properties to the cells. The two novel strains might possess a class IV polyhydroxyalcanoate (PHA) synthase operon involved in the P3HB production pathway. Overall, the polyphasic taxonomic analysis shows that these two novel strains are adapted to harsh environments such as decaying wood where the organic matter is difficult to access, and can contribute to the degradation of dead wood. These strains represent novel species of the genus Acidisoma, for which the names Acidisoma silvae sp. nov. and Acidisomacellulosilytica sp. nov. are proposed. The type strains of Acidisoma silvae and Acidisomacellulosilytica are, respectively, HW T2.11T (DSM 111006T; UBOCC-M-3364T) and HW T5.17T (DSM 111007T; UBOCC-M-3365T).
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Affiliation(s)
- Sophie Mieszkin
- Laboratoire de Microbiologie des Environnements Extrêmes LM2E, Université de Brest, CNRS, Ifremer, IUEM, Rue Dumont d’Urville, F-29280 Plouzané, France; (E.P.); (C.S.-C.); (K.A.)
- Centre INRAE-Grand Est-Nancy, Université de Lorraine, INRAE, UMR IAM, 54280 Champenoux, F-54000 Nancy, France;
- Correspondence:
| | - Eva Pouder
- Laboratoire de Microbiologie des Environnements Extrêmes LM2E, Université de Brest, CNRS, Ifremer, IUEM, Rue Dumont d’Urville, F-29280 Plouzané, France; (E.P.); (C.S.-C.); (K.A.)
| | - Stéphane Uroz
- Centre INRAE-Grand Est-Nancy, Université de Lorraine, INRAE, UMR IAM, 54280 Champenoux, F-54000 Nancy, France;
| | - Christelle Simon-Colin
- Laboratoire de Microbiologie des Environnements Extrêmes LM2E, Université de Brest, CNRS, Ifremer, IUEM, Rue Dumont d’Urville, F-29280 Plouzané, France; (E.P.); (C.S.-C.); (K.A.)
| | - Karine Alain
- Laboratoire de Microbiologie des Environnements Extrêmes LM2E, Université de Brest, CNRS, Ifremer, IUEM, Rue Dumont d’Urville, F-29280 Plouzané, France; (E.P.); (C.S.-C.); (K.A.)
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3
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Bao Y, Jin X, Guo C, Lu G, Dang Z. Sulfate-reducing bacterial community shifts in response to acid mine drainage in the sediment of the Hengshi watershed, South China. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:2822-2834. [PMID: 32895792 DOI: 10.1007/s11356-020-10248-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Accepted: 07/21/2020] [Indexed: 06/11/2023]
Abstract
Sulfate-reducing bacteria (SRB) are an attractive option for treating acid mine drainage (AMD) and are considered to be of great significance in the natural attenuation of AMD, but the available information regarding the highly diverse SRB community in AMD sites is not comprehensive. The Hengshi River, which is continually contaminated by AMD from upstream mining areas, was selected as a study site for investigation of the distribution, diversity, and abundance of SRB. Overall, high-throughput sequencing of the 16S rRNA and dsrB genes revealed the high diversity, richness, and OTU numbers of SRB communities, suggesting the existence of active sulfate reduction in the study area. Further analysis demonstrated that AMD contamination decreased the richness and diversity of the microbial community and SRB community, and led to spatiotemporal shifts in the overall composition and structure of sediment microbial and SRB communities along the Hengshi watershed. However, the sulfate reduction activity was high in the midstream, even though AMD pollution remained heavy in this area. Spatial distributions of SRB community indicated that species of Clostridia may be more tolerant of AMD contamination than other species, because of their predominance in the SRB communities. In addition, the results of CCA revealed that environmental parameters, such as pH, TS content, and Fe content, can significantly influence total microbial and SRB community structure, and dissolved organic carbon was another important factor structuring the SRB community. This study extends our knowledge of the distribution of indigenous SRB communities and their potential roles in natural AMD attenuation.
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Affiliation(s)
- Yanping Bao
- School of Environment and Energy, South China University of Technology, 510006, Guangzhou, People's Republic of China
- School of Environment and Chemical Engineering, Foshan University, Foshan, 528000, People's Republic of China
| | - Xiaohu Jin
- School of Environment and Energy, South China University of Technology, 510006, Guangzhou, People's Republic of China
| | - Chuling Guo
- School of Environment and Energy, South China University of Technology, 510006, Guangzhou, People's Republic of China.
- The Key Lab of Pollution Control and Ecosystem Restoration in Industry Clusters, Ministry of Education, South China University of Technology, Guangzhou, 510006, People's Republic of China.
| | - Guining Lu
- School of Environment and Energy, South China University of Technology, 510006, Guangzhou, People's Republic of China
- The Key Lab of Pollution Control and Ecosystem Restoration in Industry Clusters, Ministry of Education, South China University of Technology, Guangzhou, 510006, People's Republic of China
| | - Zhi Dang
- School of Environment and Energy, South China University of Technology, 510006, Guangzhou, People's Republic of China.
- The Key Lab of Pollution Control and Ecosystem Restoration in Industry Clusters, Ministry of Education, South China University of Technology, Guangzhou, 510006, People's Republic of China.
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4
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Reis MP, Suhadolnik MLS, Dias MF, Ávila MP, Motta AM, Barbosa FAR, Nascimento AMA. Characterizing a riverine microbiome impacted by extreme disturbance caused by a mining sludge tsunami. CHEMOSPHERE 2020; 253:126584. [PMID: 32278186 DOI: 10.1016/j.chemosphere.2020.126584] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Revised: 03/18/2020] [Accepted: 03/21/2020] [Indexed: 06/11/2023]
Abstract
Studies on disturbance events in riverine systems caused by environmental disasters and their effects on microbial diversity are scarce. Here, we evaluated the impact of the collapse of an iron ore dam holding approximately 50 million cubic meters of waste on both water and sediment microbiomes by deeply sequencing the 16S rRNA gene. Samples were taken from two impacted rivers and one reference river 7, 30 and 150 days postdisturbance. The impacted community structure changed greatly over spatiotemporal scales, being less diverse and more uneven, particularly on day 7 for the do Carmo River (the closest to the dam). However, the reference community structure remained similar between sampling events. Moreover, the impacted sediments were positively correlated with metals. The taxa abundance varied greatly over spatiotemporal scales, allowing for the identification of several potential bioindicators, e.g., Comamonadaceae, Novosphingobium, Sediminibacterium and Bacteriovorax. Our results showed that the impacted communities consisted mostly of Fe(II) oxidizers and Fe(III) reducers, aromatic compound degraders and predator bacteria. Network analysis showed a highly interconnected microbiome whose interactions switched from positive to negative or vice versa between the impacted and reference communities. This work revealed potential molecular signatures associated with the rivers heavily impacted by metals that might be useful sentinels for predicting riverine health.
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Affiliation(s)
- Mariana P Reis
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, 31270-901, Brazil
| | - Maria Luíza S Suhadolnik
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, 31270-901, Brazil
| | - Marcela F Dias
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, 31270-901, Brazil
| | - Marcelo P Ávila
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, 31270-901, Brazil
| | - Amanda M Motta
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, 31270-901, Brazil
| | - Francisco A R Barbosa
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, 31270-901, Brazil
| | - Andréa M A Nascimento
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, 31270-901, Brazil.
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5
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Hujslová M, Gryndlerová H, Bystrianský L, Hršelová H, Gryndler M. Biofilm and planktonic microbial communities in highly acidic soil (pH < 3) in the Soos National Nature Reserve, Czech Republic. Extremophiles 2020; 24:577-591. [PMID: 32449144 DOI: 10.1007/s00792-020-01177-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Accepted: 05/07/2020] [Indexed: 10/24/2022]
Abstract
Biofilm formation is a typical life strategy used by microorganisms populating acidic water systems. The same strategy might be used by microbes in highly acidic soils that are, however, neglected in this regard. In the present study, the microbial community in such highly acidic soil in the Soos National Nature Reserve (Czech Republic) has been investigated using high-throughput DNA sequencing and the organisms associated with biofilm life mode and those preferring planktonic life were distinguished using the biofilm trap technique. Our data show the differences between biofilm and planktonic microbiota fraction, although the majority of the organisms were capable of using both life modes. The by far most abundant prokaryotic genus was Acidiphilium and fungi were identified among the most abundant eukaryotic elements in biofilm formations. On the other hand, small flagellates from diverse taxonomical groups predominated in plankton. The application of cellulose amendment as well as the depth of sampling significantly influenced the composition of the detected microbial community.
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Affiliation(s)
- Martina Hujslová
- Institute of Microbiology, Academy of Sciences of the Czech Republic, v.v.i., Vídeňská 1083, 14220, Prague 4, Czech Republic.
| | - Hana Gryndlerová
- Institute of Microbiology, Academy of Sciences of the Czech Republic, v.v.i., Vídeňská 1083, 14220, Prague 4, Czech Republic
| | - Lukáš Bystrianský
- Faculty of Science, Jan Evangelista Purkyně University in Ústí nad Labem, České mládeže 8, 40096, Ústí nad Labem, Czech Republic
| | - Hana Hršelová
- Institute of Microbiology, Academy of Sciences of the Czech Republic, v.v.i., Vídeňská 1083, 14220, Prague 4, Czech Republic
| | - Milan Gryndler
- Faculty of Science, Jan Evangelista Purkyně University in Ústí nad Labem, České mládeže 8, 40096, Ústí nad Labem, Czech Republic
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6
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Bao Y, Guo C, Lu G, Yi X, Wang H, Dang Z. Role of microbial activity in Fe(III) hydroxysulfate mineral transformations in an acid mine drainage-impacted site from the Dabaoshan Mine. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 616-617:647-657. [PMID: 29103647 DOI: 10.1016/j.scitotenv.2017.10.273] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Revised: 10/26/2017] [Accepted: 10/26/2017] [Indexed: 06/07/2023]
Abstract
Fe(III) hydroxysulfate minerals are secondary minerals commonly found in acid mine drainage (AMD) sites and have a major impact on water and soil quality in these environments. While previous studies showed that the Fe(III) hydroxysulfate mineral transformation could be mediated by some bacterial strains under laboratory conditions, the role of indigenous microbial activity in Fe(III) hydroxysulfate mineral transformation in natural environment has received little attention. In this study, microcosms were constructed with AMD-affected river water and sediment from the Dabaoshan Mine that was either left unamended or enriched with nutrients (lactate, nitrogen, and phosphorus (LNP)) and biosynthetic minerals (schwertmannite or jarosite). The results show that microbial activity played a decisive role in the mineralogical transformation of schwertmannite/jarosite in the AMD-contaminated site when organic carbon was available. The accumulation of Fe(II) and sulfide in microcosms amended with LNP indicates that schwertmannite/jarosite transformation is mediated by microbial reduction. XRD, SEM and FTIR analyses suggest that schwertmannite was completely transformed to goethite in the Sch-LNP microcosms at the end of their incubation. Jarosite in the Jar-LNP microcosms was also transformed to goethite, but at a much slower rate than schwertmannite. Bacterial community analysis reveals that the stimulated indigenous bacteria promote the mineralogical transformation of schwertmannite/jarosite. Most of these bacteria, including Geobacter, Desulfosporosinus, Geothrix, Desulfurispora, Desulfovibrio, and Anaeromyxobacter, are known to reduce iron and/or sulfate. The mineralogical transformation of schwertmannite and jarosite exerts significant control on the geochemistry of AMD-contaminated systems.
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Affiliation(s)
- Yanping Bao
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, PR China
| | - Chuling Guo
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, PR China; The Key Lab of Pollution Control and Ecosystem Restoration in Industry Clusters, Ministry of Education, South China University of Technology, Guangzhou 510006, PR China.
| | - Guining Lu
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, PR China; The Key Lab of Pollution Control and Ecosystem Restoration in Industry Clusters, Ministry of Education, South China University of Technology, Guangzhou 510006, PR China
| | - Xiaoyun Yi
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, PR China; The Key Lab of Pollution Control and Ecosystem Restoration in Industry Clusters, Ministry of Education, South China University of Technology, Guangzhou 510006, PR China
| | - Han Wang
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, PR China
| | - Zhi Dang
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, PR China; The Key Lab of Pollution Control and Ecosystem Restoration in Industry Clusters, Ministry of Education, South China University of Technology, Guangzhou 510006, PR China
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7
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Arsène-Ploetze F, Chiboub O, Lièvremont D, Farasin J, Freel KC, Fouteau S, Barbe V. Adaptation in toxic environments: comparative genomics of loci carrying antibiotic resistance genes derived from acid mine drainage waters. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2018; 25:1470-1483. [PMID: 29090447 DOI: 10.1007/s11356-017-0535-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Accepted: 10/19/2017] [Indexed: 06/07/2023]
Abstract
Several studies have suggested the existence of a close relationship between antibiotic-resistant phenotypes and resistance to other toxic compounds such as heavy metals, which involve co-resistance or cross-resistance mechanisms. A metagenomic library was previously constructed in Escherichia coli with DNA extracted from the bacterial community inhabiting an acid mine drainage (AMD) site highly contaminated with heavy metals. Here, we conducted a search for genes involved in antibiotic resistance using this previously constructed library. In particular, resistance to antibiotics was observed among five clones carrying four different loci originating from CARN5 and CARN2, two genomes reconstructed from the metagenomic data. Among the three CARN2 loci, two carry genes homologous to those previously proposed to be involved in antibiotic resistance. The third CARN2 locus carries a gene encoding a membrane transporter with an unknown function and was found to confer bacterial resistance to rifampicin, gentamycin, and kanamycin. The genome of Thiomonas delicata DSM 16361 and Thiomonas sp. X19 were sequenced in this study. Homologs of genes carried on these three CARN2 loci were found in these genomes, two of these loci were found in genomic islands. Together, these findings confirm that AMD environments contaminated with several toxic metals also constitute habitats for bacteria that function as reservoirs for antibiotic resistance genes.
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Affiliation(s)
- Florence Arsène-Ploetze
- Laboratoire Génétique Moléculaire, Génomique et Microbiologie, UMR7156, CNRS-Université de Strasbourg, Strasbourg, France.
- Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, Strasbourg, France.
| | - Olfa Chiboub
- Laboratoire Génétique Moléculaire, Génomique et Microbiologie, UMR7156, CNRS-Université de Strasbourg, Strasbourg, France
| | - Didier Lièvremont
- Laboratoire Génétique Moléculaire, Génomique et Microbiologie, UMR7156, CNRS-Université de Strasbourg, Strasbourg, France
- Institut de Chimie de Strasbourg, UMR7177 CNRS-Université de Strasbourg, Strasbourg, France
| | - Julien Farasin
- Laboratoire Génétique Moléculaire, Génomique et Microbiologie, UMR7156, CNRS-Université de Strasbourg, Strasbourg, France
| | - Kelle C Freel
- Laboratoire Génétique Moléculaire, Génomique et Microbiologie, UMR7156, CNRS-Université de Strasbourg, Strasbourg, France
| | - Stephanie Fouteau
- Laboratoire de Biologie Moléculaire pour l'Etude des Génomes, (LBioMEG), CEA/DRF/IBFJ/Genoscope, Evry, France
| | - Valérie Barbe
- Laboratoire de Biologie Moléculaire pour l'Etude des Génomes, (LBioMEG), CEA/DRF/IBFJ/Genoscope, Evry, France
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8
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Crognale S, D'Annibale A, Pesciaroli L, Stazi SR, Petruccioli M. Fungal Community Structure and As-Resistant Fungi in a Decommissioned Gold Mine Site. Front Microbiol 2017; 8:2202. [PMID: 29170658 PMCID: PMC5684174 DOI: 10.3389/fmicb.2017.02202] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Accepted: 10/26/2017] [Indexed: 01/16/2023] Open
Abstract
Although large quantities of heavy metal laden wastes are released in an uncontrolled manner by gold mining activities with ensuing contamination of the surrounding areas, there is scant information on the mycobiota of gold-mine sites. Thus, the present study was aimed to describe the fungal community structure in three differently As- and Hg-polluted soils collected from the Pestarena decommissioned site by using Illumina® metabarcoding. Fungal richness was found to increase as the contamination level increased while biodiversity was not related to the concentrations of inorganic toxicants. Within the phylum Zygomigota which, irrespective of the contamination level, was predominant in all the soils under study, the most abundant genera were Mucor and Mortierella. The relative abundances of Basidiomycota, instead, tended to raise as the contamination increased; within this phylum the most abundant genera were Cryptococcus and Pseudotomentella. The abundance of Ascomycota, ranging from about 8 to 21%, was not related to the contamination level. The relative abundances of those genera (i.e., Penicillium, Trichoderma, and Chaetomium), the cultivable isolates of which exhibited significant As-resistance, were lower than the set threshold (0.5%). Mass balances obtained from As-exposure experiments with these isolates showed that the main mechanisms involved in counteracting the toxicant were accumulation and, above all, volatilization, the respective extents of which ranged from 0.6 to 5.9% and from 6.4 to 31.2% in dependence of the isolate.
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Affiliation(s)
- Silvia Crognale
- Department for Innovation in Biological Systems, Food and Forestry, University of Tuscia, Viterbo, Italy
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9
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Morawe M, Hoeke H, Wissenbach DK, Lentendu G, Wubet T, Kröber E, Kolb S. Acidotolerant Bacteria and Fungi as a Sink of Methanol-Derived Carbon in a Deciduous Forest Soil. Front Microbiol 2017; 8:1361. [PMID: 28790984 PMCID: PMC5523551 DOI: 10.3389/fmicb.2017.01361] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2017] [Accepted: 07/05/2017] [Indexed: 02/03/2023] Open
Abstract
Methanol is an abundant atmospheric volatile organic compound that is released from both living and decaying plant material. In forest and other aerated soils, methanol can be consumed by methanol-utilizing microorganisms that constitute a known terrestrial sink. However, the environmental factors that drive the biodiversity of such methanol-utilizers have been hardly resolved. Soil-derived isolates of methanol-utilizers can also often assimilate multicarbon compounds as alternative substrates. Here, we conducted a comparative DNA stable isotope probing experiment under methylotrophic (only [13C1]-methanol was supplemented) and combined substrate conditions ([12C1]-methanol and alternative multi-carbon [13Cu]-substrates were simultaneously supplemented) to (i) identify methanol-utilizing microorganisms of a deciduous forest soil (European beech dominated temperate forest in Germany), (ii) assess their substrate range in the soil environment, and (iii) evaluate their trophic links to other soil microorganisms. The applied multi-carbon substrates represented typical intermediates of organic matter degradation, such as acetate, plant-derived sugars (xylose and glucose), and a lignin-derived aromatic compound (vanillic acid). An experimentally induced pH shift was associated with substantial changes of the diversity of active methanol-utilizers suggesting that soil pH was a niche-defining factor of these microorganisms. The main bacterial methanol-utilizers were members of the Beijerinckiaceae (Bacteria) that played a central role in a detected methanol-based food web. A clear preference for methanol or multi-carbon substrates as carbon source of different Beijerinckiaceae-affiliated phylotypes was observed suggesting a restricted substrate range of the methylotrophic representatives. Apart from Bacteria, we also identified the yeasts Cryptococcus and Trichosporon as methanol-derived carbon-utilizing fungi suggesting that further research is needed to exclude or prove methylotrophy of these fungi.
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Affiliation(s)
- Mareen Morawe
- Department of Ecological Microbiology, University of BayreuthBayreuth, Germany
| | - Henrike Hoeke
- Department of Molecular Systems Biology, Helmholtz Centre for Environmental ResearchLeipzig, Germany.,Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmacy, University of LeipzigLeipzig, Germany
| | - Dirk K Wissenbach
- Institute of Forensic Medicine, University Hospital JenaJena, Germany
| | - Guillaume Lentendu
- Department of Ecology, University of KaiserslauternKaiserslautern, Germany
| | - Tesfaye Wubet
- Department of Soil Ecology, Helmholtz Centre for Environmental ResearchLeipzig, Germany
| | - Eileen Kröber
- Institute of Landscape Biogeochemistry, Leibniz Centre for Landscape ResearchMüncheberg, Germany
| | - Steffen Kolb
- Department of Ecological Microbiology, University of BayreuthBayreuth, Germany.,Institute of Landscape Biogeochemistry, Leibniz Centre for Landscape ResearchMüncheberg, Germany
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10
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Hamidou Soumana I, Linz B, Harvill ET. Environmental Origin of the Genus Bordetella. Front Microbiol 2017; 8:28. [PMID: 28174558 PMCID: PMC5258731 DOI: 10.3389/fmicb.2017.00028] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2016] [Accepted: 01/05/2017] [Indexed: 01/01/2023] Open
Abstract
Members of the genus Bordetella include human and animal pathogens that cause a variety of respiratory infections, including whooping cough in humans. Despite the long known ability to switch between a within-animal and an extra-host lifestyle under laboratory growth conditions, no extra-host niches of pathogenic Bordetella species have been defined. To better understand the distribution of Bordetella species in the environment, we probed the NCBI nucleotide database with the 16S ribosomal RNA (16S rRNA) gene sequences from pathogenic Bordetella species. Bacteria of the genus Bordetella were frequently found in soil, water, sediment, and plants. Phylogenetic analyses of their 16S rRNA gene sequences showed that Bordetella recovered from environmental samples are evolutionarily ancestral to animal-associated species. Sequences from environmental samples had a significantly higher genetic diversity, were located closer to the root of the phylogenetic tree and were present in all 10 identified sequence clades, while only four sequence clades possessed animal-associated species. The pathogenic bordetellae appear to have evolved from ancestors in soil and/or water. We show that, despite being animal-adapted pathogens, Bordetella bronchiseptica, and Bordetella hinzii have preserved the ability to grow and proliferate in soil. Our data implicate soil as a probable environmental origin of Bordetella species, including the animal-pathogenic lineages. Soil may further constitute an environmental niche, allowing for persistence and dissemination of the bacterial pathogens. Spread of pathogenic bordetellae from an environmental reservoir such as soil may potentially explain their wide distribution as well as frequent disease outbreaks that start without an obvious infectious source.
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Affiliation(s)
- Illiassou Hamidou Soumana
- Department of Infectious Diseases, University of GeorgiaAthens, GA, USA; Center for Vaccines and Immunology, University of GeorgiaAthens, GA, USA
| | - Bodo Linz
- Center for Vaccines and Immunology, University of GeorgiaAthens, GA, USA; Department of Veterinary and Biomedical Sciences, Pennsylvania State UniversityUniversity Park, PA, USA
| | - Eric T Harvill
- Department of Infectious Diseases, University of GeorgiaAthens, GA, USA; Center for Vaccines and Immunology, University of GeorgiaAthens, GA, USA; Department of Veterinary and Biomedical Sciences, Pennsylvania State UniversityUniversity Park, PA, USA
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Volant A, Héry M, Desoeuvre A, Casiot C, Morin G, Bertin PN, Bruneel O. Spatial Distribution of Eukaryotic Communities Using High-Throughput Sequencing Along a Pollution Gradient in the Arsenic-Rich Creek Sediments of Carnoulès Mine, France. MICROBIAL ECOLOGY 2016; 72:608-620. [PMID: 27535039 DOI: 10.1007/s00248-016-0826-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2015] [Accepted: 07/22/2016] [Indexed: 06/06/2023]
Abstract
Microscopic eukaryotes play a key role in ecosystem functioning, but their diversity remains largely unexplored in most environments. To advance our knowledge of eukaryotic microorganisms and the factors that structure their communities, high-throughput sequencing was used to characterize their diversity and spatial distribution along the pollution gradient of the acid mine drainage at Carnoulès (France). A total of 16,510 reads were retrieved leading to the identification of 323 OTUs after normalization. Phylogenetic analysis revealed a quite diverse eukaryotic community characterized by a total of eight high-level lineages including 37 classes. The majority of sequences were clustered in four main groups: Fungi, Stramenopiles, Alveolata and Viridiplantae. The Reigous sediments formed a succession of distinct ecosystems hosting contrasted eukaryotic communities whose structure appeared to be at least partially correlated with sediment mineralogy. The concentration of arsenic in the sediment was shown to be a significant factor driving the eukaryotic community structure along this continuum.
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Affiliation(s)
- A Volant
- Laboratoire HydroSciences Montpellier, UMR 5569, Université de Montpellier, CC0057 (MSE), 163 rue Auguste Broussonet, 34090, Montpellier, France.
| | - M Héry
- Laboratoire HydroSciences Montpellier, UMR 5569, Université de Montpellier, CC0057 (MSE), 163 rue Auguste Broussonet, 34090, Montpellier, France
| | - A Desoeuvre
- Laboratoire HydroSciences Montpellier, UMR 5569, Université de Montpellier, CC0057 (MSE), 163 rue Auguste Broussonet, 34090, Montpellier, France
| | - C Casiot
- Laboratoire HydroSciences Montpellier, UMR 5569, Université de Montpellier, CC0057 (MSE), 163 rue Auguste Broussonet, 34090, Montpellier, France
| | - G Morin
- Institut de Minéralogie et de Physique des Milieux Condensés, IMPMC, UMR 7590 (CNRS, Université Pierre et Marie Curie/Paris 6), 4 place Jussieu, 75252, Paris, France
| | - P N Bertin
- Laboratoire de Génétique Moléculaire, Génomique, Microbiologie, GMGM, UMR 7156 (Université de Strasbourg, CNRS), Département Microorganismes, Génomes, Environnement, 28 Rue Goethe, 67083, Strasbourg, France
| | - O Bruneel
- Laboratoire HydroSciences Montpellier, UMR 5569, Université de Montpellier, CC0057 (MSE), 163 rue Auguste Broussonet, 34090, Montpellier, France
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Wang Y, Yasuda T, Sharmin S, Kanao T, Kamimura K. Analysis of the microbial community in moderately acidic drainage from the Yanahara pyrite mine in Japan. Biosci Biotechnol Biochem 2014; 78:1274-82. [DOI: 10.1080/09168451.2014.915735] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Abstract
Acid rock drainage (ARD) originating from the Yasumi-ishi tunnel near the main tunnel of the Yanahara mine in Japan was characterized to be moderately acidic (pH 4.1) and contained iron at a low concentration (51 mg/L). The composition of the microbial community was determined by sequence analysis of 16S rRNA genes using PCR and denaturing gradient gel electrophoresis. The analysis of the obtained sequences showed their similarity to clones recently detected in other moderately acidic mine drainages. Uncultured bacteria related to Ferrovum- and Gallionella-like clones were dominant in the microbial community. Analyses using specific primers for acidophilic iron- or sulfur-oxidizing bacteria, Acidithiobacillus ferrooxidans, Leptospirillum spp., Acidithiobacillus caldus, Acidithiobacillus thiooxidans, and Sulfobacillus spp. revealed the absence of these bacteria in the microbial community in ARD from the Yasumi-ishi tunnel. Clones affiliated with a member of the order Thermoplasmatales were detected as the dominant archaea in the ARD microbial population.
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Affiliation(s)
- Yang Wang
- Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan
| | - Takashi Yasuda
- Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan
| | - Sultana Sharmin
- Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan
| | - Tadayoshi Kanao
- Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan
| | - Kazuo Kamimura
- Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan
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