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Power JF, Carere CR, Welford HE, Hudson DT, Lee KC, Moreau JW, Ettema TJG, Reysenbach AL, Lee CK, Colman DR, Boyd ES, Morgan XC, McDonald IR, Craig Cary S, Stott MB. A genus in the bacterial phylum Aquificota appears to be endemic to Aotearoa-New Zealand. Nat Commun 2024; 15:179. [PMID: 38167814 PMCID: PMC10762115 DOI: 10.1038/s41467-023-43960-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 11/24/2023] [Indexed: 01/05/2024] Open
Abstract
Allopatric speciation has been difficult to examine among microorganisms, with prior reports of endemism restricted to sub-genus level taxa. Previous microbial community analysis via 16S rRNA gene sequencing of 925 geothermal springs from the Taupō Volcanic Zone (TVZ), Aotearoa-New Zealand, revealed widespread distribution and abundance of a single bacterial genus across 686 of these ecosystems (pH 1.2-9.6 and 17.4-99.8 °C). Here, we present evidence to suggest that this genus, Venenivibrio (phylum Aquificota), is endemic to Aotearoa-New Zealand. A specific environmental niche that increases habitat isolation was identified, with maximal read abundance of Venenivibrio occurring at pH 4-6, 50-70 °C, and low oxidation-reduction potentials. This was further highlighted by genomic and culture-based analyses of the only characterised species for the genus, Venenivibrio stagnispumantis CP.B2T, which confirmed a chemolithoautotrophic metabolism dependent on hydrogen oxidation. While similarity between Venenivibrio populations illustrated that dispersal is not limited across the TVZ, extensive amplicon, metagenomic, and phylogenomic analyses of global microbial communities from DNA sequence databases indicates Venenivibrio is geographically restricted to the Aotearoa-New Zealand archipelago. We conclude that geographic isolation, complemented by physicochemical constraints, has resulted in the establishment of an endemic bacterial genus.
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Affiliation(s)
- Jean F Power
- Thermophile Research Unit, Te Aka Mātuatua | School of Science, Te Whare Wānanga o Waikato | University of Waikato, Hamilton, 3240, Aotearoa New Zealand
| | - Carlo R Carere
- Te Tari Pūhanga Tukanga Matū | Department of Chemical and Process Engineering, Te Whare Wānanga o Waitaha | University of Canterbury, Christchurch, 8140, Aotearoa New Zealand
| | - Holly E Welford
- Te Kura Pūtaiao Koiora | School of Biological Sciences, Te Whare Wānanga o Waitaha | University of Canterbury, Christchurch, 8140, Aotearoa New Zealand
| | - Daniel T Hudson
- Te Tari Moromoroiti me te Ārai Mate | Department of Microbiology and Immunology, Te Whare Wānanga o Ōtākou | University of Otago, Dunedin, 9054, Aotearoa New Zealand
| | - Kevin C Lee
- Te Kura Pūtaiao | School of Science, Te Wānanga Aronui o Tāmaki Makau Rau | Auckland University of Technology, Auckland, 1010, Aotearoa New Zealand
| | - John W Moreau
- School of Geographical & Earth Sciences, University of Glasgow, Glasgow, G12 8RZ, UK
| | - Thijs J G Ettema
- Laboratory of Microbiology, Wageningen University & Research, 6708, WE, Wageningen, the Netherlands
| | | | - Charles K Lee
- Thermophile Research Unit, Te Aka Mātuatua | School of Science, Te Whare Wānanga o Waikato | University of Waikato, Hamilton, 3240, Aotearoa New Zealand
| | - Daniel R Colman
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT, 59717, USA
| | - Eric S Boyd
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT, 59717, USA
| | - Xochitl C Morgan
- Te Tari Moromoroiti me te Ārai Mate | Department of Microbiology and Immunology, Te Whare Wānanga o Ōtākou | University of Otago, Dunedin, 9054, Aotearoa New Zealand
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, 02115, USA
| | - Ian R McDonald
- Thermophile Research Unit, Te Aka Mātuatua | School of Science, Te Whare Wānanga o Waikato | University of Waikato, Hamilton, 3240, Aotearoa New Zealand
| | - S Craig Cary
- Thermophile Research Unit, Te Aka Mātuatua | School of Science, Te Whare Wānanga o Waikato | University of Waikato, Hamilton, 3240, Aotearoa New Zealand.
| | - Matthew B Stott
- Te Kura Pūtaiao Koiora | School of Biological Sciences, Te Whare Wānanga o Waitaha | University of Canterbury, Christchurch, 8140, Aotearoa New Zealand.
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2
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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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3
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Colman DR, Veach A, Stefánsson A, Wurch L, Belisle BS, Podar PT, Yang Z, Klingeman D, Senba K, Murakami KS, Kristjánsson JK, Björnsdóttir SH, Boyd ES, Podar M. Tectonic and geological setting influence hot spring microbiology. Environ Microbiol 2023; 25:2481-2497. [PMID: 37553090 DOI: 10.1111/1462-2920.16472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 07/12/2023] [Indexed: 08/10/2023]
Abstract
Hydrothermal systems form at divergent and convergent boundaries of lithospheric plates and within plates due to weakened crust and mantle plumes, playing host to diverse microbial ecosystems. Little is known of how differences in tectonic setting influence the geochemical and microbial compositions of these hydrothermal ecosystems. Here, coordinated geochemical and microbial community analyses were conducted on 87 high-temperature (>65°C) water and sediment samples from hot springs in Yellowstone National Park, Wyoming, USA (n = 41; mantle plume setting), Iceland (n = 41, divergent boundary), and Japan (n = 5; convergent boundary). Region-specific variation in geochemistry and sediment-associated 16S rRNA gene amplicon sequence variant (ASV) composition was observed, with 16S rRNA gene assemblages being nearly completely distinguished by region and pH being the most explanatory parameter within regions. Several low abundance ASVs exhibited cosmopolitan distributions across regions, while most high-abundance ASVs were only identified in specific regions. The presence of some cosmopolitan ASVs across regions argues against dispersal limitation primarily shaping the distribution of taxa among regions. Rather, the results point to local tectonic and geologic characteristics shaping the geochemistry of continental hydrothermal systems that then select for distinct microbial assemblages. These results provide new insights into the co-evolution of hydrothermal systems and their microbial communities.
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Affiliation(s)
- Daniel R Colman
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, Montana, USA
| | - Allison Veach
- Department of Integrative Biology, University of Texas at San Antonio, San Antonio, Texas, USA
| | - Andri Stefánsson
- Institute of Earth Sciences, University of Iceland, Reykjavik, Iceland
| | - Louie Wurch
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
- Department of Biology, James Madison University, Harrisonburg, Virginia, USA
| | - B Shafer Belisle
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Peter T Podar
- School of Engineering, Vanderbilt University, Nashville, Tennessee, USA
| | - Zamin Yang
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Dawn Klingeman
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Kazuyo Senba
- Department of Microbiology, Beppu University, Beppu, Oita, Japan
| | - Katsuhiko S Murakami
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, State College, Pennsylvania, USA
| | | | | | - Eric S Boyd
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, Montana, USA
| | - Mircea Podar
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
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4
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Lai D, Hedlund BP, Mau RL, Jiao JY, Li J, Hayer M, Dijkstra P, Schwartz E, Li WJ, Dong H, Palmer M, Dodsworth JA, Zhou EM, Hungate BA. Resource partitioning and amino acid assimilation in a terrestrial geothermal spring. THE ISME JOURNAL 2023; 17:2112-2122. [PMID: 37741957 PMCID: PMC10579274 DOI: 10.1038/s41396-023-01517-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 08/31/2023] [Accepted: 09/13/2023] [Indexed: 09/25/2023]
Abstract
High-temperature geothermal springs host simplified microbial communities; however, the activities of individual microorganisms and their roles in the carbon cycle in nature are not well understood. Here, quantitative stable isotope probing (qSIP) was used to track the assimilation of 13C-acetate and 13C-aspartate into DNA in 74 °C sediments in Gongxiaoshe Hot Spring, Tengchong, China. This revealed a community-wide preference for aspartate and a tight coupling between aspartate incorporation into DNA and the proliferation of aspartate utilizers during labeling. Both 13C incorporation into DNA and changes in the abundance of taxa during incubations indicated strong resource partitioning and a significant phylogenetic signal for aspartate incorporation. Of the active amplicon sequence variants (ASVs) identified by qSIP, most could be matched with genomes from Gongxiaoshe Hot Spring or nearby springs with an average nucleotide similarity of 99.4%. Genomes corresponding to aspartate primary utilizers were smaller, near-universally encoded polar amino acid ABC transporters, and had codon preferences indicative of faster growth rates. The most active ASVs assimilating both substrates were not abundant, suggesting an important role for the rare biosphere in the community response to organic carbon addition. The broad incorporation of aspartate into DNA over acetate by the hot spring community may reflect dynamic cycling of cell lysis products in situ or substrates delivered during monsoon rains and may reflect N limitation.
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Affiliation(s)
- Dengxun Lai
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV, USA
| | - Brian P Hedlund
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV, USA.
- Nevada Institute for Personalized Medicine, University of Nevada Las Vegas, Las Vegas, NV, USA.
| | - Rebecca L Mau
- Center for Ecosystem Science and Society, Northern Arizona University and Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
| | - Jian-Yu Jiao
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Junhui Li
- Center for Ecosystem Science and Society, Northern Arizona University and Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
| | - Michaela Hayer
- Center for Ecosystem Science and Society, Northern Arizona University and Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
| | - Paul Dijkstra
- Center for Ecosystem Science and Society, Northern Arizona University and Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
| | - Egbert Schwartz
- Center for Ecosystem Science and Society, Northern Arizona University and Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Hailiang Dong
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Beijing, China and Department of Geology and Environmental Earth Science, Miami University, Oxford, OH, USA
| | - Marike Palmer
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV, USA
| | - Jeremy A Dodsworth
- Department of Biology, California State University, San Bernardino, CA, USA
| | - En-Min Zhou
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV, USA
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
- School of Resource Environment and Earth Science, Yunnan University, Kunming, China
| | - Bruce A Hungate
- Center for Ecosystem Science and Society, Northern Arizona University and Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA.
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5
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Barosa B, Ferrillo A, Selci M, Giardina M, Bastianoni A, Correggia M, di Iorio L, Bernardi G, Cascone M, Capuozzo R, Intoccia M, Price R, Vetriani C, Cordone A, Giovannelli D. Mapping the microbial diversity associated with different geochemical regimes in the shallow-water hydrothermal vents of the Aeolian archipelago, Italy. Front Microbiol 2023; 14:1134114. [PMID: 37637107 PMCID: PMC10452888 DOI: 10.3389/fmicb.2023.1134114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Accepted: 07/25/2023] [Indexed: 08/29/2023] Open
Abstract
Shallow-water hydrothermal vents are unique marine environments ubiquitous along the coast of volcanically active regions of the planet. In contrast to their deep-sea counterparts, primary production at shallow-water vents relies on both photoautotrophy and chemoautotrophy. Such processes are supported by a range of geochemical regimes driven by different geological settings. The Aeolian archipelago, located in the southern Tyrrhenian sea, is characterized by intense hydrothermal activity and harbors some of the best sampled shallow-water vents of the Mediterranean Sea. Despite this, the correlation between microbial diversity, geochemical regimes and geological settings of the different volcanic islands of the archipelago is largely unknown. Here, we report the microbial diversity associated with six distinct shallow-water hydrothermal vents of the Aeolian Islands using a combination of 16S rRNA amplicon sequencing along with physicochemical and geochemical measurements. Samples were collected from biofilms, fluids and sediments from shallow vents on the islands of Lipari, Panarea, Salina, and Vulcano. Two new shallow vent locations are described here for the first time. Our results show the presence of diverse microbial communities consistent in their composition with the local geochemical regimes. The shallow water vents of the Aeolian Islands harbor highly diverse microbial community and should be included in future conservation efforts.
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Affiliation(s)
- Bernardo Barosa
- Department of Biology, University of Naples “Federico II”, Naples, Italy
| | | | - Matteo Selci
- Department of Biology, University of Naples “Federico II”, Naples, Italy
| | - Marco Giardina
- Department of Biology, University of Naples “Federico II”, Naples, Italy
| | - Alessia Bastianoni
- Department of Biology, University of Naples “Federico II”, Naples, Italy
| | - Monica Correggia
- Department of Biology, University of Naples “Federico II”, Naples, Italy
| | - Luciano di Iorio
- Department of Biology, University of Naples “Federico II”, Naples, Italy
| | | | - Martina Cascone
- Department of Biology, University of Naples “Federico II”, Naples, Italy
| | - Rosaria Capuozzo
- Department of Biology, University of Naples “Federico II”, Naples, Italy
| | - Michele Intoccia
- Department of Biology, University of Naples “Federico II”, Naples, Italy
| | - Roy Price
- School of Marine and Atmospheric Sciences, Stony Brook, NY, United States
| | - Costantino Vetriani
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ, United States
- Department of Marine and Coastal Science, Rutgers University, New Brunswick, NJ, United States
| | - Angelina Cordone
- Department of Biology, University of Naples “Federico II”, Naples, Italy
| | - Donato Giovannelli
- Department of Biology, University of Naples “Federico II”, Naples, Italy
- Department of Marine and Coastal Science, Rutgers University, New Brunswick, NJ, United States
- Istituto per le Risorse Biologiche e Biotecnologiche Marine, Consiglio Nazionale Delle Ricerche, CNR-IRBIM, Ancona, Italy
- Earth-Life Science Institute, Tokyo Institute of Technology, Ookayama, Tokyo, Japan
- Marine Chemistry and Geochemistry Department–Woods Hole Oceanographic Institution, Woods Hole, MA, United States
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6
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Zhang FQ, Liu J, Chen XJ. Comparative analysis of bacterial diversity in two hot springs in Hefei, China. Sci Rep 2023; 13:5832. [PMID: 37037855 PMCID: PMC10086057 DOI: 10.1038/s41598-023-32853-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Accepted: 04/03/2023] [Indexed: 04/12/2023] Open
Abstract
Hot springs are extreme ecological environments of microbes. The study is the first comparative analysis of bacterial diversity of Tangchi and Bantang hot spring water samples collected in Hefei, China, which is conducive to the further development and utilization of microbial resources in hot springs. Illumina MiSeq system was utilized to sequence and analyze the bacterial 16S rRNA gene from hot spring water samples by bioinformatics, to probe into the bacterial abundance and diversity of two hot springs in Hefei. Results revealed that prevalent bacterial phyla in Tangchi hot spring were Bacillota and Aquificota, and the prevalent bacterial genus was Hydrogenobacter; prevalent phyla in Bantang hot spring were Pseudomonadota followed by Actinobacteriota, and prevalent genera were CL500-29_marine_group and Polynucleobacter. More species and higher evenness in Bantang hot spring than those in Tangchi hot spring. In MetaCyc pathway analysis, the major pathways of metabolism existed in the bacteria from the two hot springs were 'pyruvate fermentation to isobutanol (engineered)', 'acetylene degradation', 'carbon fixation pathways in prokaryotes', 'nitrate reduction I (denitrification)', 'methanogenesis from acetate', 'superpathway of glucose and xylose degradation', etc.
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Affiliation(s)
- Feng-Qin Zhang
- College of Chemistry and Material Engineering, Chaohu University, Chaohu, 238024, Anhui, China
| | - Jun Liu
- College of Biology and Food Engineering, Anhui Polytechnic University, Wuhu, 241000, Anhui, China
| | - Xiao-Ju Chen
- College of Chemistry and Material Engineering, Chaohu University, Chaohu, 238024, Anhui, China.
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7
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Yin Z, Ye L, Jing C. Genome-Resolved Metagenomics and Metatranscriptomics Reveal that Aquificae Dominates Arsenate Reduction in Tengchong Geothermal Springs. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:16473-16482. [PMID: 36227700 DOI: 10.1021/acs.est.2c05764] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Elevated arsenic (As) is common in geothermal springs, shaping the evolution of As metabolism genes and As transforming microbes. Herein, genome-level microbial metabolisms and As cycling strategies in Tengchong geothermal springs were demonstrated for the first time based on metagenomic and metatranscriptomic analyses. Sulfur cycling was dominated by Aquificae oxidizing thiosulfate via the sox system, fueling the respiration and carbon dioxide fixation processes. Arsenate reduction via arsC [488.63 ± 271.60 transcripts per million (TPM)] and arsenite efflux via arsB (442.98 ± 284.81 TPM) were the primary detoxification pathway, with most genes and transcripts contributed by the members in phylum Aquificae. A complete arsenotrophic cycle was also transcriptionally active as evidenced by the detection of aioA transcripts and arrA transcript reads mapped onto metagenome-assembled genomes (MAGs) affiliated with Crenarchaeota. MAGs affiliated with Aquificae had great potential of reducing arsenate via arsC and fixing nitrogen and carbon dioxide via nifDHK and reductive tricarboxylic acid (rTCA) cycle, respectively. Aquificae's arsenate reduction potential via arsC was observed for the first time at the transcriptional level. This study expands the diversity of the arsC-based arsenate-reducing community and highlights the importance of Aquificae to As biogeochemistry.
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Affiliation(s)
- Zhipeng Yin
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Li Ye
- Shandong Key Laboratory of Environmental Processes and Health, School of Environmental Science and Engineering, Shandong University, Qingdao 266237, China
| | - Chuanyong Jing
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Shandong Key Laboratory of Environmental Processes and Health, School of Environmental Science and Engineering, Shandong University, Qingdao 266237, China
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8
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Song ZQ, Wang L, Liang F, Zhou Q, Pei D, Jiang H, Li WJ. nifH gene expression and diversity in geothermal springs of Tengchong, China. Front Microbiol 2022; 13:980924. [PMID: 36160261 PMCID: PMC9493357 DOI: 10.3389/fmicb.2022.980924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 08/08/2022] [Indexed: 11/20/2022] Open
Abstract
Terrestrial hot springs have been suggested to harbor diverse diazotrophic lineages by using DNA-based nifH gene phylogenetic analysis. However, only a small amount of diazotrophs were ever confirmed to perform nitrogen fixation. In order to explore the compositions of active diazotrophic populations in hot springs, the in situ expression and diversity of nifH and 16S rRNA genes were investigated in the sediments of hot springs (pH 4.3-9.1; temperature 34-84°C) in Tengchong, China, by using high-throughput sequencing. The results showed that active diazotrophs were diverse in the studied Tengchong hot springs. The main active diazotrophs in high-temperature hot springs were affiliated with Aquificae, while those in low-temperature hot springs belonged to Cyanobacteria and Nitrospirae. Such dominance of Aquificae and Nitrospirae of diazotrophs has not been reported in other ecosystems. This suggests that hot springs may harbor unique active diazotrophs in comparison with other type of ecosystems. Furthermore, there were significant differences in the phylogenetic lineages of diazotrophs between hot springs of Tengchong and other regions, indicating that diazotrophs have geographical distribution patterns. Statistical analysis suggests that the expression and distribution of nifH gene were influenced by temperature and concentrations of ammonia and sulfur seem in Tengchong hot springs. These findings avail us to understand element cycling mediated by diazotrophs in hot spring ecosystems.
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Affiliation(s)
- Zhao-Qi Song
- College of Biology and Food, Shangqiu Normal University, Shangqiu, China
| | - Li Wang
- College of Biology and Food, Shangqiu Normal University, Shangqiu, China
| | - Feng Liang
- College of Biology and Food, Shangqiu Normal University, Shangqiu, China
| | - Qingfeng Zhou
- College of Biology and Food, Shangqiu Normal University, Shangqiu, China
| | - Dongli Pei
- College of Biology and Food, Shangqiu Normal University, Shangqiu, China
| | - Hongchen Jiang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, China
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
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9
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Incomplete denitrification phenotypes in diverse Thermus species from diverse geothermal spring sediments and adjacent soils in southwest China. Extremophiles 2022; 26:23. [PMID: 35802188 PMCID: PMC9270275 DOI: 10.1007/s00792-022-01272-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Accepted: 06/06/2022] [Indexed: 01/22/2023]
Abstract
A few members of the bacterial genus Thermus have been shown to be incomplete denitrifiers, terminating with nitrite (NO2−) or nitrous oxide (N2O). However, the denitrification abilities of the genus as a whole remain poorly characterized. Here, we describe diverse denitrification phenotypes and genotypes of a collection of 24 strains representing ten species, all isolated from a variety of geothermal systems in China. Confirmed terminal products of nitrate reduction were nitrite or N2O, while nitric oxide (NO) was inferred as the terminal product in some strains. Most strains produced N2O; complete denitrification was not observed. Denitrification phenotypes were largely consistent with the presence of denitrification genes, and strains of the same species often had the same denitrification phenotypes and largely syntenous denitrification gene clusters. Genes for nirS and nirK coexisted in three Thermus brockianus and three Thermus oshimai genomes, which is a unique hallmark of some denitrifying Thermus strains and may be ecologically important. These results show that incomplete denitrification phenotypes are prominent, but variable, within and between Thermus species. The incomplete denitrification phenotypes described here suggest Thermus species may play important roles in consortial denitrification in high-temperature terrestrial biotopes where sufficient supply of oxidized inorganic nitrogen exists.
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10
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Keshari N, Zhao Y, Das SK, Zhu T, Lu X. Cyanobacterial Community Structure and Isolates From Representative Hot Springs of Yunnan Province, China Using an Integrative Approach. Front Microbiol 2022; 13:872598. [PMID: 35547135 PMCID: PMC9083006 DOI: 10.3389/fmicb.2022.872598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 02/28/2022] [Indexed: 11/15/2022] Open
Abstract
Cyanobacteria from the representative hot springs of Yunnan Province, China are explored for their diversity and community composition following an integrative approach of cultivation-independent and -dependent studies and further isolation of potential taxa for future biotechnological perspective. 16S rRNA amplicon sequencing of microbial mats in these hot springs with temperature ranging from 38 to 90°C revealed Cyanobacteria and Proteobacteria constituting a bounteous portion of the bacterial community. The combined approach of 16S rRNA amplicon sequencing and phenotypic analysis revealed the diversity of cyanobacteria (a total of 45 genera). Out of these, a total of 19 cyanobacterial taxa belonging to 6 genera and 10 species were isolated as individuals with the possibility of biotechnological utilization. These isolates were subjected to a thorough morphological study and molecular characterization using 16S rRNA gene sequencing for identification and understanding their phylogeny. The identity and phenotypic and genotypic characteristics of 7 cyanobacterial isolates are not identical to any known cyanobacterial species, generating scope for future taxonomic novelties. Preliminary experiments based on high-temperature (50°C) cultivation showed that most of the isolates were thermotolerant and suggested for their high biotechnological usage potential.
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Affiliation(s)
- Nitin Keshari
- CAS Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China.,Shandong Energy Institute, Qingdao, China.,Qingdao New Energy Shandong Laboratory, Qingdao, China
| | - Yang Zhao
- CAS Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China.,Shandong Energy Institute, Qingdao, China.,Qingdao New Energy Shandong Laboratory, Qingdao, China
| | - Sudipta Kumar Das
- Centre of Excellence in Integrated Omics and Computational Biology, Utkal University, Bhubaneswar, India
| | - Tao Zhu
- CAS Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China.,Shandong Energy Institute, Qingdao, China.,Qingdao New Energy Shandong Laboratory, Qingdao, China.,College of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Xuefeng Lu
- CAS Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China.,Shandong Energy Institute, Qingdao, China.,Qingdao New Energy Shandong Laboratory, Qingdao, China.,College of Life Science, University of Chinese Academy of Sciences, Beijing, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
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11
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Kochetkova TV, Podosokorskaya OA, Elcheninov AG, Kublanov IV. Diversity of Thermophilic Prokaryotes Inhabiting Russian Natural Hot Springs. Microbiology (Reading) 2022. [DOI: 10.1134/s0026261722010064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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12
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Minerals Determined a Special Ecological Niche and Selectively Enriched Microbial Species from Bulk Water Communities in Hot Springs. Microorganisms 2021; 9:microorganisms9051020. [PMID: 34068582 PMCID: PMC8151621 DOI: 10.3390/microorganisms9051020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2021] [Revised: 04/29/2021] [Accepted: 05/07/2021] [Indexed: 12/21/2022] Open
Abstract
Minerals provide physical niches and supply nutrients or serve as electron donors/acceptors for microorganism survival and growth, and thus minerals and microbes co-evolved. Yet, little is known about how sediment minerals impact microbial community assembly in hot springs and to what extent mineralogical composition influences microbial community composition and diversity. Here the influences of minerals on thermophiles in Tengchong hot springs were revealed by network analysis of field samples, as well as in-situ microcosm experiments with minerals. A molecular ecological network was constructed based on high throughput sequencing data of 16S rRNA gene, with a combination of water geochemistry and sedimentary mineralogical compositions. Six modules were identified and this highly modular network structure represents the microbial preference to different abiotic factors, consequently resulting in niche partitioning in sedimentary communities in hot springs. Diverse mineralogical compositions generated special niches for microbial species. Subsequently, the in-situ microcosm experiments with four minerals (aragonite, albite, K-feldspar, and quartz) and spring water were conducted in a silicate-hosted alkaline spring (i.e., Gmq) and a carbonate-hosted neutral hot spring (i.e., Gxs) for 70 days. Different microbial preferences were observed among different mineral types (carbonate versus silicate). Aragonite microcosms in Gmq spring enriched archaeal genera Sulfophobococcus and Aeropyrum within the order Desulfurococcales by comparison with both in-situ water and silicate microcosms. Sulfophobococcus was also accumulated in Gxs aragonite microcosms, but the contribution to overall dissimilarity is much lower than that in Gmq spring. Besides, Caldimicrobium was a bacterial genus enriched in Gxs aragonite microcosms, in contrast to in-situ water and silicate microcosms, whereas Candidatus Kryptobacter and Thermus were more abundant in silicate microcosms. The differences in microbial accumulations among different mineral types in the same spring implied that mineral chemistry may exert extra deterministic selective pressure in drawing certain species from the bulk water communities, in addition to stochastic absorption on mineral surface. Taken together, our results highlight the special niche partitioning determined by mineralogical compositions and further confirm that minerals could be used as “fishing bait” to enrich certain rare microbial species.
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13
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Thomas SC, Payne D, Tamadonfar KO, Seymour CO, Jiao JY, Murugapiran SK, Lai D, Lau R, Bowen BP, Silva LP, Louie KB, Huntemann M, Clum A, Spunde A, Pillay M, Palaniappan K, Varghese N, Mikhailova N, Chen IM, Stamatis D, Reddy TBK, O'Malley R, Daum C, Shapiro N, Ivanova N, Kyrpides NC, Woyke T, Eloe-Fadrosh E, Hamilton TL, Dijkstra P, Dodsworth JA, Northen TR, Li WJ, Hedlund BP. Genomics, Exometabolomics, and Metabolic Probing Reveal Conserved Proteolytic Metabolism of Thermoflexus hugenholtzii and Three Candidate Species From China and Japan. Front Microbiol 2021; 12:632731. [PMID: 34017316 PMCID: PMC8129789 DOI: 10.3389/fmicb.2021.632731] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 03/02/2021] [Indexed: 01/21/2023] Open
Abstract
Thermoflexus hugenholtzii JAD2T, the only cultured representative of the Chloroflexota order Thermoflexales, is abundant in Great Boiling Spring (GBS), NV, United States, and close relatives inhabit geothermal systems globally. However, no defined medium exists for T. hugenholtzii JAD2T and no single carbon source is known to support its growth, leaving key knowledge gaps in its metabolism and nutritional needs. Here, we report comparative genomic analysis of the draft genome of T. hugenholtzii JAD2T and eight closely related metagenome-assembled genomes (MAGs) from geothermal sites in China, Japan, and the United States, representing “Candidatus Thermoflexus japonica,” “Candidatus Thermoflexus tengchongensis,” and “Candidatus Thermoflexus sinensis.” Genomics was integrated with targeted exometabolomics and 13C metabolic probing of T. hugenholtzii. The Thermoflexus genomes each code for complete central carbon metabolic pathways and an unusually high abundance and diversity of peptidases, particularly Metallo- and Serine peptidase families, along with ABC transporters for peptides and some amino acids. The T. hugenholtzii JAD2T exometabolome provided evidence of extracellular proteolytic activity based on the accumulation of free amino acids. However, several neutral and polar amino acids appear not to be utilized, based on their accumulation in the medium and the lack of annotated transporters. Adenine and adenosine were scavenged, and thymine and nicotinic acid were released, suggesting interdependency with other organisms in situ. Metabolic probing of T. hugenholtzii JAD2T using 13C-labeled compounds provided evidence of oxidation of glucose, pyruvate, cysteine, and citrate, and functioning glycolytic, tricarboxylic acid (TCA), and oxidative pentose-phosphate pathways (PPPs). However, differential use of position-specific 13C-labeled compounds showed that glycolysis and the TCA cycle were uncoupled. Thus, despite the high abundance of Thermoflexus in sediments of some geothermal systems, they appear to be highly focused on chemoorganotrophy, particularly protein degradation, and may interact extensively with other microorganisms in situ.
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Affiliation(s)
- Scott C Thomas
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, NV, United States
| | - Devon Payne
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, NV, United States
| | - Kevin O Tamadonfar
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, NV, United States
| | - Cale O Seymour
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, NV, United States
| | - Jian-Yu Jiao
- School of Life Sciences, Sun Yat-sen University, Guangzhou, China.,State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory, Zhuhai, China
| | - Senthil K Murugapiran
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, NV, United States.,Department of Plant and Microbial Biology, The BioTechnology Institute, University of Minnesota, St. Paul, MN, United States
| | - Dengxun Lai
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, NV, United States
| | - Rebecca Lau
- The Department of Energy Joint Genome Institute, Berkeley, CA, United States.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Benjamin P Bowen
- The Department of Energy Joint Genome Institute, Berkeley, CA, United States.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Leslie P Silva
- The Department of Energy Joint Genome Institute, Berkeley, CA, United States.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Katherine B Louie
- The Department of Energy Joint Genome Institute, Berkeley, CA, United States.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Marcel Huntemann
- The Department of Energy Joint Genome Institute, Berkeley, CA, United States.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Alicia Clum
- The Department of Energy Joint Genome Institute, Berkeley, CA, United States.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Alex Spunde
- The Department of Energy Joint Genome Institute, Berkeley, CA, United States.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Manoj Pillay
- The Department of Energy Joint Genome Institute, Berkeley, CA, United States.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Krishnaveni Palaniappan
- The Department of Energy Joint Genome Institute, Berkeley, CA, United States.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Neha Varghese
- The Department of Energy Joint Genome Institute, Berkeley, CA, United States.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Natalia Mikhailova
- The Department of Energy Joint Genome Institute, Berkeley, CA, United States.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - I-Min Chen
- The Department of Energy Joint Genome Institute, Berkeley, CA, United States.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Dimitrios Stamatis
- The Department of Energy Joint Genome Institute, Berkeley, CA, United States.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - T B K Reddy
- The Department of Energy Joint Genome Institute, Berkeley, CA, United States.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Ronan O'Malley
- The Department of Energy Joint Genome Institute, Berkeley, CA, United States.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Chris Daum
- The Department of Energy Joint Genome Institute, Berkeley, CA, United States.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Nicole Shapiro
- The Department of Energy Joint Genome Institute, Berkeley, CA, United States.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Natalia Ivanova
- The Department of Energy Joint Genome Institute, Berkeley, CA, United States.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Nikos C Kyrpides
- The Department of Energy Joint Genome Institute, Berkeley, CA, United States.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Tanja Woyke
- The Department of Energy Joint Genome Institute, Berkeley, CA, United States.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Emiley Eloe-Fadrosh
- The Department of Energy Joint Genome Institute, Berkeley, CA, United States.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Trinity L Hamilton
- Department of Plant and Microbial Biology, The BioTechnology Institute, University of Minnesota, St. Paul, MN, United States
| | - Paul Dijkstra
- Department of Biological Sciences, Center of Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, United States
| | - Jeremy A Dodsworth
- Department of Biology, California State University, San Bernardino, CA, United States
| | - Trent R Northen
- The Department of Energy Joint Genome Institute, Berkeley, CA, United States.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Wen-Jun Li
- School of Life Sciences, Sun Yat-sen University, Guangzhou, China.,State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory, Zhuhai, China
| | - Brian P Hedlund
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, NV, United States.,Nevada Institute of Personalized Medicine, University of Nevada, Las Vegas, Las Vegas, NV, United States
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14
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Sun Y, Wang S, Liu X, He Y, Wu H, Xie W, Li N, Hou W, Dong H. Iron availability is a key factor for freshwater cyanobacterial survival against saline stress. ENVIRONMENTAL RESEARCH 2021; 194:110592. [PMID: 33333036 DOI: 10.1016/j.envres.2020.110592] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 12/02/2020] [Accepted: 12/02/2020] [Indexed: 06/12/2023]
Abstract
Estuaries are among the most productive ecosystems and dynamic environments on Earth. Varying salinity is the most important challenge for phytoplankton survival in estuaries. In order to investigate the role of iron nutrition on phytoplankton survival under salinity stress, a freshwater cyanobacterial strain was cultivated in media added with different proportions of seawater (measured with siderophore activities), and supplied with gel-immobilized ferrihydrite as iron source. Results showed that the strain grew well in media with 0% seawater supplied with ferrihydrite as iron source. Surprisingly, the biomasses in media with 50% seawater, with more newly excreted siderophore, were similar to those with 0% seawater, but better than those with 6.25%, 12.5% and 25% seawater. Smaller iron isotopic discriminations between the cyanobacterial cells associated iron and dissolved iron were observed in media with 0% and 50% seawater suggested that higher fractions of iron uptake from aqueous dissolved iron reservoir by these comparatively larger biomasses. In summary, this study proved that iron availability plays a key role in cyanobacterial survival under varying salinity stress, and suggested that siderophores introduced by seawater may accelerate iron dissolution, increase iron availability, and make cyanobacterial cells overcome the adverse effects of high-salinity, and indicated that siderophore excretion is a kind of survival strategy for phytoplankton in face of salinity stress.
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Affiliation(s)
- Yuxuan Sun
- State Key Laboratory of Biogeosciences and Environmental Geology and Institute of Earth Sciences, China University of Geosciences, Beijing, 100083, China
| | - Shang Wang
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Xiaolei Liu
- State Key Laboratory of Biogeosciences and Environmental Geology and Institute of Earth Sciences, China University of Geosciences, Beijing, 100083, China
| | - Yongsheng He
- State Key Laboratory of Biogeosciences and Environmental Geology and Institute of Earth Sciences, China University of Geosciences, Beijing, 100083, China
| | - Hongjie Wu
- State Key Laboratory of Biogeosciences and Environmental Geology and Institute of Earth Sciences, China University of Geosciences, Beijing, 100083, China
| | - Wei Xie
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai) and School of Marine Sciences, Sun Yat-sen University, Zhuhai, 519082, China
| | - Nan Li
- Key Laboratory of Environment Change and Resources Use in Beibu Gulf, Ministry of Education (Nanning Normal University), Nanning, 530001, China
| | - Weiguo Hou
- State Key Laboratory of Biogeosciences and Environmental Geology and Institute of Earth Sciences, China University of Geosciences, Beijing, 100083, China.
| | - Hailiang Dong
- State Key Laboratory of Biogeosciences and Environmental Geology and Institute of Earth Sciences, China University of Geosciences, Beijing, 100083, China.
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15
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Hot in Cold: Microbial Life in the Hottest Springs in Permafrost. Microorganisms 2020; 8:microorganisms8091308. [PMID: 32867302 PMCID: PMC7565842 DOI: 10.3390/microorganisms8091308] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 08/22/2020] [Accepted: 08/25/2020] [Indexed: 12/26/2022] Open
Abstract
Chukotka is an arctic region located in the continuous permafrost zone, but thermal springs are abundant there. In this study, for the first time, the microbial communities of the Chukotka hot springs (CHS) biofilms and sediments with temperatures 54–94 °C were investigated and analyzed by NGS sequencing of 16S rRNA gene amplicons. In microbial mats (54–75 °C), phototrophic bacteria of genus Chloroflexus dominated (up to 89% of all prokaryotes), while Aquificae were the most numerous at higher temperatures in Fe-rich sediments and filamentous “streamers” (up to 92%). The electron donors typical for Aquificae, such as H2S and H2, are absent or present only in trace amounts, and the prevalence of Aquificae might be connected with their ability to oxidize the ferrous iron present in CHS sediments. Armatimonadetes, Proteobacteria, Deinococcus-Thermus, Dictyoglomi, and Thermotogae, as well as uncultured bacteria (candidate divisions Oct-Spa1-106, GAL15, and OPB56), were numerous, and Cyanobacteria were present in low numbers. Archaea (less than 8% of the total community of each tested spring) belonged to Bathyarchaeota, Aigarchaeota, and Thaumarchaeota. The geographical location and the predominantly autotrophic microbial community, built on mechanisms other than the sulfur cycle-based ones, make CHS a special and unique terrestrial geothermal ecosystem.
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16
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The Effect of Spring Water Geochemistry on Copper Proteins in Tengchong Hot Springs, China. Appl Environ Microbiol 2020; 86:AEM.00581-20. [PMID: 32358007 DOI: 10.1128/aem.00581-20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Accepted: 04/26/2020] [Indexed: 12/28/2022] Open
Abstract
Copper (Cu) is an essential trace metal cofactor for a variety of proteins; however, excess Cu is toxic to most organisms. Cu homeostasis is maintained by a complex machinery of Cu binding proteins that control the uptake, transport, sequestration, and efflux of Cu ions. Despite the importance of Cu binding proteins in electron transfer, substrate oxidation, superoxide dismutation, and denitrification, little information exists about microbial Cu utilization in extreme environments, where the geochemical conditions may affect Cu bioavailability. Using metagenomic data from 9 hot springs in Tengchong, China, which range in temperature from 42°C to 96°C and in pH from 2.3 to 9, the effects of pH, temperature, and spring geochemistry on the distribution of Cu binding domains of proteins and oxidoreductases were studied. Dissolved Cu and Cu binding domains were detected across all temperature and pH gradients. Cu binding domains of cytochrome c oxidase subunits, heavy-metal-associated domains, and nitrous oxide reductase were detected at all sites. DoxB, a quinol oxidase, and other quinol oxidase subunits were the dominant Cu binding oxidoreductase subunits present at low-pH and high-temperature sites, whereas cbb 3-type cytochrome c oxidase subunits were dominant at high-pH and high-temperature sites. Additionally, aa 3-type cytochrome c oxidase was more prominent than cbb 3-type cytochrome c oxidase under circumneutral-pH conditions. This suggests that the type of cytochrome c oxidase pathway and the Cu proteins employed by microbes to carry out important functions such as energy acquisition and efflux of excess Cu are affected by the physicochemical conditions of the springs.IMPORTANCE Copper is present in a variety of proteins and is required to carry out essential functions by all organisms. However, in hot spring environments, copper availability may be limited due to the high temperatures and the wide range in pH. The significance of our research is in relating the physicochemical environment to the distribution of copper proteins across hot spring environments, which provides increased understanding of primary functions and adaptions in these environments.
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17
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Massello FL, Chan CS, Chan KG, Goh KM, Donati E, Urbieta MS. Meta-Analysis of Microbial Communities in Hot Springs: Recurrent Taxa and Complex Shaping Factors beyond pH and Temperature. Microorganisms 2020; 8:microorganisms8060906. [PMID: 32560103 PMCID: PMC7356817 DOI: 10.3390/microorganisms8060906] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Revised: 06/05/2020] [Accepted: 06/09/2020] [Indexed: 11/16/2022] Open
Abstract
The study of microbial communities from extreme environments is a fascinating topic. With every study, biologists and ecologists reveal interesting facts and questions that dispel the old belief that these are inhospitable environments. In this work, we assess the microbial diversity of three hot springs from Neuquén, Argentina, using high-throughput amplicon sequencing. We predicted a distinct metabolic profile in the acidic and the circumneutral samples, with the first ones being dominated by chemolithotrophs and the second ones by chemoheterotrophs. Then, we collected data of the microbial communities of hot springs around the world in an effort to comprehend the roles of pH and temperature as shaping factors. Interestingly, there was a covariation between both parameters and the phylogenetic distance between communities; however, neither of them could explain much of the microbial profile in an ordination model. Moreover, there was no correlation between alpha diversity and these parameters. Therefore, the microbial communities' profile seemed to have complex shaping factors beyond pH and temperature. Lastly, we looked for taxa associated with different environmental conditions. Several such taxa were found. For example, Hydrogenobaculum was frequently present in acidic springs, as was the Sulfolobaceae family; on the other hand, Candidatus Hydrothermae phylum was strongly associated with circumneutral conditions. Interestingly, some singularities related to sites featuring certain taxa were also observed.
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Affiliation(s)
- Francisco L. Massello
- CINDEFI (CCT, La Plata-CONICET, UNLP), Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, 1900 Buenos Aires, Argentina; (F.L.M.); (E.D.)
| | - Chia Sing Chan
- Faculty of Biosciences and Medical Engineering, Universiti Teknologi Malaysia, Skudai 81310, Malaysia; (C.S.C.); (K.M.G.)
| | - Kok-Gan Chan
- Division of Genetics and Molecular Biology, Faculty of Science, Institute of Biological Sciences, University of Malaya, Kuala Lumpur 50603, Malaysia;
| | - Kian Mau Goh
- Faculty of Biosciences and Medical Engineering, Universiti Teknologi Malaysia, Skudai 81310, Malaysia; (C.S.C.); (K.M.G.)
| | - Edgardo Donati
- CINDEFI (CCT, La Plata-CONICET, UNLP), Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, 1900 Buenos Aires, Argentina; (F.L.M.); (E.D.)
| | - María Sofía Urbieta
- CINDEFI (CCT, La Plata-CONICET, UNLP), Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, 1900 Buenos Aires, Argentina; (F.L.M.); (E.D.)
- Correspondence:
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18
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Cavalazzi B, Barbieri R, Gómez F, Capaccioni B, Olsson-Francis K, Pondrelli M, Rossi A, Hickman-Lewis K, Agangi A, Gasparotto G, Glamoclija M, Ori G, Rodriguez N, Hagos M. The Dallol Geothermal Area, Northern Afar (Ethiopia)-An Exceptional Planetary Field Analog on Earth. ASTROBIOLOGY 2019; 19:553-578. [PMID: 30653331 PMCID: PMC6459281 DOI: 10.1089/ast.2018.1926] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
The Dallol volcano and its associated hydrothermal field are located in a remote area of the northern Danakil Depression in Ethiopia, a region only recently appraised after decades of inaccessibility due to severe political instability and the absence of infrastructure. The region is notable for hosting environments at the very edge of natural physical-chemical extremities. It is surrounded by a wide, hyperarid salt plain and is one of the hottest (average annual temperatureDallol: 36-38°C) and most acidic natural systems (pHDallol ≈0) on Earth. Spectacular geomorphologies and mineral deposits produced by supersaturated hydrothermal waters and brines are the result of complex interactions between active and inactive hydrothermal alteration of the bedrock, sulfuric hot springs and pools, fumaroles and geysers, and recrystallization processes driven by hydrothermal waters, degassing, and rapid evaporation. The study of planetary field analog environments plays a crucial role in characterizing the physical and chemical boundaries within which life can exist on Earth and other planets. It is essential for the definition and assessment of the conditions of habitability on other planets, including the possibility for biosignature preservation and in situ testing of technologies for life detection. The Dallol area represents an excellent Mars analog environment given that the active volcanic environment, the associated diffuse hydrothermalism and hydrothermal alteration, and the vast acidic sulfate deposits are reminiscent of past hydrothermal activity on Mars. The work presented in this paper is an overview of the Dallol volcanic area and its hydrothermal field that integrates previous literature with observations and results obtained from field surveys and monitoring coupled with sample characterization. In so doing, we highlight its exceptional potential as a planetary field analog as well as a site for future astrobiological and exploration programs.
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Affiliation(s)
- B. Cavalazzi
- Dipartimento di Scienze Biologiche, Geologiche e Ambientali, Università di Bologna, Bologna, Italy
- Department of Geology, University of Johannesburg, Johannesburg, South Africa
- Address correspondence to: Barbara Cavalazzi, Dipartimento di Scienze Biologiche, Geologiche e Ambientali - BiGeA, Università di Bologna, Via Zamboni 67, I-40126 Bologna, Italy
| | - R. Barbieri
- Dipartimento di Scienze Biologiche, Geologiche e Ambientali, Università di Bologna, Bologna, Italy
| | - F. Gómez
- Centro de Astrobiologia and Instituto Nacional de Técnica Aeroespacial, Madrid, Spain
| | - B. Capaccioni
- Dipartimento di Scienze Biologiche, Geologiche e Ambientali, Università di Bologna, Bologna, Italy
| | - K. Olsson-Francis
- School of Environment, Earth and Ecosystem Sciences, The Open University, Milton Keynes, United Kingdom
| | - M. Pondrelli
- Int'l Research School of Planetary Sciences, Università d'Annunzio, Chieti Scalo, Italy
| | | | - K. Hickman-Lewis
- Dipartimento di Scienze Biologiche, Geologiche e Ambientali, Università di Bologna, Bologna, Italy
- CNRS Centre de Biophysique Moléculaire, Orléans, France
| | - A. Agangi
- Department of Geology, University of Johannesburg, Johannesburg, South Africa
| | - G. Gasparotto
- Dipartimento di Scienze Biologiche, Geologiche e Ambientali, Università di Bologna, Bologna, Italy
| | - M. Glamoclija
- Department of Earth and Environmental Sciences, Rutgers University, Newark, New Jersey, USA
| | - G.G. Ori
- Int'l Research School of Planetary Sciences, Università d'Annunzio, Chieti Scalo, Italy
| | - N. Rodriguez
- Centro de Astrobiologia and Instituto Nacional de Técnica Aeroespacial, Madrid, Spain
| | - M. Hagos
- Department of Earth Sciences, Mekelle University, Mekelle, Ethiopia
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Amin A, Ahmed I, Salam N, Kim BY, Singh D, Zhi XY, Xiao M, Li WJ. Diversity and Distribution of Thermophilic Bacteria in Hot Springs of Pakistan. MICROBIAL ECOLOGY 2017; 74:116-127. [PMID: 28105510 DOI: 10.1007/s00248-017-0930-1] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Accepted: 01/02/2017] [Indexed: 06/06/2023]
Abstract
Chilas and Hunza areas, located in the Main Mantle Thrust and Main Karakoram Thrust of the Himalayas, host a range of geochemically diverse hot springs. This Himalayan geothermal region encompassed hot springs ranging in temperature from 60 to 95 °C, in pH from 6.2 to 9.4, and in mineralogy from bicarbonates (Tato Field), sulfates (Tatta Pani) to mixed type (Murtazaabad). Microbial community structures in these geothermal springs remained largely unexplored to date. In this study, we report a comprehensive, culture-independent survey of microbial communities in nine samples from these geothermal fields by employing a bar-coded pyrosequencing technique. The bacterial phyla Proteobacteria and Chloroflexi were dominant in all samples from Tato Field, Tatta Pani, and Murtazaabad. The community structures however depended on temperature, pH, and physicochemical parameters of the geothermal sites. The Murtazaabad hot springs with relatively higher temperature (90-95 °C) favored the growth of phylum Thermotogae, whereas the Tatta Pani thermal spring site TP-H3-b (60 °C) favored the phylum Proteobacteria. At sites with low silica and high temperature, OTUs belonging to phylum Chloroflexi were dominant. Deep water areas of the Murtazaabad hot springs favored the sulfur-reducing bacteria. About 40% of the total OTUs obtained from these samples were unclassified or uncharacterized, suggesting the presence of many undiscovered and unexplored microbiota. This study has provided novel insights into the nature of ecological interactions among important taxa in these communities, which in turn will help in determining future study courses in these sites.
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Affiliation(s)
- Arshia Amin
- Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education, Yunnan Institute of Microbiology, Yunnan University, Kunming, 650091, People's Republic of China
- Institute of Microbial Culture Collection of Pakistan (IMCCP), National Agricultural Research Centre (NARC), Islamabad, 45500, Pakistan
- Department of Microbiology, Quaid-e-Azam University, Islamabad, 45320, Pakistan
| | - Iftikhar Ahmed
- Institute of Microbial Culture Collection of Pakistan (IMCCP), National Agricultural Research Centre (NARC), Islamabad, 45500, Pakistan.
| | - Nimaichand Salam
- State Key Laboratory of Biocontrol and Guandong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Byung-Yong Kim
- Chun Lab Inc., Seoul National University, Seoul, 151-742, Republic of South Korea
| | - Dharmesh Singh
- Environmental Genomics Division, National Environmental Engineering Research Institute (CSIR-NEERI), Nagpur, 440024, India
| | - Xiao-Yang Zhi
- Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education, Yunnan Institute of Microbiology, Yunnan University, Kunming, 650091, People's Republic of China
| | - Min Xiao
- State Key Laboratory of Biocontrol and Guandong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Wen-Jun Li
- Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education, Yunnan Institute of Microbiology, Yunnan University, Kunming, 650091, People's Republic of China.
- State Key Laboratory of Biocontrol and Guandong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China.
- Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Ürümqi, 830011, People's Republic of China.
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Liu L, Salam N, Jiao JY, Jiang HC, Zhou EM, Yin YR, Ming H, Li WJ. Diversity of Culturable Thermophilic Actinobacteria in Hot Springs in Tengchong, China and Studies of their Biosynthetic Gene Profiles. MICROBIAL ECOLOGY 2016; 72:150-162. [PMID: 27048448 DOI: 10.1007/s00248-016-0756-2] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2015] [Accepted: 03/21/2016] [Indexed: 06/05/2023]
Abstract
The class Actinobacteria has been a goldmine for the discovery of antibiotics and has attracted interest from both academics and industries. However, an absence of novel approaches during the last few decades has limited the discovery of new microbial natural products useful for industries. Scientists are now focusing on the ecological aspects of diverse environments including unexplored or underexplored habitats and extreme environments in the search for new metabolites. This paper reports on the diversity of culturable actinobacteria associated with hot springs located in Tengchong County, Yunnan Province, southwestern China. A total of 58 thermophilic actinobacterial strains were isolated from the samples collected from ten hot springs distributed over three geothermal fields (e.g., Hehua, Rehai, and Ruidian). Phylogenetic positions and their biosynthetic profiles were analyzed by sequencing 16S rRNA gene and three biosynthetic gene clusters (KS domain of PKS-I, KSα domain of PKS-II and A domain of NRPS). On the basis of 16S rRNA gene phylogenetic analysis, the 58 strains were affiliated with 12 actinobacterial genera: Actinomadura Micromonospora, Microbispora, Micrococcus, Nocardiopsis, Nonomuraea, Promicromonospora, Pseudonocardia, Streptomyces, Thermoactinospora, Thermocatellispora, and Verrucosispora, of which the two novel genera Thermoactinospora and Thermocatellisopora were recently described from among these strains. Considering the biosynthetic potential of these actinobacterial strains, 22 were positive for PCR amplification of at least one of the three biosynthetic gene clusters (PKS-I, PKS-II, and NRPS). These actinobacteria were further subjected to antimicrobial assay against five opportunistic human pathogens (Acinetobacter baumannii, Escherichia coli, Micrococcus luteus, Staphylococcus aureus and Streptococcus faecalis). All of the 22 strains that were positive for PCR amplification of at least one of the biosynthetic gene domains exhibited antimicrobial activities against at least one of the five test organisms. Among the remaining 36 actinobacteria that are negative for PCR amplification of the domains for the biosynthetic genes, 33 strains showed antimicrobial activities against at least one of the five test pathogens. In summary, the findings presented in this study emphasized the importance of underexplored habitats such as Tengchong hot springs as potential sources for search of bioactive molecules.
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Affiliation(s)
- Lan Liu
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Nimaichand Salam
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Jian-Yu Jiao
- Yunnan Institute of Microbiology, Yunnan University, Kunming, China
- Medical Faculty of Kunming University of Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Hong-Chen Jiang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, China.
| | - En-Min Zhou
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
- Yunnan Institute of Microbiology, Yunnan University, Kunming, China
| | - Yi-Rui Yin
- Yunnan Institute of Microbiology, Yunnan University, Kunming, China
| | - Hong Ming
- Yunnan Institute of Microbiology, Yunnan University, Kunming, China
- College of Life Sciences and Technology, Xinxiang Medical University, Xinxiang, China
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China.
- Yunnan Institute of Microbiology, Yunnan University, Kunming, China.
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Microbial communities and arsenic biogeochemistry at the outflow of an alkaline sulfide-rich hot spring. Sci Rep 2016; 6:25262. [PMID: 27126380 PMCID: PMC4850476 DOI: 10.1038/srep25262] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Accepted: 03/21/2016] [Indexed: 02/03/2023] Open
Abstract
Alkaline sulfide-rich hot springs provide a unique environment for microbial community and arsenic (As) biogeochemistry. In this study, a representative alkaline sulfide-rich hot spring, Zimeiquan in the Tengchong geothermal area, was chosen to study arsenic geochemistry and microbial community using Illumina MiSeq sequencing. Over 0.26 million 16S rRNA sequence reads were obtained from 5-paired parallel water and sediment samples along the hot spring’s outflow channel. High ratios of As(V)/AsSum (total combined arsenate and arsenite concentrations) (0.59–0.78), coupled with high sulfide (up to 5.87 mg/L), were present in the hot spring’s pools, which suggested As(III) oxidation occurred. Along the outflow channel, AsSum increased from 5.45 to 13.86 μmol/L, and the combined sulfide and sulfate concentrations increased from 292.02 to 364.28 μmol/L. These increases were primarily attributed to thioarsenic transformation. Temperature, sulfide, As and dissolved oxygen significantly shaped the microbial communities between not only the pools and downstream samples, but also water and sediment samples. Results implied that the upstream Thermocrinis was responsible for the transformation of thioarsenic to As(III) and the downstream Thermus contributed to derived As(III) oxidation. This study improves our understanding of microbially-mediated As transformation in alkaline sulfide-rich hot springs.
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Jiang Z, Li P, Jiang D, Dai X, Zhang R, Wang Y, Wang Y. Microbial Community Structure and Arsenic Biogeochemistry in an Acid Vapor-Formed Spring in Tengchong Geothermal Area, China. PLoS One 2016; 11:e0146331. [PMID: 26761709 PMCID: PMC4711897 DOI: 10.1371/journal.pone.0146331] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2015] [Accepted: 12/16/2015] [Indexed: 11/24/2022] Open
Abstract
Arsenic biogeochemistry has been studied extensively in acid sulfate-chloride hot springs, but not in acid sulfate hot springs with low chloride. In this study, Zhenzhuquan in Tengchong geothermal area, a representative acid sulfate hot spring with low chloride, was chosen to study arsenic geochemistry and microbial community structure using Illumina MiSeq sequencing. Over 0.3 million 16S rRNA sequence reads were obtained from 6-paired parallel water and sediment samples along its outflow channel. Arsenic oxidation occurred in the Zhenxhuquan pool, with distinctly high ratios of arsenate to total dissolved arsenic (0.73–0.86). Coupled with iron and sulfur oxidation along the outflow channel, arsenic accumulated in downstream sediments with concentrations up to 16.44 g/kg and appeared to significantly constrain their microbial community diversity. These oxidations might be correlated with the appearance of some putative functional microbial populations, such as Aquificae and Pseudomonas (arsenic oxidation), Sulfolobus (sulfur and iron oxidation), Metallosphaera and Acidicaldus (iron oxidation). Temperature, total organic carbon and dissolved oxygen significantly shaped the microbial community structure of upstream and downstream samples. In the upstream outflow channel region, most microbial populations were microaerophilic/anaerobic thermophiles and hyperthermophiles, such as Sulfolobus, Nocardia, Fervidicoccus, Delftia, and Ralstonia. In the downstream region, aerobic heterotrophic mesophiles and thermophiles were identified, including Ktedonobacteria, Acidicaldus, Chthonomonas and Sphingobacteria. A total of 72.41–95.91% unassigned-genus sequences were derived from the downstream high arsenic sediments 16S rRNA clone libraries. This study could enable us to achieve an integrated understanding on arsenic biogeochemistry in acid hot springs.
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Affiliation(s)
- Zhou Jiang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, People's Republic of China
- School of Environmental Studies, China University of Geosciences, Wuhan, People's Republic of China
| | - Ping Li
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, People's Republic of China
- * E-mail: (PL); (YXW)
| | - Dawei Jiang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, People's Republic of China
| | - Xinyue Dai
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, People's Republic of China
- School of Environmental Studies, China University of Geosciences, Wuhan, People's Republic of China
| | - Rui Zhang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, People's Republic of China
| | - Yanhong Wang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, People's Republic of China
| | - Yanxin Wang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, People's Republic of China
- School of Environmental Studies, China University of Geosciences, Wuhan, People's Republic of China
- * E-mail: (PL); (YXW)
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Li H, Yang Q, Li J, Gao H, Li P, Zhou H. The impact of temperature on microbial diversity and AOA activity in the Tengchong Geothermal Field, China. Sci Rep 2015; 5:17056. [PMID: 26608685 PMCID: PMC4660298 DOI: 10.1038/srep17056] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Accepted: 10/20/2015] [Indexed: 02/07/2023] Open
Abstract
Using a culture-independent method that combines CARD-FISH, qPCR and 16S rDNA, we investigated the abundance, community structure and diversity of microbes along a steep thermal gradient (50–90 °C) in the Tengchong Geothermal Field. We found that Bacteria and Archaea abundance changed markedly with temperature changes and that the number of cells was lowest at high temperatures (90.8 °C). Under low-temperature conditions (52.3–74.6 °C), the microbial communities were dominated by Bacteria, which accounted for 60–80% of the total number of cells. At 74.6 °C, Archaea were dominant, and at 90.8 °C, they accounted for more than 90% of the total number of cells. Additionally, the microbial communities at high temperatures (74.6–90.8 °C) were substantially simpler than those at the low-temperature sites. Only a few genera (e.g., bacterial Caldisericum, Thermotoga and Thermoanaerobacter, archaeal Vulcanisaeta and Hyperthermus) often dominated in high-temperature environments. Additionally, a positive correlation between Ammonia-Oxidizing Archaea (AOA) activity and temperature was detected. AOA activity increased from 17 to 52 pmol of NO2− per cell d−1 with a temperature change from 50 to 70 °C.
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Affiliation(s)
- Haizhou Li
- School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Qunhui Yang
- State Key Laboratory of Marine Geology, School of Ocean and Earth Science, Tongji University, Shanghai 200092, China
| | - Jian Li
- School of Engineering, Anhui Agricultural University, Hefei 230000, China
| | - Hang Gao
- State Key Laboratory of Marine Geology, School of Ocean and Earth Science, Tongji University, Shanghai 200092, China
| | - Ping Li
- School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Huaiyang Zhou
- State Key Laboratory of Marine Geology, School of Ocean and Earth Science, Tongji University, Shanghai 200092, China
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Dodsworth JA, Ong JC, Williams AJ, Dohnalkova AC, Hedlund BP. Thermocrinis jamiesonii sp. nov., a thiosulfate-oxidizing, autotropic thermophile isolated from a geothermal spring. Int J Syst Evol Microbiol 2015; 65:4769-4775. [PMID: 26419502 DOI: 10.1099/ijsem.0.000647] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
An obligately thermophilic, chemolithotrophic, microaerophilic bacterium, designated strain GBS1T, was isolated from the water column of Great Boiling Spring, Nevada, USA. Thiosulfate was required for growth. Although capable of autotrophy, growth of GBS1T was enhanced in the presence of acetate, peptone or Casamino acids. Growth occurred at 70-85 °C with an optimum at 80 °C, at pH 6.50-7.75 with an optimum at pH 7.25, with 0.5-8 % oxygen with an optimum at 1-2 % and with ≤ 200 mM NaCl. The doubling time under optimal growth conditions was 1.3 h, with a final mean cell density of 6.2 ± 0.5 × 107 cells ml- 1. Non-motile, rod-shaped cells 1.4-2.4 × 0.4-0.6 μm in size occurred singly or in pairs. The major cellular fatty acids (>5 % of the total) were C20 : 1ω9c, C18 : 0, C16 : 0 and C20 : 0. Phylogenetic analysis of the GBS1T 16S rRNA gene sequence indicated an affiliation with Thermocrinis ruber and other species of the genus Thermocrinis, but determination of 16S rRNA gene sequence similarity ( ≤ 97.10 %) and in silico estimated DNA-DNA hybridization values ( ≤ 18.4 %) with the type strains of recognized Thermocrinis species indicate that the novel strain is distinct from described species. Based on phenotypic, genotypic and phylogenetic characteristics, a novel species, Thermocrinis jamiesonii sp. nov., is proposed, with GBS1T ( = JCM 19133T = DSM 27162T) as the type strain.
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Affiliation(s)
- Jeremy A Dodsworth
- Department of Biology, California State University, San Bernardino, CA 92407, USA.,School of Life Sciences, University of Nevada, Las Vegas, NV 89154, USA
| | - John C Ong
- School of Life Sciences, University of Nevada, Las Vegas, NV 89154, USA
| | - Amanda J Williams
- School of Life Sciences, University of Nevada, Las Vegas, NV 89154, USA
| | - Alice C Dohnalkova
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Brian P Hedlund
- School of Life Sciences, University of Nevada, Las Vegas, NV 89154, USA
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