1
|
Arisan D, Moya-Beltrán A, Rojas-Villalobos C, Issotta F, Castro M, Ulloa R, Chiacchiarini PA, Díez B, Martín AJM, Ñancucheo I, Giaveno A, Johnson DB, Quatrini R. Acidithiobacillia class members originating at sites within the Pacific Ring of Fire and other tectonically active locations and description of the novel genus ' Igneacidithiobacillus'. Front Microbiol 2024; 15:1360268. [PMID: 38633703 PMCID: PMC11021618 DOI: 10.3389/fmicb.2024.1360268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 02/21/2024] [Indexed: 04/19/2024] Open
Abstract
Recent studies have expanded the genomic contours of the Acidithiobacillia, highlighting important lacunae in our comprehension of the phylogenetic space occupied by certain lineages of the class. One such lineage is 'Igneacidithiobacillus', a novel genus-level taxon, represented by 'Igneacidithiobacillus copahuensis' VAN18-1T as its type species, along with two other uncultivated metagenome-assembled genomes (MAGs) originating from geothermally active sites across the Pacific Ring of Fire. In this study, we investigate the genetic and genomic diversity, and the distribution patterns of several uncharacterized Acidithiobacillia class strains and sequence clones, which are ascribed to the same 16S rRNA gene sequence clade. By digging deeper into this data and contributing to novel MAGs emerging from environmental studies in tectonically active locations, the description of this novel genus has been consolidated. Using state-of-the-art genomic taxonomy methods, we added to already recognized taxa, an additional four novel Candidate (Ca.) species, including 'Ca. Igneacidithiobacillus chanchocoensis' (mCHCt20-1TS), 'Igneacidithiobacillus siniensis' (S30A2T), 'Ca. Igneacidithiobacillus taupoensis' (TVZ-G3 TS), and 'Ca. Igneacidithiobacillus waiarikiensis' (TVZ-G4 TS). Analysis of published data on the isolation, enrichment, cultivation, and preliminary microbiological characterization of several of these unassigned or misassigned strains, along with the type species of the genus, plus the recoverable environmental data from metagenomic studies, allowed us to identify habitat preferences of these taxa. Commonalities and lineage-specific adaptations of the seven species of the genus were derived from pangenome analysis and comparative genomic metabolic reconstruction. The findings emerging from this study lay the groundwork for further research on the ecology, evolution, and biotechnological potential of the novel genus 'Igneacidithiobacillus'.
Collapse
Affiliation(s)
- Dilanaz Arisan
- Facultad de Medicina y Ciencia, Universidad San Sebastián, Santiago, Chile
- Centro Científico y Tecnológico de Excelencia Ciencia & Vida, Santiago, Chile
| | - Ana Moya-Beltrán
- Departamento de Informática y Computación, Facultad de Ingeniería, Universidad Tecnológica Metropolitana, Santiago, Chile
| | - Camila Rojas-Villalobos
- Centro Científico y Tecnológico de Excelencia Ciencia & Vida, Santiago, Chile
- Facultad de Ingeniería, Arquitectura y Diseño, Universidad San Sebastián, Santiago, Chile
| | - Francisco Issotta
- Centro Científico y Tecnológico de Excelencia Ciencia & Vida, Santiago, Chile
- Biological Sciences Faculty, Pontifical Catholic University of Chile, Santiago, Chile
- Millennium Institute Center for Genome Regulation (CGR), Santiago, Chile
| | - Matías Castro
- Instituto Milenio de Oceanografía (IMO), Universidad de Concepción, Concepción, Chile
| | - Ricardo Ulloa
- PROBIEN (CCT Patagonia Confluencia-CONICET, UNCo), Facultad de Ingeniería, Departamento de Química, Universidad Nacional del Comahue, Neuquén, Argentina
| | - Patricia A. Chiacchiarini
- PROBIEN (CCT Patagonia Confluencia-CONICET, UNCo), Facultad de Ingeniería, Departamento de Química, Universidad Nacional del Comahue, Neuquén, Argentina
| | - Beatriz Díez
- Biological Sciences Faculty, Pontifical Catholic University of Chile, Santiago, Chile
- Millennium Institute Center for Genome Regulation (CGR), Santiago, Chile
- Center for Climate and Resilience Research (CR), Santiago, Chile
| | - Alberto J. M. Martín
- Centro Científico y Tecnológico de Excelencia Ciencia & Vida, Santiago, Chile
- Facultad de Ingeniería, Arquitectura y Diseño, Universidad San Sebastián, Santiago, Chile
| | - Iván Ñancucheo
- Facultad de Ingeniería y Tecnología, Universidad San Sebastián, Lientur, Concepción, Chile
| | - Alejandra Giaveno
- PROBIEN (CCT Patagonia Confluencia-CONICET, UNCo), Facultad de Ingeniería, Departamento de Química, Universidad Nacional del Comahue, Neuquén, Argentina
| | - D. Barrie Johnson
- College of Natural Sciences, Bangor University, Bangor, United Kingdom
- Faculty of Health and Life Sciences, Coventry University, Coventry, United Kingdom
- Natural History Museum, London, United Kingdom
| | - Raquel Quatrini
- Facultad de Medicina y Ciencia, Universidad San Sebastián, Santiago, Chile
- Centro Científico y Tecnológico de Excelencia Ciencia & Vida, Santiago, Chile
| |
Collapse
|
2
|
Marín-Paredes R, Bolívar-Torres HH, Coronel-Gaytán A, Martínez-Romero E, Servín-Garcidueñas LE. A Metagenome from a Steam Vent in Los Azufres Geothermal Field Shows an Abundance of Thermoplasmatales archaea and Bacteria from the Phyla Actinomycetota and Pseudomonadota. Curr Issues Mol Biol 2023; 45:5849-5864. [PMID: 37504286 PMCID: PMC10378326 DOI: 10.3390/cimb45070370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 07/09/2023] [Accepted: 07/10/2023] [Indexed: 07/29/2023] Open
Abstract
Los Azufres National Park is a geothermal field that has a wide number of thermal manifestations; nevertheless, the microbial communities in many of these environments remain unknown. In this study, a metagenome from a sediment sample from Los Azufres National Park was sequenced. In this metagenome, we found that the microbial diversity corresponds to bacteria (Actinomycetota, Pseudomonadota), archaea (Thermoplasmatales and Candidatus Micrarchaeota and Candidatus Parvarchaeota), eukarya (Cyanidiaceae), and viruses (Fussellovirus and Caudoviricetes). The functional annotation showed genes related to the carbon fixation pathway, sulfur metabolism, genes involved in heat and cold shock, and heavy-metal resistance. From the sediment, it was possible to recover two metagenome-assembled genomes from Ferrimicrobium and Cuniculiplasma. Our results showed that there are a large number of microorganisms in Los Azufres that deserve to be studied.
Collapse
Affiliation(s)
- Roberto Marín-Paredes
- Laboratorio de Microbiómica, Escuela Nacional de Estudios Superiores Unidad Morelia, Universidad Nacional Autónoma de México, Morelia 58341, Mexico
| | - Hermes H Bolívar-Torres
- Escuela de Ciencias Biológicas, Universidad Pedagógica y Tecnológica de Colombia, Tunja 150003, Colombia
| | - Alberto Coronel-Gaytán
- Laboratorio de Microbiómica, Escuela Nacional de Estudios Superiores Unidad Morelia, Universidad Nacional Autónoma de México, Morelia 58341, Mexico
| | | | - Luis E Servín-Garcidueñas
- Laboratorio de Microbiómica, Escuela Nacional de Estudios Superiores Unidad Morelia, Universidad Nacional Autónoma de México, Morelia 58341, Mexico
- Laboratorio Nacional de Análisis y Síntesis Ecológica, Escuela Nacional de Estudios Superiores Unidad Morelia, Morelia 58341, Mexico
| |
Collapse
|
3
|
Frolov EN, Lebedinsky AV, Elcheninov AG, Kublanov IV. Taxonomic proposal for a deep branching bacterial phylogenetic lineage: transfer of the family Thermodesulfobiaceae to Thermodesulfobiales ord. nov., Thermodesulfobiia classis nov. and Thermodesulfobiota phyl. nov. Syst Appl Microbiol 2023; 46:126388. [PMID: 36493506 DOI: 10.1016/j.syapm.2022.126388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 11/20/2022] [Accepted: 11/28/2022] [Indexed: 12/03/2022]
Abstract
The family Thermodesulfobiaceae, comprising one genus Thermodesulfobium with two validly published species, is currently assigned to order Thermoanaerobacterales within the class Clostridia of the phylum Bacillota. At the same time, the very first 16S rRNA gene sequence-based phylogenetic studies of representatives of the genus pointed out great differences between Thermodesulfobium and other members of the phylum Bacillota. Subsequent studies of new Thermodesulfobium representatives supported deep phylogenetic branching of this lineage within bacterial tree, implying that it represents a novel phylum. The results of the phylogenomic analysis performed in the frames of the present work confirm previous findings and suggest that Thermodesulfobium represents a distinct phylum-level lineage. Thus, we propose the transfer of the family Thermodesulfobiaceae to the new order Thermodesulfobiales within the new class Thermodesulfobiia and the new phylum Thermodesulfobiota.
Collapse
Affiliation(s)
- Evgenii N Frolov
- Winogradsky Institute of Microbiology, Federal Research Center of Biotechnology, Russian Academy of Sciences, 60-let Oktyabrya prospect, 7, bld. 2, 119071 Moscow, Russia.
| | - Alexander V Lebedinsky
- Winogradsky Institute of Microbiology, Federal Research Center of Biotechnology, Russian Academy of Sciences, 60-let Oktyabrya prospect, 7, bld. 2, 119071 Moscow, Russia
| | - Alexander G Elcheninov
- Winogradsky Institute of Microbiology, Federal Research Center of Biotechnology, Russian Academy of Sciences, 60-let Oktyabrya prospect, 7, bld. 2, 119071 Moscow, Russia
| | - Ilya V Kublanov
- Winogradsky Institute of Microbiology, Federal Research Center of Biotechnology, Russian Academy of Sciences, 60-let Oktyabrya prospect, 7, bld. 2, 119071 Moscow, Russia
| |
Collapse
|
4
|
Peña-Ocaña BA, Ovando-Ovando CI, Puente-Sánchez F, Tamames J, Servín-Garcidueñas LE, González-Toril E, Gutiérrez-Sarmiento W, Jasso-Chávez R, Ruíz-Valdiviezo VM. Metagenomic and metabolic analyses of poly-extreme microbiome from an active crater volcano lake. ENVIRONMENTAL RESEARCH 2022; 203:111862. [PMID: 34400165 DOI: 10.1016/j.envres.2021.111862] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 08/02/2021] [Accepted: 08/05/2021] [Indexed: 06/13/2023]
Abstract
El Chichón volcano is one of the most active volcanoes in Mexico. Previous studies have described its poly-extreme conditions and its bacterial composition, although the functional features of the complete microbiome have not been characterized yet. By using metabarcoding analysis, metagenomics, metabolomics and enzymology techniques, the microbiome of the crater lake was characterized in this study. New information is provided on the taxonomic and functional diversity of the representative Archaea phyla, Crenarchaeota and Euryarchaeota, as well as those that are representative of Bacteria, Thermotogales and Aquificae. With culture of microbial consortia and with the genetic information collected from the natural environment sampling, metabolic interactions were identified between prokaryotes, which can withstand multiple extreme conditions. The existence of a close relationship between the biogeochemical cycles of carbon and sulfur in an active volcano has been proposed, while the relationship in the energy metabolism of thermoacidophilic bacteria and archaea in this multi-extreme environment was biochemically revealed for the first time. These findings contribute towards understanding microbial metabolism under extreme conditions, and provide potential knowledge pertaining to "microbial dark matter", which can be applied to biotechnological processes and evolutionary studies.
Collapse
Affiliation(s)
- Betsy Anaid Peña-Ocaña
- Tecnologico Nacional de México / IT de Tuxtla Gutierrez, Tuxtla Gutiérrez, Chiapas, Mexico; Departamento de Bioquímica, Instituto Nacional de Cardiología, Mexico City, Mexico
| | | | - Fernando Puente-Sánchez
- Microbiome Analysis Laboratory, Systems Biology Department, Centro Nacional de Biotecnología, CSIC, Madrid, Spain; Department of Aquatic Sciences and Assessment, Swedish University for Agricultural Sciences (SLU), Lennart Hjelms väg 9, 756 51, Uppsala, Sweden
| | - Javier Tamames
- Microbiome Analysis Laboratory, Systems Biology Department, Centro Nacional de Biotecnología, CSIC, Madrid, Spain
| | | | | | | | - Ricardo Jasso-Chávez
- Departamento de Bioquímica, Instituto Nacional de Cardiología, Mexico City, Mexico.
| | | |
Collapse
|
5
|
The Microbial Composition in Circumneutral Thermal Springs from Chignahuapan, Puebla, Mexico Reveals the Presence of Particular Sulfur-Oxidizing Bacterial and Viral Communities. Microorganisms 2020; 8:microorganisms8111677. [PMID: 33137872 PMCID: PMC7692377 DOI: 10.3390/microorganisms8111677] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Revised: 09/11/2020] [Accepted: 09/17/2020] [Indexed: 12/28/2022] Open
Abstract
Terrestrial thermal springs are widely distributed globally, and these springs harbor a broad diversity of organisms of biotechnological interest. In Mexico, few studies exploring this kind of environment have been described. In this work, we explore the microbial community in Chignahuapan hot springs, which provides clues to understand these ecosystems' diversity. We assessed the diversity of the microorganism communities in a hot spring environment with a metagenomic shotgun approach. Besides identifying similarities and differences with other ecosystems, we achieved a systematic comparison against 11 metagenomic samples from diverse localities. The Chignahuapan hot springs show a particular prevalence of sulfur-oxidizing bacteria from the genera Rhodococcus, Thermomonas, Thiomonas, Acinetobacter, Sulfurovum, and Bacillus, highlighting those that are different from other recovered bacterial populations in circumneutral hot springs environments around the world. The co-occurrence analysis of the bacteria and viruses in these environments revealed that within the Rhodococcus, Thiomonas, Thermonas, and Bacillus genera, the Chignahuapan samples have specific species of bacteria with a particular abundance, such as Rhodococcus erytropholis. The viruses in the circumneutral hot springs present bacteriophages within the order Caudovirales (Siphoviridae, Myoviridae, and Podoviridae), but the family of Herelleviridae was the most abundant in Chignahuapan samples. Furthermore, viral auxiliary metabolic genes were identified, many of which contribute mainly to the metabolism of cofactors and vitamins as well as carbohydrate metabolism. Nevertheless, the viruses and bacteria present in the circumneutral environments contribute to the sulfur cycle. This work represents an exhaustive characterization of a community structure in samples collected from hot springs in Mexico and opens opportunities to identify organisms of biotechnological interest.
Collapse
|
6
|
Zhang Q, Campos M, Larama G, Acuña JJ, Valenzuela B, Solis F, Zamorano P, Araya R, Sadowsky MJ, Jorquera MA. Composition and predicted functions of the bacterial community in spouting pool sediments from the El Tatio Geyser field in Chile. Arch Microbiol 2020; 203:389-397. [PMID: 32816051 DOI: 10.1007/s00203-020-02020-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 08/03/2020] [Accepted: 08/10/2020] [Indexed: 10/23/2022]
Abstract
The El Tatio Geyser Field (ETGF), located in Northern Chile, is the main geyser field in the southern hemisphere. Despite this, details of its microbial ecology are still unknown. Here, we briefly report on the composition and predicted functions of the bacterial community in spouting pool sediments from the ETGF as revealed by high-throughput sequencing of 16S rRNA genes. Results of this analysis showed that while there were differences in richness and diversity between samples, bacterial communities were primarily dominated by the phyla Proteobacteria, followed Firmicutes, Bacteroidetes, Acidobacteria, and Chloroflexi. Analyses of predicted functional activity indicated that the functions were mostly attributed to chemoheterotrophy and aerobic chemoheterotrophy, followed by sulfur (respiration of sulfur compounds and sulfate) and nitrogen (nitrate reduction, respiration of nitrogen and nitrate) cycling. Taken together, our results suggest a high diversity in taxonomy and predictive functions of bacterial communities in sediments from spouting pools. This study provides fundamentally important information on the structure and function predictive functions of microbiota communities in spouting pools. Moreover, since the ETGF is intensively visited and impacted by tens of thousands of tourists every year, our results can be used to help guide the design of sustainable conservation strategies.
Collapse
Affiliation(s)
- Qian Zhang
- The BioTechnology Institute, University of Minnesota, 140 Gortner Lab, 1479 Gortner Ave, St Paul, MN, 55108-6106, USA
| | - Marco Campos
- Laboratorio de Ecología Microbiana Aplicada (EMALAB), Departamento de Ciencias Químicas y Recursos Naturales, Universidad de La Frontera, Ave. Francisco Salazar 01145, Temuco, Chile.,Network for Extreme Environment Research (NEXER), Scientific and Technological Bioresource Nucleus (BIOREN), Universidad de La Frontera, Ave. Francisco Salazar 01145, Temuco, Chile
| | - Giovanni Larama
- Laboratorio de Ecología Microbiana Aplicada (EMALAB), Departamento de Ciencias Químicas y Recursos Naturales, Universidad de La Frontera, Ave. Francisco Salazar 01145, Temuco, Chile.,Network for Extreme Environment Research (NEXER), Scientific and Technological Bioresource Nucleus (BIOREN), Universidad de La Frontera, Ave. Francisco Salazar 01145, Temuco, Chile
| | - Jacquelinne J Acuña
- Laboratorio de Ecología Microbiana Aplicada (EMALAB), Departamento de Ciencias Químicas y Recursos Naturales, Universidad de La Frontera, Ave. Francisco Salazar 01145, Temuco, Chile.,Network for Extreme Environment Research (NEXER), Scientific and Technological Bioresource Nucleus (BIOREN), Universidad de La Frontera, Ave. Francisco Salazar 01145, Temuco, Chile
| | - Bernardita Valenzuela
- Laboratorio de Extremófilos, Instituto Antofagasta, Universidad de Antofagasta, Av. Angamos 601, Antofagasta, Chile
| | - Francisco Solis
- Laboratorio de Extremófilos, Instituto Antofagasta, Universidad de Antofagasta, Av. Angamos 601, Antofagasta, Chile
| | - Pedro Zamorano
- Laboratorio de Extremófilos, Instituto Antofagasta, Universidad de Antofagasta, Av. Angamos 601, Antofagasta, Chile.,Departamento Biomédico, Universidad de Antofagasta, Antofagasta, Chile
| | - Rubén Araya
- Instituto de Ciencias Naturales Alexander von Humboldt, Universidad de Antofagasta, Av. Angamos 601, Antofagasta, Chile
| | - Michael J Sadowsky
- The BioTechnology Institute, University of Minnesota, 140 Gortner Lab, 1479 Gortner Ave, St Paul, MN, 55108-6106, USA.,Department of Soil, Water, and Climate, and Department of Plant and Microbial Biology, University of Minnesota, 439 Borlaug Hall 1991 Upper Buford Circle, St. Paul, MN, 55108, USA
| | - Milko A Jorquera
- Laboratorio de Ecología Microbiana Aplicada (EMALAB), Departamento de Ciencias Químicas y Recursos Naturales, Universidad de La Frontera, Ave. Francisco Salazar 01145, Temuco, Chile. .,Network for Extreme Environment Research (NEXER), Scientific and Technological Bioresource Nucleus (BIOREN), Universidad de La Frontera, Ave. Francisco Salazar 01145, Temuco, Chile.
| |
Collapse
|
7
|
Brito EMS, Rodríguez-Galván M, Hernández-Espino LG, Caretta CA, Goñi-Urriza M, Malm O, Torres JPM, Guyoneaud R. Prospecting bacterial consortia from a geothermal site for metals biotransformation. Biodegradation 2020; 31:235-247. [PMID: 32676947 DOI: 10.1007/s10532-020-09906-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Accepted: 07/01/2020] [Indexed: 11/30/2022]
Abstract
Biomats that flourished in a fumarole located on the geothermal site Los Azufres (Mexico) were used as inocula to select aerobic and sulfate-reducing bacteria consortia for studying their capacity to reduce hexavalent chromium [Cr(VI)], aiming to use these consortia in biotransformation technologies. The sample site is characterized by slightly warm (nearly 27 [Formula: see text]C), acid (pH 3) and about hypoxic (1.8 mg L[Formula: see text] of dissolved oxygen) conditions. Four culture systems (2 aerobic and 2 anaerobic) were investigated, including their enzymatic activity, capacity to produce biofilms, and an analysis of the total bacterial populations. For the anaerobic condition (using sulfate and sulfur as electron acceptors), four pH values (from 2 to 8) and four carbon sources (pyruvate, glycerol, Na-lactate and Na-acetate) were probed. Significant biological Cr(VI) removal was observed for all the pH values probed, particularly during the first 12 h, being more effective at the most acid conditions. At a pH value of 4 and using pyruvate as carbon source, 100 mg L[Formula: see text] of Cr(VI) were completely depleted in less than 12 h, while the use of Na-lactate was less effective but still reasonable. These results indicate that sulfate-reducing bacteria consortia from geothermal sites like the one studied here are capable of biotransforming Cr(VI) and have the potential to provide metal bioremediation technologies.
Collapse
Affiliation(s)
- E M S Brito
- Environmental Microbiology and Applied Molecular Biology Lab., Dept. Environmental Eng., DI-CGT, Universidad de Guanajuato (UG), Guanajuato, Mexico
| | - M Rodríguez-Galván
- Environmental Microbiology and Applied Molecular Biology Lab., Dept. Environmental Eng., DI-CGT, Universidad de Guanajuato (UG), Guanajuato, Mexico
| | - L G Hernández-Espino
- Environmental Microbiology and Applied Molecular Biology Lab., Dept. Environmental Eng., DI-CGT, Universidad de Guanajuato (UG), Guanajuato, Mexico
| | - C A Caretta
- Dept. of Astronomy, DCNE-CGT, Universidad de Guanajuato (UG), Guanajuato, Mexico.
| | - M Goñi-Urriza
- Environmental Microbiology Group, EEM-UMR IPREM 5254, Université de Pau et des Pays de l'Adour (UPPA), Pau, France
| | - O Malm
- Radioisotopes Lab. (LREPF), IBCCF, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - J P M Torres
- Micropollutants Lab., IBCCF, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - R Guyoneaud
- Environmental Microbiology Group, EEM-UMR IPREM 5254, Université de Pau et des Pays de l'Adour (UPPA), Pau, France
| |
Collapse
|
8
|
Massello FL, Chan CS, Chan KG, Goh KM, Donati E, Urbieta MS. Meta-Analysis of Microbial Communities in Hot Springs: Recurrent Taxa and Complex Shaping Factors beyond pH and Temperature. Microorganisms 2020; 8:microorganisms8060906. [PMID: 32560103 PMCID: PMC7356817 DOI: 10.3390/microorganisms8060906] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Revised: 06/05/2020] [Accepted: 06/09/2020] [Indexed: 11/16/2022] Open
Abstract
The study of microbial communities from extreme environments is a fascinating topic. With every study, biologists and ecologists reveal interesting facts and questions that dispel the old belief that these are inhospitable environments. In this work, we assess the microbial diversity of three hot springs from Neuquén, Argentina, using high-throughput amplicon sequencing. We predicted a distinct metabolic profile in the acidic and the circumneutral samples, with the first ones being dominated by chemolithotrophs and the second ones by chemoheterotrophs. Then, we collected data of the microbial communities of hot springs around the world in an effort to comprehend the roles of pH and temperature as shaping factors. Interestingly, there was a covariation between both parameters and the phylogenetic distance between communities; however, neither of them could explain much of the microbial profile in an ordination model. Moreover, there was no correlation between alpha diversity and these parameters. Therefore, the microbial communities' profile seemed to have complex shaping factors beyond pH and temperature. Lastly, we looked for taxa associated with different environmental conditions. Several such taxa were found. For example, Hydrogenobaculum was frequently present in acidic springs, as was the Sulfolobaceae family; on the other hand, Candidatus Hydrothermae phylum was strongly associated with circumneutral conditions. Interestingly, some singularities related to sites featuring certain taxa were also observed.
Collapse
Affiliation(s)
- Francisco L. Massello
- CINDEFI (CCT, La Plata-CONICET, UNLP), Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, 1900 Buenos Aires, Argentina; (F.L.M.); (E.D.)
| | - Chia Sing Chan
- Faculty of Biosciences and Medical Engineering, Universiti Teknologi Malaysia, Skudai 81310, Malaysia; (C.S.C.); (K.M.G.)
| | - Kok-Gan Chan
- Division of Genetics and Molecular Biology, Faculty of Science, Institute of Biological Sciences, University of Malaya, Kuala Lumpur 50603, Malaysia;
| | - Kian Mau Goh
- Faculty of Biosciences and Medical Engineering, Universiti Teknologi Malaysia, Skudai 81310, Malaysia; (C.S.C.); (K.M.G.)
| | - Edgardo Donati
- CINDEFI (CCT, La Plata-CONICET, UNLP), Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, 1900 Buenos Aires, Argentina; (F.L.M.); (E.D.)
| | - María Sofía Urbieta
- CINDEFI (CCT, La Plata-CONICET, UNLP), Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, 1900 Buenos Aires, Argentina; (F.L.M.); (E.D.)
- Correspondence:
| |
Collapse
|
9
|
Analysis of the Microbiome (Bathing Biome) in Geothermal Waters from an Australian Balneotherapy Centre. WATER 2020. [DOI: 10.3390/w12061705] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Balneotherapy is an ancient practice which remains commonplace throughout the world due to perceived health benefits that include relief of arthritis, fibromyalgia and relaxation. However, bathing environments are not sterile and natural spring waters may harbour natural microbial populations that include potential pathogens. We elucidated the microbial community from water taken from the borehole, pre-filter water (chlorinated, cold and post-bathing water) and post-filter water at a commercial Australian natural hot spring bathing facility. Thiobacillus, Sphingobium and Agrobacterium were the predominant genera in samples collected from the borehole. The predominant genera changed to Sphingobium, Parvibaculum and Achromobacter following chloride treatment and Azospira replaced the Achromobacter once the water reached ambient temperature and was stored ready to be used by bathers. The microbial community changed again following use by bathers, dominated by Pseudomonas, although Sphingobium persisted. No total or faecal coliforms were observed in any of the samples except for the post-bathing water; even there, their presence was at very low concentration (2.3 cfu/mL). These results confirm the lack of pathogens present in these hot spring waters but also suggests that good management of post-bathing water is required especially if the water is used for borehole water recharge.
Collapse
|
10
|
Willis G, Nancucheo I, Hedrich S, Giaveno A, Donati E, Johnson DB. Enrichment and isolation of acid-tolerant sulfate-reducing microorganisms in the anoxic, acidic hot spring sediments from Copahue volcano, Argentina. FEMS Microbiol Ecol 2020; 95:5610214. [PMID: 31665270 DOI: 10.1093/femsec/fiz175] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 10/28/2019] [Indexed: 01/21/2023] Open
Abstract
The geothermal Copahue-Caviahue (GCC) system (Argentina) is an extreme acidic environment, dominated by the activity of Copahue volcano. Environments characterised by low pH values, such as volcanic areas, are of particular interest for the search of acidophilic microorganisms with application in biotechnological processes. In this work, sulfate-reducing microorganisms were investigated in geothermal acidic, anaerobic zones from GCC system. Sediment samples from Agua del Limón (AL1), Las Máquinas (LMa2), Las Maquinitas (LMi) and Baño 9 (B9-2, B9-3) were found to be acidic (pH values 2.1-3.0) to moderate acidic (5.1-5.2), containing small total organic carbon values, and ferric iron precipitates. The organic electron donor added to the enrichment was completely oxidised to CO2. Bacteria related to 'Desulfobacillus acidavidus' strain CL4 were found to be dominant (67-83% of the total number of clones) in the enrichment cultures, and their presence was confirmed by their isolation on overlay plates. Other bacteria were also detected with lower abundance (6-20% of the total number of clones), with representatives of the genera Acidithiobacillus, Sulfobacillus, Alicyclobacillus and Athalassotoga/Mesoaciditoga. These enrichment and isolates found at low pH confirm the presence of anaerobic activities in the acidic sediments from the geothermal Copahue-Caviahue system.
Collapse
Affiliation(s)
- Graciana Willis
- CINDEFI (CONICET-UNLP), Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Calle 47 y 115, 1900 La Plata, Argentina
| | - Ivan Nancucheo
- Facultad de Ingeniería y Tecnología, Universidad San Sebastián, Lientur 1457, Concepción 4080871, Chile
| | - Sabrina Hedrich
- Federal Institute for Geosciences and Natural Resources, Resource Geochemistry, Stilleweg 2, 30655 Hannover, Germany
| | - Alejandra Giaveno
- PROBIEN (CONICET-UNCo), Departamento de Química, Facultad de Ingeniería, Universidad Nacional del Comahue, Buenos Aires 1400, 8300 Neuquén, Argentina
| | - Edgardo Donati
- CINDEFI (CONICET-UNLP), Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Calle 47 y 115, 1900 La Plata, Argentina
| | - David Barrie Johnson
- School of Natural Sciences, Bangor University, Deiniol Road, Bangor, LL57 2UW, UK
| |
Collapse
|
11
|
An integrated microbiological and electrochemical approach to determine distributions of Fe metabolism in acid mine drainage-induced "iron mound" sediments. PLoS One 2019; 14:e0213807. [PMID: 30913215 PMCID: PMC6435174 DOI: 10.1371/journal.pone.0213807] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Accepted: 02/28/2019] [Indexed: 11/21/2022] Open
Abstract
Fe(III)-rich deposits referred to as “iron mounds” develop when Fe(II)-rich acid mine drainage (AMD) emerges at the terrestrial surface, and aeration of the fluids induces oxidation of Fe(II), with subsequent precipitation of Fe(III) phases. As Fe(III) phases accumulate in these systems, O2 gradients may develop in the sediments and influence the distributions and extents of aerobic and anaerobic microbiological Fe metabolism, and in turn the solubility of Fe. To determine how intrusion of O2 into iron mound sediments influences microbial community composition and Fe metabolism, we incubated samples of these sediments in a column format. O2 was only supplied through the top of the columns, and microbiological, geochemical, and electrochemical changes at discrete depths were determined with time. Despite the development of dramatic gradients in dissolved Fe(II) concentrations, indicating Fe(II) oxidation in shallower portions and Fe(III) reduction in the deeper portions, microbial communities varied little with depth, suggesting the metabolic versatility of organisms in the sediments with respect to Fe metabolism. Additionally, the availability of O2 in shallow portions of the sediments influenced Fe metabolism in deeper, O2-free sediments. Total potential (EH + self-potential) measurements at discrete depths in the columns indicated that Fe transformations and electron transfer processes were occurring through the sediments and could explain the impact of O2 on Fe metabolism past where it penetrates into the sediments. This work shows that O2 availability (or lack of it) minimally influences microbial communities, but influences microbial activities beyond its penetration depth in AMD-derived Fe(III) rich sediments. Our results indicate that O2 can modulate Fe redox state and solubility in larger volumes of iron mound sediments than only those directly exposed to O2.
Collapse
|
12
|
Brito EMS, Romero-Núñez VM, Caretta CA, Bertin P, Valerdi-Negreros JC, Guyoneaud R, Goñi-Urriza M. The bacterial diversity on steam vents from Paricutín and Sapichu volcanoes. Extremophiles 2019; 23:249-263. [PMID: 30712189 DOI: 10.1007/s00792-019-01078-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2018] [Accepted: 01/22/2019] [Indexed: 01/30/2023]
Abstract
Vapor steam vents are prevailing structures on geothermal sites in which local geochemical conditions allow the development of extremophilic microorganisms. We describe the structure of the prokaryotic community able to grow on the walls and rocks of such microecosystems in two terrestrial Mexican volcanoes: Paricutín (PI and PII samples) and its satellite Sapichu (S sample). The investigated samples showed similar diversity indices, with few dominant OTUs (abundance > 1%): 21, 16 and 23, respectively for PI, PII and S. However, each steam vent showed a particular community profile: PI was dominated by photosynthetic bacteria (Cyanobacteria and Chloroflexia class), PII by Actinobacteria and Proteobacteria, and S by Ktedonobacteria class, Acidobacteria and Cyanobacteria phyla. Concerning the predicted metabolic potential, we found a dominance of cellular pathways, especially the ones for energy generation with metabolisms for sulfur respiration, nitrogen fixation, methanogenesis, carbon fixation, photosynthesis, and metals, among others. We suggest a different maturity stage for the three studied fumaroles, from the youngest (PI) to the oldest (S and PII), also influenced by the temperature and other geochemical parameters. Furthermore, four anaerobic strains were isolated, belonging to Clostridia class (Clostridium sphenoides, C. swellfunanium and Anaerocolumna cellulosilytica) and to Bacilli class (Paenibacillus azoreducens).
Collapse
Affiliation(s)
| | - Víctor Manuel Romero-Núñez
- Ingeniería Ambiental, División de Ingenierías (CGT), Universidad de Guanajuato, Guanajuato, Gto., Mexico
| | - César Augusto Caretta
- Departamento de Astronomía, División de Ciencias Naturales y Exactas (CGT), Universidad de Guanajuato, Guanajuato, Gto., Mexico
| | - Pierre Bertin
- Equipe Génomique, Structure et Traduction, Inst. Biologie Intégrative de la Cellule (I2BC) CNRS-UMR9198, Universitè Paris-Sud, 91405, Orsay Cedex, France
| | | | - Rémy Guyoneaud
- CNRS/Universitè de Pau et des Pays de l'Adour/E2S, Institut des Sciences Analytiques et de Physicochimie pour l'Environnement et les Matériaux, Environmental Microbiology Group, UMR 5254, 64000, Pau, France
| | - Marisol Goñi-Urriza
- CNRS/Universitè de Pau et des Pays de l'Adour/E2S, Institut des Sciences Analytiques et de Physicochimie pour l'Environnement et les Matériaux, Environmental Microbiology Group, UMR 5254, 64000, Pau, France
| |
Collapse
|
13
|
Rüffel V, Maar M, Dammbrück MN, Hauröder B, Neu TR, Meier J. Thermodesulfobium sp. strain 3baa, an acidophilic sulfate reducing bacterium forming biofilms triggered by mineral precipitation. Environ Microbiol 2018; 20:3717-3731. [PMID: 30105784 DOI: 10.1111/1462-2920.14374] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Revised: 08/01/2018] [Accepted: 08/05/2018] [Indexed: 01/22/2023]
Abstract
Sulfate reducing prokaryotes are promising candidates for the remediation of acidic metal-rich waste waters. However, only few acidophilic species have been described to date. Chemolithoautotrophic strain 3baa was isolated from sediments of an acidic mine pit lake. Based on its 16S-rRNA gene sequence it belongs to the genus Thermodesulfobium. It was identified as an acidophile growing in artificial pore water medium in the range of pH 2.6-6.6. Though the highest sulfate reduction rates were obtained at the lower end of this range, elongated cells and extended lag phases demonstrated acid stress. Sulfate reduction at low pH was accompanied by the formation of mineral precipitates strongly adhering to solid surfaces. A structural investigation by laser scanning microscopy, electron microscopy and X-ray microanalysis revealed the formation of Al hydroxides and Fe sulfides which were densely populated by cells. Al hydroxides precipitated first, enabling initial cell attachment. Colonization of solid surfaces coincided with increased sulfate reducing activity indicating more favourable growth conditions within biofilms compared with free-living cells. These findings point out the importance of cell-mineral interaction for biofilm formation and contribute to our understanding how sulfate reducing prokaryotes thrive in both natural and engineered systems at low pH.
Collapse
Affiliation(s)
- Viola Rüffel
- Institute for Integrated Natural Sciences, University Koblenz-Landau, 56070, Koblenz, Germany
| | - Mona Maar
- Institute for Integrated Natural Sciences, University Koblenz-Landau, 56070, Koblenz, Germany
| | - Markus N Dammbrück
- Institute for Integrated Natural Sciences, University Koblenz-Landau, 56070, Koblenz, Germany
| | - Bärbel Hauröder
- Department of Pathology, Electron Microscopy, Bundeswehr Central Hospital Coblenz, 56070, Koblenz, Germany
| | - Thomas R Neu
- Department of River Ecology, Helmholtz Centre of Environmental Research - UFZ, 39114, Magdeburg, Germany
| | - Jutta Meier
- Institute for Integrated Natural Sciences, University Koblenz-Landau, 56070, Koblenz, Germany
| |
Collapse
|
14
|
Prieto-Barajas CM, Valencia-Cantero E, Santoyo G. Microbial mat ecosystems: Structure types, functional diversity, and biotechnological application. ELECTRON J BIOTECHN 2018. [DOI: 10.1016/j.ejbt.2017.11.001] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
|
15
|
Prieto-Barajas CM, Alfaro-Cuevas R, Valencia-Cantero E, Santoyo G. Effect of seasonality and physicochemical parameters on bacterial communities in two hot spring microbial mats from Araró, Mexico. REV MEX BIODIVERS 2017. [DOI: 10.1016/j.rmb.2017.07.010] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
|
16
|
Bacterial diversity in fumarole environments of the Paricutín volcano, Michoacán (Mexico). Extremophiles 2017; 21:499-511. [DOI: 10.1007/s00792-017-0920-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2016] [Accepted: 02/13/2017] [Indexed: 10/20/2022]
|
17
|
An overview of siderophores for iron acquisition in microorganisms living in the extreme. Biometals 2016; 29:551-71. [PMID: 27457587 DOI: 10.1007/s10534-016-9949-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Accepted: 07/08/2016] [Indexed: 12/11/2022]
Abstract
Siderophores are iron-chelating molecules produced by microbes when intracellular iron concentrations are low. Low iron triggers a cascade of gene activation, allowing the cell to survive due to the synthesis of important proteins involved in siderophore synthesis and transport. Generally, siderophores are classified by their functional groups as catecholates, hydroxamates and hydroxycarboxylates. Although other chemical structural modifications and functional groups can be found. The functional groups participate in the iron-chelating process when the ferri-siderophore complex is formed. Classified as acidophiles, alkaliphiles, halophiles, thermophiles, psychrophiles, piezophiles, extremophiles have particular iron requirements depending on the environmental conditions in where they grow. Most of the work done in siderophore production by extremophiles is based in siderophore concentration and/or genomic studies determining the presence of siderophore synthesis and transport genes. Siderophores produced by extremophiles are not well known and more work needs to be done to elucidate chemical structures and their role in microorganism survival and metal cycling in extreme environments.
Collapse
|
18
|
Florentino AP, Brienza C, Stams AJM, Sánchez-Andrea I. Desulfurella amilsii sp. nov., a novel acidotolerant sulfur-respiring bacterium isolated from acidic river sediments. Int J Syst Evol Microbiol 2015; 66:1249-1253. [PMID: 26704766 DOI: 10.1099/ijsem.0.000866] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel acidotolerant and moderately thermophilic sulfur-reducing bacterium was isolated from sediments of the Tinto River (Spain), an extremely acidic environment. Strain TR1T stained Gram-negative, and was obligately anaerobic, non-spore-forming and motile. Cells were short rods (1.5-2 × 0.5-0.7 μm), appearing singly or in pairs. Strain TR1T was catalase-negative and slightly oxidase-positive. Urease activity and indole formation were absent, but gelatin hydrolysis was present. Growth was observed at 20-52 °C with an optimum close to 50 °C, and a pH range of 3-7 with optimum between pH 6 and 6.5. Yeast extract was essential for growth, but extra vitamins were not required. In the presence of sulfur, strain TR1T grew with acetate, formate, lactate, pyruvate, stearate, arginine and H2/CO2. All substrates were completely oxidized and H2S and CO2 were the only metabolic products detected. Besides elemental sulfur, thiosulfate was used as an electron acceptor. The isolate also grew by disproportionation of elemental sulfur. The predominant cellular fatty acids were saturated components: C16 : 0, anteiso-C17 : 0 and C18 : 0. The only quinone component detected was menaquinone MK-7(H2). The G+C content of the genomic DNA was 34 mol%. The isolate is affiliated to the genus Desulfurella of the class Deltaproteobacteria, sharing 97 % 16S rRNA gene sequence similarity with the four species described in the genus Desulfurella. Considering the distinct physiological and phylogenetic characteristics, strain TR1T represents a novel species within the genus Desulfurella, for which the name Desulfurella amilsii sp. nov. is proposed. The type strain is TR1T ( = DSM 29984T = JCM 30680T).
Collapse
Affiliation(s)
- Anna P Florentino
- Laboratory of Microbiology, Wageningen University, Dreijenplein 10, 6703 HB Wageningen, The Netherlands.,Sub-department of Environmental Technology, Wageningen University, Bornse Weilanden 9, 6708 WG Wageningen, The Netherlands
| | - Claudio Brienza
- Laboratory of Microbiology, Wageningen University, Dreijenplein 10, 6703 HB Wageningen, The Netherlands
| | - Alfons J M Stams
- Laboratory of Microbiology, Wageningen University, Dreijenplein 10, 6703 HB Wageningen, The Netherlands.,CEB-Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - Irene Sánchez-Andrea
- Laboratory of Microbiology, Wageningen University, Dreijenplein 10, 6703 HB Wageningen, The Netherlands
| |
Collapse
|
19
|
Florentino AP, Weijma J, Stams AJM, Sánchez-Andrea I. Sulfur Reduction in Acid Rock Drainage Environments. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2015; 49:11746-55. [PMID: 26356416 DOI: 10.1021/acs.est.5b03346] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Microbiological suitability of acidophilic sulfur reduction for metal recovery was explored by enriching sulfur reducers from acidic sediments at low pH (from 2 to 5) with hydrogen, glycerol, methanol and acetate as electron donors at 30 °C. The highest levels of sulfide in the enrichments were detected at pH 3 with hydrogen and pH 4 with acetate. Cloning and sequencing of the 16S rRNA gene showed dominance of the deltaproteobacterial sulfur-reducing genus Desulfurella in all the enrichments and subsequently an acidophilic strain (TR1) was isolated. Strain TR1 grew at a broad range of pH (3-7) and temperature (20-50 °C) and showed good metal tolerance (Pb(2+), Zn(2+), Cu(2+), Ni(2+)), especially for Ni(2+) and Pb(2+), with maximal tolerated concentrations of 0.09 and 0.03 mM, respectively. Different sources of sulfur were tested in the enrichments, from which biosulfur showed fastest growth (doubling time of 1.9 days), followed by colloidal, chemical and sublimated sulfur (doubling times of 2.2, 2.5, and 3.6 days, respectively). Strain TR1's physiological traits make it a good candidate to cope with low pH and high metal concentration in biotechnological processes for treatment of metal-laden acidic streams at low and moderately high temperature.
Collapse
Affiliation(s)
- Anna P Florentino
- Laboratory of Microbiology, Wageningen University , Stippeneng 4, 6708 WE Wageningen, The Netherlands
- Sub-department of Environmental Technology, Wageningen University , Bornse Weilanden 9, 6708 WG Wageningen, The Netherlands
| | - Jan Weijma
- Sub-department of Environmental Technology, Wageningen University , Bornse Weilanden 9, 6708 WG Wageningen, The Netherlands
| | - Alfons J M Stams
- Laboratory of Microbiology, Wageningen University , Stippeneng 4, 6708 WE Wageningen, The Netherlands
- CEB-Centre of Biological Engineering, University of Minho, Campus de Gualtar , 4710-057, Braga, Portugal
| | - Irene Sánchez-Andrea
- Laboratory of Microbiology, Wageningen University , Stippeneng 4, 6708 WE Wageningen, The Netherlands
| |
Collapse
|