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Zhang Z, Liu T, Li X, Ye Q, Bangash HI, Zheng J, Peng N. Metagenome-assembled genomes reveal carbohydrate degradation and element metabolism of microorganisms inhabiting Tengchong hot springs, China. ENVIRONMENTAL RESEARCH 2023; 238:117144. [PMID: 37716381 DOI: 10.1016/j.envres.2023.117144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 08/31/2023] [Accepted: 09/13/2023] [Indexed: 09/18/2023]
Abstract
A hot spring is a distinctive aquatic environment that provides an excellent system to investigate microorganisms and their function in elemental cycling processes. Previous studies of terrestrial hot springs have been mostly focused on the microbial community, one special phylum or category, or genes involved in a particular metabolic step, while little is known about the overall functional metabolic profiles of microorganisms inhabiting the terrestrial hot springs. Here, we analyzed the microbial community structure and their functional genes based on metagenomic sequencing of six selected hot springs with different temperature and pH conditions. We sequenced a total of 11 samples from six hot springs and constructed 162 metagenome-assembled genomes (MAGs) with completeness above 70% and contamination lower than 10%. Crenarchaeota, Euryarchaeota and Aquificae were found to be the dominant phyla. Functional annotation revealed that bacteria encode versatile carbohydrate-active enzymes (CAZYmes) for the degradation of complex polysaccharides, while archaea tend to assimilate C1 compounds through carbon fixation. Under nitrogen-deficient conditions, there were correspondingly fewer genes involved in nitrogen metabolism, while abundant and diverse set of genes participating in sulfur metabolism, particularly those associated with sulfide oxidation and thiosulfate disproportionation. In summary, archaea and bacteria residing in the hot springs display distinct carbon metabolism fate, while sharing the common energy preference through sulfur metabolism. Overall, this research contributes to a better comprehension of biogeochemistry of terrestrial hot springs.
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Affiliation(s)
- Zhufeng Zhang
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, People's Republic of China
| | - Tao Liu
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, People's Republic of China.
| | - Xudong Li
- State Key Laboratory of Agricultural Microbiology, Hubei Key Laboratory of Agricultural Bioinformatics, Huazhong Agricultural University, Wuhan, Hubei, People's Republic of China
| | - Qing Ye
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, People's Republic of China
| | - Hina Iqbal Bangash
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, People's Republic of China
| | - Jinshui Zheng
- State Key Laboratory of Agricultural Microbiology, Hubei Key Laboratory of Agricultural Bioinformatics, Huazhong Agricultural University, Wuhan, Hubei, People's Republic of China
| | - Nan Peng
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, People's Republic of China.
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Influence of Geochemistry in the Tropical Hot Springs on Microbial Community Structure and Function. Curr Microbiol 2022; 80:4. [PMID: 36434287 DOI: 10.1007/s00284-022-03118-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 11/10/2022] [Indexed: 11/26/2022]
Abstract
Thermophiles inhabiting high temperatures are considered primitive microorganisms on early Earth. In this regard, several works have demonstrated microbial community composition in geothermal environments. Despite that, studies on hot springs located in the Indian subcontinent viz., Surajkund in the district Hazaribag, Jharkhand; Bakreshwar in the district Birbhum, West Bengal; Tantloi in the district Dumka, and Sidpur in the district Pakur, Jharkhand are scanty. Nonetheless, the metagenomic analysis of these hot springs showed significant differences in the predominant phyla corresponding to geochemical properties. The Chloroflexi, Proteobacteria, Actinobacteria, Deinococcus-Thermus, and Firmicutes were dominant phyla in all the samples. In contrast, Meiothermus was more in comparatively low-temperature hot springs. In addition, archaeal phyla, Euryarchaeota, Candidatus Bathyarchaeota, and Crenarchaeota were predominant in all samples. The canonical correspondence analysis (CCA) showed the abundance of Deinococcus, Thermus, Pyrobaculum, Kocuria, and Geodermatophilus positively correlated with the aqueous concentration of sulfate, fluoride, and argon in relatively high-temperature (≥ 72 °C) hot springs. However, at a lower temperature (≤ 63 °C), Thermodesulfovibrio, Caldilinea, Chloroflexus, Meiothermus, and Tepidimonas are positively correlated with the concentration of zinc, iron, and dissolved oxygen. Further, hierarchical clustering exhibits variations in its functional attributes depending on the temperature gradients. Metagenome analysis predicted carbon, methane, sulfur, and nitrogen metabolism genes, indicating a wide range of bacteria and archaea habitation in these hot springs. In addition, identified several genes encode polyketide biosynthesis pathways. The present study described the microbial community composition and function in the tropical hot springs and their relationship with the environmental variables.
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Twing KI, Ward LM, Kane ZK, Sanders A, Price RE, Pendleton HL, Giovannelli D, Brazelton WJ, McGlynn SE. Microbial ecology of a shallow alkaline hydrothermal vent: Strýtan Hydrothermal Field, Eyjafördur, northern Iceland. Front Microbiol 2022; 13:960335. [PMID: 36466646 PMCID: PMC9713835 DOI: 10.3389/fmicb.2022.960335] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 08/05/2022] [Indexed: 10/20/2023] Open
Abstract
Strýtan Hydrothermal Field (SHF) is a submarine system located in Eyjafördur in northern Iceland composed of two main vents: Big Strýtan and Arnarnesstrýtan. The vents are shallow, ranging from 16 to 70 m water depth, and vent high pH (up to 10.2), moderate temperature (T max ∼70°C), anoxic, fresh fluids elevated in dissolved silica, with slightly elevated concentrations of hydrogen and methane. In contrast to other alkaline hydrothermal vents, SHF is unique because it is hosted in basalt and therefore the high pH is not created by serpentinization. While previous studies have assessed the geology and geochemistry of this site, the microbial diversity of SHF has not been explored in detail. Here we present a microbial diversity survey of the actively venting fluids and chimneys from Big Strýtan and Arnarnesstrýtan, using 16S rRNA gene amplicon sequencing. Community members from the vent fluids are mostly aerobic heterotrophic bacteria; however, within the chimneys oxic, low oxygen, and anoxic habitats could be distinguished, where taxa putatively capable of acetogenesis, sulfur-cycling, and hydrogen metabolism were observed. Very few archaea were observed in the samples. The inhabitants of SHF are more similar to terrestrial hot spring samples than other marine sites. It has been hypothesized that life on Earth (and elsewhere in the solar system) could have originated in an alkaline hydrothermal system, however all other studied alkaline submarine hydrothermal systems to date are fueled by serpentinization. SHF adds to our understandings of hydrothermal vents in relationship to microbial diversity, evolution, and possibly the origin of life.
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Affiliation(s)
- Katrina I. Twing
- School of Biological Sciences, The University of Utah, Salt Lake City, UT, United States
- Department of Microbiology, Weber State University, Ogden, UT, United States
| | - L. M. Ward
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, Japan
- Department of Geosciences, Smith College, Northampton, MA, United States
| | - Zachary K. Kane
- Department of Microbiology, Weber State University, Ogden, UT, United States
| | - Alexa Sanders
- Department of Microbiology, Weber State University, Ogden, UT, United States
| | - Roy Edward Price
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY, United States
| | - H. Lizethe Pendleton
- School of Biological Sciences, The University of Utah, Salt Lake City, UT, United States
| | - Donato Giovannelli
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, Japan
- Department of Biology, University of Naples “Federico II”, Naples, Italy
| | - William J. Brazelton
- School of Biological Sciences, The University of Utah, Salt Lake City, UT, United States
| | - Shawn E. McGlynn
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, Japan
- Center for Sustainable Resource Science, RIKEN, Saitama, Japan
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Peach JT, Mueller RC, Skorupa DJ, Mesle MM, Kanta S, Boltinghouse E, Sharon B, Copié V, Bothner B, Peyton BM. Longitudinal analysis of the Five Sisters hot springs in Yellowstone National Park reveals a dynamic thermoalkaline environment. Sci Rep 2022; 12:18707. [PMID: 36333441 PMCID: PMC9636164 DOI: 10.1038/s41598-022-22047-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 10/07/2022] [Indexed: 11/06/2022] Open
Abstract
Research focused on microbial populations of thermoalkaline springs has been driven in a large part by the lure of discovering functional enzymes with industrial applications in high-pH and high temperature environments. While several studies have focused on understanding the fundamental ecology of these springs, the small molecule profiles of thermoalkaline springs have largely been overlooked. To better understand how geochemistry, small molecule composition, and microbial communities are connected, we conducted a three-year study of the Five Sisters (FS) springs that included high-resolution geochemical measurements, 16S rRNA sequencing of the bacterial and archaeal community, and mass spectrometry-based metabolite and extracellular small molecule characterization. Integration of the four datasets facilitated a comprehensive analysis of the interwoven thermoalkaline spring system. Over the course of the study, the microbial population responded to changing environmental conditions, with archaeal populations decreasing in both relative abundance and diversity compared to bacterial populations. Decreases in the relative abundance of Archaea were associated with environmental changes that included decreased availability of specific nitrogen- and sulfur-containing extracellular small molecules and fluctuations in metabolic pathways associated with nitrogen cycling. This multi-factorial analysis demonstrates that the microbial community composition is more closely correlated with pools of extracellular small molecules than with the geochemistry of the thermal springs. This is a novel finding and suggests that a previously overlooked component of thermal springs may have a significant impact on microbial community composition.
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Affiliation(s)
- Jesse T. Peach
- grid.41891.350000 0001 2156 6108Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717 USA
| | - Rebecca C. Mueller
- grid.41891.350000 0001 2156 6108Thermal Biology Institute, Montana State University, Bozeman, MT 59717 USA ,grid.41891.350000 0001 2156 6108Chemical and Biological Engineering Department, Center for Biofilm Engineering, Montana State University, Bozeman, MT 59717 USA
| | - Dana J. Skorupa
- grid.41891.350000 0001 2156 6108Thermal Biology Institute, Montana State University, Bozeman, MT 59717 USA ,grid.41891.350000 0001 2156 6108Chemical and Biological Engineering Department, Center for Biofilm Engineering, Montana State University, Bozeman, MT 59717 USA
| | - Margaux M. Mesle
- grid.41891.350000 0001 2156 6108Thermal Biology Institute, Montana State University, Bozeman, MT 59717 USA ,grid.41891.350000 0001 2156 6108Chemical and Biological Engineering Department, Center for Biofilm Engineering, Montana State University, Bozeman, MT 59717 USA
| | - Sutton Kanta
- grid.41891.350000 0001 2156 6108Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717 USA
| | - Eric Boltinghouse
- grid.41891.350000 0001 2156 6108Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717 USA
| | - Bailey Sharon
- grid.41891.350000 0001 2156 6108Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717 USA
| | - Valerie Copié
- grid.41891.350000 0001 2156 6108Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717 USA
| | - Brian Bothner
- grid.41891.350000 0001 2156 6108Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717 USA ,grid.41891.350000 0001 2156 6108Thermal Biology Institute, Montana State University, Bozeman, MT 59717 USA
| | - Brent M. Peyton
- grid.41891.350000 0001 2156 6108Thermal Biology Institute, Montana State University, Bozeman, MT 59717 USA ,grid.41891.350000 0001 2156 6108Chemical and Biological Engineering Department, Center for Biofilm Engineering, Montana State University, Bozeman, MT 59717 USA ,grid.41891.350000 0001 2156 6108Department of Biological and Chemical Engineering, Montana State University, Bozeman, MT 59717 USA
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5
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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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Podosokorskaya OA, Kochetkova TV, Novikov AA, Toshchakov SV, Elcheninov AG, Kublanov IV. Tenuifilum thalassicum gen. nov., sp. nov., a novel moderate thermophilic anaerobic bacterium from a Kunashir Island shallow hot spring representing a new family Tenuifilaceae fam. nov. in the class Bacteroidia. Syst Appl Microbiol 2020; 43:126126. [DOI: 10.1016/j.syapm.2020.126126] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 07/15/2020] [Accepted: 07/16/2020] [Indexed: 01/23/2023]
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7
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Kumar R, Sharma RC. Microbial diversity in relation to physico-chemical properties of hot water ponds located in the Yamunotri landscape of Garhwal Himalaya. Heliyon 2020; 6:e04850. [PMID: 32954033 PMCID: PMC7486430 DOI: 10.1016/j.heliyon.2020.e04850] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Revised: 04/07/2020] [Accepted: 09/02/2020] [Indexed: 11/15/2022] Open
Abstract
The current study includes the assessment of physico-chemical characteristics along with the microbial diversity of hot water samples collected from three important sacred hot water springs of the Uttarakhand Himalaya close to the world-famous Hindu shrine Yamunotri temple. Hot water samples were collected for two consecutive years 2015-2016 in two sampling operations each year. A total of fifteen physico-chemical attributes of hot water were recorded. Microbes of hot water ponds were characterized by morphological, biochemical, MALDI-TOF MS, and molecular approaches. A total of twenty-two microbial strains were identified from the Surya Kund with water temperature ranging between 86 °C and 89 °C; twenty-two microbial strains were identified from the Draupadi Kund with water temperature ranging between 65 °C and 69 °C and twenty-one microbial strains were identified from the Yamunotri Tapt Kund with water temperature ranging between 45 °C and 48 °C during the study period. The present study on the assessment of physico-chemical characteristics and thermophilic microbial diversity of all the three hot water springs can be a useful reference for further studies on similar aspects in other parts of the Himalaya. The available data will also help to understand the reasons behind the curative properties of these hot water springs. This baseline information will also be instrumental for the conservation and management of these hot water springs.
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Affiliation(s)
- Rahul Kumar
- Laboratory of Environmental Microbiology and Biotechnology, Department of Environmental Sciences, H.N.B. Garhwal University (A Central University), Srinagar Garhwal, 246174, Uttarakhand, India
| | - Ramesh C. Sharma
- Laboratory of Environmental Microbiology and Biotechnology, Department of Environmental Sciences, H.N.B. Garhwal University (A Central University), Srinagar Garhwal, 246174, Uttarakhand, India
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White LM, Shibuya T, Vance SD, Christensen LE, Bhartia R, Kidd R, Hoffmann A, Stucky GD, Kanik I, Russell MJ. Simulating Serpentinization as It Could Apply to the Emergence of Life Using the JPL Hydrothermal Reactor. ASTROBIOLOGY 2020; 20:307-326. [PMID: 32125196 DOI: 10.1089/ast.2018.1949] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The molecules feeding life's emergence are thought to have been provided through the hydrothermal interactions of convecting carbonic ocean waters with minerals comprising the early Hadean oceanic crust. Few laboratory experiments have simulated ancient hydrothermal conditions to test this conjecture. We used the JPL hydrothermal flow reactor to investigate CO2 reduction in simulated ancient alkaline convective systems over 3 days (T = 120°C, P = 100 bar, pH = 11). H2-rich hydrothermal simulant and CO2-rich ocean simulant solutions were periodically driven in 4-h cycles through synthetic mafic and ultramafic substrates and Fe>Ni sulfides. The resulting reductants included micromoles of HS- and formate accompanied possibly by micromoles of acetate and intermittent minor bursts of methane as ascertained by isotopic labeling. The formate concentrations directly correlated with the CO2 input as well as with millimoles of Mg2+ ions, whereas the acetate did not. Also, tens of micromoles of methane were drawn continuously from the reactor materials during what appeared to be the onset of serpentinization. These results support the hypothesis that formate may have been delivered directly to a branch of an emerging acetyl coenzyme-A pathway, thus obviating the need for the very first hydrogenation of CO2 to be made in a hydrothermal mound. Another feed to early metabolism could have been methane, likely mostly leached from primary CH4 present in the original Hadean crust or emanating from the mantle. That a small volume of methane was produced sporadically from the 13CO2-feed, perhaps from transient occlusions, echoes the mixed results and interpretations from other laboratories. As serpentinization and hydrothermal leaching can occur wherever an ocean convects within anhydrous olivine- and sulfide-rich crust, these results may be generalized to other wet rocky planets and moons in our solar system and beyond.
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Affiliation(s)
- Lauren M White
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California
- Department of Chemistry and Biochemistry, University of California at Santa Barbara, Santa Barbara, California
- Project Systems Engineering, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California
| | - Takazo Shibuya
- Department of Subsurface Geobiological Analysis and Research (D-SUGAR), Project Team for Development of New-generation Research Protocol for Submarine Resources, and Research and Development (RandD), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
- Research and Development (RandD) Center for Submarine Resources, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Steven D Vance
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California
| | - Lance E Christensen
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California
| | - Rohit Bhartia
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California
| | - Richard Kidd
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California
| | - Adam Hoffmann
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California
| | - Galen D Stucky
- Department of Chemistry and Biochemistry, University of California at Santa Barbara, Santa Barbara, California
- Materials Department, University of California at Santa Barbara, Santa Barbara, California
| | - Isik Kanik
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California
| | - Michael J Russell
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California
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Li L, Ma Z(S. Global Microbiome Diversity Scaling in Hot Springs With DAR (Diversity-Area Relationship) Profiles. Front Microbiol 2019; 10:118. [PMID: 30853941 PMCID: PMC6395440 DOI: 10.3389/fmicb.2019.00118] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Accepted: 01/18/2019] [Indexed: 11/20/2022] Open
Abstract
The spatial distribution of biodiversity (i.e., the biogeography) of the hot-spring microbiome is critical for understanding the microbial ecosystems in hot springs. We investigated the microbiome diversity scaling (changes) over space by analyzing the diversity-area relationship (DAR), which is an extension to classic SAR (species-area relationship) law in biogeography. We built DAR models for archaea and bacteria with 16S-rRNA sequencing datasets from 165 hot springs globally. From the DAR models, we sketch out the biogeographic maps of hot-spring microbiomes by constructing: (i) DAR profile-measuring the archaea or bacteria diversity scaling over space (areas); (ii) PDO (pair-wise diversity overlap or similarity) profile-estimating the PDO between two hot springs; (iii) MAD (maximal accrual diversity) profile-predicting the global MAD; (iv) LRD/LGD (ratio of local diversity to regional or global diversity) profile. We further investigated the differences between archaea and bacteria in their biogeographic maps. For example, the comparison of DAR-profile maps revealed that the archaea diversity is more heterogeneous (i.e., more diverse) or scaling faster than the bacterial diversity does in terms of species numbers (species richness), but is less heterogeneous (i.e., less diverse) or scaling slower than bacteria when the diversity (Hill numbers) were weighted in favor of more abundant dominant species. When the diversity is weighted equally in terms of species abundances, archaea, and bacteria are equally heterogeneous over space or scaling at the same rate. Finally, unified DAR models (maps) were built with the combined datasets of archaea and bacteria.
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Affiliation(s)
- Lianwei Li
- Computational Biology and Medical Ecology Lab, State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Kunming College of Life Sciences, University of Chinese Academy of Sciences, Kunming, China
| | - Zhanshan (Sam) Ma
- Computational Biology and Medical Ecology Lab, State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Kunming College of Life Sciences, University of Chinese Academy of Sciences, Kunming, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
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10
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Mandl K, Cantelmo C, Gruber E, Faber F, Friedrich B, Zaller JG. Effects of Glyphosate-, Glufosinate- and Flazasulfuron-Based Herbicides on Soil Microorganisms in a Vineyard. BULLETIN OF ENVIRONMENTAL CONTAMINATION AND TOXICOLOGY 2018; 101:562-569. [PMID: 30229276 PMCID: PMC6223855 DOI: 10.1007/s00128-018-2438-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Accepted: 09/03/2018] [Indexed: 05/23/2023]
Abstract
In a vineyard we examined the effects of broad-spectrum herbicides with three different active ingredients (glyphosate, glufosinate, flazasulfuron) on soil microorganisms. Mechanical weeding served as control treatment. Treatments were applied within grapevine rows and soil samples taken from there in 10-20 cm depth 77 days after application. Fungi were analyzed using classical sequencing technology and bacteria using next-generation sequencing. The number of colony-forming units (CFU) comprising bacteria, yeasts and molds was higher under flazasulfuron compared to all other treatments which had similar CFU levels. Abundance of the fungus Mucor was higher under flazasulfuron than glufosinate and mechanical weeding; Mucor was absent under glyphosate. Several other fungi taxa were exclusively found under a specific treatment. Up to 160 different bacteria species were found - some of them for the first time in vineyard soils. Total bacterial counts under herbicides were on average 260% higher than under mechanical weeding; however due to high variability this was not statistically significant. We suggest that herbicide-induced alterations of soil microorganisms could have knock-on effects on other parts of the grapevine system.
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Affiliation(s)
- Karin Mandl
- Federal College and Research Center for Viticulture and Pomology, Wienerstraße 74, 3400, Klosterneuburg, Austria
| | - Clemens Cantelmo
- Federal College and Research Center for Viticulture and Pomology, Wienerstraße 74, 3400, Klosterneuburg, Austria
- Institute of Zoology, University of Natural Resources and Life Sciences, Vienna, Gregor-Mendel-Straße 33, 1180, Vienna, Austria
| | - Edith Gruber
- Institute of Zoology, University of Natural Resources and Life Sciences, Vienna, Gregor-Mendel-Straße 33, 1180, Vienna, Austria
| | - Florian Faber
- Federal College and Research Center for Viticulture and Pomology, Wienerstraße 74, 3400, Klosterneuburg, Austria
| | - Barbara Friedrich
- Federal College and Research Center for Viticulture and Pomology, Wienerstraße 74, 3400, Klosterneuburg, Austria
| | - Johann G Zaller
- Institute of Zoology, University of Natural Resources and Life Sciences, Vienna, Gregor-Mendel-Straße 33, 1180, Vienna, Austria.
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Lavrentyeva EV, Radnagurueva AA, Barkhutova DD, Belkova NL, Zaitseva SV, Namsaraev ZB, Gorlenko VM, Namsaraev BB. Bacterial Diversity and Functional Activity of Microbial Communities in Hot Springs of the Baikal Rift Zone. Microbiology (Reading) 2018; 87:272-281. [DOI: 10.1134/s0026261718020078] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Indexed: 07/26/2024] Open
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12
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Chiriac CM, Baricz A, Szekeres E, Rudi K, Dragoș N, Coman C. Microbial Composition and Diversity Patterns in Deep Hyperthermal Aquifers from the Western Plain of Romania. MICROBIAL ECOLOGY 2018; 75:38-51. [PMID: 28702708 DOI: 10.1007/s00248-017-1031-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 06/28/2017] [Indexed: 06/07/2023]
Abstract
A limited number of studies have investigated the biodiversity in deep continental hyperthermal aquifers and its influencing factors. Here, we present the first description of microbial communities inhabiting the Pannonian and Triassic hyperthermal aquifers from the Western Plain of Romania, the first one being considered a deposit of "fossilized waters," while the latter is embedded in the hydrological cycle due to natural refilling. The 11 investigated drillings have an open interval between 952 and 3432 m below the surface, with collected water temperatures ranging between 47 and 104 °C, these being the first microbial communities characterized in deep continental water deposits with outflow temperatures exceeding 80 °C. The abundances of bacterial 16S rRNA genes varied from approximately 105-106 mL-1 in the Pannonian to about 102-104 mL-1 in the Triassic aquifer. A 16S rRNA gene metabarcoding analysis revealed distinct microbial communities in the two water deposits, especially in the rare taxa composition. The Pannonian aquifer was dominated by the bacterial genera Hydrogenophilus and Thermodesulfobacterium, together with archaeal methanogens from the Methanosaeta and Methanothermobacter groups. Firmicutes was prevalent in the Triassic deposit with a large number of OTUs affiliated to Thermoanaerobacteriaceae, Thermacetogenium, and Desulfotomaculum. Species richness, evenness, and phylogenetic diversity increased alongside with the abundance of mesophiles, their presence in the Triassic aquifer being most probably caused by the refilling with large quantities of meteoric water in the Carpathian Mountains. Altogether, our results show that the particular physico-cheminal characteristics of each aquifer, together with the water refilling possibilities, seem to determine the microbial community structure.
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Affiliation(s)
- Cecilia M Chiriac
- NIRDBS, Institute of Biological Research, 48 Republicii street, 400015, Cluj-Napoca, Romania
- Molecular Biology and Biotechnology Department, Faculty of Biology and Geology, Babeş-Bolyai University, Cluj-Napoca, Romania
| | - Andreea Baricz
- NIRDBS, Institute of Biological Research, 48 Republicii street, 400015, Cluj-Napoca, Romania
- Molecular Biology and Biotechnology Department, Faculty of Biology and Geology, Babeş-Bolyai University, Cluj-Napoca, Romania
| | - Edina Szekeres
- NIRDBS, Institute of Biological Research, 48 Republicii street, 400015, Cluj-Napoca, Romania
- Molecular Biology and Biotechnology Department, Faculty of Biology and Geology, Babeş-Bolyai University, Cluj-Napoca, Romania
| | - Knut Rudi
- Chemistry, Biotechnology and Food Science Department, Norwegian University of Life Sciences, Aas, Norway
| | - Nicolae Dragoș
- NIRDBS, Institute of Biological Research, 48 Republicii street, 400015, Cluj-Napoca, Romania
- Molecular Biology and Biotechnology Department, Faculty of Biology and Geology, Babeş-Bolyai University, Cluj-Napoca, Romania
| | - Cristian Coman
- NIRDBS, Institute of Biological Research, 48 Republicii street, 400015, Cluj-Napoca, Romania.
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Yang Y, Mu Y, Zeng XC, Wu W, Yuan J, Liu Y, Guoji E, Luo F, Chen X, Li H, Wang J. Functional genes and thermophilic microorganisms responsible for arsenite oxidation from the shallow sediment of an untraversed hot spring outlet. ECOTOXICOLOGY (LONDON, ENGLAND) 2017; 26:490-501. [PMID: 28251437 DOI: 10.1007/s10646-017-1779-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 02/08/2017] [Indexed: 06/06/2023]
Abstract
Hot Springs have unique geochemical features. Microorganisms-mediated arsenite oxidation is one of the major biogeochemical processes occurred in some hot springs. This study aimed to understand the diversities of genes and microorganisms involved in arsenite oxidation from the outlet of an untraversed hot spring located at an altitude of 4226 m. Microcosm assay indicated that the microbial community from the hot spring was able to efficiently oxidize As(III) using glucose, lactic acid, yeast extract or sodium bicarbonate as the sole carbon source. The microbial community contained 7 phyla of microorganisms, of which Proteobacteria and Firmicutes are largely dominant; this composition is unique and differs significantly from those of other described hot springs. Twenty one novel arsenite oxidase genes were identified from the samples, which are affiliated with the arsenite oxidase families of α-Proteobacteria, β-Proteobacteria or Archaea; this highlights the high diversity of the arsenite-oxidizing microorganisms from the hot spring. A cultivable arsenite-oxidizer Chelatococcu sp. GHS311 was also isolated from the sample using enrichment technique. It can completely convert 75.0 mg/L As(III) into As(V) in 18 days at 45 °C. The arsenite oxidase of GHS311 shares the maximal sequence identity (84.7%) to that of Hydrogenophaga sp. CL3, a non-thermotolerant bacterium. At the temperature lower than 30 °C or higher than 65 °C, the growth of this strain was completely inhibited. These data help us to better understand the diversity and functional features of the thermophilic arsenite-oxidizing microorganisms from hot springs.
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Affiliation(s)
- Ye Yang
- State Key Laboratory of Biogeology and Environmental Geology & Department of Biological Science and Technology, School of Environmental Studies, China University of Geosciences (Wuhan), Wuhan, 430074, People's Republic of China
| | - Yao Mu
- State Key Laboratory of Biogeology and Environmental Geology & Department of Biological Science and Technology, School of Environmental Studies, China University of Geosciences (Wuhan), Wuhan, 430074, People's Republic of China
| | - Xian-Chun Zeng
- State Key Laboratory of Biogeology and Environmental Geology & Department of Biological Science and Technology, School of Environmental Studies, China University of Geosciences (Wuhan), Wuhan, 430074, People's Republic of China.
| | - Weiwei Wu
- State Key Laboratory of Biogeology and Environmental Geology & Department of Biological Science and Technology, School of Environmental Studies, China University of Geosciences (Wuhan), Wuhan, 430074, People's Republic of China
| | - Jie Yuan
- State Key Laboratory of Biogeology and Environmental Geology & Department of Biological Science and Technology, School of Environmental Studies, China University of Geosciences (Wuhan), Wuhan, 430074, People's Republic of China
| | - Yichen Liu
- State Key Laboratory of Biogeology and Environmental Geology & Department of Biological Science and Technology, School of Environmental Studies, China University of Geosciences (Wuhan), Wuhan, 430074, People's Republic of China
| | - E Guoji
- State Key Laboratory of Biogeology and Environmental Geology & Department of Biological Science and Technology, School of Environmental Studies, China University of Geosciences (Wuhan), Wuhan, 430074, People's Republic of China
| | - Feng Luo
- School of Medicine, Jianghan University, Wuhan, 430056, People's Republic of China.
| | - Xiaoming Chen
- State Key Laboratory of Biogeology and Environmental Geology & Department of Biological Science and Technology, School of Environmental Studies, China University of Geosciences (Wuhan), Wuhan, 430074, People's Republic of China
| | - Hao Li
- State Key Laboratory of Biogeology and Environmental Geology & Department of Biological Science and Technology, School of Environmental Studies, China University of Geosciences (Wuhan), Wuhan, 430074, People's Republic of China
| | - Jianing Wang
- State Key Laboratory of Biogeology and Environmental Geology & Department of Biological Science and Technology, School of Environmental Studies, China University of Geosciences (Wuhan), Wuhan, 430074, People's Republic of China
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14
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Pérez-Rodríguez I, Rawls M, Coykendall DK, Foustoukos DI. Deferrisoma palaeochoriense sp. nov., a thermophilic, iron(III)-reducing bacterium from a shallow-water hydrothermal vent in the Mediterranean Sea. Int J Syst Evol Microbiol 2015; 66:830-836. [PMID: 26610851 DOI: 10.1099/ijsem.0.000798] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel thermophilic, anaerobic, mixotrophic bacterium, designated strain MAG-PB1T, was isolated from a shallow-water hydrothermal vent system in Palaeochori Bay off the coast of the island of Milos, Greece. The cells were Gram-negative, rugose, short rods, approximately 1.0 μm long and 0.5 μm wide. Strain MAG-PB1T grew at 30-70 °C (optimum 60 °C), 0-50 g NaCl l- 1 (optimum 15-20 g l- 1) and pH 5.5-8.0 (optimum pH 6.0). Generation time under optimal conditions was 2.5 h. Optimal growth occurred under chemolithoautotrophic conditions with H2 as the energy source and CO2 as the carbon source. Fe(III), Mn(IV), arsenate and selenate were used as electron acceptors. Peptone, tryptone, Casamino acids, sucrose, yeast extract, d-fructose, α-d-glucose and ( - )-d-arabinose also served as electron donors. No growth occurred in the presence of lactate or formate. The G+C content of the genomic DNA was 66.7 mol%. Phylogenetic analysis of the 16S rRNA gene sequence indicated that this organism is closely related to Deferrisoma camini, the first species of a recently described genus in the Deltaproteobacteria. Based on the 16S rRNA gene phylogenetic analysis and on physiological, biochemical and structural characteristics, the strain was found to represent a novel species, for which the name Deferrisoma palaeochoriense sp. nov. is proposed. The type strain is MAG-PB1T ( = JCM 30394T = DSM 29363T).
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Affiliation(s)
| | - Matthew Rawls
- Geophysical Laboratory, Carnegie Institution of Washington, Washington DC, 20015, USA.,Department of Oceanic, Atmospheric and Earth Sciences, George Mason University, Fairfax, VA 22030, USA
| | - D Katharine Coykendall
- US Geological Survey, National Fish Health Research Laboratory, Leetown Science Center, Kearneysville, WV 25430, USA
| | - Dionysis I Foustoukos
- Geophysical Laboratory, Carnegie Institution of Washington, Washington DC, 20015, USA
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Rozanov AS, Bryanskaya AV, Malup TK, Meshcheryakova IA, Lazareva EV, Taran OP, Ivanisenko TV, Ivanisenko VA, Zhmodik SM, Kolchanov NA, Peltek SE. Molecular analysis of the benthos microbial community in Zavarzin thermal spring (Uzon Caldera, Kamchatka, Russia). BMC Genomics 2014; 15 Suppl 12:S12. [PMID: 25563397 PMCID: PMC4303939 DOI: 10.1186/1471-2164-15-s12-s12] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Background Geothermal areas are of great interest for the study of microbial communities. The results of such investigations can be used in a variety of fields (ecology, microbiology, medicine) to answer fundamental questions, as well as those with practical benefits. Uzon caldera is located in the Uzon-Geyser depression that is situated in the centre of the Karym-Semyachin region of the East Kamchatka graben-synclinorium. The microbial communities of Zavarzin spring are well studied; however, its benthic microbial mat has not been previously described. Results Pyrosequencing of the V3 region of the 16S rRNA gene was used to study the benthic microbial community of the Zavarzin thermal spring (Uzon Caldera, Kamchatka). The community is dominated by bacteria (>95% of all sequences), including thermophilic, chemoorganotrophic Caldiserica (33.0%) and Dictyoglomi (24.8%). The benthic community and the previously examined planktonic community of Zavarzin spring have qualitatively similar, but quantitatively different, compositions. Conclusions In this study, we performed a metagenomic analysis of the benthic microbial mat of Zavarzin spring. We compared this benthic community to microbial communities found in the water and of an integral probe consisting of water and bottom sediments. Various phylogenetic groups of microorganisms, including potentially new ones, represent the full-fledged trophic system of Zavarzin. A thorough geochemical study of the spring was performed.
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16
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Rothery RA, Weiner JH. Shifting the metallocentric molybdoenzyme paradigm: the importance of pyranopterin coordination. J Biol Inorg Chem 2014; 20:349-72. [PMID: 25267303 DOI: 10.1007/s00775-014-1194-6] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Accepted: 09/15/2014] [Indexed: 01/10/2023]
Abstract
In this review, we test the hypothesis that pyranopterin coordination plays a critical role in defining substrate reactivities in the four families of mononuclear molybdenum and tungsten enzymes (Mo/W-enzymes). Enzyme families containing a single pyranopterin dithiolene chelate have been demonstrated to have reactivity towards two (sulfite oxidase, SUOX-fold) and five (xanthine dehydrogenase, XDH-fold) types of substrate, whereas the major family of enzymes containing a bis-pyranopterin dithiolene chelate (dimethylsulfoxide reductase, DMSOR-fold) is reactive towards eight types of substrate. A second bis-pyranopterin enzyme (aldehyde oxidoreductase, AOR-fold) family catalyzes a single type of reaction. The diversity of reactions catalyzed by each family correlates with active site variability, and also with the number of pyranopterins and their coordination by the protein. In the case of the AOR-fold enzymes, inflexibility of pyranopterin coordination correlates with their limited substrate specificity (oxidation of aldehydes). In examples of the SUOX-fold and DMSOR-fold enzymes, we observe three types of histidine-containing charge-transfer relays that can: (1) connect the piperazine ring of the pyranopterin to the substrate-binding site (SUOX-fold enzymes); (2) provide inter-pyranopterin communication (DMSOR-fold enzymes); and (3) connect a pyran ring oxygen to deeply buried water molecules (the DMSOR-fold NarGHI-type nitrate reductases). Finally, sequence data mining reveals a number of bacterial species whose predicted proteomes contain large numbers (up to 64) of Mo/W-enzymes, with the DMSOR-fold enzymes being dominant. These analyses also reveal an inverse correlation between Mo/W-enzyme content and pathogenicity.
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Affiliation(s)
- Richard A Rothery
- Department of Biochemistry, University of Alberta, Edmonton, AB, T6G 2H7, Canada
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