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Mehić S, Saltikov C. Genome sequence and characterisation of a freshwater photoarsenotroph, Cereibacter azotoformans strain ORIO, isolated from sediments capable of cyclic light-dark arsenic oxidation and reduction. Environ Microbiol 2023; 25:3738-3752. [PMID: 37974504 DOI: 10.1111/1462-2920.16542] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 11/01/2023] [Indexed: 11/19/2023]
Abstract
A freshwater photosynthetic arsenite-oxidizing bacterium, Cereibacter azotoformans strain ORIO, was isolated from Owens River, CA, USA. The waters from Owens River are elevated in arsenic and serve as the headwaters to the Los Angeles Aqueduct. The complete genome sequence of strain ORIO is 4.8 Mb genome (68% G + C content) and comprises two chromosomes and six plasmids. Taxonomic analysis placed ORIO within the Cereibacter genus (formerly Rhodobacter). The ORIO genome contains arxB2 AB1 CD (encoding an arsenite oxidase), arxXSR (regulators) and several ars arsenic resistance genes all co-localised on a 136 kb plasmid, named pORIO3. Phylogenetic analysis of ArxA, the molybdenum-containing arsenite oxidase catalytic subunit, demonstrated photoarsenotrophy is likely to occur within members of the Alphaproteobacteria. ORIO is a mixotroph, oxidises arsenite to arsenate (As(V)) photoheterotrophically, and expresses arxA in cultures grown with arsenite. Further ecophysiology studies with Owens River sediment demonstrated the interconversion of arsenite and As(V) was dependent on light-dark cycling. arxA and arrA (As(V) respiratory reductase) genes were detected in the light-dark cycled sediment metagenomes suggesting syntrophic interactions among arsenotrophs. This work establishes C. azotoformans str. ORIO as a new model organism for studying photoarsenotrophy and light-dark arsenic biogeochemical cycling.
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Affiliation(s)
- Sanjin Mehić
- Department of Microbiology and Environmental Toxicology, University of California Santa Cruz, Santa Cruz, California, USA
| | - Chad Saltikov
- Department of Microbiology and Environmental Toxicology, University of California Santa Cruz, Santa Cruz, California, USA
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2
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Barbosa C, Tamayo-Leiva J, Alcorta J, Salgado O, Daniele L, Morata D, Díez B. Effects of hydrogeochemistry on the microbial ecology of terrestrial hot springs. Microbiol Spectr 2023; 11:e0024923. [PMID: 37754764 PMCID: PMC10581198 DOI: 10.1128/spectrum.00249-23] [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: 01/19/2023] [Accepted: 07/13/2023] [Indexed: 09/28/2023] Open
Abstract
Temperature, pH, and hydrochemistry of terrestrial hot springs play a critical role in shaping thermal microbial communities. However, the interactions of biotic and abiotic factors at this terrestrial-aquatic interface are still not well understood on a global scale, and the question of how underground events influence microbial communities remains open. To answer this, 11 new samples obtained from the El Tatio geothermal field were analyzed by 16S rRNA amplicon sequencing (V4 region), along with 191 samples from previous publications obtained from the Taupo Volcanic Zone, the Yellowstone Plateau Volcanic Field, and the Eastern Tibetan Plateau, with their temperature, pH, and major ion concentration. Microbial alpha diversity was lower in acid-sulfate waters, and no significant correlations were found with temperature. However, moderate correlations were observed between chemical parameters such as pH (mostly constrained to temperatures below 70°C), SO4 2- and abundances of members of the phyla Armatimonadota, Deinococcota, Chloroflexota, Campilobacterota, and Thermoplasmatota. pH and SO4 2- gradients were explained by phase separation of sulfur-rich hydrothermal fluids and oxidation of reduced sulfur in the steam phase, which were identified as key processes shaping these communities. Ordination and permutational analysis of variance showed that temperature, pH, and major element hydrochemistry explain only 24% of the microbial community structure. Therefore, most of the variance remained unexplained, suggesting that other environmental or biotic factors are also involved and highlighting the environmental complexity of the ecosystem and its great potential to test niche theory ecological associated questions. IMPORTANCE This is the first approach to investigate whether geothermal processes could have an influence on the ecology of thermal microbial communities on a global scale. In addition to temperature and pH, microbial communities are structured by sulfate concentrations, which depends on the tectono-magmatic settings (such as the depth of magmatic chambers) and the local settings (such as the availability of a confining layer separating NaCl waters from steam after phase separation) and the possibility of mixing with more diluted fluids. Comparison of microbial communities from different geothermal areas by homogeneous sequence processing showed that no significant geographic distance decay was detected on the microbial communities according to Bray-Curtis, Jaccard, unweighted, and weighted Unifrac similarity/dissimilarity indices. Instead, an ancient potential divergence in the same taxonomic groups is suggested between globally distant thermal zones.
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Affiliation(s)
- Carla Barbosa
- Department of Geology, University of Chile, Santiago, Chile
- Andean Geothermal Center of Excellence (CEGA-Fondap), University of Chile, Santiago, Chile
| | - Javier Tamayo-Leiva
- Department of Molecular Genetics and Microbiology, Pontifical Catholic University of Chile, Santiago, Chile
- Center for Climate and Resilience Research (CR)2, University of Chile, Santiago, Chile
- Millennium Institute Center of Genome Regulation (CGR), Santiago, Chile
| | - Jaime Alcorta
- Department of Molecular Genetics and Microbiology, Pontifical Catholic University of Chile, Santiago, Chile
- Millennium Institute Center of Genome Regulation (CGR), Santiago, Chile
| | - Oscar Salgado
- Department of Molecular Genetics and Microbiology, Pontifical Catholic University of Chile, Santiago, Chile
- Laboratorio de Bioinformática, Facultad de Educación, Universidad Adventista de Chile, Chillán, Chile
| | - Linda Daniele
- Department of Geology, University of Chile, Santiago, Chile
- Andean Geothermal Center of Excellence (CEGA-Fondap), University of Chile, Santiago, Chile
| | - Diego Morata
- Department of Geology, University of Chile, Santiago, Chile
- Andean Geothermal Center of Excellence (CEGA-Fondap), University of Chile, Santiago, Chile
| | - Beatríz Díez
- Department of Molecular Genetics and Microbiology, Pontifical Catholic University of Chile, Santiago, Chile
- Center for Climate and Resilience Research (CR)2, University of Chile, Santiago, Chile
- Millennium Institute Center of Genome Regulation (CGR), Santiago, Chile
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3
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Colman DR, Lindsay MR, Harnish A, Bilbrey EM, Amenabar MJ, Selensky MJ, Fecteau KM, Debes RV, Stott MB, Shock EL, Boyd ES. Seasonal hydrologic and geologic forcing drive hot spring geochemistry and microbial biodiversity. Environ Microbiol 2021; 23:4034-4053. [PMID: 34111905 DOI: 10.1111/1462-2920.15617] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 05/10/2021] [Accepted: 05/29/2021] [Indexed: 01/31/2023]
Abstract
Hot springs integrate hydrologic and geologic processes that vary over short- and long-term time scales. However, the influence of temporal hydrologic and geologic change on hot spring biodiversity is unknown. Here, we coordinated near-weekly, cross-seasonal (~140 days) geochemical and microbial community analyses of three widely studied hot springs with local precipitation data in Yellowstone National Park. One spring ('HFS') exhibited statistically significant, coupled microbial and geochemical variation across seasons that was associated with recent precipitation patterns. Two other spring communities, 'CP' and 'DS', exhibited minimal to no variation across seasons. Variability in the seasonal response of springs is attributed to differences in the timing and extent of aquifer recharge with oxidized near-surface water from precipitation. This influx of oxidized water is associated with changes in community composition, and in particular, the abundances of aerobic sulfide-/sulfur-oxidizers that can acidify waters. During sampling, a new spring formed after a period of heavy precipitation and its successional dynamics were also influenced by surface water recharge. Collectively, these results indicate that changes in short-term hydrology associated with precipitation can impact hot spring geochemistry and microbial biodiversity. These results point to potential susceptibility of certain hot springs and their biodiversity to sustained, longer-term hydrologic changes.
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Affiliation(s)
- Daniel R Colman
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT, 59717, USA
| | - Melody R Lindsay
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT, 59717, USA
| | - Annette Harnish
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT, 59717, USA
| | - Evan M Bilbrey
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT, 59717, USA
| | - Maximiliano J Amenabar
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT, 59717, USA
| | - Matthew J Selensky
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT, 59717, USA
| | | | - Randall V Debes
- School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287, USA
| | - Matthew B Stott
- School of Biological Sciences, University of Canterbury, Christchurch, 8140, New Zealand
| | - Everett L Shock
- School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287, USA.,School of Earth and Space Exploration, Arizona State University, Tempe, AZ, 85287, USA
| | - Eric S Boyd
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT, 59717, USA
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4
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Palmer M, Hedlund BP, Roux S, Tsourkas PK, Doss RK, Stamereilers C, Mehta A, Dodsworth JA, Lodes M, Monsma S, Glavina del Rio T, Schoenfeld TW, Eloe-Fadrosh EA, Mead DA. Diversity and Distribution of a Novel Genus of Hyperthermophilic Aquificae Viruses Encoding a Proof-Reading Family-A DNA Polymerase. Front Microbiol 2020; 11:583361. [PMID: 33281778 PMCID: PMC7689252 DOI: 10.3389/fmicb.2020.583361] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 10/16/2020] [Indexed: 12/27/2022] Open
Abstract
Despite the high abundance of Aquificae in many geothermal systems, these bacteria are difficult to culture and no viruses infecting members of this phylum have been isolated. Here, we describe the complete, circular dsDNA Uncultivated Virus Genome (UViG) of Thermocrinis Octopus Spring virus (TOSV), derived from metagenomic data, along with eight related UViGs representing three additional viral species. Despite low overall similarity among viruses from different hot springs, the genomes shared a high degree of synteny, and encoded numerous genes for nucleotide metabolism, including a PolA-type DNA polymerase polyprotein with likely accessory functions, a DNA Pol III sliding clamp, a thymidylate kinase, a DNA gyrase, a helicase, and a DNA methylase. Also present were conserved genes predicted to code for phage capsid, large and small subunits of terminase, portal protein, holin, and lytic transglycosylase, all consistent with a distant relatedness to cultivated Caudovirales. These viruses are predicted to infect Aquificae, as multiple CRISPR spacers matching the viral genomes were identified within the genomes and metagenomic contigs from these bacteria. Based on the predicted atypical bi-directional replication strategy, low sequence similarity to known viral genomes, and unique position in gene-sharing networks, we propose a new putative genus, "Pyrovirus," in the order Caudovirales.
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Affiliation(s)
- Marike Palmer
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, NV, United States
| | - Brian P. Hedlund
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, NV, United States
- Nevada Institute of Personalized Medicine, University of Nevada, Las Vegas, Las Vegas, NV, United States
| | - Simon Roux
- Department of Energy Joint Genome Institute, Berkeley, CA, United States
| | - Philippos K. Tsourkas
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, NV, United States
- Nevada Institute of Personalized Medicine, University of Nevada, Las Vegas, Las Vegas, NV, United States
| | - Ryan K. Doss
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, NV, United States
| | - Casey Stamereilers
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, NV, United States
| | - Astha Mehta
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, NV, United States
| | - Jeremy A. Dodsworth
- Department of Biology, California State University, San Bernardino, CA, United States
| | | | - Scott Monsma
- Lucigen Corporation, Middleton, WI, United States
| | | | | | | | - David A. Mead
- Varigen Biosciences Corporation, Madison, WI, United States
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5
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Colman DR, Lindsay MR, Amenabar MJ, Fernandes-Martins MC, Roden ER, Boyd ES. Phylogenomic analysis of novel Diaforarchaea is consistent with sulfite but not sulfate reduction in volcanic environments on early Earth. THE ISME JOURNAL 2020; 14:1316-1331. [PMID: 32066874 PMCID: PMC7174415 DOI: 10.1038/s41396-020-0611-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 01/28/2020] [Accepted: 02/04/2020] [Indexed: 12/27/2022]
Abstract
The origin(s) of dissimilatory sulfate and/or (bi)sulfite reducing organisms (SRO) remains enigmatic despite their importance in global carbon and sulfur cycling since at least 3.4 Ga. Here, we describe novel, deep-branching archaeal SRO populations distantly related to other Diaforarchaea from two moderately acidic thermal springs. Dissimilatory (bi)sulfite reductase homologs, DsrABC, encoded in metagenome assembled genomes (MAGs) from spring sediments comprise one of the earliest evolving Dsr lineages. DsrA homologs were expressed in situ under moderately acidic conditions. MAGs lacked genes encoding proteins that activate sulfate prior to (bi)sulfite reduction. This is consistent with sulfide production in enrichment cultures provided sulfite but not sulfate. We suggest input of volcanic sulfur dioxide to anoxic spring-water yields (bi)sulfite and moderately acidic conditions that favor its stability and bioavailability. The presence of similar volcanic springs at the time SRO are thought to have originated (>3.4 Ga) may have supplied (bi)sulfite that supported ancestral SRO. These observations coincide with the lack of inferred SO42- reduction capacity in nearly all organisms with early-branching DsrAB and which are near universally found in hydrothermal environments.
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Affiliation(s)
- Daniel R Colman
- Department of Microbiology & Immunology, Montana State University, Bozeman, MT, 59717, USA
| | - Melody R Lindsay
- Department of Microbiology & Immunology, Montana State University, Bozeman, MT, 59717, USA
| | - Maximiliano J Amenabar
- Department of Microbiology & Immunology, Montana State University, Bozeman, MT, 59717, USA
| | | | - Eric R Roden
- Department of Geoscience, University of Wisconsin, Madison, WI, USA
- NASA Astrobiology Institute, Mountain View, CA, USA
| | - Eric S Boyd
- Department of Microbiology & Immunology, Montana State University, Bozeman, MT, 59717, USA.
- NASA Astrobiology Institute, Mountain View, CA, USA.
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6
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Bose D, Mukhopadhyay S. Comparative genomics of a few members of the family Aquificaceae on the basis of their codon usage profile. GENE REPORTS 2019. [DOI: 10.1016/j.genrep.2018.11.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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7
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Cousins CR, Fogel M, Bowden R, Crawford I, Boyce A, Cockell C, Gunn M. Biogeochemical probing of microbial communities in a basalt-hosted hot spring at Kverkfjöll volcano, Iceland. GEOBIOLOGY 2018; 16:507-521. [PMID: 29856116 DOI: 10.1111/gbi.12291] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Accepted: 04/24/2018] [Indexed: 06/08/2023]
Abstract
We investigated bacterial and archaeal communities along an ice-fed surficial hot spring at Kverkfjöll volcano-a partially ice-covered basaltic volcano at Vatnajökull glacier, Iceland, using biomolecular (16S rRNA, apsA, mcrA, amoA, nifH genes) and stable isotope techniques. The hot spring environment is characterized by high temperatures and low dissolved oxygen concentrations at the source (68°C and <1 mg/L (±0.1%)) changing to lower temperatures and higher dissolved oxygen downstream (34.7°C and 5.9 mg/L), with sulfate the dominant anion (225 mg/L at the source). Sediments are comprised of detrital basalt, low-temperature alteration phases and pyrite, with <0.4 wt. % total organic carbon (TOC). 16S rRNA gene profiles reveal that organisms affiliated with Hydrogenobaculum (54%-87% bacterial population) and Thermoproteales (35%-63% archaeal population) dominate the micro-oxic hot spring source, while sulfur-oxidizing archaea (Sulfolobales, 57%-82%), and putative sulfur-oxidizing and heterotrophic bacterial groups dominate oxic downstream environments. The δ13 Corg (‰ V-PDB) values for sediment TOC and microbial biomass range from -9.4‰ at the spring's source decreasing to -12.6‰ downstream. A reverse effect isotope fractionation of ~3‰ between sediment sulfide (δ34 S ~0‰) and dissolved water sulfate (δ34 S +3.2‰), and δ18 O values of ~ -5.3‰ suggest pyrite forms abiogenically from volcanic sulfide, followed by abiogenic and microbial oxidation. These environments represent an unexplored surficial geothermal environment analogous to transient volcanogenic habitats during putative "snowball Earth" scenarios and volcano-ice geothermal environments on Mars.
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Affiliation(s)
- Claire R Cousins
- School of Earth and Environmental Science, University of St Andrews, St Andrews, UK
| | - Marilyn Fogel
- Department of Earth Sciences, University of California Riverside, Riverside, California
| | - Roxane Bowden
- Geophysical Laboratory, Carnegie Institution of Washington, Washington, District of Columbia
| | | | | | - Charles Cockell
- School of Physics and Astronomy, University of Edinburgh, Edinburgh, UK
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8
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De Anda V, Zapata-Peñasco I, Poot-Hernandez AC, Eguiarte LE, Contreras-Moreira B, Souza V. MEBS, a software platform to evaluate large (meta)genomic collections according to their metabolic machinery: unraveling the sulfur cycle. Gigascience 2018; 6:1-17. [PMID: 29069412 PMCID: PMC5737871 DOI: 10.1093/gigascience/gix096] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Accepted: 10/01/2017] [Indexed: 01/30/2023] Open
Abstract
The increasing number of metagenomic and genomic sequences has dramatically improved our understanding of microbial diversity, yet our ability to infer metabolic capabilities in such datasets remains challenging. We describe the Multigenomic Entropy Based Score pipeline (MEBS), a software platform designed to evaluate, compare, and infer complex metabolic pathways in large “omic” datasets, including entire biogeochemical cycles. MEBS is open source and available through https://github.com/eead-csic-compbio/metagenome_Pfam_score. To demonstrate its use, we modeled the sulfur cycle by exhaustively curating the molecular and ecological elements involved (compounds, genes, metabolic pathways, and microbial taxa). This information was reduced to a collection of 112 characteristic Pfam protein domains and a list of complete-sequenced sulfur genomes. Using the mathematical framework of relative entropy (H΄), we quantitatively measured the enrichment of these domains among sulfur genomes. The entropy of each domain was used both to build up a final score that indicates whether a (meta)genomic sample contains the metabolic machinery of interest and to propose marker domains in metagenomic sequences such as DsrC (PF04358). MEBS was benchmarked with a dataset of 2107 non-redundant microbial genomes from RefSeq and 935 metagenomes from MG-RAST. Its performance, reproducibility, and robustness were evaluated using several approaches, including random sampling, linear regression models, receiver operator characteristic plots, and the area under the curve metric (AUC). Our results support the broad applicability of this algorithm to accurately classify (AUC = 0.985) hard-to-culture genomes (e.g., Candidatus Desulforudis audaxviator), previously characterized ones, and metagenomic environments such as hydrothermal vents, or deep-sea sediment. Our benchmark indicates that an entropy-based score can capture the metabolic machinery of interest and can be used to efficiently classify large genomic and metagenomic datasets, including uncultivated/unexplored taxa.
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Affiliation(s)
- Valerie De Anda
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, 70-275, Coyoacán 04510, D.F., México
| | - Icoquih Zapata-Peñasco
- Dirección de Investigación en Transformación de Hidrocarburos, Instituto Mexicano del Petróleo, Eje Central Lázaro Cárdenas, Norte 152, Col. San Bartolo Atepehuacan, 07730, México
| | - Augusto Cesar Poot-Hernandez
- Departamento de Ingeniería de Sistemas Computacionales y Automatización. Sección de Ingeniería de Sistemas Computacionales. Instituto de Investigaciones en Matemáticas Aplicadas y en Sistemas. Circuito Escolar 3000, Cd. Universitaria, 04510 Ciudad de México
| | - Luis E Eguiarte
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, 70-275, Coyoacán 04510, D.F., México
| | - Bruno Contreras-Moreira
- Estación Experimental de Aula Dei, Consejo Superior de Investigaciones Científicas (EEAD-CSIC), Avda. Montañana, 1005, Zaragoza 50059, Spain.,Fundación ARAID, calle María de Luna 11, 50018 Zaragoza, Spain
| | - Valeria Souza
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, 70-275, Coyoacán 04510, D.F., México
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9
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Ward L, Taylor MW, Power JF, Scott BJ, McDonald IR, Stott MB. Microbial community dynamics in Inferno Crater Lake, a thermally fluctuating geothermal spring. THE ISME JOURNAL 2017; 11:1158-1167. [PMID: 28072418 PMCID: PMC5437927 DOI: 10.1038/ismej.2016.193] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Revised: 10/21/2016] [Accepted: 11/19/2016] [Indexed: 11/08/2022]
Abstract
Understanding how microbial communities respond and adjust to ecosystem perturbation is often difficult to interpret due to multiple and often simultaneous variations in observed conditions. In this research, we investigated the microbial community dynamics of Inferno Crater Lake, an acidic geothermal spring in New Zealand with a unique thermal cycle that varies between 30 and 80 °C over a period of 40-60 days. Using a combination of next-generation sequencing, geochemical analysis and quantitative PCR we found that the microbial community composition was predominantly chemolithotrophic and strongly associated with the thermal cycle. At temperatures >65 °C, the microbial community was dominated almost exclusively by sulphur-oxidising archaea (Sulfolobus-like spp.). By contrast, at mesophilic temperatures the community structure was more mixed, comprising both archaea and bacteria but dominated primarily by chemolithotrophic sulphur and hydrogen oxidisers. Multivariate analysis of physicochemical data confirmed that temperature was the only significant variable associated with community turnover. This research contributes to our understanding of microbial community dynamics in variable environments, using a naturally alternating system as a model and extends our limited knowledge of acidophile ecology in geothermal habitats.
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Affiliation(s)
- Laura Ward
- GNS Science, Wairakei Research Centre, Wairakei, Taup, New Zealand
- University of Auckland, School of Biological Sciences, Auckland, New Zealand
| | - Michael W Taylor
- University of Auckland, School of Biological Sciences, Auckland, New Zealand
| | - Jean F Power
- GNS Science, Wairakei Research Centre, Wairakei, Taup, New Zealand
| | - Bradley J Scott
- GNS Science, Wairakei Research Centre, Wairakei, Taup, New Zealand
| | - Ian R McDonald
- University of Waikato, School of Science, Hamilton, New Zealand
| | - Matthew B Stott
- GNS Science, Wairakei Research Centre, Wairakei, Taup, New Zealand
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10
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Geesey GG, Barkay T, King S. Microbes in mercury-enriched geothermal springs in western North America. THE SCIENCE OF THE TOTAL ENVIRONMENT 2016; 569-570:321-331. [PMID: 27344121 DOI: 10.1016/j.scitotenv.2016.06.080] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Revised: 06/11/2016] [Accepted: 06/12/2016] [Indexed: 06/06/2023]
Abstract
Because geothermal environments contain mercury (Hg) from natural sources, microorganisms that evolved in these systems have likely adapted to this element. Knowledge of the interactions between microorganisms and Hg in geothermal systems may assist in understanding the long-term evolution of microbial adaptation to Hg with relevance to other environments where Hg is introduced from anthropogenic sources. A number of microbiological studies with supporting geochemistry have been conducted in geothermal systems across western North America. Approximately 1 in 5 study sites include measurements of Hg. Of all prokaryotic taxa reported across sites with microbiological and accompanying physicochemical data, 42% have been detected at sites in which Hg was measured. Genes specifying Hg reduction and detoxification by microorganisms were detected in a number of hot springs across the region. Archaeal-like sequences, representing two crenarchaeal orders and one order each of the Euryarchaeota and Thaumarchaeota, dominated in metagenomes' MerA (the mercuric reductase protein) inventories, while bacterial homologs were mostly found in one deeply sequenced metagenome. MerA homologs were more frequently found in metagenomes of microbial communities in acidic springs than in circumneutral or high pH geothermal systems, possibly reflecting higher bioavailability of Hg under acidic conditions. MerA homologs were found in hot springs prokaryotic isolates affiliated with Bacteria and Archaea taxa. Acidic sites with high Hg concentrations contain more of Archaea than Bacteria taxa, while the reverse appears to be the case in circumneutral and high pH sites with high Hg concentrations. However, MerA was detected in only a small fraction of the Archaea and Bacteria taxa inhabiting sites containing Hg. Nevertheless, the presence of MerA homologs and their distribution patterns in systems, in which Hg has yet to be measured, demonstrates the potential for detoxification by Hg reduction in these geothermal systems, particularly the low pH springs that are dominated by Archaea.
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Affiliation(s)
- Gill G Geesey
- Department of Microbiology and Immunology, Thermal Biology Institute, Montana State University, Bozeman, MT 59717-3520, USA.
| | - Tamar Barkay
- Department of Biochemistry and Microbiology, Graduate Program in Ecology and Evolution, Rutgers University, New Brunswick, NJ 08901-8525, USA.
| | - Sue King
- 2908 3rd Avenue North, Great Falls, MT 59401, USA.
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11
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Beam JP, Bernstein HC, Jay ZJ, Kozubal MA, Jennings RD, Tringe SG, Inskeep WP. Assembly and Succession of Iron Oxide Microbial Mat Communities in Acidic Geothermal Springs. Front Microbiol 2016; 7:25. [PMID: 26913020 PMCID: PMC4753309 DOI: 10.3389/fmicb.2016.00025] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Accepted: 01/11/2016] [Indexed: 11/25/2022] Open
Abstract
Biomineralized ferric oxide microbial mats are ubiquitous features on Earth, are common in hot springs of Yellowstone National Park (YNP, WY, USA), and form due to direct interaction between microbial and physicochemical processes. The overall goal of this study was to determine the contribution of different community members to the assembly and succession of acidic high-temperature Fe(III)-oxide mat ecosystems. Spatial and temporal changes in Fe(III)-oxide accretion and the abundance of relevant community members were monitored over 70 days using sterile glass microscope slides incubated in the outflow channels of two acidic geothermal springs (pH = 3–3.5; temperature = 68–75°C) in YNP. Hydrogenobaculum spp. were the most abundant taxon identified during early successional stages (4–40 days), and have been shown to oxidize arsenite, sulfide, and hydrogen coupled to oxygen reduction. Iron-oxidizing populations of Metallosphaera yellowstonensis were detected within 4 days, and reached steady-state levels within 14–30 days, corresponding to visible Fe(III)-oxide accretion. Heterotrophic archaea colonized near 30 days, and emerged as the dominant functional guild after 70 days and in mature Fe(III)-oxide mats (1–2 cm thick). First-order rate constants of Fe(III)-oxide accretion ranged from 0.046 to 0.05 day−1, and in situ microelectrode measurements showed that the oxidation of Fe(II) is limited by the diffusion of O2 into the Fe(III)-oxide mat. The formation of microterracettes also implicated O2 as a major variable controlling microbial growth and subsequent mat morphology. The assembly and succession of Fe(III)-oxide mat communities follows a repeatable pattern of colonization by lithoautotrophic organisms, and the subsequent growth of diverse organoheterotrophs. The unique geochemical signatures and micromorphology of extant biomineralized Fe(III)-oxide mats are also useful for understanding other Fe(II)-oxidizing systems.
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Affiliation(s)
- Jacob P Beam
- Department of Land Resources and Environmental Sciences, Thermal Biology Institute, Montana State University Bozeman, MT, USA
| | - Hans C Bernstein
- Department of Chemical and Biological Engineering, Center for Biofilm Engineering, Montana State UniversityBozeman, MT, USA; Biodetection Science and Biological Science Division, Pacific Northwest National LaboratoryRichland, WA, USA
| | - Zackary J Jay
- Department of Land Resources and Environmental Sciences, Thermal Biology Institute, Montana State UniversityBozeman, MT, USA; Department of Chemical and Biological Engineering, Center for Biofilm Engineering, Montana State UniversityBozeman, MT, USA
| | - Mark A Kozubal
- Department of Land Resources and Environmental Sciences, Thermal Biology Institute, Montana State University Bozeman, MT, USA
| | - Ryan deM Jennings
- Department of Land Resources and Environmental Sciences, Thermal Biology Institute, Montana State University Bozeman, MT, USA
| | - Susannah G Tringe
- United States Department of Energy Joint Genome Institute Walnut Creek, CA, USA
| | - William P Inskeep
- Department of Land Resources and Environmental Sciences, Thermal Biology Institute, Montana State University Bozeman, MT, USA
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12
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Gudbergsdóttir SR, Menzel P, Krogh A, Young M, Peng X. Novel viral genomes identified from six metagenomes reveal wide distribution of archaeal viruses and high viral diversity in terrestrial hot springs. Environ Microbiol 2015; 18:863-74. [PMID: 26439881 DOI: 10.1111/1462-2920.13079] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Accepted: 09/30/2015] [Indexed: 11/27/2022]
Abstract
Limited by culture-dependent methods the number of viruses identified from thermophilic Archaea and Bacteria is still very small. In this study we retrieved viral sequences from six hot spring metagenomes isolated worldwide, revealing a wide distribution of four archaeal viral families, Ampullaviridae, Bicaudaviridae, Lipothrixviridae and Rudiviridae. Importantly, we identified 10 complete or near complete viral genomes allowing, for the first time, an assessment of genome conservation and evolution of the Ampullaviridae family as well as Sulfolobus Monocaudavirus 1 (SMV1)-related viruses. Among the novel genomes, one belongs to a putative thermophilic virus infecting the bacterium Hydrogenobaculum, for which no virus has been reported in the literature. Moreover, a high viral diversity was observed in the metagenomes, especially among the Lipothrixviridae, as indicated by the large number of unique contigs and the lack of a completely assembled genome for this family. This is further supported by the large number of novel genes in the complete and partial genomes showing no sequence similarities to public databases. CRISPR analysis revealed hundreds of novel CRISPR loci and thousands of novel CRISPR spacers from each metagenome, reinforcing the notion of high viral diversity in the thermal environment.
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Affiliation(s)
| | - Peter Menzel
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, Copenhagen N, DK-2200, Denmark
| | - Anders Krogh
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, Copenhagen N, DK-2200, Denmark
| | - Mark Young
- Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT, 59717-3150, USA
| | - Xu Peng
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, Copenhagen N, DK-2200, Denmark
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13
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Hedlund BP, Reysenbach AL, Huang L, Ong JC, Liu Z, Dodsworth JA, Ahmed R, Williams AJ, Briggs BR, Liu Y, Hou W, Dong H. Isolation of diverse members of the Aquificales from geothermal springs in Tengchong, China. Front Microbiol 2015; 6:157. [PMID: 25774153 PMCID: PMC4343020 DOI: 10.3389/fmicb.2015.00157] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Accepted: 02/11/2015] [Indexed: 11/28/2022] Open
Abstract
The order Aquificales (phylum Aquificae) consists of thermophilic and hyperthermophilic bacteria that are prominent in many geothermal systems, including those in Tengchong, Yunnan Province, China. However, Aquificales have not previously been isolated from Tengchong. We isolated five strains of Aquificales from diverse springs (temperature 45.2–83.3°C and pH 2.6–9.1) in the Rehai Geothermal Field from sites in which Aquificales were abundant. Phylogenetic analysis showed that four of the strains belong to the genera Hydrogenobacter, Hydrogenobaculum, and Sulfurihydrogenibium, including strains distant enough to likely justify new species of Hydrogenobacter and Hydrogenobaculum. The additional strain may represent a new genus in the Hydrogenothermaceae. All strains were capable of aerobic respiration under microaerophilic conditions; however, they had variable capacity for chemolithotrophic oxidation of hydrogen and sulfur compounds and nitrate reduction.
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Affiliation(s)
- Brian P Hedlund
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV, USA ; Nevada Institute of Personalized Medicine, University of Nevada Las Vegas, Las Vegas, NV, USA
| | - Anna-Louise Reysenbach
- Biology Department and Center for Life in Extreme Environments, Portland State University Portland, OR, USA
| | - Liuquin Huang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences Beijing, China
| | - John C Ong
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV, USA
| | - Zizhang Liu
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences Beijing, China
| | - Jeremy A Dodsworth
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV, USA ; Department of Biology, California State University San Bernardino San Bernardino, CA, USA
| | - Reham Ahmed
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV, USA
| | - Amanda J Williams
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV, USA
| | - Brandon R Briggs
- Department of Geology and Environmental Earth Science, Miami University, Oxford, OH, USA
| | - Yitai Liu
- Biology Department and Center for Life in Extreme Environments, Portland State University Portland, OR, USA
| | - Weiguo Hou
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences Beijing, China
| | - Hailiang Dong
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences Beijing, China ; Department of Geology and Environmental Earth Science, Miami University, Oxford, OH, USA
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14
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Brinkmann-Chen S, Cahn JKB, Arnold FH. Uncovering rare NADH-preferring ketol-acid reductoisomerases. Metab Eng 2014; 26:17-22. [PMID: 25172159 DOI: 10.1016/j.ymben.2014.08.003] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2014] [Revised: 08/01/2014] [Accepted: 08/19/2014] [Indexed: 11/25/2022]
Abstract
All members of the ketol-acid reductoisomerase (KARI) enzyme family characterized to date have been shown to prefer the nicotinamide adenine dinucleotide phosphate hydride (NADPH) cofactor to nicotinamide adenine dinucleotide hydride (NADH). However, KARIs with the reversed cofactor preference are desirable for industrial applications, including anaerobic fermentation to produce branched-chain amino acids. By applying insights gained from structural and engineering studies of this enzyme family to a comprehensive multiple sequence alignment of KARIs, we identified putative NADH-utilizing KARIs and characterized eight whose catalytic efficiencies using NADH were equal to or greater than NADPH. These are the first naturally NADH-preferring KARIs reported and demonstrate that this property has evolved independently multiple times, using strategies unlike those used previously in the laboratory to engineer a KARI cofactor switch.
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Affiliation(s)
- S Brinkmann-Chen
- California Institute of Technology, Division of Chemistry and Chemical Engineering, 1200 E California Blvd, MC 210-41, Pasadena, CA 91125, USA.
| | - J K B Cahn
- California Institute of Technology, Division of Chemistry and Chemical Engineering, 1200 E California Blvd, MC 210-41, Pasadena, CA 91125, USA.
| | - F H Arnold
- California Institute of Technology, Division of Chemistry and Chemical Engineering, 1200 E California Blvd, MC 210-41, Pasadena, CA 91125, USA.
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15
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16
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Meyer JL, Huber JA. Strain-level genomic variation in natural populations of Lebetimonas from an erupting deep-sea volcano. ISME JOURNAL 2013; 8:867-80. [PMID: 24257443 DOI: 10.1038/ismej.2013.206] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2013] [Revised: 10/02/2013] [Accepted: 10/13/2013] [Indexed: 11/09/2022]
Abstract
Chemolithoautotrophic Epsilonproteobacteria are ubiquitous in sulfidic, oxygen-poor habitats, including hydrothermal vents, marine oxygen minimum zones, marine sediments and sulfidic caves and have a significant role in cycling carbon, hydrogen, nitrogen and sulfur in these environments. The isolation of diverse strains of Epsilonproteobacteria and the sequencing of their genomes have revealed that this group has the metabolic potential to occupy a wide range of niches, particularly at dynamic deep-sea hydrothermal vents. We expand on this body of work by examining the population genomics of six strains of Lebetimonas, a vent-endemic, thermophilic, hydrogen-oxidizing Epsilonproteobacterium, from a single seamount in the Mariana Arc. Using Lebetimonas as a model for anaerobic, moderately thermophilic organisms in the warm, anoxic subseafloor environment, we show that genomic content is highly conserved and that recombination is limited between closely related strains. The Lebetimonas genomes are shaped by mobile genetic elements and gene loss as well as the acquisition of novel functional genes by horizontal gene transfer, which provide the potential for adaptation and microbial speciation in the deep sea. In addition, these Lebetimonas genomes contain two operons of nitrogenase genes with different evolutionary origins. Lebetimonas expressed nifH during growth with nitrogen gas as the sole nitrogen source, thus providing the first evidence of nitrogen fixation in any Epsilonproteobacteria from deep-sea hydrothermal vents. In this study, we provide a comparative overview of the genomic potential within the Nautiliaceae as well as among more distantly related hydrothermal vent Epsilonproteobacteria to broaden our understanding of microbial adaptation and diversity in the deep sea.
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Affiliation(s)
- Julie L Meyer
- Marine Biological Laboratory, Josephine Bay Paul Center, Woods Hole, MA, USA
| | - Julie A Huber
- Marine Biological Laboratory, Josephine Bay Paul Center, Woods Hole, MA, USA
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17
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Boyd ES, Peters JW. New insights into the evolutionary history of biological nitrogen fixation. Front Microbiol 2013; 4:201. [PMID: 23935594 PMCID: PMC3733012 DOI: 10.3389/fmicb.2013.00201] [Citation(s) in RCA: 108] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2013] [Accepted: 06/26/2013] [Indexed: 12/03/2022] Open
Abstract
Nitrogenase, which catalyzes the ATP-dependent reduction of dinitrogen (N2) to ammonia (NH3), accounts for roughly half of the bioavailable nitrogen supporting extant life. The fundamental requirement for fixed forms of nitrogen for life on Earth, both at present and in the past, has led to broad and significant interest in the origin and evolution of biological N2 fixation. One key question is whether the limited availability of fixed nitrogen was a factor in life's origin or whether there were ample sources of fixed nitrogen produced by abiotic processes or delivered through the weathering of bolide impact materials to support this early life. If the latter, the key questions become what were the characteristics of the environment that precipitated the evolution of this oxygen sensitive process, when did this occur, and how was its subsequent evolutionary history impacted by the advent of oxygenic photosynthesis and the rise of oxygen in the Earth's biosphere. Since the availability of fixed sources of nitrogen capable of supporting early life is difficult to glean from the geologic record, there are limited means to get direct insights into these questions. Indirect insights, however, can be gained through phylogenetic studies of nitrogenase structural gene products and additional gene products involved in the biosynthesis of the complex metal-containing prosthetic groups associated with this enzyme complex. Insights gained from such studies, as reviewed herein, challenge traditional models for the evolution of biological nitrogen fixation and provide the basis for the development of new conceptual models that explain the stepwise evolution of this highly complex life sustaining process.
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Affiliation(s)
- Eric S Boyd
- Department of Chemistry and Biochemistry and Department of Microbiology, Montana State University Bozeman, MT, USA
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18
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Takacs-Vesbach C, Inskeep WP, Jay ZJ, Herrgard MJ, Rusch DB, Tringe SG, Kozubal MA, Hamamura N, Macur RE, Fouke BW, Reysenbach AL, McDermott TR, Jennings RD, Hengartner NW, Xie G. Metagenome sequence analysis of filamentous microbial communities obtained from geochemically distinct geothermal channels reveals specialization of three aquificales lineages. Front Microbiol 2013; 4:84. [PMID: 23755042 PMCID: PMC3665934 DOI: 10.3389/fmicb.2013.00084] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2012] [Accepted: 03/25/2013] [Indexed: 02/01/2023] Open
Abstract
The Aquificales are thermophilic microorganisms that inhabit hydrothermal systems worldwide and are considered one of the earliest lineages of the domain Bacteria. We analyzed metagenome sequence obtained from six thermal "filamentous streamer" communities (∼40 Mbp per site), which targeted three different groups of Aquificales found in Yellowstone National Park (YNP). Unassembled metagenome sequence and PCR-amplified 16S rRNA gene libraries revealed that acidic, sulfidic sites were dominated by Hydrogenobaculum (Aquificaceae) populations, whereas the circum-neutral pH (6.5-7.8) sites containing dissolved sulfide were dominated by Sulfurihydrogenibium spp. (Hydrogenothermaceae). Thermocrinis (Aquificaceae) populations were found primarily in the circum-neutral sites with undetectable sulfide, and to a lesser extent in one sulfidic system at pH 8. Phylogenetic analysis of assembled sequence containing 16S rRNA genes as well as conserved protein-encoding genes revealed that the composition and function of these communities varied across geochemical conditions. Each Aquificales lineage contained genes for CO2 fixation by the reverse-TCA cycle, but only the Sulfurihydrogenibium populations perform citrate cleavage using ATP citrate lyase (Acl). The Aquificaceae populations use an alternative pathway catalyzed by two separate enzymes, citryl-CoA synthetase (Ccs), and citryl-CoA lyase (Ccl). All three Aquificales lineages contained evidence of aerobic respiration, albeit due to completely different types of heme Cu oxidases (subunit I) involved in oxygen reduction. The distribution of Aquificales populations and differences among functional genes involved in energy generation and electron transport is consistent with the hypothesis that geochemical parameters (e.g., pH, sulfide, H2, O2) have resulted in niche specialization among members of the Aquificales.
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Cai F, Axen SD, Kerfeld CA. Evidence for the widespread distribution of CRISPR-Cas system in the Phylum Cyanobacteria. RNA Biol 2013; 10:687-93. [PMID: 23628889 DOI: 10.4161/rna.24571] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Members of the phylum Cyanobacteria inhabit ecologically diverse environments. However, the CRISPR-Cas (clustered regularly interspaced short palindromic repeats, CRISPR associated genes), an extremely adaptable defense system, has not been surveyed in this phylum. We analyzed 126 cyanobacterial genomes and, surprisingly, found CRISPR-Cas in the majority except the marine subclade (Synechococcus and Prochlorococcus), in which cyanophages are a known force shaping their evolution. Multiple observations of CRISPR loci in the absence of cas1/cas2 genes may represent an early stage of losing a CRISPR-Cas locus. Our findings reveal the widespread distribution of their role in the phylum Cyanobacteria and provide a first step to systematically understanding CRISPR-Cas systems in cyanobacteria.
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Affiliation(s)
- Fei Cai
- U.S. Department of Energy-Joint Genome Institute, Walnut Creek, CA, USA
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