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Chen JS, Hussain B, Tsai HC, Nagarajan V, Koner S, Hsu BM. Analysis and interpretation of hot springs water, biofilms, and sediment bacterial community profiling and their metabolic potential in the area of Taiwan geothermal ecosystem. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 856:159115. [PMID: 36181827 DOI: 10.1016/j.scitotenv.2022.159115] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 09/21/2022] [Accepted: 09/25/2022] [Indexed: 06/16/2023]
Abstract
Microorganisms developed a mechanism that copes with heat, acidity, and high dissolved metal concentrations that likely first evolved. The geothermal fluids emerging in the geothermal springs of Taiwan, located at a subduction zone, are still under signs of progress in the characterization of the various microbial taxonomic changes over time. However, no systematic studies have been performed to compare water, biofilms, and sediment bacterial communities and the primary driving force of dissolved and mineral substrates capable of supporting microbial metabolism. In this study, 16S rRNA gene sequencing was employed for bacterial community exploration, and their potential metabolic pathways involved from water, biofilms, and sediment samples, collected from the geothermal valley (Ti-re-ku). Metagenomic data revealed that the water samples had higher bacterial diversity and richness than biofilms and sediment samples. At the genus level, Alicyclobacillus, Thiomonas, Acidocella, Metallibacterium, Picrophilus, and Legionella were significantly abundant in the water samples. The biofilms were rich in Aciditerrimonas, Bacillus, Acidithiobacillus, and Lysinibacillus, whereas the sediment samples were abundant in Sulfobacillus. The PICRUSt2-predicted functional results revealed that heavy metal-related functions such as heavy-metal exporter system, cobalt‑zinc‑cadmium resistance, arsenical pump, high-affinity nickel-transport, and copper resistance metabolisms were significant in the water samples. Moreover, sulfur-related pathways such as thiosulfate oxidation, dissimilatory sulfate reduction, and assimilatory sulfate reduction were important in water samples, followed by biofilms and sediment. Therefore, our findings highlighted the comparative taxonomic diversity and functional composition contributions to geothermal fluid, with implications for understanding the evolution and ecological niche dimension of microbes which are the key to geothermal ecosystem function.
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Affiliation(s)
- Jung-Sheng Chen
- Department of Medical Research, E-Da Hospital, Kaohsiung City 824, Taiwan
| | - Bashir Hussain
- Department of Earth and Environmental Sciences, National Chung Cheng University, Chiayi County 621, Taiwan; Department of Biomedical Sciences, National Chung Cheng University, Chiayi County 621, Taiwan
| | - Hsin-Chi Tsai
- Department of Psychiatry, School of Medicine, Tzu Chi University, Hualien 970, Taiwan; Department of Psychiatry, Tzu-Chi General Hospital, Hualien 970, Taiwan
| | - Viji Nagarajan
- Department of Earth and Environmental Sciences, National Chung Cheng University, Chiayi County 621, Taiwan
| | - Suprokash Koner
- Department of Earth and Environmental Sciences, National Chung Cheng University, Chiayi County 621, Taiwan; Department of Biomedical Sciences, National Chung Cheng University, Chiayi County 621, Taiwan
| | - Bing-Mu Hsu
- Department of Earth and Environmental Sciences, National Chung Cheng University, Chiayi County 621, Taiwan; Center for Innovative Research on Aging Society (CIRAS), National Chung Cheng University, Chiayi County 621, Taiwan.
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Mueller RC, Peach JT, Skorupa DJ, Copié V, Bothner B, Peyton BM. An emerging view of the diversity, ecology and function of Archaea in alkaline hydrothermal environments. FEMS Microbiol Ecol 2021; 97:6021323. [PMID: 33501490 DOI: 10.1093/femsec/fiaa246] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 12/01/2020] [Indexed: 11/15/2022] Open
Abstract
The described diversity within the domain Archaea has recently expanded due to advances in sequencing technologies, but many habitats that likely harbor novel lineages of archaea remain understudied. Knowledge of archaea within natural and engineered hydrothermal systems, such as hot springs and engineered subsurface habitats, has been steadily increasing, but the majority of the work has focused on archaea living in acidic or circumneutral environments. The environmental pressures exerted by the combination of high temperatures and high pH likely select for divergent communities and distinct metabolic pathways from those observed in acidic or circumneutral systems. In this review, we examine what is currently known about the archaea found in thermoalkaline environments, focusing on the detection of novel lineages and knowledge of the ecology, metabolic pathways and functions of these populations and communities. We also discuss the potential of emerging multi-omics approaches, including proteomics and metabolomics, to enhance our understanding of archaea within extreme thermoalkaline systems.
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Affiliation(s)
- Rebecca C Mueller
- Department of Chemical and Biological Engineering, Montana State University,Bozeman, MT 59717, PO Box 173920, USA.,Thermal Biology Institute, Montana State University, Bozeman, MT 59717, PO Box 173142, USA
| | - Jesse T Peach
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, PO Box 173400, USA
| | - Dana J Skorupa
- Department of Chemical and Biological Engineering, Montana State University,Bozeman, MT 59717, PO Box 173920, USA.,Thermal Biology Institute, Montana State University, Bozeman, MT 59717, PO Box 173142, USA
| | - Valerie Copié
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, PO Box 173400, USA.,Thermal Biology Institute, Montana State University, Bozeman, MT 59717, PO Box 173142, USA
| | - Brian Bothner
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, PO Box 173400, USA.,Thermal Biology Institute, Montana State University, Bozeman, MT 59717, PO Box 173142, USA
| | - Brent M Peyton
- Department of Chemical and Biological Engineering, Montana State University,Bozeman, MT 59717, PO Box 173920, USA.,Thermal Biology Institute, Montana State University, Bozeman, MT 59717, PO Box 173142, USA
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Podar PT, Yang Z, Björnsdóttir SH, Podar M. Comparative Analysis of Microbial Diversity Across Temperature Gradients in Hot Springs From Yellowstone and Iceland. Front Microbiol 2020; 11:1625. [PMID: 32760379 PMCID: PMC7372906 DOI: 10.3389/fmicb.2020.01625] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2020] [Accepted: 06/22/2020] [Indexed: 11/21/2022] Open
Abstract
Geothermal hot springs are a natural setting to study microbial adaptation to a wide range of temperatures reaching up to boiling. Temperature gradients lead to distinct microbial communities that inhabit their optimum niches. We sampled three alkaline, high temperature (80-100°C) hot springs in Yellowstone and Iceland that had cooling outflows and whose microbial communities had not been studied previously. The microbial composition in sediments and mats was determined by DNA sequencing of rRNA gene amplicons. Over three dozen phyla of Archaea and Bacteria were identified, representing over 1700 distinct organisms. We observed a significant non-linear reduction in the number of microbial taxa as the temperature increased from warm (38°C) to boiling. At high taxonomic levels, the community structure was similar between the Yellowstone and Iceland hot springs. We identified potential endemism at the genus level, especially in thermophilic phototrophs, which may have been potentially driven by distinct environmental conditions and dispersal limitations.
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Affiliation(s)
- Peter T. Podar
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Zamin Yang
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | | | - Mircea Podar
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
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4
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Archaeal community compositions in tilapia pond systems and their influencing factors. World J Microbiol Biotechnol 2018; 34:43. [PMID: 29492679 DOI: 10.1007/s11274-018-2412-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Accepted: 01/12/2018] [Indexed: 10/17/2022]
Abstract
Archaea, like the bacterial communities are gradually being realized as key players in the biogeochemical progress of water ecosystems. In this study, tilapia aquaculture ponds were used for an in-depth understanding of archaeal community compositions in water and surface sediment. Some of the main functions, as well as the communities' response patterns, to time variations, pond differences and some physio-chemical parameters were investigated. The results revealed the dominant phylum in both the water and surface sediment, as Euryarchaeota, while, the most abundant classes were: Halobacteria and Methanomicrobia respectively. Significant differences in the archaeal community compositions in the water and surface sediment, were observed in the early stages of cultivation, which became minimal at the later stage of the GIFT tilapia cultivation. Additionally to the differences in the most abundant classes, more OTUs were observed in water samples than in surface sediment samples. The methane generation could be attributed to the large proportion of methanogens found in both pond water and in the surface sediment. Furthermore, the archaeal community compositions in water and the surface sediment were shaped mainly by temporal variations and pond differences respectively. In the pond water, the archaeal community compositions were highly co-related to the concentration changes of ammonia, sulfate and total nitrogen; while in the surface sediment, the correlation to the content changes was significant in total phosphorus. The archaeal community compositions in surface sediment should be considered as an indicator for future environmental capacity studies in aquaculture.
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Rozanov AS, Bryanskaya AV, Ivanisenko TV, Malup TK, Peltek SE. Biodiversity of the microbial mat of the Garga hot spring. BMC Evol Biol 2017; 17:254. [PMID: 29297382 PMCID: PMC5751763 DOI: 10.1186/s12862-017-1106-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
BACKGROUND Microbial mats are a good model system for ecological and evolutionary analysis of microbial communities. There are more than 20 alkaline hot springs on the banks of the Barguzin river inflows. Water temperature reaches 75 °C and pH is usually 8.0-9.0. The formation of microbial mats is observed in all hot springs. Microbial communities of hot springs of the Baikal rift zone are poorly studied. Garga is the biggest hot spring in this area. RESULTS In this study, we investigated bacterial and archaeal diversity of the Garga hot spring (Baikal rift zone, Russia) using 16S rRNA metagenomic sequencing. We studied two types of microbial communities: (i) small white biofilms on rocks in the points with the highest temperature (75 °C) and (ii) continuous thick phototrophic microbial mats observed at temperatures below 70 °C. Archaea (mainly Crenarchaeota; 19.8% of the total sequences) were detected only in the small biofilms. The high abundance of Archaea in the sample from hot springs of the Baikal rift zone supplemented our knowledge of the distribution of Archaea. Most archaeal sequences had low similarity to known Archaea. In the microbial mats, primary products were formed by cyanobacteria of the genus Leptolyngbya. Heterotrophic microorganisms were mostly represented by Actinobacteria and Proteobacteria in all studied samples of the microbial mats. Planctomycetes, Chloroflexi, and Chlorobi were abundant in the middle layer of the microbial mats, while heterotrophic microorganisms represented mostly by Firmicutes (Clostridia, strict anaerobes) dominated in the bottom part. Besides prokaryotes, we detect some species of Algae with help of detection their chloroplasts 16 s rRNA. CONCLUSIONS High abundance of Archaea in samples from hot springs of the Baikal rift zone supplemented our knowledge of the distribution of Archaea. Most archaeal sequences had low similarity to known Archaea. Metagenomic analysis of microbial communities of the microbial mat of Garga hot spring showed that the three studied points sampled at 70 °C, 55 °C, and 45 °C had similar species composition. Cyanobacteria of the genus Leptolyngbya dominated in the upper layer of the microbial mat. Chloroflexi and Chlorobi were less abundant and were mostly observed in the middle part of the microbial mat. We detected domains of heterotrophic organisms in high abundance (Proteobacteria, Firmicutes, Verrucomicrobia, Planctomicetes, Bacteroidetes, Actinobacteria, Thermi), according to metabolic properties of known relatives, which can form complete cycles of carbon, sulphur, and nitrogen in the microbial mat. The studied microbial mats evolved in early stages of biosphere formation. They can live autonomously, providing full cycles of substances and preventing live activity products poisoning.
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Affiliation(s)
- Alexey Sergeevich Rozanov
- Federal Research Center Institute of Cytology and Genetics, the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.
| | - Alla Victorovna Bryanskaya
- Federal Research Center Institute of Cytology and Genetics, the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Timofey Vladimirovich Ivanisenko
- Federal Research Center Institute of Cytology and Genetics, the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.,Novosibirsk State University, Novosibirsk, Russia
| | - Tatyana Konstantinovna Malup
- Federal Research Center Institute of Cytology and Genetics, the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Sergey Evgenievich Peltek
- Federal Research Center Institute of Cytology and Genetics, the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
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Fan L, Song C, Meng S, Qiu L, Zheng Y, Wu W, Qu J, Li D, Zhang C, Hu G, Chen J. Spatial distribution of planktonic bacterial and archaeal communities in the upper section of the tidal reach in Yangtze River. Sci Rep 2016; 6:39147. [PMID: 27966673 PMCID: PMC5155431 DOI: 10.1038/srep39147] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Accepted: 11/18/2016] [Indexed: 12/14/2022] Open
Abstract
Bacterioplankton and archaeaplankton communities play key roles in the biogeochemical processes of water, and they may be affected by many factors. In this study, we used high-throughput 16S rRNA gene sequencing to profile planktonic bacterial and archaeal community compositions in the upper section of the tidal reach in Yangtze River. We found that the predominant bacterial phyla in this river section were Proteobacteria, Firmicutes, and Actinobacteria, whereas the predominant archaeal classes were Halobacteria, Methanomicrobia, and unclassified Euryarchaeota. Additionally, the bacterial and archaeal community compositions, richnesses, functional profiles, and ordinations were affected by the spatial heterogeneity related to the concentration changes of sulphate or nitrate. Notably, the bacterial community was more sensitive than the archaeal community to changes in the spatial characteristics of this river section. These findings provide important insights into the distributions of bacterial and archaeal communities in natural water habitats.
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Affiliation(s)
- Limin Fan
- Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Scientific Observing and Experimental Station of Fishery Resources and Environment in the Lower Reaches of the Yangtze River, Wuxi 214081, China
| | - Chao Song
- Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Scientific Observing and Experimental Station of Fishery Resources and Environment in the Lower Reaches of the Yangtze River, Wuxi 214081, China
| | - Shunlong Meng
- Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Scientific Observing and Experimental Station of Fishery Resources and Environment in the Lower Reaches of the Yangtze River, Wuxi 214081, China
| | - Liping Qiu
- Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Scientific Observing and Experimental Station of Fishery Resources and Environment in the Lower Reaches of the Yangtze River, Wuxi 214081, China
| | - Yao Zheng
- Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Scientific Observing and Experimental Station of Fishery Resources and Environment in the Lower Reaches of the Yangtze River, Wuxi 214081, China
| | - Wei Wu
- Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Scientific Observing and Experimental Station of Fishery Resources and Environment in the Lower Reaches of the Yangtze River, Wuxi 214081, China
| | - Jianhong Qu
- Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Scientific Observing and Experimental Station of Fishery Resources and Environment in the Lower Reaches of the Yangtze River, Wuxi 214081, China
| | - Dandan Li
- Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Scientific Observing and Experimental Station of Fishery Resources and Environment in the Lower Reaches of the Yangtze River, Wuxi 214081, China
| | - Cong Zhang
- Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Scientific Observing and Experimental Station of Fishery Resources and Environment in the Lower Reaches of the Yangtze River, Wuxi 214081, China
| | - Gengdong Hu
- Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Scientific Observing and Experimental Station of Fishery Resources and Environment in the Lower Reaches of the Yangtze River, Wuxi 214081, China
| | - Jiazhang Chen
- Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Scientific Observing and Experimental Station of Fishery Resources and Environment in the Lower Reaches of the Yangtze River, Wuxi 214081, China
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7
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Panda AK, Bisht SS, De Mandal S, Kumar NS. Bacterial and archeal community composition in hot springs from Indo-Burma region, North-east India. AMB Express 2016; 6:111. [PMID: 27832517 PMCID: PMC5104702 DOI: 10.1186/s13568-016-0284-y] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Accepted: 11/02/2016] [Indexed: 11/24/2022] Open
Abstract
Bacterial and archaeal diversity of two alkaline Indian hot springs, Jakrem (Meghalaya) and Yumthang (Sikkim), were studied. Thirteen major bacterial phyla were identified of which Firmicutes, Chloroflexi and Thermi were dominant in Jakrem and Proteobacteria in Yumthang. The dominant genera were Clostridium, Chloroflexus and Meiothermus at Jakrem (water temperature 46 °C, pH 9) and Thiobacillus, Sulfuritalea at Yumthang (water temperature 39 °C, pH 8) hot springs. The four Euryarchaeota taxa that were observed in both the hot springs were Methanoculleus, Methanosaeta, Methanosarcina and Methanocorposculum. Elstera litoralis, Thiovirga sp., Turneriella sp. were observed for the first time in association with hot springs along with Tepidibacter sp., Ignavibacterium sp., Teribacillus sp. and Dechloromonas sp. Individual bacterial phyla were found to be specifically correlated with certain physico-chemical factors such as temperature, dissolved SiO2, elemental S, total sulphide, calcium concentrations in hot spring water. Bacterial reads involved in sulfur cycle were identified in both16S rRNA gene library and sulfur metabolism may play key physiological functions in this hot spring. Members within Desulfobacterales and Thermodesulfovibrionaceae were identified and hypothesized their role in regulating sulfur cycle. The presence of many taxonomically unsolved sequences in the 16S rRNA gene tag datasets from these hot springs could be a sign of novel microbe richness in these less known hot water bodies of Northeastern India.
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Sakai HD, Kurosawa N. Exploration and isolation of novel thermophiles in frozen enrichment cultures derived from a terrestrial acidic hot spring. Extremophiles 2016; 20:207-14. [PMID: 26860120 DOI: 10.1007/s00792-016-0815-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Accepted: 01/28/2016] [Indexed: 11/25/2022]
Abstract
An isolation strategy, exploring novel microorganisms in frozen enrichment cultures (ENFE), which uses a combination of enrichment culture and 16S rRNA gene clone analysis, was evaluated for isolating uncultured thermophiles from a terrestrial acidic hot spring. The procedure comprised (a) multiple enrichment cultures under various conditions, (b) cryostorage of all enrichments, (c) microbial community analyses of the enrichments using 16S rRNA gene sequences, and (d) purification of microorganisms from enrichments containing previously uncultured microorganisms. The enrichments were performed under a total of 36 conditions, and 16 of these enrichments yielded positive microbial growth with the detection of three previously uncultured archaea. Two of the three previously uncultured archaea, strains HS-1 and HS-3, were successfully isolated. Strain HS-1 and HS-3 represented a novel lineage of the order Sulfolobales and novel species of the genus Sulfolobus, respectively. Although innovative isolation methods play strategic roles in isolating previously uncultured microorganisms, the ENFE strategy showed potential for characterizing and isolating such microorganisms using conventional media and techniques.
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Affiliation(s)
- Hiroyuki D Sakai
- Department of Science and Engineering for Sustainable Innovation, Faculty of Science and Engineering, Soka University, 1-236 Tangi-machi, Hachioji, Tokyo 192-8577, Japan
| | - Norio Kurosawa
- Department of Science and Engineering for Sustainable Innovation, Faculty of Science and Engineering, Soka University, 1-236 Tangi-machi, Hachioji, Tokyo 192-8577, Japan.
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Wall K, Cornell J, Bizzoco RW, Kelley ST. Biodiversity hot spot on a hot spot: novel extremophile diversity in Hawaiian fumaroles. Microbiologyopen 2015; 4:267-281. [PMID: 25565172 PMCID: PMC4398508 DOI: 10.1002/mbo3.236] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2014] [Revised: 11/18/2014] [Accepted: 11/24/2014] [Indexed: 02/01/2023] Open
Abstract
Fumaroles (steam vents) are the most common, yet least understood, microbial habitat in terrestrial geothermal settings. Long believed too extreme for life, recent advances in sample collection and DNA extraction methods have found that fumarole deposits and subsurface waters harbor a considerable diversity of viable microbes. In this study, we applied culture-independent molecular methods to explore fumarole deposit microbial assemblages in 15 different fumaroles in four geographic locations on the Big Island of Hawai'i. Just over half of the vents yielded sufficient high-quality DNA for the construction of 16S ribosomal RNA gene sequence clone libraries. The bacterial clone libraries contained sequences belonging to 11 recognized bacterial divisions and seven other division-level phylogenetic groups. Archaeal sequences were less numerous, but similarly diverse. The taxonomic composition among fumarole deposits was highly heterogeneous. Phylogenetic analysis found cloned fumarole sequences were related to microbes identified from a broad array of globally distributed ecotypes, including hot springs, terrestrial soils, and industrial waste sites. Our results suggest that fumarole deposits function as an “extremophile collector” and may be a hot spot of novel extremophile biodiversity.
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Affiliation(s)
- Kate Wall
- Department of Biology, San Diego State University, 5500 Campanile Drive, San Diego, California
| | - Jennifer Cornell
- Department of Biology, San Diego State University, 5500 Campanile Drive, San Diego, California
| | - Richard W Bizzoco
- Department of Biology, San Diego State University, 5500 Campanile Drive, San Diego, California
| | - Scott T Kelley
- Department of Biology, San Diego State University, 5500 Campanile Drive, San Diego, California
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10
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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] [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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Song ZQ, Wang FP, Zhi XY, Chen JQ, Zhou EM, Liang F, Xiao X, Tang SK, Jiang HC, Zhang CL, Dong H, Li WJ. Bacterial and archaeal diversities in Yunnan and Tibetan hot springs, China. Environ Microbiol 2012; 15:1160-75. [PMID: 23126508 DOI: 10.1111/1462-2920.12025] [Citation(s) in RCA: 94] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2011] [Revised: 09/17/2012] [Accepted: 10/09/2012] [Indexed: 11/27/2022]
Abstract
Thousands of hot springs are located in the north-eastern part of the Yunnan-Tibet geothermal zone, which is one of the most active geothermal areas in the world. However, a comprehensive and detailed understanding of microbial diversity in these hot springs is still lacking. In this study, bacterial and archaeal diversities were investigated in 16 hot springs (pH 3.2-8.6; temperature 47-96°C) in Yunnan Province and Tibet, China by using a barcoded 16S rRNA gene-pyrosequencing approach. Aquificae, Proteobacteria, Firmicutes, Deinococcus-Thermus and Bacteroidetes comprised the large portion of the bacterial communities in acidic hot springs. Non-acidic hot springs harboured more and variable bacterial phyla than acidic springs. Desulfurococcales and unclassified Crenarchaeota were the dominated groups in archaeal populations from most of the non-acidic hot springs; whereas, the archaeal community structure in acidic hot springs was simpler and characterized by Sulfolobales and Thermoplasmata. The phylogenetic analyses showed that Aquificae and Crenarchaeota were predominant in the investigated springs and possessed many phylogenetic lineages that have never been detected in other hot springs in the world. Thus findings from this study significantly improve our understanding of microbial diversity in terrestrial hot springs.
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Affiliation(s)
- Zhao-Qi Song
- Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education, Laboratory for Conservation and Utilization of Bio-resources, Yunnan Institute of Microbiology, Yunnan University, Kunming, 650091, China
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