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Ugwuanyi IR, Steele A, Glamoclija M. Microbial Ecology of an Arctic Travertine Geothermal Spring: Implications for Biosignature Preservation and Astrobiology. ASTROBIOLOGY 2024; 24:734-753. [PMID: 38985714 DOI: 10.1089/ast.2023.0130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/12/2024]
Abstract
Jotun springs in Svalbard, Norway, is a rare warm environment in the Arctic that actively forms travertine. In this study, we assessed the microbial ecology of Jotun's active (aquatic) spring and dry spring transects. We evaluated the microbial preservation potential and mode, as well as the astrobiological relevance of the travertines to marginal carbonates mapped at Jezero Crater on Mars (the Mars 2020 landing site). Our results revealed that microbial communities exhibited spatial dynamics controlled by temperature, fluid availability, and geochemistry. Amorphous carbonates and silica precipitated within biofilm and on the surface of filamentous microorganisms. The water discharged at the source is warm, with near neutral pH, and undersaturated in silica. Hence, silicification possibly occurred through cooling, dehydration, and partially by a microbial presence or activities that promote silica precipitation. CO2 degassing and possible microbial contributions induced calcite precipitation and travertine formation. Jotun revealed that warm systems that are not very productive in carbonate formation may still produce significant carbonate buildups and provide settings favorable for fossilization through silicification and calcification. Our findings suggest that the potential for amorphous silica precipitation may be essential for Jezero Crater's marginal carbonates because it significantly increases the preservation potential of putative martian organisms.
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Affiliation(s)
- Ifeoma R Ugwuanyi
- Department of Earth and Environmental Sciences, Rutgers University, Newark, New Jersey, USA
| | - Andrew Steele
- Earth and Planets Laboratory, Carnegie Institution for Science, Washington, District of Columbia, USA
| | - Mihaela Glamoclija
- Department of Earth and Environmental Sciences, Rutgers University, Newark, New Jersey, USA
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2
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Rowe L, Dowd SE, Davidson K, Kovarik C, VanAken M, Jarabek A, Taylor C. Comparing microbial populations from diverse hydrothermal features in Yellowstone National Park: hot springs and mud volcanoes. Front Microbiol 2024; 15:1409664. [PMID: 38993494 PMCID: PMC11236564 DOI: 10.3389/fmicb.2024.1409664] [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: 03/30/2024] [Accepted: 05/30/2024] [Indexed: 07/13/2024] Open
Abstract
Geothermal features, such as hot springs and mud volcanoes, host diverse microbial life, including many extremophile organisms. The physicochemical parameters of the geothermal feature, such as temperature, pH, and heavy metal concentration, can influence the alpha and beta diversity of microbial life in these environments, as can spatiotemporal differences between sites and sampling. In this study, water and sediment samples were collected and analyzed from eight geothermal sites at Yellowstone National Park, including six hot springs, a mud volcano, and an acidic lake within the same week in July 2019, and these geothermal sites varied greatly in their temperature, pH, and chemical composition. All samples were processed and analyzed with the same methodology and taxonomic profiles and alpha and beta diversity metrics determined with 16S rRNA sequencing. These microbial diversity results were then analyzed with respect to pH, temperature, and chemical composition of the geothermal features. Results indicated that predominant microbial species varied greatly depending on the physicochemical composition of the geothermal site, with decreases in pH and increases in dissolved heavy metals in the water corresponding to decreases in alpha diversity, especially in the sediment samples. Similarly, sites with acidic pH values had more similar microbial populations (beta diversity) to one another than to relatively neutral or alkaline pH geothermal sites. This study suggests that pH and/or heavy metal concentration is a more important driver for microbial diversity and population profile than the temperature for these sites and is also the first reported microbial diversity study for multiple geothermal sites in Yellowstone National Park, including the relatively new mud volcano Black Dragon's Caldron, which erupted in 1948.
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Affiliation(s)
- Laura Rowe
- Department of Chemistry, Eastern Kentucky University, Richmond, KY, United States
- Department of Chemistry, Valparaiso University, Valparaiso, IN, United States
| | - Scot E. Dowd
- Molecular Research LP (MR DNA Lab), Shallowater, TX, United States
| | - Kelly Davidson
- Department of Chemistry, Valparaiso University, Valparaiso, IN, United States
| | - Claire Kovarik
- Department of Chemistry, Valparaiso University, Valparaiso, IN, United States
| | - Michayla VanAken
- Department of Chemistry, Valparaiso University, Valparaiso, IN, United States
| | - Alyssa Jarabek
- Department of Chemistry, Valparaiso University, Valparaiso, IN, United States
| | - Churro Taylor
- Department of Chemistry, Eastern Kentucky University, Richmond, KY, United States
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Sriaporn C, Komonjinda S, Awiphan S, Santitharangkun S, Banjongprasert C, Osathanunkul M, Ramsiri B. Mineralogical and microbial characterization of alkali hot spring microbial mats and deposits in Pong Dueat Pa Pae hot spring, Northern Thailand. Extremophiles 2024; 28:29. [PMID: 38900286 DOI: 10.1007/s00792-024-01343-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Accepted: 05/27/2024] [Indexed: 06/21/2024]
Abstract
Hot spring environments encompass broad physicochemical ranges, in which temperature and pH account for crucial factors shaping hot spring microbial community and diversity. However, the presence of photosynthetic microbial mats adjacent to boiling hot spring vents, where fluid temperatures extend beyond photosynthetic capability, questions the microbial profiles and the actual temperatures of such adjacent mats. Therefore, this study aims to characterize thermophilic microbial communities at Pong Dueat Pa Pae hot spring using next-generation sequencing, including investigating hot spring mineralogy. Results suggest that Pong Dueat Pa Pae hot spring precipitates comprise mainly silica which also acts as the main preservative medium for microbial permineralization. Molecular results revealed the presence of cyanobacterial and Chloroflexi species in the thick, orange and green subaerial mats surrounding the vents, suggesting the mats would be at least 30 °C cooler than source vents despite constantly receiving geyser splashes. Bacterial abundance was considerably higher than archaeal (97.9% versus 2.1%). Cyanobacterial (mainly Synechococcus and Leptolygbya) and Chloroflexi species (mainly Roseiflexus) accounted for almost half (40.04%) of the bacterial community, while DHVEG-6 and Thaumarchaeota comprised dominant members (> 90%) of the archaeal fraction. This study updates and provides insights into thermophilic microbial community composition and mineralogy of hot springs in Thailand.
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Affiliation(s)
- C Sriaporn
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
| | - S Komonjinda
- Department of Physics and Materials Science, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand.
| | - S Awiphan
- National Astronomical Research Institute of Thailand (Public Organization), Chiang Mai, Thailand
| | - S Santitharangkun
- Department of Geology, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
| | - C Banjongprasert
- Department of Physics and Materials Science, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
| | - M Osathanunkul
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
| | - B Ramsiri
- Huai Nam Dang National Park, Protected Areas Regional Office 16, Department of National Parks, Wildlife and Plant Conservation, Chiang Mai, Thailand
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Qi YL, Chen YT, Xie YG, Li YX, Rao YZ, Li MM, Xie QJ, Cao XR, Chen L, Qu YN, Yuan ZX, Xiao ZC, Lu L, Jiao JY, Shu WS, Li WJ, Hedlund BP, Hua ZS. Analysis of nearly 3000 archaeal genomes from terrestrial geothermal springs sheds light on interconnected biogeochemical processes. Nat Commun 2024; 15:4066. [PMID: 38744885 PMCID: PMC11094006 DOI: 10.1038/s41467-024-48498-5] [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: 09/07/2023] [Accepted: 05/02/2024] [Indexed: 05/16/2024] Open
Abstract
Terrestrial geothermal springs are physicochemically diverse and host abundant populations of Archaea. However, the diversity, functionality, and geological influences of these Archaea are not well understood. Here we explore the genomic diversity of Archaea in 152 metagenomes from 48 geothermal springs in Tengchong, China, collected from 2016 to 2021. Our dataset is comprised of 2949 archaeal metagenome-assembled genomes spanning 12 phyla and 392 newly identified species, which increases the known species diversity of Archaea by ~48.6%. The structures and potential functions of the archaeal communities are strongly influenced by temperature and pH, with high-temperature acidic and alkaline springs favoring archaeal abundance over Bacteria. Genome-resolved metagenomics and metatranscriptomics provide insights into the potential ecological niches of these Archaea and their potential roles in carbon, sulfur, nitrogen, and hydrogen metabolism. Furthermore, our findings illustrate the interplay of competition and cooperation among Archaea in biogeochemical cycles, possibly arising from overlapping functional niches and metabolic handoffs. Taken together, our study expands the genomic diversity of Archaea inhabiting geothermal springs and provides a foundation for more incisive study of biogeochemical processes mediated by Archaea in geothermal ecosystems.
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Affiliation(s)
- Yan-Ling Qi
- Chinese Academy of Sciences Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, 230026, China
| | - Ya-Ting Chen
- Institute for Disaster Management and Reconstruction, Sichuan University-Hong Kong Polytechnic University, Chengdu, 610207, China
| | - Yuan-Guo Xie
- Chinese Academy of Sciences Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, 230026, China
| | - Yu-Xian Li
- Chinese Academy of Sciences Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, 230026, China
| | - Yang-Zhi Rao
- Chinese Academy of Sciences Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, 230026, China
| | - Meng-Meng Li
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, PR China
| | - Qi-Jun Xie
- Chinese Academy of Sciences Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, 230026, China
| | - Xing-Ru Cao
- Chinese Academy of Sciences Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, 230026, China
| | - Lei Chen
- Chinese Academy of Sciences Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, 230026, China
| | - Yan-Ni Qu
- Chinese Academy of Sciences Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, 230026, China
| | - Zhen-Xuan Yuan
- Chinese Academy of Sciences Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, 230026, China
| | - Zhi-Chao Xiao
- Chinese Academy of Sciences Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, 230026, China
| | - Lu Lu
- College of Environmental Science and Engineering, China West Normal University, Nanchong, 637009, China
| | - Jian-Yu Jiao
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, PR China
| | - Wen-Sheng Shu
- School of Life Sciences, South China Normal University, Guangzhou, PR China
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, PR China.
| | - Brian P Hedlund
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV, 89154, USA.
- Nevada Institute of Personalized Medicine, University of Nevada Las Vegas, Las Vegas, NV, 89154, USA.
| | - Zheng-Shuang Hua
- Chinese Academy of Sciences Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, 230026, China.
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Wu D, Zou Y, Xiao J, Mo L, Lek S, Chen B, Fu Q, Guo Z. The spatiotemporal variations of microbial community in relation to water quality in a tropical drinking water reservoir, Southmost China. Front Microbiol 2024; 15:1354784. [PMID: 38770023 PMCID: PMC11102952 DOI: 10.3389/fmicb.2024.1354784] [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: 01/16/2024] [Accepted: 04/08/2024] [Indexed: 05/22/2024] Open
Abstract
It is well-known that water quality has great significance on microbial community composition in aquatic environments. In this study, we detected water column indicates the microbial community composition of nine sampling sites over two seasons using Illumina TruSeq sequencing in Songtao Reservoir, Hainan Province, Southmost China. The study indicated that the dominant phylum was Actinobacteria, Proteobacteria, Bacteroidetes, and Cyanobacteria. The diversity parameters showed that the microbial community composition had significant spatiotemporal variations, including the significantly higher Shannon index and Simpson index upstream than those midstream and downstream. Besides, there were significantly higher Chao1 index, Shannon index, and Simpson index in winter than in summer. Principal coordinates analysis (PCoA) showed the microbial structural composition had significant seasonal differences. The results of microbial community composition further revealed that the eutrophication level upstream was higher than that of midstream and downstream. The redundancy analysis (RDA) diagram indicated that the abundance of microbiology species significantly correlated with temperature, total phosphorus, Se, and Ni. Furthermore, the mantel's test showed that the temperature and total phosphorus significantly affected the community composition of archaea and bacteria. Overall, our finding here partially validated our hypothesis that the spatiotemporal variations of microbial community composition are significantly related to nutrients, physicochemical factors and metals, which has been unknown previously in tropical drinking waterbodies. This study substantially contributed to understanding of the composition of microbial community in tropical drinking water reservoirs and the main environmental driving factors in tropical zones. It also provided a reference for the management of reservoir operation to ensure drinking water safe.
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Affiliation(s)
- Di Wu
- School of Life and Health Sciences, Key Laboratory of Tropical Biological Resources of Ministry of Education, State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, China
| | - Ying Zou
- School of Life and Health Sciences, Key Laboratory of Tropical Biological Resources of Ministry of Education, State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, China
| | - Juan Xiao
- School of Life and Health Sciences, Key Laboratory of Tropical Biological Resources of Ministry of Education, State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, China
| | - Ling Mo
- Institute of Environmental Sciences, Haikou, Hainan Province, China
| | - Sovan Lek
- School of Life and Health Sciences, Key Laboratory of Tropical Biological Resources of Ministry of Education, State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, China
- Laboratoire Evolution & Diversité Biologique, Université Paul Sabatier, Toulouse, France
| | - Bo Chen
- National Health Commission of the People's Republic of China Key Laboratory of Control of Tropical Diseases Control, School of Tropical Medicine, Hainan Medical University, Haikou, Hainan, China
| | - Qiongyao Fu
- National Health Commission of the People's Republic of China Key Laboratory of Control of Tropical Diseases Control, School of Tropical Medicine, Hainan Medical University, Haikou, Hainan, China
| | - Zhiqiang Guo
- School of Life and Health Sciences, Key Laboratory of Tropical Biological Resources of Ministry of Education, State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, China
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6
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Kut P, Garcia-Pichel F. Nimble vs. torpid responders to hydration pulse duration among soil microbes. Commun Biol 2024; 7:455. [PMID: 38609432 PMCID: PMC11015016 DOI: 10.1038/s42003-024-06141-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 04/03/2024] [Indexed: 04/14/2024] Open
Abstract
Environmental parameters vary in time, and variability is inherent in soils, where microbial activity follows precipitation pulses. The expanded pulse-reserve paradigm (EPRP) contends that arid soil microorganisms have adaptively diversified in response to pulse regimes differing in frequency and duration. To test this, we incubate Chihuahuan Desert soil microbiomes under separate treatments in which 60 h of hydration was reached with pulses of different pulse duration (PD), punctuated by intervening periods of desiccation. Using 16S rRNA gene amplicon data, we measure treatment effects on microbiome net growth, growth efficiency, diversity, and species composition, tracking the fate of 370 phylotypes (23% of those detected). Consistent with predictions, microbial diversity is a direct, saturating function of PD. Increasingly larger shifts in community composition are detected with decreasing PD, as specialist phylotypes become more prominent. One in five phylotypes whose fate was tracked responds consistently to PD, some preferring short pulses (nimble responders; NIRs) and some longer pulses (torpid responders; TORs). For pulses shorter than a day, microbiome growth efficiency is an inverse function of PD, as predicted. We conclude that PD in pulsed soil environments constitutes a major driver of microbial community assembly and function, largely consistent with the EPRP predictions.
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Affiliation(s)
- Patrick Kut
- Center for Fundamental and Applied Microbiomics and School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | - Ferran Garcia-Pichel
- Center for Fundamental and Applied Microbiomics and School of Life Sciences, Arizona State University, Tempe, AZ, USA.
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7
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Pantiora PD, Georgakis ND, Premetis GE, Labrou NE. Metagenomic analysis of hot spring soil for mining a novel thermostable enzybiotic. Appl Microbiol Biotechnol 2024; 108:163. [PMID: 38252132 PMCID: PMC10803476 DOI: 10.1007/s00253-023-12979-2] [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: 08/17/2023] [Revised: 12/06/2023] [Accepted: 12/20/2023] [Indexed: 01/23/2024]
Abstract
The misuse and overuse of antibiotics have contributed to a rapid emergence of antibiotic-resistant bacterial pathogens. This global health threat underlines the urgent need for innovative and novel antimicrobials. Endolysins derived from bacteriophages or prophages constitute promising new antimicrobials (so-called enzybiotics), exhibiting the ability to break down bacterial peptidoglycan (PG). In the present work, metagenomic analysis of soil samples, collected from thermal springs, allowed the identification of a prophage-derived endolysin that belongs to the N-acetylmuramoyl-L-alanine amidase type 2 (NALAA-2) family and possesses a LysM (lysin motif) region as a cell wall binding domain (CWBD). The enzyme (Ami1) was cloned and expressed in Escherichia coli, and its bactericidal and lytic activity was characterized. The results indicate that Ami1 exhibits strong bactericidal and antimicrobial activity against a broad range of bacterial pathogens, as well as against isolated peptidoglycan (PG). Among the examined bacterial pathogens, Ami1 showed highest bactericidal activity against Staphylococcus aureus sand Staphylococcus epidermidis cells. Thermostability analysis revealed a melting temperature of 64.2 ± 0.6 °C. Overall, these findings support the potential that Ami1, as a broad spectrum antimicrobial agent, could be further assessed as enzybiotic for the effective treatment of bacterial infections. KEY POINTS: • Metagenomic analysis allowed the identification of a novel prophage endolysin • The endolysin belongs to type 2 amidase family with lysin motif region • The endolysin displays high thermostability and broad bactericidal spectrum.
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Affiliation(s)
- Panagiota D Pantiora
- Laboratory of Enzyme Technology, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, 75 Iera Odos Street, GR-11855, Athens, Greece
| | - Nikolaos D Georgakis
- Laboratory of Enzyme Technology, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, 75 Iera Odos Street, GR-11855, Athens, Greece
| | - Georgios E Premetis
- Laboratory of Enzyme Technology, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, 75 Iera Odos Street, GR-11855, Athens, Greece
| | - Nikolaos E Labrou
- Laboratory of Enzyme Technology, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, 75 Iera Odos Street, GR-11855, Athens, Greece.
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Chen JS, Hussain B, Tsai HC, Nagarajan V, Kumar RS, Lin IC, Hsu BM. Deciphering microbial communities and their unique metabolic repertoire across rock-soil-plant continuum in the Dayoukeng fumarolic geothermal field of the Tatun Volcano Group. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:7330-7344. [PMID: 38158533 DOI: 10.1007/s11356-023-31313-x] [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: 05/08/2023] [Accepted: 11/28/2023] [Indexed: 01/03/2024]
Abstract
High temperature and sulfur concentrations in geothermal sulfur fumaroles host unique microbial ecosystems with niche-specific metabolic diversity and physiological functions. In this study, the microbial communities and their functionalities associated with the Dayoukeng geothermal field and the rock-soil-plant continuum were investigated to underpin the microbial modulation at different distances from the fumaroles source. At the phylum level, Bacteroidota, Planctomycetota, Armatimonadota, and Patescibacteria were abundant in plant samples; Elusimicrobiota and Desulfobacterota were in the rock samples while Nitrospirota, Micrarchaeota, and Deinococcota were dominant in the soil samples. Acidophilic thermophiles were enriched in samples within close proximity to the fumaroles, primarily at a distance of 1 m. The sulfur and iron-oxidizing acidophilic bacterial genera such as Acidothiobacillus and Sulfobacillus were abundant in the rock samples. The thermoacidophilic archaeon Acidianus and acidophilic bacteria Acidiphilium were abundant in the soil samples. Additionally, Thermosporothrix and Acidothermus were found abundant in the plant samples. The results of the functional annotation indicated that dark sulfur oxidation, iron oxidation, and hydrogen oxidation pathways were abundant in the soil samples up to 1 m from the fumaroles, while methanogenic and fermentation pathways were more prevalent in the soil samples located 10 m from the fumaroles. Interestingly, the results of this study indicated a higher microbial richness and abundance of acidophilic communities in the soils and plants compared to the rocks of the DYK fumarolic geothermal field.
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Affiliation(s)
- Jung-Sheng Chen
- Department of Medical Research, E-Da Hospital, I-Shou University, Kaohsiung, Taiwan
| | - Bashir Hussain
- Department of Earth and Environmental Sciences, National Chung Cheng University, Minxiong, Chiayi County, Taiwan
- Department of Biomedical Sciences, National Chung Cheng University, Minxiong, Chiayi County, Taiwan
| | - Hsin-Chi Tsai
- Department of Psychiatry, School of Medicine, Tzu Chi University, Hualien, Taiwan
- Department of Psychiatry, Tzu-Chi General Hospital, Hualien, Taiwan
| | - Viji Nagarajan
- Department of Earth and Environmental Sciences, National Chung Cheng University, Minxiong, Chiayi County, Taiwan
| | - Rajendran Senthil Kumar
- Department of Earth and Environmental Sciences, National Chung Cheng University, Minxiong, Chiayi County, Taiwan
| | - I-Ching Lin
- Department of Family Medicine, Asia University Hospital, Taichung, Taiwan
- Department of Kinesiology, Health and Leisure, Chienkuo Technology University, Chenghua, Taiwan
| | - Bing-Mu Hsu
- Department of Earth and Environmental Sciences, National Chung Cheng University, Minxiong, Chiayi County, Taiwan.
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Bonthond G, Beermann J, Gutow L, Neumann A, Barboza FR, Desiderato A, Fofonova V, Helber SB, Khodami S, Kraan C, Neumann H, Rohde S, Schupp PJ. Benthic microbial biogeographic trends in the North Sea are shaped by an interplay of environmental drivers and bottom trawling effort. ISME COMMUNICATIONS 2023; 3:132. [PMID: 38102238 PMCID: PMC10724143 DOI: 10.1038/s43705-023-00336-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 11/09/2023] [Accepted: 11/16/2023] [Indexed: 12/17/2023]
Abstract
Microbial composition and diversity in marine sediments are shaped by environmental, biological, and anthropogenic processes operating at different scales. However, our understanding of benthic microbial biogeography remains limited. Here, we used 16S rDNA amplicon sequencing to characterize benthic microbiota in the North Sea from the top centimeter of 339 sediment samples. We utilized spatially explicit statistical models, to disentangle the effects of the different predictors, including bottom trawling intensity, a prevalent industrial fishing practice which heavily impacts benthic ecosystems. Fitted models demonstrate how the geographic interplay of different environmental and anthropogenic drivers shapes the diversity, structure and potential metabolism of benthic microbial communities. Sediment properties were the primary determinants, with diversity increasing with sediment permeability but also with mud content, highlighting different underlying processes. Additionally, diversity and structure varied with total organic matter content, temperature, bottom shear stress and bottom trawling. Changes in diversity associated with bottom trawling intensity were accompanied by shifts in predicted energy metabolism. Specifically, with increasing trawling intensity, we observed a transition toward more aerobic heterotrophic and less denitrifying predicted metabolism. Our findings provide first insights into benthic microbial biogeographic patterns on a large spatial scale and illustrate how anthropogenic activity such as bottom trawling may influence the distribution and abundances of microbes and potential metabolism at macroecological scales.
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Affiliation(s)
- Guido Bonthond
- Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University Oldenburg, Schleusenstrasse 1, 26382, Wilhelmshaven, Germany.
| | - Jan Beermann
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Am Handelshafen 12, 27570, Bremerhaven, Germany
| | - Lars Gutow
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Am Handelshafen 12, 27570, Bremerhaven, Germany
| | | | | | - Andrea Desiderato
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Am Handelshafen 12, 27570, Bremerhaven, Germany
- Department of Invertebrate Zoology and Hydrobiology, University of Lodz, 90-136, Lodz, Poland
| | - Vera Fofonova
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Am Handelshafen 12, 27570, Bremerhaven, Germany
| | - Stephanie B Helber
- Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University Oldenburg, Schleusenstrasse 1, 26382, Wilhelmshaven, Germany
| | - Sahar Khodami
- Senckenberg am Meer Wilhelmshaven, German Centre for Marine Biodiversity Research, Südstrand 44, 26382, Wilhelmshaven, Germany
| | - Casper Kraan
- Thünen Institute of Sea Fisheries, Herwigstraße 31, 27572, Bremerhaven, Germany
| | - Hermann Neumann
- Thünen Institute of Sea Fisheries, Herwigstraße 31, 27572, Bremerhaven, Germany
| | - Sven Rohde
- Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University Oldenburg, Schleusenstrasse 1, 26382, Wilhelmshaven, Germany
| | - Peter J Schupp
- Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University Oldenburg, Schleusenstrasse 1, 26382, Wilhelmshaven, Germany
- Helmholtz Institute for Functional Marine Biodiversity at the University of Oldenburg (HIFMB), Ammerländer Heerstrasse 231, D-26129, Oldenburg, Germany
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10
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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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11
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Kostešić E, Mitrović M, Kajan K, Marković T, Hausmann B, Orlić S, Pjevac P. Microbial Diversity and Activity of Biofilms from Geothermal Springs in Croatia. MICROBIAL ECOLOGY 2023; 86:2305-2319. [PMID: 37209180 PMCID: PMC10640420 DOI: 10.1007/s00248-023-02239-1] [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: 03/03/2023] [Accepted: 05/07/2023] [Indexed: 05/22/2023]
Abstract
Hot spring biofilms are stable, highly complex microbial structures. They form at dynamic redox and light gradients and are composed of microorganisms adapted to the extreme temperatures and fluctuating geochemical conditions of geothermal environments. In Croatia, a large number of poorly investigated geothermal springs host biofilm communities. Here, we investigated the microbial community composition of biofilms collected over several seasons at 12 geothermal springs and wells. We found biofilm microbial communities to be temporally stable and highly dominated by Cyanobacteria in all but one high-temperature sampling site (Bizovac well). Of the physiochemical parameters recorded, temperature had the strongest influence on biofilm microbial community composition. Besides Cyanobacteria, the biofilms were mainly inhabited by Chloroflexota, Gammaproteobacteria, and Bacteroidota. In a series of incubations with Cyanobacteria-dominated biofilms from Tuhelj spring and Chloroflexota- and Pseudomonadota-dominated biofilms from Bizovac well, we stimulated either chemoorganotrophic or chemolithotrophic community members, to determine the fraction of microorganisms dependent on organic carbon (in situ predominantly produced via photosynthesis) versus energy derived from geochemical redox gradients (here simulated by addition of thiosulfate). We found surprisingly similar levels of activity in response to all substrates in these two distinct biofilm communities, and observed microbial community composition and hot spring geochemistry to be poor predictors of microbial activity in the study systems.
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Affiliation(s)
- Ema Kostešić
- Division of Materials Chemistry, Ruđer Bošković Institute, Zagreb, Croatia
| | - Maja Mitrović
- Division of Materials Chemistry, Ruđer Bošković Institute, Zagreb, Croatia
| | - Katarina Kajan
- Division of Materials Chemistry, Ruđer Bošković Institute, Zagreb, Croatia
- Center of Excellence for Science and Technology-Integration of Mediterranean Region (STIM), Split, Croatia
| | | | - Bela Hausmann
- Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna, Vienna, Austria
- Department of Laboratory Medicine, Medical University of Vienna, Vienna, Austria
| | - Sandi Orlić
- Division of Materials Chemistry, Ruđer Bošković Institute, Zagreb, Croatia
- Center of Excellence for Science and Technology-Integration of Mediterranean Region (STIM), Split, Croatia
| | - Petra Pjevac
- Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna, Vienna, Austria.
- Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria.
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12
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Akaçin İ, Ersoy Ş, Doluca O, Güngörmüşler M. Using custom-built primers and nanopore sequencing to evaluate CO-utilizer bacterial and archaeal populations linked to bioH 2 production. Sci Rep 2023; 13:17025. [PMID: 37813931 PMCID: PMC10562470 DOI: 10.1038/s41598-023-44357-3] [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: 04/14/2023] [Accepted: 10/06/2023] [Indexed: 10/11/2023] Open
Abstract
The microbial community composition of five distinct thermophilic hot springs was effectively described in this work, using broad-coverage nanopore sequencing (ONT MinION sequencer). By examining environmental samples from the same source, but from locations with different temperatures, bioinformatic analysis revealed dramatic changes in microbial diversity and archaeal abundance. More specifically, no archaeal presence was reported with universal bacterial primers, whereas a significant archaea presence and also a wider variety of bacterial species were reported. These results revealed the significance of primer preference for microbiomes in extreme environments. Bioinformatic analysis was performed by aligning the reads to 16S microbial databases for identification using three different alignment methods, Epi2Me (Fastq 16S workflow), Kraken, and an in-house BLAST tool, including comparison at the genus and species levels. As a result, this approach to data analysis had a significant impact on the genera identified, and thus, it is recommended that use of multiple analysis tools to support findings on taxonomic identification using the 16S region until more precise bioinformatics tools become available. This study presents the first compilation of the ONT-based inventory of the hydrogen producers in the designated hot springs in Türkiye.
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Affiliation(s)
- İlayda Akaçin
- Division of Bioengineering, Graduate School, Izmir University of Economics, Sakarya Caddesi No: 156, 35330, Balçova, Izmir, Türkiye
| | - Şeymanur Ersoy
- Division of Bioengineering, Graduate School, Izmir University of Economics, Sakarya Caddesi No: 156, 35330, Balçova, Izmir, Türkiye
| | - Osman Doluca
- Division of Bioengineering, Graduate School, Izmir University of Economics, Sakarya Caddesi No: 156, 35330, Balçova, Izmir, Türkiye
- Department of Biomedical Engineering, Faculty of Engineering, Izmir University of Economics, Sakarya Caddesi No: 156, 35330, Balçova, Izmir, Türkiye
| | - Mine Güngörmüşler
- Division of Bioengineering, Graduate School, Izmir University of Economics, Sakarya Caddesi No: 156, 35330, Balçova, Izmir, Türkiye.
- Department of Genetics and Bioengineering, Faculty of Engineering, Izmir University of Economics, Sakarya Caddesi No: 156, 35330, Balçova, Izmir, Türkiye.
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13
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Bendia AG, Moreira JCF, Ferreira JCN, Romano RG, Ferreira IGC, Franco DC, Evangelista H, Montone RC, Pellizari VH. Insights into Antarctic microbiomes: diversity patterns for terrestrial and marine habitats. AN ACAD BRAS CIENC 2023; 95:e20211442. [PMID: 37820122 DOI: 10.1590/0001-3765202320211442] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 08/27/2022] [Indexed: 10/13/2023] Open
Abstract
Microorganisms in Antarctica are recognized for having crucial roles in ecosystems functioning and biogeochemical cycles. To explore the diversity and composition of microbial communities through different terrestrial and marine Antarctic habitats, we analyze 16S rRNA sequence datasets from fumarole and marine sediments, soil, snow and seawater environments. We obtained measures of alpha- and beta-diversities, as well as we have identified the core microbiome and the indicator microbial taxa of a particular habitat. Our results showed a unique microbial community structure according to each habitat, including specific taxa composing each microbiome. Marine sediments harbored the highest microbial diversity among the analyzed habitats. In the fumarole sediments, the core microbiome was composed mainly of thermophiles and hyperthermophilic Archaea, while in the majority of soil samples Archaea was absent. In the seawater samples, the core microbiome was mainly composed by cultured and uncultured orders usually identified on Antarctic pelagic ecosystems. Snow samples exhibited common taxa previously described for habitats of the Antarctic Peninsula, which suggests long-distance dispersal processes occurring from the Peninsula to the Continent. This study contributes as a baseline for further efforts on evaluating the microbial responses to environmental conditions and future changes.
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Affiliation(s)
- Amanda G Bendia
- Universidade de São Paulo (USP), Departamento de Oceanografia Biológica, Instituto Oceanográfico, Cidade Universitária, Praça do Oceanográfico, 191, 05508-900 São Paulo, SP, Brazil
| | - Julio Cezar F Moreira
- Universidade de São Paulo (USP), Departamento de Oceanografia Biológica, Instituto Oceanográfico, Cidade Universitária, Praça do Oceanográfico, 191, 05508-900 São Paulo, SP, Brazil
| | - Juliana C N Ferreira
- Universidade de São Paulo (USP), Departamento de Oceanografia Biológica, Instituto Oceanográfico, Cidade Universitária, Praça do Oceanográfico, 191, 05508-900 São Paulo, SP, Brazil
| | - Renato G Romano
- Universidade de São Paulo (USP), Departamento de Oceanografia Biológica, Instituto Oceanográfico, Cidade Universitária, Praça do Oceanográfico, 191, 05508-900 São Paulo, SP, Brazil
| | - Ivan G C Ferreira
- Universidade de São Paulo (USP), Departamento de Oceanografia Biológica, Instituto Oceanográfico, Cidade Universitária, Praça do Oceanográfico, 191, 05508-900 São Paulo, SP, Brazil
| | - Diego C Franco
- Universidade de São Paulo (USP), Departamento de Oceanografia Biológica, Instituto Oceanográfico, Cidade Universitária, Praça do Oceanográfico, 191, 05508-900 São Paulo, SP, Brazil
| | - Heitor Evangelista
- Universidade do Estado do Rio de Janeiro (UERJ), Instituto de Biologia Roberto Alcantara Gomes, Maracanã, 20550-013 Rio de Janeiro, RJ, Brazil
| | - Rosalinda C Montone
- Universidade de São Paulo (USP), Departamento de Oceanografia Física, Química e Geológica, Instituto Oceanográfico, Cidade Universitária, Praça do Oceanográfico, 191, 05508-900 São Paulo, SP, Brazil
| | - Vivian Helena Pellizari
- Universidade de São Paulo (USP), Departamento de Oceanografia Biológica, Instituto Oceanográfico, Cidade Universitária, Praça do Oceanográfico, 191, 05508-900 São Paulo, SP, Brazil
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14
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Kumar S, Najar IN, Sharma P, Tamang S, Mondal K, Das S, Sherpa MT, Thakur N. Temperature - A critical abiotic paradigm that governs bacterial heterogeneity in natural ecological system. ENVIRONMENTAL RESEARCH 2023; 234:116547. [PMID: 37422118 DOI: 10.1016/j.envres.2023.116547] [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: 03/27/2023] [Revised: 06/28/2023] [Accepted: 07/01/2023] [Indexed: 07/10/2023]
Abstract
A baseline data has been presented here to prove that among the abiotic factors, temperature is the most critical factor that regulates and governs the bacterial diversity in a natural ecosystem. Present study in Yumesamdong hot springs riverine vicinity (Sikkim), parades a gamut of bacterial communities in it and hosts them from semi-frigid region (- 4-10 °C) to fervid region (50-60 °C) via an intermediate region (25-37 °C) within the same ecosystem. This is an extremely rare intriguing natural ecosystem that has no anthropogenic disturbances nor any artificial regulation of temperature. We scanned the bacterial flora through both the culture-dependent and culture-independent techniques in this naturally complex thermally graded habitat. High-throughput sequencing gave bacterial and archaeal phyla representatives of over 2000 species showcasing their biodiversity. Proteobacteria, Firmicutes, Bacteroidetes and Chloroflexi were the predominant phyla. A concave down-curve significance was found in temperature-abundance correlation as the number of microbial taxa decreased when the temperature increased from warm (35 °C) to hot (60 °C). Firmicutes showed significant linear increase from cold to hot environment whereas Proteobacteria followed the opposite trend. No significant correlation was observed for physicochemical parameters against the bacterial diversity. However, only temperature has shown significant positive correlation to the predominant phyla at their respective thermal gradients. The antibiotic resistance patterns correlated with temperature gradient where the prevalence of antibiotic resistance was higher in case of mesophiles than that of psychrophiles and there was no resistance in thermophiles. The antibiotic resistant genes obtained were solely from mesophiles as it conferred high resistance at mesophilic conditions enabling them to adapt and metabolically compete for survival. Our study concludes that the temperature is a major factor that plays a significant contribution in shaping the bacterial community structure in any thermal gradient edifice.
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Affiliation(s)
- Santosh Kumar
- Department of Microbiology, School of Life Sciences, Sikkim University, Gangtok, 737102, Sikkim, India
| | - Ishfaq Nabi Najar
- Department of Microbiology, School of Life Sciences, Sikkim University, Gangtok, 737102, Sikkim, India
| | - Prayatna Sharma
- Department of Microbiology, School of Life Sciences, Sikkim University, Gangtok, 737102, Sikkim, India
| | - Sonia Tamang
- Department of Microbiology, School of Life Sciences, Sikkim University, Gangtok, 737102, Sikkim, India
| | - Krishnendu Mondal
- Department of Microbiology, Vidyasagar University, Midnapore, 721102, India
| | - Sayak Das
- Department of Life Science & Bioinformatics, HK School of Life Sciences, Assam University, Silchar, 788011, Assam, India
| | - Mingma Thundu Sherpa
- Department of Microbiology, School of Life Sciences, Sikkim University, Gangtok, 737102, Sikkim, India
| | - Nagendra Thakur
- Department of Microbiology, School of Life Sciences, Sikkim University, Gangtok, 737102, Sikkim, India.
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15
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Barbosa C, Tamayo-Leiva J, Alcorta J, Salgado O, Daniele L, Morata D, Díez B. Effects of hydrogeochemistry on the microbial ecology of terrestrial hot springs. Microbiol Spectr 2023; 11:e0024923. [PMID: 37754764 PMCID: PMC10581198 DOI: 10.1128/spectrum.00249-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 07/13/2023] [Indexed: 09/28/2023] Open
Abstract
Temperature, pH, and hydrochemistry of terrestrial hot springs play a critical role in shaping thermal microbial communities. However, the interactions of biotic and abiotic factors at this terrestrial-aquatic interface are still not well understood on a global scale, and the question of how underground events influence microbial communities remains open. To answer this, 11 new samples obtained from the El Tatio geothermal field were analyzed by 16S rRNA amplicon sequencing (V4 region), along with 191 samples from previous publications obtained from the Taupo Volcanic Zone, the Yellowstone Plateau Volcanic Field, and the Eastern Tibetan Plateau, with their temperature, pH, and major ion concentration. Microbial alpha diversity was lower in acid-sulfate waters, and no significant correlations were found with temperature. However, moderate correlations were observed between chemical parameters such as pH (mostly constrained to temperatures below 70°C), SO4 2- and abundances of members of the phyla Armatimonadota, Deinococcota, Chloroflexota, Campilobacterota, and Thermoplasmatota. pH and SO4 2- gradients were explained by phase separation of sulfur-rich hydrothermal fluids and oxidation of reduced sulfur in the steam phase, which were identified as key processes shaping these communities. Ordination and permutational analysis of variance showed that temperature, pH, and major element hydrochemistry explain only 24% of the microbial community structure. Therefore, most of the variance remained unexplained, suggesting that other environmental or biotic factors are also involved and highlighting the environmental complexity of the ecosystem and its great potential to test niche theory ecological associated questions. IMPORTANCE This is the first approach to investigate whether geothermal processes could have an influence on the ecology of thermal microbial communities on a global scale. In addition to temperature and pH, microbial communities are structured by sulfate concentrations, which depends on the tectono-magmatic settings (such as the depth of magmatic chambers) and the local settings (such as the availability of a confining layer separating NaCl waters from steam after phase separation) and the possibility of mixing with more diluted fluids. Comparison of microbial communities from different geothermal areas by homogeneous sequence processing showed that no significant geographic distance decay was detected on the microbial communities according to Bray-Curtis, Jaccard, unweighted, and weighted Unifrac similarity/dissimilarity indices. Instead, an ancient potential divergence in the same taxonomic groups is suggested between globally distant thermal zones.
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Affiliation(s)
- Carla Barbosa
- Department of Geology, University of Chile, Santiago, Chile
- Andean Geothermal Center of Excellence (CEGA-Fondap), University of Chile, Santiago, Chile
| | - Javier Tamayo-Leiva
- Department of Molecular Genetics and Microbiology, Pontifical Catholic University of Chile, Santiago, Chile
- Center for Climate and Resilience Research (CR)2, University of Chile, Santiago, Chile
- Millennium Institute Center of Genome Regulation (CGR), Santiago, Chile
| | - Jaime Alcorta
- Department of Molecular Genetics and Microbiology, Pontifical Catholic University of Chile, Santiago, Chile
- Millennium Institute Center of Genome Regulation (CGR), Santiago, Chile
| | - Oscar Salgado
- Department of Molecular Genetics and Microbiology, Pontifical Catholic University of Chile, Santiago, Chile
- Laboratorio de Bioinformática, Facultad de Educación, Universidad Adventista de Chile, Chillán, Chile
| | - Linda Daniele
- Department of Geology, University of Chile, Santiago, Chile
- Andean Geothermal Center of Excellence (CEGA-Fondap), University of Chile, Santiago, Chile
| | - Diego Morata
- Department of Geology, University of Chile, Santiago, Chile
- Andean Geothermal Center of Excellence (CEGA-Fondap), University of Chile, Santiago, Chile
| | - Beatríz Díez
- Department of Molecular Genetics and Microbiology, Pontifical Catholic University of Chile, Santiago, Chile
- Center for Climate and Resilience Research (CR)2, University of Chile, Santiago, Chile
- Millennium Institute Center of Genome Regulation (CGR), Santiago, Chile
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16
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Deore KS, Dhakephalkar PK, Dagar SS. Phylogenetically and physiologically diverse methanogenic archaea inhabit the Indian hot spring environments. Arch Microbiol 2023; 205:332. [PMID: 37707605 DOI: 10.1007/s00203-023-03661-2] [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: 03/24/2023] [Revised: 08/10/2023] [Accepted: 08/15/2023] [Indexed: 09/15/2023]
Abstract
Mesophilic and thermophilic methanogens belonging to the hydrogenotrophic, methylotrophic, and acetotrophic groups were isolated from Indian hot spring environments using BY and BCYT growth media. Following initial Hinf I-based PCR-RFLP screening, 70 methanogens were sequenced to ascertain their identity. These methanogens were phylogenetically and physiologically diverse and represented different taxa distributed across three physiological groups, i.e., hydrogenotrophs (53), methylotrophs (14) and acetotrophs (3). Overall, methanogens representing three families, five genera, and ten species, including two putative novel species, were recognized. The highest number and diversity of methanogens was observed at 40 ℃, dominated by Methanobacterium (10; 3 species), Methanosarcina (9; 3 species), Methanothermobacter (7; 2 species), Methanomethylovorans (5; 1 species) and Methanoculleus (3; 1 species). Both putative novel methanogen species were isolated at 40 ℃ and belonged to the genera Methanosarcina and Methanobacterium. At 55 ℃, limited diversity was observed, and resulted in the isolation of only two genera of methanogens, i.e., Methanothermobacter (28; 2 species) and Methanosarcina (4; 1 species). At 70 ℃, only members of the genus Methanothermobacter (5; 2 species) were isolated, whereas no methanogen could be cultured at 85 ℃. Ours is the first study that documents the extensive range of cultivable methanogenic archaea inhabiting hot springs across various geothermal provinces of India.
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Affiliation(s)
- Kasturi Shirish Deore
- Bioenergy Group, Agharkar Research Institute, Gopal Ganesh Agarkar Road, Pune, 411004, India
- Savitribai Phule Pune University, Ganeshkhind, Pune, India
| | - Prashant K Dhakephalkar
- Bioenergy Group, Agharkar Research Institute, Gopal Ganesh Agarkar Road, Pune, 411004, India
- Savitribai Phule Pune University, Ganeshkhind, Pune, India
| | - Sumit Singh Dagar
- Bioenergy Group, Agharkar Research Institute, Gopal Ganesh Agarkar Road, Pune, 411004, India.
- Savitribai Phule Pune University, Ganeshkhind, Pune, India.
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17
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Sriaporn C, Campbell KA, Van Kranendonk MJ, Handley KM. Bacterial and archaeal community distributions and cosmopolitanism across physicochemically diverse hot springs. ISME COMMUNICATIONS 2023; 3:80. [PMID: 37596308 PMCID: PMC10439147 DOI: 10.1038/s43705-023-00291-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Revised: 08/01/2023] [Accepted: 08/04/2023] [Indexed: 08/20/2023]
Abstract
Terrestrial hot springs harbor diverse microbial communities whose compositions are shaped by the wide-ranging physico-chemistries of individual springs. The effect of enormous physico-chemical differences on bacterial and archaeal distributions and population structures is little understood. We therefore analysed the prevalence and relative abundance of bacteria and archaea in the sediments (n = 76) of hot spring features, in the Taupō Volcanic Zone (New Zealand), spanning large differences in major anion water chemistry, pH (2.0-7.5), and temperature (17.5-92.9 °C). Community composition, based on 16S rRNA amplicon sequence variants (ASVs) was strongly influenced by both temperature and pH. However, certain lineages characterized diverse hot springs. At the domain level, bacteria and archaea shared broadly equivalent community abundances across physico-chemically diverse springs, despite slightly lower bacteria-to-archaea ratios and microbial 16S rRNA gene concentrations at higher temperatures. Communities were almost exclusively dominated by Proteobacteria, Euryarchaeota or Crenarchaeota. Eight archaeal and bacterial ASVs from Thermoplasmatales, Desulfurellaceae, Mesoaciditogaceae and Acidithiobacillaceae were unusually prevalent (present in 57.9-84.2% of samples) and abundant (1.7-12.0% sample relative abundance), and together comprised 44% of overall community abundance. Metagenomic analyses generated multiple populations associated with dominant ASVs, and showed characteristic traits of each lineage for sulfur, nitrogen and hydrogen metabolism. Differences in metabolic gene composition and genome-specific metabolism delineated populations from relatives. Genome coverage calculations showed that populations associated with each lineage were distributed across a physicochemically broad range of hot springs. Results imply that certain bacterial and archaeal lineages harbor different population structures and metabolic potentials for colonizing diverse hot spring environments.
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Affiliation(s)
- Chanenath Sriaporn
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
| | - Kathleen A Campbell
- School of Environment & Te Ao Mārama - Centre for Fundamental Inquiry, The University of Auckland, Auckland, New Zealand
| | - Martin J Van Kranendonk
- Australian Centre for Astrobiology, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, Australia
| | - Kim M Handley
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand.
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18
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Ohore OE, Ifon BE, Wang Y, Kazmi SSUH, Zhang J, Sanganyado E, Jiao X, Liu W, Wang Z. Vertical changes in water depth and environmental variables drove the antibiotics and antibiotic resistomes distribution, and microbial food web structures in the estuary and marine ecosystems. ENVIRONMENT INTERNATIONAL 2023; 178:108118. [PMID: 37517178 DOI: 10.1016/j.envint.2023.108118] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 06/29/2023] [Accepted: 07/25/2023] [Indexed: 08/01/2023]
Abstract
The influence of vertical changes in water depth on emerging pollutants distribution and microbial food web remains elusive. We investigated the influence of vertical transition in water depth on the environmental variables, antibiotics and antibiotic resistomes, and microbial community structures in estuary and marine ecosystems (0-50 m). Stepwise multiple linear regression model showed that among investigated environmental variables, change in water salinity was the most influential factor dictating the fluoroquinolone and macrolides concentrations, while dissolved oxygen and turbidity were the key influencers of sulfonamides and beta-lactam concentrations, respectively. Bacterial and eukaryotic diversity and niche breadth significantly increased with the increasing water depth. Ecosystem food web structure at the bottom depths was more stable than at the middle and surface depths. At the surface depth, the top 5 keystone genera were Cryothecomonas, Syndiniales, Achromobacter, Pseudopirsonia, and Karlodinium. Whereas Eugregarinorida, Neptuniibacter, Mychonastes, Novel_Apicomplexa_Class_1, Aplanochytrium and Dietzia, Halodaphnea, Luminiphilus, Aplanochytrium, Maullinia dominated the top 5 genera at the middle and the bottom depth, respectively. Absolute abundance of antibiotic resistance genes (ARGs) was drastically increased at the surface depth compared with the middle and bottom depths. Abundance of the top 10 ARGs and mobile genetic elements (MGEs) detected including tnpA-05, aadA2-03, mexF, aadA1, intI-1(clinic), qacEdelta1-02, aadA-02, qacEdelta1-01, cmlA1-01, and aadA-01 were amplified at the surface depth. This study demonstrated that ARGs abundance was disproportionate to bacterial diversity, and anthropogenic disturbances, confinement, MGEs, and ecosystem stability play primary roles in the fate of ARGs. The findings of this study also implicate that vertical changes in the water depth on environmental conditions can influence antibiotic concentrations and microbial community dramatically.
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Affiliation(s)
- Okugbe Ebiotubo Ohore
- Guangdong Provincial Key Laboratory of Marine Disaster Prediction and Prevention, and Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou 515063, China
| | - Binessi Edouard Ifon
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Laboratory of Physical Chemistry, University of Abomey-Calavi, Republic of Benin, Cotonou 01 BP 4521, Benin
| | - Yuwen Wang
- Guangdong Provincial Key Laboratory of Marine Disaster Prediction and Prevention, and Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou 515063, China
| | - Syed Shabi Ul Hassan Kazmi
- Guangdong Provincial Key Laboratory of Marine Disaster Prediction and Prevention, and Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou 515063, China
| | - Jingli Zhang
- Department of Clinical Medicine, Shantou University Medical College, Shantou, Guangdong 515041, China
| | - Edmond Sanganyado
- Department of Applied Sciences, Northumbria University, Newcastle Upon Tyne NE2 4PB, UK
| | - Xiaoyang Jiao
- Department of Cell Biology and Genetics, Shantou University Medical College, Shantou, Guangdong 515041, China
| | - Wenhua Liu
- Guangdong Provincial Key Laboratory of Marine Disaster Prediction and Prevention, and Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou 515063, China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
| | - Zhen Wang
- Guangdong Provincial Key Laboratory of Marine Disaster Prediction and Prevention, and Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou 515063, China.
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19
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Wang X, Yin Y, Yu Z, Shen G, Cheng H, Tao S. Distinct distribution patterns of the abundant and rare bacteria in high plateau hot spring sediments. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 863:160832. [PMID: 36521602 DOI: 10.1016/j.scitotenv.2022.160832] [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: 09/17/2022] [Revised: 12/02/2022] [Accepted: 12/06/2022] [Indexed: 06/17/2023]
Abstract
The diversity and distribution patterns of the abundant and rare microbial sub-communities in hot spring ecosystems and their assembly mechanisms are poorly understood. The present study investigated the diversity and distribution patterns of the total, abundant, conditionally rare, and always rare taxa in the low- and moderate-temperature hot spring sediments on the Tibetan Plateau based on high-throughput 16S rRNA gene sequencing, and explored their major environmental drivers. The diversity of these four bacterial taxa showed no significant change between the low-temperature and moderate-temperature hot spring sediments, whereas the bacterial compositions were obviously different. Stochasticity dominated the bacterial sub-community assemblages, while heterogeneous selection also played an important role in shaping the abundant and conditionally rare taxa between the low-temperature and moderate-temperature hot spring sediments. No significant difference in the topological properties of co-occurrence networks was found between the conditionally rare and abundant taxa, and the connections between the paired operational taxonomic units (OTUs) were almost positive. The diversity of the total, abundant, and conditionally rare taxa was governed by the salinity of hot spring sediments, while that of the always rare taxa was determined by the content of S element. In contrast, temperature had significant direct effect on the composition of the total, abundant, and conditionally rare taxa, but relatively weak influence on that of the always rare taxa. Besides, salinity was another major environmental factor driving the composition of the abundant and rare sub-communities in the hot spring sediments. These results reveal the assembly processes and major environmental drivers that shaped different bacterial sub-communities in the hot spring sediments on the Tibetan Plateau, and indicate the importance of conditionally rare taxa in constructing bacterial communities. These findings enhance the current understanding of the ecological mechanisms maintaining the ecosystem stability and services in extreme environment.
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Affiliation(s)
- Xiaojie Wang
- State Key Laboratory of Organic Geochemistry, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China; University of Chinese Academy of Sciences, Beijing 100049, China; MOE Laboratory for Earth Surface Processes, College of Urban and Environmental Sciences, Peking University, Beijing 100871, China
| | - Yue Yin
- MOE Laboratory for Earth Surface Processes, College of Urban and Environmental Sciences, Peking University, Beijing 100871, China
| | - Zhiqiang Yu
- State Key Laboratory of Organic Geochemistry, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
| | - Guofeng Shen
- MOE Laboratory for Earth Surface Processes, College of Urban and Environmental Sciences, Peking University, Beijing 100871, China
| | - Hefa Cheng
- MOE Laboratory for Earth Surface Processes, College of Urban and Environmental Sciences, Peking University, Beijing 100871, China.
| | - Shu Tao
- MOE Laboratory for Earth Surface Processes, College of Urban and Environmental Sciences, Peking University, Beijing 100871, China
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20
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Taxonomic Diversity of the Microbial Biofilms Collected along the Thermal Streams on Kunashir Island. ECOLOGIES 2023. [DOI: 10.3390/ecologies4010009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
Abstract
Hot springs are known as highly adverse extreme environments where thermophilic and hyperthermophilic microorganisms can survive. We describe taxonomic diversity of several microbial biofilms collected along water temperature gradient in hot streams in the aquatic system of the Stolbovskie hot springs on Kunashir Island, Kurils, Russia. The taxonomic composition of the studied microbial communities was assessed by the 16S rRNA gene metabarcoding for bacteria and archaea, and by the 18S rRNA gene metabarcoding for protists. Richness and diversity of bacteria in the geothermal microbial communities decreased with the increase of temperature, while for archaea, the tendency was the opposite. Ciliophora was the most represented taxon of protists. The biofilms of various kinds that we found in a very local area of the geothermal system were different from each other by taxonomic composition, and the level of their taxonomic diversity was significantly influenced by water temperature.
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21
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Ugwuanyi IR, Fogel ML, Bowden R, Steele A, De Natale G, Troise C, Somma R, Piochi M, Mormone A, Glamoclija M. Comparative metagenomics at Solfatara and Pisciarelli hydrothermal systems in Italy reveal that ecological differences across substrates are not ubiquitous. Front Microbiol 2023; 14:1066406. [PMID: 36819055 PMCID: PMC9930910 DOI: 10.3389/fmicb.2023.1066406] [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: 10/10/2022] [Accepted: 01/06/2023] [Indexed: 02/04/2023] Open
Abstract
Introduction Continental hydrothermal systems (CHSs) are geochemically complex, and they support microbial communities that vary across substrates. However, our understanding of these variations across the complete range of substrates in CHS is limited because many previous studies have focused predominantly on aqueous settings. Methods Here we used metagenomes in the context of their environmental geochemistry to investigate the ecology of different substrates (i.e., water, mud and fumarolic deposits) from Solfatara and Pisciarelli. Results and Discussion Results indicate that both locations are lithologically similar with distinct fluid geochemistry. In particular, all substrates from Solfatara have similar chemistry whereas Pisciarelli substrates have varying chemistry; with water and mud from bubbling pools exhibiting high SO4 2- and NH4 + concentrations. Species alpha diversity was found to be different between locations but not across substrates, and pH was shown to be the most important driver of both diversity and microbial community composition. Based on cluster analysis, microbial community structure differed significantly between Pisciarelli substrates but not between Solfatara substrates. Pisciarelli mud pools, were dominated by (hyper)thermophilic archaea, and on average, bacteria dominated Pisciarelli fumarolic deposits and all investigated Solfatara environments. Carbon fixation and sulfur oxidation were the most important metabolic pathways fueled by volcanic outgassing at both locations. Together, results demonstrate that ecological differences across substrates are not a widespread phenomenon but specific to the system. Therefore, this study demonstrates the importance of analyzing different substrates of a CHS to understand the full range of microbial ecology to avoid biased ecological assessments.
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Affiliation(s)
- Ifeoma R. Ugwuanyi
- Department of Earth and Environmental Sciences, Rutgers University, Newark, NJ, United States,Ifeoma R. Ugwuanyi, ✉
| | - Marilyn L. Fogel
- EDGE Institute, University of California, Riverside, Riverside, CA, United States
| | - Roxane Bowden
- Earth and Planets Laboratory, Carnegie Institution for Science, Washington, DC, United States
| | - Andrew Steele
- Earth and Planets Laboratory, Carnegie Institution for Science, Washington, DC, United States
| | - Giuseppe De Natale
- Istituto Nazionale di Geofisica e Vulcanologia, Osservatorio Vesuviano, Naples, Italy,Consiglio Nazionale delle Ricerche INO, Naples, Italy
| | - Claudia Troise
- Istituto Nazionale di Geofisica e Vulcanologia, Osservatorio Vesuviano, Naples, Italy,Consiglio Nazionale delle Ricerche INO, Naples, Italy
| | - Renato Somma
- Istituto Nazionale di Geofisica e Vulcanologia, Osservatorio Vesuviano, Naples, Italy,Consiglio Nazionale delle Ricerche IRISS, Naples, Italy
| | - Monica Piochi
- Istituto Nazionale di Geofisica e Vulcanologia, Osservatorio Vesuviano, Naples, Italy
| | - Angela Mormone
- Istituto Nazionale di Geofisica e Vulcanologia, Osservatorio Vesuviano, Naples, Italy
| | - Mihaela Glamoclija
- Department of Earth and Environmental Sciences, Rutgers University, Newark, NJ, United States,*Correspondence: Mihaela Glamoclija, ✉
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22
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Zhang HS, Feng QD, Zhang DY, Zhu GL, Yang L. Bacterial community structure in geothermal springs on the northern edge of Qinghai-Tibet plateau. Front Microbiol 2023; 13:994179. [PMID: 37180363 PMCID: PMC10172933 DOI: 10.3389/fmicb.2022.994179] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 12/13/2022] [Indexed: 03/19/2023] Open
Abstract
Introduction:In order to reveal the composition of the subsurface hydrothermal bacterial community in the zones of magmatic tectonics and their response to heat storage environments.Methods:In this study, we performed hydrochemical analysis and regional sequencing of the 16S rRNA microbial V4-V5 region in 7 Pleistocene and Lower Neogene hot water samples from the Gonghe basin.Results:Two geothermal hot spring reservoirs in the study area were found to be alkaline reducing environments with a mean temperature of 24.83°C and 69.28°C, respectively, and the major type of hydrochemistry was SO4-Cl·Na. The composition and structure of microorganisms in both types of geologic thermal storage were primarily controlled by temperature, reducing environment intensity, and hydrogeochemical processes. Only 195 ASVs were shared across different temperature environments, and the dominant bacterial genera in recent samples from temperate hot springs were Thermus and Hydrogenobacter, with both genera being typical of thermophiles. The correlation analysis showed that the overall level of relative abundance of the subsurface hot spring relied on a high temperature and a slightly alkaline reducing environment. Nearly all of the top 4 species in the abundance level (53.99% of total abundance) were positively correlated with temperature and pH, whereas they were negatively correlated with ORP (oxidation–reduction potential), nitrate, and bromine ions.Discussion:In general, the composition of bacteria in the groundwater in the study area was sensitive to the response of the thermal storage environment and also showed a relationship with geochemical processes, such as gypsum dissolution, mineral oxidation, etc.
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23
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Fernandes-Martins MC, Colman DR, Boyd ES. Relationships between fluid mixing, biodiversity, and chemosynthetic primary productivity in Yellowstone hot springs. Environ Microbiol 2023; 25:1022-1040. [PMID: 36651919 DOI: 10.1111/1462-2920.16340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 01/14/2023] [Indexed: 01/19/2023]
Abstract
The factors that influence biodiversity and productivity of hydrothermal ecosystems are not well understood. Here we investigate the relationship between fluid mixing, biodiversity, and chemosynthetic primary productivity in three co-localized hot springs (RSW, RSN, and RSE) in Yellowstone National Park that have different geochemistry. All three springs are sourced by reduced hydrothermal fluid, but RSE and RSN receive input of vapour phase gas and oxidized groundwaters, with input of both being substantially higher in RSN. Metagenomic sequencing revealed that communities in RSN were more biodiverse than those of RSE and RSW in all dimensions evaluated. Microcosm activity assays indicate that rates of dissolved inorganic carbon (DIC) uptake were also higher in RSN than in RSE and RSW. Together, these results suggest that increased mixing of reduced volcanic fluid with oxidized fluids generates additional niche space capable of supporting increasingly biodiverse communities that are more productive. These results provide insight into the factors that generate and maintain chemosynthetic biodiversity in hydrothermal systems and that influence the distribution, abundance, and diversity of microbial life in communities supported by chemosynthesis. These factors may also extend to other ecosystems not supported by photosynthesis, including the vast subterranean biosphere and biospheres beneath ice sheets and glaciers.
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Affiliation(s)
| | - Daniel R Colman
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, Montana, USA
| | - Eric S Boyd
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, Montana, USA
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24
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Chen JS, Hussain B, Tsai HC, Nagarajan V, Koner S, Hsu BM. Analysis and interpretation of hot springs water, biofilms, and sediment bacterial community profiling and their metabolic potential in the area of Taiwan geothermal ecosystem. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 856:159115. [PMID: 36181827 DOI: 10.1016/j.scitotenv.2022.159115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 09/21/2022] [Accepted: 09/25/2022] [Indexed: 06/16/2023]
Abstract
Microorganisms developed a mechanism that copes with heat, acidity, and high dissolved metal concentrations that likely first evolved. The geothermal fluids emerging in the geothermal springs of Taiwan, located at a subduction zone, are still under signs of progress in the characterization of the various microbial taxonomic changes over time. However, no systematic studies have been performed to compare water, biofilms, and sediment bacterial communities and the primary driving force of dissolved and mineral substrates capable of supporting microbial metabolism. In this study, 16S rRNA gene sequencing was employed for bacterial community exploration, and their potential metabolic pathways involved from water, biofilms, and sediment samples, collected from the geothermal valley (Ti-re-ku). Metagenomic data revealed that the water samples had higher bacterial diversity and richness than biofilms and sediment samples. At the genus level, Alicyclobacillus, Thiomonas, Acidocella, Metallibacterium, Picrophilus, and Legionella were significantly abundant in the water samples. The biofilms were rich in Aciditerrimonas, Bacillus, Acidithiobacillus, and Lysinibacillus, whereas the sediment samples were abundant in Sulfobacillus. The PICRUSt2-predicted functional results revealed that heavy metal-related functions such as heavy-metal exporter system, cobalt‑zinc‑cadmium resistance, arsenical pump, high-affinity nickel-transport, and copper resistance metabolisms were significant in the water samples. Moreover, sulfur-related pathways such as thiosulfate oxidation, dissimilatory sulfate reduction, and assimilatory sulfate reduction were important in water samples, followed by biofilms and sediment. Therefore, our findings highlighted the comparative taxonomic diversity and functional composition contributions to geothermal fluid, with implications for understanding the evolution and ecological niche dimension of microbes which are the key to geothermal ecosystem function.
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Affiliation(s)
- Jung-Sheng Chen
- Department of Medical Research, E-Da Hospital, Kaohsiung City 824, Taiwan
| | - Bashir Hussain
- Department of Earth and Environmental Sciences, National Chung Cheng University, Chiayi County 621, Taiwan; Department of Biomedical Sciences, National Chung Cheng University, Chiayi County 621, Taiwan
| | - Hsin-Chi Tsai
- Department of Psychiatry, School of Medicine, Tzu Chi University, Hualien 970, Taiwan; Department of Psychiatry, Tzu-Chi General Hospital, Hualien 970, Taiwan
| | - Viji Nagarajan
- Department of Earth and Environmental Sciences, National Chung Cheng University, Chiayi County 621, Taiwan
| | - Suprokash Koner
- Department of Earth and Environmental Sciences, National Chung Cheng University, Chiayi County 621, Taiwan; Department of Biomedical Sciences, National Chung Cheng University, Chiayi County 621, Taiwan
| | - Bing-Mu Hsu
- Department of Earth and Environmental Sciences, National Chung Cheng University, Chiayi County 621, Taiwan; Center for Innovative Research on Aging Society (CIRAS), National Chung Cheng University, Chiayi County 621, Taiwan.
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25
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Das S, Najar IN, Sherpa MT, Kumari A, Thakur N. Post-monsoon seasonal variation of prokaryotic diversity in solfataric soil from the North Sikkim hot spring. Int Microbiol 2022; 26:281-294. [PMID: 36478539 DOI: 10.1007/s10123-022-00298-x] [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: 04/24/2022] [Revised: 10/29/2022] [Accepted: 11/07/2022] [Indexed: 12/12/2022]
Abstract
The solfataric soil sediments of the hot springs of Sikkim located at Yume Samdung and Lachen valley were studied for deciphering the bacterial diversity. The main aim here is to present a comparative study and generate a baseline data on the post-monsoon seasonal variation for the months of October and December, analyzed through 16S rRNA V3-V4 amplicon sequencing. The results have shown that there is not much variation at phylum level in the month of October in all the three hot springs such as New Yume Samdung (NYS), Old Yume Samdung (OYS), and Tarum (TAR) hot spring. The abundant phyla mainly present were Firmicutes, followed by Proteobacteria, Actinobacteria, and Bacteroidetes. Similarly, in the month of December, Firmicutes, Proteobacteria, Actinobacteria, and Bacteroidetes were prevalent; however, the percent relative abundance of these phyla in the month of December is relatively less. Besides this decrease in percent abundance, it was interestingly seen that relatively more phyla were found contributing towards the bacterial diversity in the month of December. Similar to phylum level, at genus level, there was not much variation seen among various prevalent genera of the three studied hot springs in both months. The major genera prevalent in both months among all the three hot springs were followed by Bacillus, Desulfotomaculum, Lactobacillus, and Paenibacillus. A similar trend was also seen at gene level that relative abundance of various genera was higher in the month of October but more genera were found to be contributing towards bacterial diversity in the month of December. Few distinct genera were found to be more abundant in the month of December such as Rhodopirellula and Blastopirellula. The results may conclude that there is not much variation in the abundance and type of bacterial communities during the post-monsoon season in the month of October and December. However, this may be assumed that there is the accumulation or increase in the bacterial communities during the winter (relatively higher temperature among hot springs) and may favor few mesophilic and more thermophilic communities as well.
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Affiliation(s)
- Sayak Das
- Department of Microbiology, School of Life Sciences, Sikkim University, 6th Mile, Samdur, Gangtok, 737102, Sikkim, India
| | - Ishfaq Nabi Najar
- Department of Microbiology, School of Life Sciences, Sikkim University, 6th Mile, Samdur, Gangtok, 737102, Sikkim, India
| | - Mingma Thundu Sherpa
- Department of Microbiology, School of Life Sciences, Sikkim University, 6th Mile, Samdur, Gangtok, 737102, Sikkim, India
| | | | - Nagendra Thakur
- Department of Microbiology, School of Life Sciences, Sikkim University, 6th Mile, Samdur, Gangtok, 737102, Sikkim, India.
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26
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Salgado O, Guajardo-Leiva S, Moya-Beltrán A, Barbosa C, Ridley C, Tamayo-Leiva J, Quatrini R, Mojica FJM, Díez B. Global phylogenomic novelty of the Cas1 gene from hot spring microbial communities. Front Microbiol 2022; 13:1069452. [DOI: 10.3389/fmicb.2022.1069452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 11/17/2022] [Indexed: 12/05/2022] Open
Abstract
The Cas1 protein is essential for the functioning of CRISPR-Cas adaptive systems. However, despite the high prevalence of CRISPR-Cas systems in thermophilic microorganisms, few studies have investigated the occurrence and diversity of Cas1 across hot spring microbial communities. Phylogenomic analysis of 2,150 Cas1 sequences recovered from 48 metagenomes representing hot springs (42–80°C, pH 6–9) from three continents, revealed similar ecological diversity of Cas1 and 16S rRNA associated with geographic location. Furthermore, phylogenetic analysis of the Cas1 sequences exposed a broad taxonomic distribution in thermophilic bacteria, with new clades of Cas1 homologs branching at the root of the tree or at the root of known clades harboring reference Cas1 types. Additionally, a new family of casposases was identified from hot springs, which further completes the evolutionary landscape of the Cas1 superfamily. This ecological study contributes new Cas1 sequences from known and novel locations worldwide, mainly focusing on under-sampled hot spring microbial mat taxa. Results herein show that circumneutral hot springs are environments harboring high diversity and novelty related to adaptive immunity systems.
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27
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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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28
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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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29
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Zhang L, Xu Z, Sun Y, Gao Y, Zhu L. Coal Mining Activities Driving the Changes in Microbial Community and Hydrochemical Characteristics of Underground Mine Water. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:13359. [PMID: 36293941 PMCID: PMC9603172 DOI: 10.3390/ijerph192013359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 10/09/2022] [Accepted: 10/13/2022] [Indexed: 06/16/2023]
Abstract
Coal mining can cause groundwater pollution, and microorganism may reflect/affect its hydrochemical characteristics, yet little is known about the microorganism's distribution characteristics and its influence on the formation and evolution of mine water quality in underground coal mines. Here, we investigated the hydrochemical characteristics and microbial communities of six typical zones in a typical North China coalfield. The results showed that hydrochemical compositions and microbial communities of the water samples displayed apparent zone-specific patterns. The microbial community diversity of the six zones followed the order of surface waters > coal roadways > water sumps ≈ rock roadways ≈ goafs > groundwater aquifers. The microbial communities corresponded to the redox sensitive indices' levels. Coal roadways and goafs were the critical zones of groundwater pollution prevention and control. During tunneling in the panel, pyrite was oxidized by sulfur-oxidizing bacteria leading to SO42- increase. With the closure of the panel and formation of the goaf, SO42- increased rapidly for a short period. However, with the time since goaf closure, sulfate-reducing bacteria (e.g., c_Thermodesulfovibrionia, Desulfobacterium_catecholicum, etc.) proportion increased significantly, leading to SO42- concentration's decrease by 42% over 12 years, indicating the long-term closed goafs had a certain self-purification ability. These findings would benefit mine water pollution prevention and control by district.
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Affiliation(s)
- Li Zhang
- School of Resources and Geosciences, China University of Mining and Technology, Xuzhou 221116, China
| | - Zhimin Xu
- School of Resources and Geosciences, China University of Mining and Technology, Xuzhou 221116, China
- Fundamental Research Laboratory for Mine Water Hazards Prevention and Controlling Technology, Xuzhou 221006, China
| | - Yajun Sun
- School of Resources and Geosciences, China University of Mining and Technology, Xuzhou 221116, China
- Fundamental Research Laboratory for Mine Water Hazards Prevention and Controlling Technology, Xuzhou 221006, China
| | - Yating Gao
- School of Resources and Geosciences, China University of Mining and Technology, Xuzhou 221116, China
| | - Lulu Zhu
- School of Resources and Geosciences, China University of Mining and Technology, Xuzhou 221116, China
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30
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Gao Y, Chen Y, Luo Y, Liu J, Tian P, Nan Z, Zhou Q. The microbiota diversity of Festuca sinensis seeds in Qinghai-Tibet Plateau and their relationship with environments. Front Microbiol 2022; 13:956489. [PMID: 35992719 PMCID: PMC9382023 DOI: 10.3389/fmicb.2022.956489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 07/01/2022] [Indexed: 11/15/2022] Open
Abstract
A total of 14 Festuca sinensis seed lots were collected from different geographical locations on the Qinghai-Tibet Plateau to study the seed microbiota and determine the abiotic (temperature, precipitation, and elevation) and biotic (Epichloë sinensis infection rate) factors likely to shape the seed microbiome. The 14 seed lots had different bacterial and fungal structures and significantly different diversities (p < 0.05). The α-diversity indices of the bacteria were significantly correlated with precipitation (p < 0.05), whereas those of the fungi were significantly correlated with temperature (p < 0.05). Microbiota analysis showed that Proteobacteria, Cyanobacteria, and Bacteroidetes were the most abundant bacteria at the phylum level in the seeds, and Ascomycota and Basidiomycota were the most abundant fungi. β-diversity analysis suggested large differences in the microbial communities of each sample. Redundancy analysis showed that temperature and precipitation were the main environmental factors that drive variations in the microbial community, at the medium-high elevation (3,000–4,500 m), the impact of temperature and precipitation on microbial community is different, and the other elevations that effect on microbial community were basically identical. Spearman's correlation analysis showed that the relative abundances of the most abundant bacterial phyla were significantly correlated with temperature (p < 0.05), whereas those of the most abundant fungal phyla were significantly correlated with precipitation (p < 0.05). E. sinensis infection rates were significantly correlated with elevation and temperature (p < 0.05). These results suggest that temperature and precipitation are the key factors driving the microbial community, that temperature and elevation also had a great influence on the E. sinensis infection rate, and that environmental factors (temperature and elevation) may further affect the microbial community by regulating the E. sinensis infection rate.
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Affiliation(s)
- Yue Gao
- State Key Laboratory of Grassland Agro-Ecosystems, Lanzhou University, Lanzhou, China
- Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Lanzhou University, Lanzhou, China
- College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Youjun Chen
- Institute of Qinghai-Tibetan Plateau, Southwest Minzu University, Chengdu, China
| | - Yang Luo
- State Key Laboratory of Grassland Agro-Ecosystems, Lanzhou University, Lanzhou, China
- Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Lanzhou University, Lanzhou, China
- College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Junying Liu
- State Key Laboratory of Grassland Agro-Ecosystems, Lanzhou University, Lanzhou, China
- Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Lanzhou University, Lanzhou, China
- College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Pei Tian
- State Key Laboratory of Grassland Agro-Ecosystems, Lanzhou University, Lanzhou, China
- Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Lanzhou University, Lanzhou, China
- College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
- *Correspondence: Pei Tian
| | - Zhibiao Nan
- State Key Laboratory of Grassland Agro-Ecosystems, Lanzhou University, Lanzhou, China
- Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Lanzhou University, Lanzhou, China
- College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Qingping Zhou
- Institute of Qinghai-Tibetan Plateau, Southwest Minzu University, Chengdu, China
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Bazzicalupo AL, Erlandson S, Branine M, Ratz M, Ruffing L, Nguyen NH, Branco S. Fungal Community Shift Along Steep Environmental Gradients from Geothermal Soils in Yellowstone National Park. MICROBIAL ECOLOGY 2022; 84:33-43. [PMID: 34468785 DOI: 10.1007/s00248-021-01848-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 08/24/2021] [Indexed: 06/13/2023]
Abstract
Geothermal soils offer unique insight into the way extreme environmental factors shape communities of organisms. However, little is known about the fungi growing in these environments and in particular how localized steep abiotic gradients affect fungal diversity. We used metabarcoding to characterize soil fungi surrounding a hot spring-fed thermal creek with water up to 84 °C and pH 10 in Yellowstone National Park. We found a significant association between fungal communities and soil variable principal components, and we identify the key trends in co-varying soil variables that explain the variation in fungal community. Saprotrophic and ectomycorrhizal fungi community profiles followed, and were significantly associated with, different soil variable principal components, highlighting potential differences in the factors that structure these different fungal trophic guilds. In addition, in vitro growth experiments in four target fungal species revealed a wide range of tolerances to pH levels but not to heat. Overall, our results documenting turnover in fungal species within a few hundred meters suggest many co-varying environmental factors structure the diverse fungal communities found in the soils of Yellowstone National Park.
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Affiliation(s)
- Anna L Bazzicalupo
- Department of Zoology, University of British Columbia, Vancouver, BC, Canada.
| | - Sonya Erlandson
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT, USA
| | - Margaret Branine
- Graduate Field of Microbiology, Cornell University, Ithaca, NY, USA
| | - Megan Ratz
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT, USA
| | - Lauren Ruffing
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT, USA
| | - Nhu H Nguyen
- Department of Tropical Plant and Soil Sciences, University of Hawaii At Manoa, Honolulu, HI, USA
| | - Sara Branco
- Department of Integrative Biology, University of Colorado Denver, Denver, CO, USA
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32
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Huber KJ, Pester M, Eichorst SA, Navarrete AA, Foesel BU. Editorial: Acidobacteria – Towards Unraveling the Secrets of a Widespread, Though Enigmatic, Phylum. Front Microbiol 2022; 13:960602. [PMID: 35814658 PMCID: PMC9267355 DOI: 10.3389/fmicb.2022.960602] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 06/06/2022] [Indexed: 11/13/2022] Open
Affiliation(s)
- Katharina J. Huber
- Department Microorganisms, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Michael Pester
- Department Microorganisms, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
- Institute for Microbiology, Technical University of Braunschweig, Braunschweig, Germany
| | - Stephanie A. Eichorst
- Department of Microbiology and Ecosystem Science, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Acacio A. Navarrete
- Graduate Program in Environmental Sciences, University Brazil, São Paulo, Brazil
| | - Bärbel U. Foesel
- Working Group Biobank, Research Unit Molecular Epidemiology, Institute of Epidemiology, Helmholtz Munich, German Research Center for Environmental Health, Neuherberg, Germany
- *Correspondence: Bärbel U. Foesel
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33
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Dynamics of Planktonic Microbial Community Associated with Saccharina japonica Seedling. JOURNAL OF MARINE SCIENCE AND ENGINEERING 2022. [DOI: 10.3390/jmse10060726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/10/2022]
Abstract
Macroalgae interact with planktonic microbes in seawater. It remains unclear how planktonic microbes interact with the environment and each other during the cultivation processes of commercially important algal species. Such an interaction is important for developing environment-friendly mariculture methods. In this study, the dynamics of the planktonic microbial community associated with Saccharina japonica were profiled during the seedling production stage, with its environmental correlation and co-occurrence pattern determined simultaneously. Microbial richness increased and positively correlated with light intensity and contents of NO3− and PO43−. A clear temporal succession of the community was observed, which coincided with changes in light intensity, dissolved oxygen, pH, and NO3− content. α-Proteobacteria, Bacteroidetes, γ-Proteobacteria, and the genera prevalent in these taxa dominated the planktonic microbial community, and their relative abundance temporally changed. A profile of keystone taxa that is different from prevalent genera was identified based on betweenness centrality scores. A modularized co-occurrence pattern was determined, in addition to intensified species-to-species interactions at the core of the co-occurrence network. These findings expanded our cognization of the planktonic microbial community in response to S. japonica cultivation.
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34
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Noell SE, Baptista MS, Smith E, McDonald IR, Lee CK, Stott MB, Amend JP, Cary SC. Unique Geothermal Chemistry Shapes Microbial Communities on Mt. Erebus, Antarctica. Front Microbiol 2022; 13:836943. [PMID: 35591982 PMCID: PMC9111169 DOI: 10.3389/fmicb.2022.836943] [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: 12/17/2021] [Accepted: 04/18/2022] [Indexed: 11/13/2022] Open
Abstract
Mt. Erebus, Antarctica, is the world's southernmost active volcano and is unique in its isolation from other major active volcanic systems and its distinctive geothermal systems. Using 16S rRNA gene amplicon sequencing and physicochemical analyses, we compared samples collected at two contrasting high-temperature (50°C-65°C) sites on Mt. Erebus: Tramway Ridge, a weather-protected high biomass site, and Western Crater, an extremely exposed low biomass site. Samples were collected along three thermal gradients, one from Western Crater and two within Tramway Ridge, which allowed an examination of the heterogeneity present at Tramway Ridge. We found distinct soil compositions between the two sites, and to a lesser extent within Tramway Ridge, correlated with disparate microbial communities. Notably, pH, not temperature, showed the strongest correlation with these differences. The abundance profiles of several microbial groups were different between the two sites; class Nitrososphaeria amplicon sequence variants (ASVs) dominated the community profiles at Tramway Ridge, whereas Acidobacteriotal ASVs were only found at Western Crater. A co-occurrence network, paired with physicochemical analyses, allowed for finer scale analysis of parameters correlated with differential abundance profiles, with various parameters (total carbon, total nitrogen, soil moisture, soil conductivity, sulfur, phosphorous, and iron) showing significant correlations. ASVs assigned to Chloroflexi classes Ktedonobacteria and Chloroflexia were detected at both sites. Based on the known metabolic capabilities of previously studied members of these groups, we predict that chemolithotrophy is a common strategy in this system. These analyses highlight the importance of conducting broader-scale metagenomics and cultivation efforts at Mt. Erebus to better understand this unique environment.
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Affiliation(s)
- Stephen E Noell
- Te Aka Mātuatua-School of Science, Te Whare Wānanga o Waikato-University of Waikato, Hamilton, New Zealand.,International Centre for Terrestrial Antarctic Research, University of Waikato, Hamilton, New Zealand
| | - Mafalda S Baptista
- International Centre for Terrestrial Antarctic Research, University of Waikato, Hamilton, New Zealand.,Interdisciplinary Centre of Marine and Environmental Research (CIIMAR/CIMAR), University of Porto, Matosinhos, Portugal.,Faculty of Sciences, University of Porto, Porto, Portugal
| | - Emily Smith
- Te Aka Mātuatua-School of Science, Te Whare Wānanga o Waikato-University of Waikato, Hamilton, New Zealand.,International Centre for Terrestrial Antarctic Research, University of Waikato, Hamilton, New Zealand
| | - Ian R McDonald
- Te Aka Mātuatua-School of Science, Te Whare Wānanga o Waikato-University of Waikato, Hamilton, New Zealand.,International Centre for Terrestrial Antarctic Research, University of Waikato, Hamilton, New Zealand
| | - Charles K Lee
- Te Aka Mātuatua-School of Science, Te Whare Wānanga o Waikato-University of Waikato, Hamilton, New Zealand.,International Centre for Terrestrial Antarctic Research, University of Waikato, Hamilton, New Zealand
| | - Matthew B Stott
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Jan P Amend
- Department of Earth Sciences, University of Southern California, Los Angeles, CA, United States.,Department of Biological Sciences, University of Southern California, Los Angeles, CA, United States
| | - S Craig Cary
- Te Aka Mātuatua-School of Science, Te Whare Wānanga o Waikato-University of Waikato, Hamilton, New Zealand.,International Centre for Terrestrial Antarctic Research, University of Waikato, Hamilton, New Zealand
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35
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Effects of Increasing Concentrations of Enrofloxacin on Co-Digestion of Pig Manure and Corn Straw. SUSTAINABILITY 2022. [DOI: 10.3390/su14105894] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Enrofloxacin (ENR) is one of the most commonly used antibiotics in pig farms. In this study, using fresh pig manure and corn straw powder as substrates, the effects of different concentrations of ENR (2.5, 10, and 20 mg/L) on anaerobic digestion in completely mixed anaerobic reactors were investigated. A relatively low concentration of ENR (2.5 mg/L) increased methane production by 47.58% compared with the control group. Among the volatile fatty acids (VFAs) in the reactors, the propionic acid content was the lowest, and the concentrations of acetic acid kinase and coenzyme F420 were highest in the first seven days during peak gas production. However, methane production in the reactors with 10 mg/L and 20 mg/L ENR decreased by 8.59% and 20.25%, respectively. Furthermore, the accelerated hydrolysis of extracellular polymeric substances causes a significant accumulation of VFA levels. The microbial community in anaerobic reactors was analyzed by 16S rRNA sequencing. Proteiniphilum was the dominant bacterial genus. In addition, ENR at 2.5 mg/L effectively increased the abundance and diversity of anaerobic microorganisms, whereas a high concentration of ENR (10 and 20 mg/L) significantly decreased these parameters. This study demonstrated that different concentrations of ENR had significantly different effects on anaerobic digestion.
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36
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Bowers RM, Nayfach S, Schulz F, Jungbluth SP, Ruhl IA, Sheremet A, Lee J, Goudeau D, Eloe-Fadrosh EA, Stepanauskas R, Malmstrom RR, Kyrpides NC, Dunfield PF, Woyke T. Dissecting the dominant hot spring microbial populations based on community-wide sampling at single-cell genomic resolution. THE ISME JOURNAL 2022; 16:1337-1347. [PMID: 34969995 PMCID: PMC9039060 DOI: 10.1038/s41396-021-01178-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Revised: 11/29/2021] [Accepted: 12/10/2021] [Indexed: 02/07/2023]
Abstract
With advances in DNA sequencing and miniaturized molecular biology workflows, rapid and affordable sequencing of single-cell genomes has become a reality. Compared to 16S rRNA gene surveys and shotgun metagenomics, large-scale application of single-cell genomics to whole microbial communities provides an integrated snapshot of community composition and function, directly links mobile elements to their hosts, and enables analysis of population heterogeneity of the dominant community members. To that end, we sequenced nearly 500 single-cell genomes from a low diversity hot spring sediment sample from Dewar Creek, British Columbia, and compared this approach to 16S rRNA gene amplicon and shotgun metagenomics applied to the same sample. We found that the broad taxonomic profiles were similar across the three sequencing approaches, though several lineages were missing from the 16S rRNA gene amplicon dataset, likely the result of primer mismatches. At the functional level, we detected a large array of mobile genetic elements present in the single-cell genomes but absent from the corresponding same species metagenome-assembled genomes. Moreover, we performed a single-cell population genomic analysis of the three most abundant community members, revealing differences in population structure based on mutation and recombination profiles. While the average pairwise nucleotide identities were similar across the dominant species-level lineages, we observed differences in the extent of recombination between these dominant populations. Most intriguingly, the creek's Hydrogenobacter sp. population appeared to be so recombinogenic that it more closely resembled a sexual species than a clonally evolving microbe. Together, this work demonstrates that a randomized single-cell approach can be useful for the exploration of previously uncultivated microbes from community composition to population structure.
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Affiliation(s)
- Robert M. Bowers
- grid.451309.a0000 0004 0449 479XU.S. Department of Energy, Joint Genome Institute, Berkeley, CA USA
| | - Stephen Nayfach
- grid.451309.a0000 0004 0449 479XU.S. Department of Energy, Joint Genome Institute, Berkeley, CA USA
| | - Frederik Schulz
- grid.451309.a0000 0004 0449 479XU.S. Department of Energy, Joint Genome Institute, Berkeley, CA USA
| | - Sean P. Jungbluth
- grid.184769.50000 0001 2231 4551Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA USA
| | - Ilona A. Ruhl
- grid.22072.350000 0004 1936 7697Department of Biological Sciences, University of Calgary, 2500 University Dr. NW, Calgary, AB T2N 1N4 Canada ,grid.419357.d0000 0001 2199 3636National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO USA
| | - Andriy Sheremet
- grid.22072.350000 0004 1936 7697Department of Biological Sciences, University of Calgary, 2500 University Dr. NW, Calgary, AB T2N 1N4 Canada
| | - Janey Lee
- grid.451309.a0000 0004 0449 479XU.S. Department of Energy, Joint Genome Institute, Berkeley, CA USA
| | - Danielle Goudeau
- grid.451309.a0000 0004 0449 479XU.S. Department of Energy, Joint Genome Institute, Berkeley, CA USA
| | - Emiley A. Eloe-Fadrosh
- grid.451309.a0000 0004 0449 479XU.S. Department of Energy, Joint Genome Institute, Berkeley, CA USA
| | - Ramunas Stepanauskas
- grid.296275.d0000 0000 9516 4913Bigelow Laboratory for Ocean Sciences, 60 Bigelow Drive, East Boothbay, ME USA
| | - Rex R. Malmstrom
- grid.451309.a0000 0004 0449 479XU.S. Department of Energy, Joint Genome Institute, Berkeley, CA USA
| | - Nikos C. Kyrpides
- grid.451309.a0000 0004 0449 479XU.S. Department of Energy, Joint Genome Institute, Berkeley, CA USA
| | - Peter F. Dunfield
- grid.22072.350000 0004 1936 7697Department of Biological Sciences, University of Calgary, 2500 University Dr. NW, Calgary, AB T2N 1N4 Canada
| | - Tanja Woyke
- U.S. Department of Energy, Joint Genome Institute, Berkeley, CA, USA.
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37
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Chen JS, Tsai HC, Hsu YL, Nagarajan V, Su HY, Hussain B, Hsu BM. Comprehensive assessment of bacterial communities and their functional profiles in the Huang Gang Creek in the Tatun Volcano Group basin, Taiwan using 16S rRNA amplicon sequencing. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2022; 234:113375. [PMID: 35278991 DOI: 10.1016/j.ecoenv.2022.113375] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 02/28/2022] [Accepted: 03/01/2022] [Indexed: 06/14/2023]
Abstract
The microbial characteristics of water bodies located in the outflow of hot springs may affect the water quality parameters of the associated river ecosystem. Using 16S rRNA amplicon sequencing, we investigated the bacterial diversity and functional profiles of the Huang Gang (HG) Creek, located in the trace metal-rich, acid-sulfate thermal springs zone of the Tatun Volcano Group (TVG). Biofilms and water samples were collected from the upstream, midstream, and geothermal valleys and downstream of the creek. The results showed that the biofilm and water samples had distinct bacterial diversity and abundance profiles. Acidophilic sulfur-oxidizing bacteria were found to be more abundant in water samples, whereas aquatic photosynthetic bacterial communities were dominant in biofilms. The water samples were contaminated with Legionella and Chlamydiae, which could contaminate the nearby river and cause clinical infections in humans. The upstream samples were highly unique and displayed higher diversity than the other sites. Moderate thermo-acidophiles were dominant in the upstream and midstream regions, whereas the geothermal valley and downstream samples were abundant in thermo-acidophiles. In addition, functional profiling revealed higher expression of sulfur, arsenic, and iron-related functions in water and lead-related functions in the biofilms of the creek. As described in previous studies, the hydrochemical properties of the HG Creek were influenced by the TVG hot springs. Our findings indicated that the hydrochemical properties of the HG Creek were highly correlated with the bacterial diversity and functional potential of running water as compared to biofilms.
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Affiliation(s)
- Jung-Sheng Chen
- Department of Medical Research, E-Da Hospital, Kaohsiung, Taiwan
| | - Hsin-Chi Tsai
- Department of Psychiatry, School of Medicine, Tzu Chi University, Hualien, Taiwan; Department of Psychiatry, Tzu-Chi General Hospital, Hualien, Taiwan
| | - Yu-Ling Hsu
- Department of Nuclear Medicine, Ditmanson Medical Foundation Chia-Yi Christian Hospital, Chiayi, Taiwan
| | - Viji Nagarajan
- Department of Earth and Environmental Sciences, National Chung Cheng University, Chiayi, Taiwan
| | - Hung-Yuan Su
- Department of Emergency Medicine, E-Da Hospital and I-Shou University, Kaohsiung, Taiwan; School of Chinese Medicine for Post Baccalaureate, I-Shou University, Kaohsiung, Taiwan
| | - Bashir Hussain
- Department of Earth and Environmental Sciences, National Chung Cheng University, Chiayi, Taiwan; Department of Biomedical Sciences, National Chung Cheng University, Chiayi, Taiwan
| | - Bing-Mu Hsu
- Department of Earth and Environmental Sciences, National Chung Cheng University, Chiayi, Taiwan.
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38
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Shu WS, Huang LN. Microbial diversity in extreme environments. Nat Rev Microbiol 2022; 20:219-235. [PMID: 34754082 DOI: 10.1038/s41579-021-00648-y] [Citation(s) in RCA: 107] [Impact Index Per Article: 53.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/01/2021] [Indexed: 01/02/2023]
Abstract
A wide array of microorganisms, including many novel, phylogenetically deeply rooted taxa, survive and thrive in extreme environments. These unique and reduced-complexity ecosystems offer a tremendous opportunity for studying the structure, function and evolution of natural microbial communities. Marker gene surveys have resolved patterns and ecological drivers of these extremophile assemblages, revealing a vast uncultured microbial diversity and the often predominance of archaea in the most extreme conditions. New omics studies have uncovered linkages between community function and environmental variables, and have enabled discovery and genomic characterization of major new lineages that substantially expand microbial diversity and change the structure of the tree of life. These efforts have significantly advanced our understanding of the diversity, ecology and evolution of microorganisms populating Earth's extreme environments, and have facilitated the exploration of microbiota and processes in more complex ecosystems.
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Affiliation(s)
- Wen-Sheng Shu
- School of Life Sciences, South China Normal University, Guangzhou, People's Republic of China.
| | - Li-Nan Huang
- School of Life Sciences, Sun Yat-sen University, Guangzhou, People's Republic of China.
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Thermophiles and carbohydrate-active enzymes (CAZymes) in biofilm microbial consortia that decompose lignocellulosic plant litters at high temperatures. Sci Rep 2022; 12:2850. [PMID: 35181739 PMCID: PMC8857248 DOI: 10.1038/s41598-022-06943-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2021] [Accepted: 02/09/2022] [Indexed: 12/19/2022] Open
Abstract
The SKY hot spring is a unique site filled with a thick layer of plant litter. With the advancement of next-generation sequencing, it is now possible to mine many new biocatalyst sequences. In this study, we aimed to (i) identify the metataxonomic of prokaryotes and eukaryotes in microbial mats using 16S and 18S rRNA markers, (ii) and explore carbohydrate degrading enzymes (CAZymes) that have a high potential for future applications. Green microbial mat, predominantly photosynthetic bacteria, was attached to submerged or floating leaves litter. At the spring head, the sediment mixture consisted of plant debris, predominantly brownish-reddish gelatinous microbial mat, pale tan biofilm, and grey-white filament biofilm. The population in the spring head had a higher percentage of archaea and hyperthermophiles than the green mat. Concurrently, we cataloged nearly 10,000 sequences of CAZymes in both green and brown biofilms using the shotgun metagenomic sequencing approach. These sequences include β-glucosidase, cellulase, xylanase, α-N-arabinofuranosidase, α-l-arabinofuranosidase, and other CAZymes. In conclusion, this work elucidated that SKY is a unique hot spring due to its rich lignocellulosic material, often absent in other hot springs. The data collected from this study serves as a repository of new thermostable macromolecules, in particular families of glycoside hydrolases.
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Abstract
Microbial community diversity is often correlated with physical environmental stresses like acidity, salinity, and temperature. For example, species diversity usually declines with increasing temperature above 20°C. However, few studies have examined whether the genetic functional diversity of community metagenomes varies in a similar way as species diversity along stress gradients. Here, we investigated bacterial communities in thermal spring sediments ranging from 21 to 88°C, representing communities of 330 to 3,800 bacterial and archaeal species based on 16S rRNA gene amplicon analysis. Metagenomes were sequenced, and Pfam abundances were used as a proxy for metagenomic functional diversity. Significant decreases in both species diversity and Pfam diversity were observed with increasing temperatures. The relationship between Pfam diversity and species diversity followed a power function with the steepest slopes in the high-temperature, low-diversity region of the gradient. Species additions to simple thermophilic communities added many new Pfams, while species additions to complex mesophilic communities added relatively fewer new Pfams, indicating that species diversity does not approach saturation as rapidly as Pfam diversity does. Many Pfams appeared to have distinct temperature ceilings of 60 to 80°C. This study suggests that temperature stress limits both taxonomic and functional diversity of microbial communities, but in a quantitatively different manner. Lower functional diversity at higher temperatures is probably due to two factors, including (i) the absence of many enzymes not adapted to thermophilic conditions, and (ii) the fact that high-temperature communities are comprised of fewer species with smaller average genomes and, therefore, contain fewer rare functions. IMPORTANCE Only recently have microbial ecologists begun to assess quantitatively how microbial species diversity correlates with environmental factors like pH, temperature, and salinity. However, still, very few studies have examined how the number of distinct biochemical functions of microbial communities, termed functional diversity, varies with the same environmental factors. Our study examined 18 microbial communities sampled across a wide temperature gradient and found that increasing temperature reduced both species and functional diversity, but in different ways. Initially, functional diversity increased sharply with increasing species diversity but eventually plateaued, following a power function. This pattern has been previously predicted in theoretical models, but our study validates this predicted power function with field metagenomic data. This study also presents a unique overview of the distribution of metabolic functions along a temperature gradient, demonstrating that many functions have temperature "ceilings" above which they are no longer found.
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Ruhl IA, Sheremet A, Furgason CC, Krause S, Bowers RM, Jarett JK, Tran TM, Grasby SE, Woyke T, Dunfield PF. GAL08, an Uncultivated Group of Acidobacteria, Is a Dominant Bacterial Clade in a Neutral Hot Spring. Front Microbiol 2022; 12:787651. [PMID: 35087491 PMCID: PMC8787282 DOI: 10.3389/fmicb.2021.787651] [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: 10/01/2021] [Accepted: 11/29/2021] [Indexed: 11/28/2022] Open
Abstract
GAL08 are bacteria belonging to an uncultivated phylogenetic cluster within the phylum Acidobacteria. We detected a natural population of the GAL08 clade in sediment from a pH-neutral hot spring located in British Columbia, Canada. To shed light on the abundance and genomic potential of this clade, we collected and analyzed hot spring sediment samples over a temperature range of 24.2–79.8°C. Illumina sequencing of 16S rRNA gene amplicons and qPCR using a primer set developed specifically to detect the GAL08 16S rRNA gene revealed that absolute and relative abundances of GAL08 peaked at 65°C along three temperature gradients. Analysis of sediment collected over multiple years and locations revealed that the GAL08 group was consistently a dominant clade, comprising up to 29.2% of the microbial community based on relative read abundance and up to 4.7 × 105 16S rRNA gene copy numbers per gram of sediment based on qPCR. Using a medium quality threshold, 25 single amplified genomes (SAGs) representing these bacteria were generated from samples taken at 65 and 77°C, and seven metagenome-assembled genomes (MAGs) were reconstructed from samples collected at 45–77°C. Based on average nucleotide identity (ANI), these SAGs and MAGs represented three separate species, with an estimated average genome size of 3.17 Mb and GC content of 62.8%. Phylogenetic trees constructed from 16S rRNA gene sequences and a set of 56 concatenated phylogenetic marker genes both placed the three GAL08 bacteria as a distinct subgroup of the phylum Acidobacteria, representing a candidate order (Ca. Frugalibacteriales) within the class Blastocatellia. Metabolic reconstructions from genome data predicted a heterotrophic metabolism, with potential capability for aerobic respiration, as well as incomplete denitrification and fermentation. In laboratory cultivation efforts, GAL08 counts based on qPCR declined rapidly under atmospheric levels of oxygen but increased slightly at 1% (v/v) O2, suggesting a microaerophilic lifestyle.
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Affiliation(s)
- Ilona A Ruhl
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Andriy Sheremet
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Chantel C Furgason
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Susanne Krause
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Robert M Bowers
- U.S. Department of Energy Joint Genome Institute, Berkeley, CA, United States
| | - Jessica K Jarett
- U.S. Department of Energy Joint Genome Institute, Berkeley, CA, United States
| | - Triet M Tran
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Stephen E Grasby
- Department of Geoscience, University of Calgary, Calgary, AB, Canada.,Geological Survey of Canada, Calgary, AB, Canada
| | - Tanja Woyke
- U.S. Department of Energy Joint Genome Institute, Berkeley, CA, United States
| | - Peter F Dunfield
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
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DeCastro ME, Escuder-Rodríguez JJ, Becerra M, Rodríguez-Belmonte E, González-Siso MI. Comparative Metagenomic Analysis of Two Hot Springs From Ourense (Northwestern Spain) and Others Worldwide. Front Microbiol 2021; 12:769065. [PMID: 34899652 PMCID: PMC8661477 DOI: 10.3389/fmicb.2021.769065] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 10/26/2021] [Indexed: 01/12/2023] Open
Abstract
With their circumneutral pH and their moderate temperature (66 and 68°C, respectively), As Burgas and Muiño da Veiga are two important human-use hot springs, previously studied with traditional culture methods, but never explored with a metagenomic approach. In the present study, we have performed metagenomic sequence-based analyses to compare the taxonomic composition and functional potential of these hot springs. Proteobacteria, Deinococcus-Thermus, Firmicutes, Nitrospirae, and Aquificae are the dominant phyla in both geothermal springs, but there is a significant difference in the abundance of these phyla between As Burgas and Muiño da Veiga. Phylum Proteobacteria dominates As Burgas ecosystem while Aquificae is the most abundant phylum in Muiño da Veiga. Taxonomic and functional analyses reveal that the variability in water geochemistry might be shaping the differences in the microbial communities inhabiting these geothermal springs. The content in organic compounds of As Burgas water promotes the presence of heterotrophic populations of the genera Acidovorax and Thermus, whereas the sulfate-rich water of Muiño da Veiga favors the co-dominance of genera Sulfurihydrogenibium and Thermodesulfovibrio. Differences in ammonia concentration exert a selective pressure toward the growth of nitrogen-fixing bacteria such as Thermodesulfovibrio in Muiño da Veiga. Temperature and pH are two important factors shaping hot springs microbial communities as was determined by comparative analysis with other thermal springs.
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Affiliation(s)
| | | | | | | | - María-Isabel González-Siso
- Grupo EXPRELA, Centro de Investigacións Científicas Avanzadas (CICA), Departamento de Bioloxía, Facultade de Ciencias, Universidade da Coruña, A Coruña, Spain
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43
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Distinct Assembly Processes and Determinants of Soil Microbial Communities between Farmland and Grassland in Arid and Semiarid Areas. Appl Environ Microbiol 2021; 87:e0101021. [PMID: 34524892 DOI: 10.1128/aem.01010-21] [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] [Indexed: 11/20/2022] Open
Abstract
It is critical to identify the assembly processes and determinants of soil microbial communities to better predict soil microbial responses to environmental change in arid and semiarid areas. Here, soils from 16 grassland-only, 9 paired grassland and farmland, and 16 farmland-only sites were collected across the central Inner Mongolia Plateau, covering a steep environmental gradient. Through analyzing the paired samples, we discovered that land uses had strong effects on soil microbial communities but weak effects on their assembly processes. For all samples, although no environmental variables were significantly correlated with the net relatedness index (NRI), both the nearest taxon index (NTI) and the β-nearest taxon index (βNTI) were most related to mean annual precipitation (MAP). With the increase of MAP, soil microbial taxa at the tips of the phylogenetic tree were more clustered, and the contribution of determinism increased. Determinism (48.6%), especially variable selection (46.3%), and stochasticity (51.4%) were almost equal in farmland, while stochasticity (75.0%) was dominant in grassland. Additionally, Mantel tests and redundancy analyses (RDA) revealed that the main determinants of soil microbial community structure were MAP in grassland but mean annual temperature (MAT) in farmland. MAP and MAT were also good predictors of the community composition (the top 200 dominant operational taxonomic units) in grassland and farmland, respectively. Collectively, in arid and semiarid areas, soil microbial communities were more sensitive to environmental change in farmland than in grassland, and unlike the major impact of MAP on grassland microbial communities, MAT was the primary driver of farmland microbial communities. IMPORTANCE As one of the most diverse organisms, soil microbes play indispensable roles in many ecological processes in arid and semiarid areas with limited macrofaunal and plant diversity, yet the mechanisms underpinning soil microbial community are not fully understood. In this study, soil microbial communities were investigated along a 500-km transect covering a steep environmental gradient across farmland and grassland in the areas. The results showed that precipitation was the main factor mediating the assembly processes. Determinism was more influential in farmland, and variable selection of farmland was twice that of grassland. Temperature mainly drove farmland microbial communities, while precipitation mainly affected grassland microbial communities. These findings provide new information about the assembly processes and determinants of soil microbial communities in arid and semiarid areas, consequently improving the predictability of the community dynamics, which have implications for sustaining soil microbial diversity and ecosystem functioning, particularly under global climate change conditions.
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Abirami B, Radhakrishnan M, Kumaran S, Wilson A. Impacts of global warming on marine microbial communities. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 791:147905. [PMID: 34126492 DOI: 10.1016/j.scitotenv.2021.147905] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 04/26/2021] [Accepted: 05/16/2021] [Indexed: 06/12/2023]
Abstract
Global warming in ocean ecosystems alters temperature, acidification, oxygen content, circulation, stratification, and nutrient inputs. Microorganisms play a dominant role in global biogeochemical cycles crucial for a planet's sustainability. Since microbial communities are highly dependent on the temperature factor, fluctuations in the same will lead to adverse effects on the microbial community organization. Throughout the Ocean, increase in evaporation rates causes the surface mixed layer to become shallower. This intensified stratification inhibits vertical transport of nutrient supplies. Such density driven processes will decrease oxygen solubility in surface waters leading to significant decrease of oxygen from future Ocean. Metabolism and diversity of microbes along with ocean biogeochemistry will be at great risk due to global warming and its related effects. As a response to the changes in temperature, alteration in the distribution of phytoplankta communities is observed all over the planet, creating changes in the primary production of the ocean causing massive impact on the biosphere. Marine microbial communities try to adapt to the changing ocean environmental conditions by responding with biogeographic range shifts, community structure modifications, and adaptive evolution. Persistence of this climate change on ocean ecosystems, in future, will pose serious threat to the metabolism and distribution of marine microbes leading to fluctuations in the biogeochemical cycles thereby affecting the overall ecosystem functioning. Genomics plays an important role in marine microbial research by providing tools to study the association between environment and organisms. The ecological and genomic perspectives of marine microbes are being investigated to design effective models to understand their physiology and evolution in a changing ocean. Mesocosm/microcosm experimental studies and field studies are in the need of the hour to evaluate the impact of climate shifts on microbial genesis.
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Affiliation(s)
- Baskaran Abirami
- Centre for Drug Discovery and Development, Sathyabama Institute of Science and Technology, Chennai 600 119, Tamil Nadu, India
| | - Manikkam Radhakrishnan
- Centre for Drug Discovery and Development, Sathyabama Institute of Science and Technology, Chennai 600 119, Tamil Nadu, India
| | - Subramanian Kumaran
- Centre for Drug Discovery and Development, Sathyabama Institute of Science and Technology, Chennai 600 119, Tamil Nadu, India
| | - Aruni Wilson
- Sathyabama Institute of Science and Technology, Chennai 600119, Tamil Nadu, India; School of Medicine, Loma Linda University, CA, USA; Musculoskeletal Disease Research Laboratory, US Department of Veteran Affairs, Loma Linda, CA, USA.
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45
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Bendia AG, Lemos LN, Mendes LW, Signori CN, Bohannan BJM, Pellizari VH. Metabolic potential and survival strategies of microbial communities across extreme temperature gradients on Deception Island volcano, Antarctica. Environ Microbiol 2021; 23:4054-4073. [PMID: 34245102 DOI: 10.1111/1462-2920.15649] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Revised: 06/16/2021] [Accepted: 06/20/2021] [Indexed: 11/27/2022]
Abstract
Active volcanoes in Antarctica have remarkable temperature and geochemical gradients that could select for a wide variety of microbial adaptive mechanisms and metabolic pathways. Deception Island is a stratovolcano flooded by the sea, resulting in contrasting ecosystems such as permanent glaciers and active fumaroles, which creates steep gradients that have been shown to affect microbial diversity. In this study, we used shotgun metagenomics and metagenome-assembled genomes to explore the metabolic potentials and survival strategies of microbial communities along an extreme temperature gradient in fumarole and glacier sediments on Deception Island. We observed that communities from a 98 °C fumarole were significantly enriched in genes related to hyperthermophilic (e.g. reverse gyrase, GroEL/GroES and thermosome) and oxidative stress responses, as well as genes related to sulfate reduction, ammonification and carbon fixation. Communities from <80 °C fumaroles possessed more genes related osmotic, cold- and heat-shock responses, and diverse metabolic potentials, such as those related to sulfur oxidation and denitrification, while glacier communities showed abundant metabolic potentials mainly related to heterotrophy. Through the reconstruction of genomes, we were able to reveal the metabolic potentials and different survival strategies of underrepresented taxonomic groups, especially those related to Nanoarchaeota, Pyrodictiaceae and thermophilic ammonia-oxidizing archaeal lineages.
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Affiliation(s)
- Amanda Gonçalves Bendia
- Departamento de Oceanografia Biológica, Instituto Oceanográfico, Universidade de São Paulo (USP), Praça do Oceanográfico, 191, São Paulo, SP, CEP 05508-120, Brazil
| | - Leandro Nascimento Lemos
- Laboratório de Biologia Celular e Molecular, Centro de Energia Nuclear na Agricultura, Universidade de São Paulo, Avenida Centenário 303, Piracicaba, SP, CEP 13416-00, Brazil
| | - Lucas William Mendes
- Laboratório de Biologia Celular e Molecular, Centro de Energia Nuclear na Agricultura, Universidade de São Paulo, Avenida Centenário 303, Piracicaba, SP, CEP 13416-00, Brazil
| | - Camila Negrão Signori
- Departamento de Oceanografia Biológica, Instituto Oceanográfico, Universidade de São Paulo (USP), Praça do Oceanográfico, 191, São Paulo, SP, CEP 05508-120, Brazil
| | - Brendan J M Bohannan
- Department of Biology, Institute of Ecology and Evolution, University of Oregon, Eugene, OR, USA
| | - Vivian Helena Pellizari
- Departamento de Oceanografia Biológica, Instituto Oceanográfico, Universidade de São Paulo (USP), Praça do Oceanográfico, 191, São Paulo, SP, CEP 05508-120, Brazil
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46
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He Q, Wang S, Hou W, Feng K, Li F, Hai W, Zhang Y, Sun Y, Deng Y. Temperature and microbial interactions drive the deterministic assembly processes in sediments of hot springs. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 772:145465. [PMID: 33571767 DOI: 10.1016/j.scitotenv.2021.145465] [Citation(s) in RCA: 70] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 01/22/2021] [Accepted: 01/24/2021] [Indexed: 06/12/2023]
Abstract
Terrestrial geothermal ecosystems, as a representative of extreme environments, exhibit a variety of geochemical gradients, and their microbes are thought to be under high stress through environmental selection. However, it is still unclear how stochasticity and biotic interactions contribute to the microbial community assembly in hot springs. Here, we investigated the assembly processes and co-occurrence patterns of microbiota (i.e. bacteria and archaea) in both water and sediments sampled from fifteen hot springs in the Tengchong area, Southwestern of China, using 16S rRNA gene sequencing combined with multivariate ecological and statistical methods. These hot springs harbored more specialists than non-geothermal ecosystems, which are well-adapted to the extreme conditions, as shown by extremely high nearest-taxon index (NTI) and narrower niche width. Habitat differentiation led to the differences in microbial diversity, species-interactions, and community assembly between water and sediment communities. The sediment community showed stronger phylogenetic clustering and was primarily governed by heterogeneous selection, while undominated stochastic processes and dispersal limitation were the major assembly processes in the water community. Temperature and ferrous iron were the major factors mediating the balance of stochastic and deterministic assembly processes in sediment communities, as evidenced by how divergences in temperature and ferrous iron increased the proportion of determinism. Microbial interactions in sediments contributed to deterministic community assembly, as indicated by more complex associations and greater responsiveness to environmental change than water community. These findings uncover the ecological processes underlying microbial communities in hot springs, and provide potential insight into understanding the mechanism to maintain microbial diversity in extreme biospheres.
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Affiliation(s)
- Qing He
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100190, China
| | - Shang Wang
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing 100085, China.
| | - Weiguo Hou
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Beijing 100083, China
| | - Kai Feng
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100190, China
| | - Fangru Li
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Beijing 100083, China
| | - Wanming Hai
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Beijing 100083, China
| | - Yidi Zhang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Beijing 100083, China
| | - Yuxuan Sun
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Beijing 100083, China
| | - Ye Deng
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100190, China
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Abstract
In recent years, natural thermal mineral waters have been gaining the special attention of the scientific community, namely in the prevention and treatment of some diseases, due to the microbial properties that exist in these habitats. The aim of this work was to characterize the physicochemical composition and the microbial taxonomic communities present in three thermal waters of the Galician region in Spain and two samples of the northern region in Portugal. These collected water samples were analyzed for physicochemical characterization and the respective hydrogenome of the waters using next generation sequencing together with 16S rRNA gene sequencing. The sequencing showed a high diversity of microorganisms in all analyzed waters; however, there is a clear bacterial predominance of Proteobacteria phylum, followed by Firmicutes, Deinococcus-Thermus, Aquificae and Nitrospira. The main physicochemical parameters responsible for the clustering within the Spanish waters were sulfur compounds (SO32− and S2−), CO32− and neutral pH, and in the Portuguese waters were Mg, Ca and Sr, nitrogen compounds (NO3− and NH4+), Na, Rb, conductivity and dry residue. This work will allow for a better understanding of the microbial community’s composition and how these microorganisms interfere in the physicochemical constitution of these waters often associated with medicinal properties. Furthermore, the hydrogenome may be used as an auxiliary tool in the practice of medical hydrology, increasing the likelihood of safe use of these unique water types.
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48
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Reichart NJ, Bowers RM, Woyke T, Hatzenpichler R. High Potential for Biomass-Degrading Enzymes Revealed by Hot Spring Metagenomics. Front Microbiol 2021; 12:668238. [PMID: 33968004 PMCID: PMC8098120 DOI: 10.3389/fmicb.2021.668238] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 03/29/2021] [Indexed: 12/24/2022] Open
Abstract
Enzyme stability and activity at elevated temperatures are important aspects in biotechnological industries, such as the conversion of plant biomass into biofuels. In order to reduce the costs and increase the efficiency of biomass conversion, better enzymatic processing must be developed. Hot springs represent a treasure trove of underexplored microbiological and protein chemistry diversity. Herein, we conduct an exploratory study into the diversity of hot spring biomass-degrading potential. We describe the taxonomic diversity and carbohydrate active enzyme (CAZyme) coding potential in 71 publicly available metagenomic datasets from 58 globally distributed terrestrial geothermal features. Through taxonomic profiling, we detected a wide diversity of microbes unique to varying temperature and pH ranges. Biomass-degrading enzyme potential included all five classes of CAZymes and we described the presence or absence of genes encoding 19 glycosyl hydrolases hypothesized to be involved with cellulose, hemicellulose, and oligosaccharide degradation. Our results highlight hot springs as a promising system for the further discovery and development of thermo-stable biomass-degrading enzymes that can be applied toward generation of renewable biofuels. This study lays a foundation for future research to further investigate the functional diversity of hot spring biomass-degrading enzymes and their potential utility in biotechnological processing.
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Affiliation(s)
- Nicholas J Reichart
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, United States.,Thermal Biology Institute, Montana State University, Bozeman, MT, United States.,Center for Biofilm Engineering, Montana State University, Bozeman, MT, United States
| | - Robert M Bowers
- Department of Energy, Joint Genome Institute, Berkeley, CA, United States
| | - Tanja Woyke
- Department of Energy, Joint Genome Institute, Berkeley, CA, United States
| | - Roland Hatzenpichler
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, United States.,Thermal Biology Institute, Montana State University, Bozeman, MT, United States.,Center for Biofilm Engineering, Montana State University, Bozeman, MT, United States
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49
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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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50
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Marietou A. Sulfate reducing microorganisms in high temperature oil reservoirs. ADVANCES IN APPLIED MICROBIOLOGY 2021; 116:99-131. [PMID: 34353505 DOI: 10.1016/bs.aambs.2021.03.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
High temperature reservoirs offer a window into the microbial life of the deep biosphere. Sulfate reducing microorganisms have been recovered from high temperature oil reservoirs around the globe and characterized using culture-dependent and culture-independent approaches. The activities of sulfate reducers contribute to reservoir souring and hydrocarbon degradation among other attracting considerable interest from the oil industry for the last 100 years. The extremes of temperature and pressure shape the activities and distribution of sulfate reducing bacteria and archaea in high temperature reservoirs. This chapter will attempt to summarize the key findings on the diversity and activities of sulfate reducing microorganisms in high temperature reservoirs.
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Affiliation(s)
- Angeliki Marietou
- Section for Microbiology, Department of Biology, Aarhus University, Aarhus, Denmark.
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