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Toshchakov SV, Izotova AO, Vinogradova EN, Kachmazov GS, Tuaeva AY, Abaev VT, Evteeva MA, Gunitseva NM, Korzhenkov AA, Elcheninov AG, Patrushev MV, Kublanov IV. Culture-Independent Survey of Thermophilic Microbial Communities of the North Caucasus. Biology (Basel) 2021; 10:biology10121352. [PMID: 34943267 PMCID: PMC8698779 DOI: 10.3390/biology10121352] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 12/09/2021] [Accepted: 12/14/2021] [Indexed: 01/04/2023]
Abstract
Simple Summary The Republic of North Ossetia-Alania, located in the southern part of the North Caucasus, possess a number of hydrothermal habitats, including both subterranean thermal reservoirs and terrestrial hot springs. At the same time, reports on microbiology of numerous geothermal sites are rather scarce for the whole North Caucasus region. In this paper, we report on the first culture-independent metabarcoding study of thermal habitats in the North Caucasus, coupled with a chemical analysis of the elemental composition of water. The results of this work include the conclusions regarding key metabolic characteristics of these habitats as well as detection of few but abundant deep lineages of uncultivated microorganisms which could be regarded as endemic. This study may represent a first step in closing the knowledge gap in extremophilic microbial communities of the North Caucasus. Abstract The Greater Caucasus is a part of seismically active Alpine–Himalayan orogenic belt and has been a center of significant volcanic activity during the Quaternary period. That led to the formation of the number of hydrothermal habitats, including subterranean thermal aquifers and surface hot springs. However, there are only a limited number of scientific works reporting on the microbial communities of these habitats. Moreover, all these reports concern only studies of specific microbial taxa, carried out using classical cultivation approaches. In this work, we present first culture-independent study of hydrotherms in the Republic of North Ossetia-Alania, located in the southern part of the North Caucasus. Using 16S metabarcoding, we analyzed the composition of the microbial communities of two subterranean thermal aquifers and terrestrial hot springs of the Karmadon valley. Analysis of correlations between the chemical composition of water and the representation of key taxa allowed us to identify the key factors determining the formation of microbial communities. In addition, we were able to identify a significant number of highly abundant deep phylogenetic lineages. Our study represents a first glance on the thermophilic microbial communities of the North Caucasus and may serve as a basis for further microbiological studies of the extreme habitats of this region.
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Affiliation(s)
- Stepan V. Toshchakov
- Kurchatov Center for Genome Research, National Research Center “Kurchatov Institute”, Ac. Kurchatov Square, 1, Moscow 123098, Russia; (A.O.I.); (E.N.V.); (M.A.E.); (N.M.G.); (A.A.K.); (M.V.P.)
- Correspondence: ; Tel.: +7-911-481-1809
| | - Anna O. Izotova
- Kurchatov Center for Genome Research, National Research Center “Kurchatov Institute”, Ac. Kurchatov Square, 1, Moscow 123098, Russia; (A.O.I.); (E.N.V.); (M.A.E.); (N.M.G.); (A.A.K.); (M.V.P.)
| | - Elizaveta N. Vinogradova
- Kurchatov Center for Genome Research, National Research Center “Kurchatov Institute”, Ac. Kurchatov Square, 1, Moscow 123098, Russia; (A.O.I.); (E.N.V.); (M.A.E.); (N.M.G.); (A.A.K.); (M.V.P.)
- Faculty of Biology, Lomonosov Moscow State University, 1-12 Leninskie Gory, Moscow 119991, Russia
| | - Gennady S. Kachmazov
- Faculty of Chemistry, Biology and Biotechnology, North Ossetian State University Named after K.L. Khetagurov, Vatutina str., 44-46, Vladikavkaz 362025, Russia; (G.S.K.); (V.T.A.)
| | - Albina Y. Tuaeva
- National Research Center Kurchatov Institute-GOSNIIGENETIKA, 1st Dorozhny Pr., 1, Moscow 117545, Russia;
| | - Vladimir T. Abaev
- Faculty of Chemistry, Biology and Biotechnology, North Ossetian State University Named after K.L. Khetagurov, Vatutina str., 44-46, Vladikavkaz 362025, Russia; (G.S.K.); (V.T.A.)
| | - Martha A. Evteeva
- Kurchatov Center for Genome Research, National Research Center “Kurchatov Institute”, Ac. Kurchatov Square, 1, Moscow 123098, Russia; (A.O.I.); (E.N.V.); (M.A.E.); (N.M.G.); (A.A.K.); (M.V.P.)
| | - Natalia M. Gunitseva
- Kurchatov Center for Genome Research, National Research Center “Kurchatov Institute”, Ac. Kurchatov Square, 1, Moscow 123098, Russia; (A.O.I.); (E.N.V.); (M.A.E.); (N.M.G.); (A.A.K.); (M.V.P.)
| | - Aleksei A. Korzhenkov
- Kurchatov Center for Genome Research, National Research Center “Kurchatov Institute”, Ac. Kurchatov Square, 1, Moscow 123098, Russia; (A.O.I.); (E.N.V.); (M.A.E.); (N.M.G.); (A.A.K.); (M.V.P.)
| | - Alexander G. Elcheninov
- Winogradsky Institute of Microbiology, Research Center of Biotechnology RAS, 60-let Oktyzbrya Av., 7/2, Moscow 119071, Russia; (A.G.E.); (I.V.K.)
| | - Maxim V. Patrushev
- Kurchatov Center for Genome Research, National Research Center “Kurchatov Institute”, Ac. Kurchatov Square, 1, Moscow 123098, Russia; (A.O.I.); (E.N.V.); (M.A.E.); (N.M.G.); (A.A.K.); (M.V.P.)
| | - Ilya V. Kublanov
- Winogradsky Institute of Microbiology, Research Center of Biotechnology RAS, 60-let Oktyzbrya Av., 7/2, Moscow 119071, Russia; (A.G.E.); (I.V.K.)
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Hackmann TJ. Accurate estimation of microbial sequence diversity with Distanced. Bioinformatics 2020; 36:728-734. [PMID: 31504180 DOI: 10.1093/bioinformatics/btz668] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Revised: 07/16/2019] [Accepted: 08/21/2019] [Indexed: 11/13/2022] Open
Abstract
MOTIVATION Microbes are the most diverse organisms on the planet. Deep sequencing of ribosomal DNA (rDNA) suggests thousands of different microbes may be present in a single sample. However, errors in sequencing have made any estimate of within-sample (alpha) diversity uncertain. RESULTS We developed a tool to estimate alpha diversity of rDNA sequences from microbes (and other sequences). Our tool, Distanced, calculates how different (distant) sequences would be without sequencing errors. It does this using a Bayesian approach. Using this approach, Distanced accurately estimated alpha diversity of rDNA sequences from bacteria and fungi. It had lower root mean square prediction error (RMSPE) than when using no tool (leaving sequencing errors uncorrected). It was also accurate with non-microbial sequences (antibody mRNA). State-of-the-art tools (DADA2 and Deblur) were far less accurate. They often had higher RMSPE than when using no tool. Distanced thus represents an improvement over existing tools. Distanced will be useful to several disciplines, given microbial diversity affects everything from human health to ecosystem function. AVAILABILITY AND IMPLEMENTATION Distanced is freely available at https://github.com/thackmann/Distanced. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Timothy J Hackmann
- Department of Animal Science, University of California, Davis, CA 95616, USA
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Romagnoli CL, Pellegrino KCM, Silva NM, Brianesi UA, Leão SC, Rabello MCDS, Viana-Niero C. Diversity of Mycobacteriaceae from aquatic environment at the São Paulo Zoological Park Foundation in Brazil. PLoS One 2020; 15:e0227759. [PMID: 31935265 DOI: 10.1371/journal.pone.0227759] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Accepted: 12/28/2019] [Indexed: 12/22/2022] Open
Abstract
We investigated the species diversity of Mycobacteriaceae in surface water samples from six environments at the zoological park in São Paulo, Brazil. Three hundred and eighty isolates were cultivated and identified by phenotypic characteristics (growth rate and pigmentation) and sequencing of hsp65, rpoB and 16S rRNA genes. The results revealed that almost 48% of the isolates could be identified at the species level; about 50% were classified at the genus level, and only less than 2% of the isolates showed an inconclusive identification. The isolates classified at the genus level and not identified were then evaluated by phylogenetic analyses using the same three concatenated target genes. The results allowed us to identify at the genus level some isolates that previously had inconclusive identification, and they also suggested the presence of putative candidate species within the sample, demonstrating that this zoological park is an important source of diversity.
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Steller LH, Nakamura E, Ota T, Sakaguchi C, Sharma M, Van Kranendonk MJ. Boron Isotopes in the Puga Geothermal System, India, and Their Implications for the Habitat of Early Life. Astrobiology 2019; 19:1459-1473. [PMID: 31287717 DOI: 10.1089/ast.2018.1966] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Boron is associated with several Archean stromatolite deposits, including the tourmaline-rich Barberton stromatolites in South Africa and tourmaline-bearing pyritic laminae associated with stromatolites of the 3.48 Ga Dresser Formation in the Pilbara Craton, Australia. Boron is also a critical element in prebiotic organic chemistry, including in the formation of ribose, a crucial component in RNA. As geological evidence and advances in prebiotic chemistry are now suggesting that hot spring activity may be associated with the origins of life, an understanding of boron and its mobility and isotopic fractionation in geothermal settings may provide important insights into the setting for the origin of life. Here, we report on the boron isotopic compositions and elemental concentrations in a range of fluid, sediment, and mineral samples from the active, boron-rich Puga geothermal system in the Himalayas, India. This includes one of the lowest boron isotope values ever recorded in modern settings: diatom-rich sediments (δ11B = -41.0‰) in a multiphase fractionation system where evaporation is not the dominant form of isotope fractionation. Instead, the extreme boron isotopic fractionation is ascribed to the incorporation of tetrahedral 10B borate anions in precipitating amorphous silica. These findings expand the known limits and drivers of boron isotope fractionation, as well as provide insight into the concentration and fractionation of boron in Archean hot spring environments.
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Affiliation(s)
- Luke H Steller
- Australian Centre for Astrobiology, and School of Biological, Earth and Environmental Sciences, University of New South Wales, Kensington, Australia
| | - Eizo Nakamura
- Pheasant Memorial Laboratory for Geochemistry and Cosmochemistry, Institute for Planetary Materials, Okayama University at Misasa, Tottori, Japan
| | - Tsutomu Ota
- Pheasant Memorial Laboratory for Geochemistry and Cosmochemistry, Institute for Planetary Materials, Okayama University at Misasa, Tottori, Japan
| | - Chie Sakaguchi
- Pheasant Memorial Laboratory for Geochemistry and Cosmochemistry, Institute for Planetary Materials, Okayama University at Misasa, Tottori, Japan
| | - Mukund Sharma
- Birbal Sahni Institute of Palaeosciences, Lucknow, India
| | - Martin J Van Kranendonk
- Australian Centre for Astrobiology, and School of Biological, Earth and Environmental Sciences, University of New South Wales, Kensington, Australia
- Pheasant Memorial Laboratory for Geochemistry and Cosmochemistry, Institute for Planetary Materials, Okayama University at Misasa, Tottori, Japan
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Crognale S, Venturi S, Tassi F, Rossetti S, Rashed H, Cabassi J, Capecchiacci F, Nisi B, Vaselli O, Morrison HG, Sogin ML, Fazi S. Microbiome profiling in extremely acidic soils affected by hydrothermal fluids: the case of the Solfatara Crater (Campi Flegrei, southern Italy). FEMS Microbiol Ecol 2018; 94:5105751. [DOI: 10.1093/femsec/fiy190] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Accepted: 09/20/2018] [Indexed: 12/20/2022] Open
Affiliation(s)
- Simona Crognale
- IRSA - CNR Water Research Institute, Via Salaria km 29.300 – CP10, 00015 Monterotondo, Rome, Italy
| | - Stefania Venturi
- IGG − CNR Institute of Geosciences and Earth Resources, Via G. La Pira 4, 50121 Florence, Italy
- Department of Earth Sciences, University of Florence, Via G. La Pira 4, 50121 Florence, Italy
| | - Franco Tassi
- IGG − CNR Institute of Geosciences and Earth Resources, Via G. La Pira 4, 50121 Florence, Italy
- Department of Earth Sciences, University of Florence, Via G. La Pira 4, 50121 Florence, Italy
| | - Simona Rossetti
- IRSA - CNR Water Research Institute, Via Salaria km 29.300 – CP10, 00015 Monterotondo, Rome, Italy
| | - Heba Rashed
- Department of Earth Sciences, University of Florence, Via G. La Pira 4, 50121 Florence, Italy
| | - Jacopo Cabassi
- IGG − CNR Institute of Geosciences and Earth Resources, Via G. La Pira 4, 50121 Florence, Italy
- Department of Earth Sciences, University of Florence, Via G. La Pira 4, 50121 Florence, Italy
| | - Francesco Capecchiacci
- IGG − CNR Institute of Geosciences and Earth Resources, Via G. La Pira 4, 50121 Florence, Italy
- Department of Earth Sciences, University of Florence, Via G. La Pira 4, 50121 Florence, Italy
| | - Barbara Nisi
- IGG – CNR Institute of Geosciences and Earth Resources, Via G. Moruzzi 1, 56124 Pisa, Italy
| | - Orlando Vaselli
- IGG − CNR Institute of Geosciences and Earth Resources, Via G. La Pira 4, 50121 Florence, Italy
- Department of Earth Sciences, University of Florence, Via G. La Pira 4, 50121 Florence, Italy
| | | | | | - Stefano Fazi
- IRSA - CNR Water Research Institute, Via Salaria km 29.300 – CP10, 00015 Monterotondo, Rome, Italy
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Mendes LW, Tsai SM. Distinct taxonomic and functional composition of soil microbiomes along the gradient forest-restinga-mangrove in southeastern Brazil. Antonie Van Leeuwenhoek 2018; 111:101-14. [PMID: 28831604 DOI: 10.1007/s10482-017-0931-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Accepted: 08/17/2017] [Indexed: 02/06/2023]
Abstract
Soil microorganisms play crucial roles in ecosystem functioning, and the central goal in microbial ecology studies is to elucidate which factors shape community structure. A better understanding of the relationship between microbial diversity, functions and environmental parameters would increase our ability to set conservation priorities. Here, the bacterial and archaeal community structure in Atlantic Forest, restinga and mangrove soils was described and compared based on shotgun metagenomics. We hypothesized that each distinct site would harbor a distinct taxonomic and functional soil community, which is influenced by environmental parameters. Our data showed that the microbiome is shaped by soil properties, with pH, base saturation, boron and iron content significantly correlated to overall community structure. When data of specific phyla were correlated to specific soil properties, we demonstrated that parameters such as boron, copper, sulfur, potassium and aluminum presented significant correlation with the most number of bacterial groups. Mangrove soil was the most distinct site and presented the highest taxonomic and functional diversity in comparison with forest and restinga soils. From the total 34 microbial phyla identified, 14 were overrepresented in mangrove soils, including several archaeal groups. Mangrove soils hosted a high abundance of sequences related to replication, survival and adaptation; forest soils included high numbers of sequences related to the metabolism of nutrients and other composts; while restinga soils included abundant genes related to the metabolism of carbohydrates. Overall, our finds show that the microbial community structure and functional potential were clearly different across the environmental gradient, followed by functional adaptation and both were related to the soil properties.
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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. ISME J 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] [What about the content of this article? (0)] [Affiliation(s)] [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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Tripathy S, Padhi SK, Mohanty S, Samanta M, Maiti NK. Analysis of the metatranscriptome of microbial communities of an alkaline hot sulfur spring revealed different gene encoding pathway enzymes associated with energy metabolism. Extremophiles 2016; 20:525-36. [DOI: 10.1007/s00792-016-0846-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Accepted: 05/31/2016] [Indexed: 10/21/2022]
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Lin KH, Liao BY, Chang HW, Huang SW, Chang TY, Yang CY, Wang YB, Lin YTK, Wu YW, Tang SL, Yu HT. Metabolic characteristics of dominant microbes and key rare species from an acidic hot spring in Taiwan revealed by metagenomics. BMC Genomics 2015; 16:1029. [PMID: 26630941 PMCID: PMC4668684 DOI: 10.1186/s12864-015-2230-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Accepted: 11/18/2015] [Indexed: 11/10/2022] Open
Abstract
Background Microbial diversity and community structures in acidic hot springs have been characterized by 16S rRNA gene-based diversity surveys. However, our understanding regarding the interactions among microbes, or between microbes and environmental factors, remains limited. Results In the present study, a metagenomic approach, followed by bioinformatics analyses, were used to predict interactions within the microbial ecosystem in Shi-Huang-Ping (SHP), an acidic hot spring in northern Taiwan. Characterizing environmental parameters and potential metabolic pathways highlighted the importance of carbon assimilatory pathways. Four distinct carbon assimilatory pathways were identified in five dominant genera of bacteria. Of those dominant carbon fixers, Hydrogenobaculum bacteria outcompeted other carbon assimilators and dominated the SHP, presumably due to their ability to metabolize hydrogen and to withstand an anaerobic environment with fluctuating temperatures. Furthermore, most dominant microbes were capable of metabolizing inorganic sulfur-related compounds (abundant in SHP). However, Acidithiobacillus ferrooxidans was the only species among key rare microbes with the capability to fix nitrogen, suggesting a key role in nitrogen cycling. In addition to potential metabolic interactions, based on the 16S rRNAs gene sequence of Nanoarchaeum-related and its potential host Ignicoccus-related archaea, as well as sequences of viruses and CRISPR arrays, we inferred that there were complex microbe-microbe interactions. Conclusions Our study provided evidence that there were numerous microbe-microbe and microbe-environment interactions within the microbial community in an acidic hot spring. We proposed that Hydrogenobaculum bacteria were the dominant microbial genus, as they were able to metabolize hydrogen, assimilate carbon and live in an anaerobic environment with fluctuating temperatures. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2230-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Kuei-Han Lin
- Department of Life Science, National Taiwan University, Taipei, 10617, Taiwan, Republic of China.
| | - Ben-Yang Liao
- Division of Biostatistics & Bioinformatics, Institute of Population Health Sciences, National Health Research Institutes, Zhunan Town, Miaoli County, 35053, Taiwan, Republic of China.
| | - Hao-Wei Chang
- Department of Life Science, National Taiwan University, Taipei, 10617, Taiwan, Republic of China. .,Molecular Microbiology and Microbial Pathogenesis Program, Division of Biology and Biomedical Science, Washington University in St. Louis, St. Louis, MO, 63130, USA.
| | - Shiao-Wei Huang
- Department of Life Science, National Taiwan University, Taipei, 10617, Taiwan, Republic of China.
| | - Ting-Yan Chang
- Division of Biostatistics & Bioinformatics, Institute of Population Health Sciences, National Health Research Institutes, Zhunan Town, Miaoli County, 35053, Taiwan, Republic of China.
| | - Cheng-Yu Yang
- Biodiversity Research Center, Academia Sinica, Taipei, 11529, Taiwan, Republic of China.
| | - Yu-Bin Wang
- Department of Life Science, National Taiwan University, Taipei, 10617, Taiwan, Republic of China. .,Institute of Information Science, Academia Sinica, Taipei, 11529, Taiwan, Republic of China.
| | - Yu-Teh Kirk Lin
- Department of Life Science, National Taiwan University, Taipei, 10617, Taiwan, Republic of China. .,Institute of Ecology and Evolutionary Biology, National Taiwan University, Taipei, 10617, Taiwan, Republic of China.
| | - Yu-Wei Wu
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA. .,Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
| | - Sen-Lin Tang
- Biodiversity Research Center, Academia Sinica, Taipei, 11529, Taiwan, Republic of China.
| | - Hon-Tsen Yu
- Department of Life Science, National Taiwan University, Taipei, 10617, Taiwan, Republic of China. .,Degree Program of Genome and Systems Biology, National Taiwan University and Academia Sinica, Taipei, 10617, Taiwan, Republic of China.
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Ittisupornrat S, Tobino T, Yamamoto K. A study of the relationship among sludge retention time, bacterial communities, and hydrolytic enzyme activities in inclined plate membrane bioreactors for the treatment of municipal wastewater. Appl Microbiol Biotechnol 2014; 98:9107-18. [DOI: 10.1007/s00253-014-5914-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2014] [Revised: 06/24/2014] [Accepted: 06/25/2014] [Indexed: 02/03/2023]
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Meyer-dombard DR, Amend JP. Geochemistry and microbial ecology in alkaline hot springs of Ambitle Island, Papua New Guinea. Extremophiles 2014; 18:763-78. [DOI: 10.1007/s00792-014-0657-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2013] [Accepted: 05/18/2014] [Indexed: 11/30/2022]
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Kuang JL, Huang LN, Chen LX, Hua ZS, Li SJ, Hu M, Li JT, Shu WS. Contemporary environmental variation determines microbial diversity patterns in acid mine drainage. ISME J 2013; 7:1038-50. [PMID: 23178673 PMCID: PMC3635239 DOI: 10.1038/ismej.2012.139] [Citation(s) in RCA: 215] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/03/2012] [Revised: 10/01/2012] [Accepted: 10/01/2012] [Indexed: 11/17/2022]
Abstract
A wide array of microorganisms survive and thrive in extreme environments. However, we know little about the patterns of, and controls over, their large-scale ecological distribution. To this end, we have applied a bar-coded 16S rRNA pyrosequencing technology to explore the phylogenetic differentiation among 59 microbial communities from physically and geochemically diverse acid mine drainage (AMD) sites across Southeast China, revealing for the first time environmental variation as the major factor explaining community differences in these harsh environments. Our data showed that overall microbial diversity estimates, including phylogenetic diversity, phylotype richness and pairwise UniFrac distance, were largely correlated with pH conditions. Furthermore, multivariate regression tree analysis also identified solution pH as a strong predictor of relative lineage abundance. Betaproteobacteria, mostly affiliated with the 'Ferrovum' genus, were explicitly predominant in assemblages under moderate pH conditions, whereas Alphaproteobacteria, Euryarchaeota, Gammaproteobacteria and Nitrospira exhibited a strong adaptation to more acidic environments. Strikingly, such pH-dependent patterns could also be observed in a subsequent comprehensive analysis of the environmental distribution of acidophilic microorganisms based on 16S rRNA gene sequences previously retrieved from globally distributed AMD and associated environments, regardless of the long-distance isolation and the distinct substrate types. Collectively, our results suggest that microbial diversity patterns are better predicted by contemporary environmental variation rather than geographical distance in extreme AMD systems.
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Affiliation(s)
- Jia-Liang Kuang
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Li-Nan Huang
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Lin-Xing Chen
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Zheng-Shuang Hua
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Sheng-Jin Li
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Min Hu
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Jin-Tian Li
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Wen-Sheng Shu
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, People's Republic of China
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Satoh T, Watanabe K, Yamamoto H, Yamamoto S, Kurosawa N. Archaeal community structures in the solfataric acidic hot springs with different temperatures and elemental compositions. Archaea 2013; 2013:723871. [PMID: 23710131 DOI: 10.1155/2013/723871] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2012] [Revised: 01/20/2013] [Accepted: 03/24/2013] [Indexed: 11/18/2022]
Abstract
Archaeal 16S rRNA gene compositions and environmental factors of four distinct solfataric acidic hot springs in Kirishima, Japan were compared. The four ponds were selected by differences of temperature and total dissolved elemental concentration as follows: (1) Pond-A: 93°C and 1679 mg L−1, (2) Pond-B: 66°C and 2248 mg L−1, (3) Pond-C: 88°C and 198 mg L−1, and (4) Pond-D: 67°C and 340 mg L−1. In total, 431 clones of 16S rRNA gene were classified into 26 phylotypes. In Pond-B, the archaeal diversity was the highest among the four, and the members of the order Sulfolobales were dominant. The Pond-D also showed relatively high diversity, and the most frequent group was uncultured thermoacidic spring clone group. In contrast to Pond-B and Pond-D, much less diverse archaeal clones were detected in Pond-A and Pond-C showing higher temperatures. However, dominant groups in these ponds were also different from each other. The members of the order Sulfolobales shared 89% of total clones in Pond-A, and the uncultured crenarchaeal groups shared 99% of total Pond-C clones. Therefore, species compositions and biodiversity were clearly different among the ponds showing different temperatures and dissolved elemental concentrations.
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15
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Jiménez DJ, Andreote FD, Chaves D, Montaña JS, Osorio-Forero C, Junca H, Zambrano MM, Baena S. Structural and functional insights from the metagenome of an acidic hot spring microbial planktonic community in the Colombian Andes. PLoS One 2012; 7:e52069. [PMID: 23251687 PMCID: PMC3522619 DOI: 10.1371/journal.pone.0052069] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2012] [Accepted: 11/15/2012] [Indexed: 12/11/2022] Open
Abstract
A taxonomic and annotated functional description of microbial life was deduced from 53 Mb of metagenomic sequence retrieved from a planktonic fraction of the Neotropical high Andean (3,973 meters above sea level) acidic hot spring El Coquito (EC). A classification of unassembled metagenomic reads using different databases showed a high proportion of Gammaproteobacteria and Alphaproteobacteria (in total read affiliation), and through taxonomic affiliation of 16S rRNA gene fragments we observed the presence of Proteobacteria, micro-algae chloroplast and Firmicutes. Reads mapped against the genomes Acidiphilium cryptum JF-5, Legionella pneumophila str. Corby and Acidithiobacillus caldus revealed the presence of transposase-like sequences, potentially involved in horizontal gene transfer. Functional annotation and hierarchical comparison with different datasets obtained by pyrosequencing in different ecosystems showed that the microbial community also contained extensive DNA repair systems, possibly to cope with ultraviolet radiation at such high altitudes. Analysis of genes involved in the nitrogen cycle indicated the presence of dissimilatory nitrate reduction to N2 (narGHI, nirS, norBCDQ and nosZ), associated with Proteobacteria-like sequences. Genes involved in the sulfur cycle (cysDN, cysNC and aprA) indicated adenylsulfate and sulfite production that were affiliated to several bacterial species. In summary, metagenomic sequence data provided insight regarding the structure and possible functions of this hot spring microbial community, describing some groups potentially involved in the nitrogen and sulfur cycling in this environment.
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Affiliation(s)
- Diego Javier Jiménez
- Colombian Center for Genomic and Bioinformatics from Extreme Environments (GeBiX), Bogotá, Colombia.
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16
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Abstract
Magnesium plays a special role in biochemistry because of its ability to coordinate six oxygen atoms efficiently in its first coordination shell. Such oxygen atoms may be part of one or two charged oxyanions, which means that Mg²⁺ can, for instance, tie together two different phosphate groups that are located at distance from each other in a macromolecule, and in this way be responsible for the folding of molecules like RNA. This property of Mg²⁺ also helps the stabilization of diphosphate and triphosphate groups of nucleotides, as well as promoting the condensation of orthophosphate to oligophosphates, like pyrophosphate and trimetaphosphate. Borates, on the other hand, are known to promote the formation of nucleobases and carbohydrates, ribose in particular, which is yet another constituent of nucleotides. The oldest borate minerals that we find on Earth today are magnesium borates. Dissolved borate stabilizes pentose sugars by forming complexes with cis-hydroxyl groups. In the furanose form of ribose, the preferential binding occurs to the 2 and 3 carbon, leaving the 5 carbon free for phosphorylation. The central role of Mg²⁺ in the function of ribozymes and its 'archaic' position in ribosomes, and the fact that magnesium generally has coordination properties different from other cations, suggests that the inorganic chemistry of magnesium had a key position in the first chemical processes leading to the origin and early evolution of life.
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Affiliation(s)
- N G Holm
- Department of Geological Sciences, Stockholm University, Stockholm, Sweden.
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Huang Q, Dong CZ, Dong RM, Jiang H, Wang S, Wang G, Fang B, Ding X, Niu L, Li X, Zhang C, Dong H. Archaeal and bacterial diversity in hot springs on the Tibetan Plateau, China. Extremophiles 2011; 15:549-63. [PMID: 21695489 DOI: 10.1007/s00792-011-0386-z] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2010] [Accepted: 06/06/2011] [Indexed: 11/24/2022]
Abstract
The diversity of archaea and bacteria was investigated in ten hot springs (elevation >4600 m above sea level) in Central and Central-Eastern Tibet using 16S rRNA gene phylogenetic analysis. The temperature and pH of these hot springs were 26-81°C and close to neutral, respectively. A total of 959 (415 and 544 for bacteria and archaea, respectively) clone sequences were obtained. Phylogenetic analysis showed that bacteria were more diverse than archaea and that these clone sequences were classified into 82 bacterial and 41 archaeal operational taxonomic units (OTUs), respectively. The retrieved bacterial clones were mainly affiliated with four known groups (i.e., Firmicutes, Proteobacteria, Cyanobacteria, Chloroflexi), which were similar to those in other neutral-pH hot springs at low elevations. In contrast, most of the archaeal clones from the Tibetan hot springs were affiliated with Thaumarchaeota, a newly proposed archaeal phylum. The dominance of Thaumarchaeota in the archaeal community of the Tibetan hot springs appears to be unique, although the exact reasons are not yet known. Statistical analysis showed that diversity indices of both archaea and bacteria were not statistically correlated with temperature, which is consistent with previous studies.
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Affiliation(s)
- Qiuyuan Huang
- Department of Geology, Miami University, Oxford, OH 45056, USA
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