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Li S, Deng Q, Xiang S, Zhang Z, Zhou Y. Study on the changes and transformation characteristics of intermediate liquid products in hydrogen sulfide production from lignite degraded by sulfate-reducing bacteria. ENVIRONMENTAL GEOCHEMISTRY AND HEALTH 2024; 46:408. [PMID: 39215874 DOI: 10.1007/s10653-024-02202-0] [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: 05/28/2024] [Accepted: 08/27/2024] [Indexed: 09/04/2024]
Abstract
The changes and transformation laws of intermediate liquid-phase products during the anaerobic degradation of lignite by sulfate-reducing bacteria in the formation of hydrogen sulfide play an important role in supplementing and improving the existing theories on the genesis of hydrogen sulfide gas in coal mines. In this paper, H2S gas and key intermediate liquid-phase products produced during the anaerobic degradation of lignite by sulfate-reducing bacteria were detected and analyzed by gas chromatography and gas chromatography-mass spectrometry. The results showed that the process of hydrogen sulfide production from lignite degradation by sulfate-reducing bacteria can be roughly divided into four stages: slow production phase, rapid growth phase, steady production phase, and slight decline phase. In this reaction system, the SO42- concentration showed a decreasing trend, the pH value showed an increasing trend, and the ORP value decreased and then slightly increased with time. Ten volatile component types were detected during the experiment: straight-chain alkanes, branched-chain alkanes, alcohols, aldehydes, ketones, olefins, amines, lipids, acids and phenols. The key components in the intermediate liquid phase products were straight chain alkanes, straight chain alkanes, acids, alcohols, phenols and amines. PAHs, alkanes, and phenols are closely related to H2S production, while amides stimulate nitrogen production. The process is divided into three stages: hydrolysis stage, H2S gas production stage, and decay stage. Liquid-phase intermediates play an important role in the formation process of coal mine BSR hydrogen sulfide and the mechanism of coal mine H2S genesis.
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Affiliation(s)
- Shuai Li
- School of Safety Science and Engineering, Henan Polytechnic University, Jiaozuo, 454003, China
| | - Qigen Deng
- School of Safety Science and Engineering, Henan Polytechnic University, Jiaozuo, 454003, China.
- State Key Laboratory Cultivation Base for Gas Geology and Gas Control, Henan Polytechnic University, Jiaozuo, 454003, China.
- Collaborative Innovation Center of Coal Safety Production of Henan Province, Jiaozuo, 454003, China.
| | - Sisi Xiang
- School of Safety Science and Engineering, Henan Polytechnic University, Jiaozuo, 454003, China
| | - Zhecheng Zhang
- School of Safety Science and Engineering, Henan Polytechnic University, Jiaozuo, 454003, China
| | - Yinzi Zhou
- School of Safety Science and Engineering, Henan Polytechnic University, Jiaozuo, 454003, China
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2
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Bassani I, Bellini R, Vizzarro A, Coti C, Pozzovivo V, Barbieri D, Pirri CF, Verga F, Menin B. Biogeochemical characterization of four depleted gas reservoirs for conversion into underground hydrogen storage. Environ Microbiol 2023; 25:3683-3702. [PMID: 37964633 DOI: 10.1111/1462-2920.16538] [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: 05/19/2023] [Accepted: 10/31/2023] [Indexed: 11/16/2023]
Abstract
Depleted gas reservoirs are a valuable option for underground hydrogen storage (UHS). However, different classes of microorganisms, which are capable of using free H2 as a reducing agent for their metabolism, inhabit deep underground formations and can potentially affect the storage. This study integrates metagenomics based on Illumina-NGS sequencing of bacterial and archaeal 16S rRNA and dsrB and mcrA functional genes to unveil the composition and the variability of indigenous microbial populations of four Italian depleted reservoirs. The obtained mcrA sequences allow us to implement the existing taxonomic database for mcrA gene sequences with newly classified sequences obtained from the Italian gas reservoirs. Moreover, the KEGG and COG predictive functional annotation was used to highlight the metabolic pathways potentially associated with hydrogenotrophic metabolisms. The analyses revealed the specificity of each reservoir microbial community, and taxonomic and functional data highlighted the presence of an enriched number of taxa, whose activity depends on both reservoir hydrochemical composition and nutrient availability, of potential relevance in the context of UHS. This study is the very first to address the profiling of the microbial population and allowed us to perform a preliminary assessment of UHS feasibility in Italy.
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Affiliation(s)
- Ilaria Bassani
- Centre for Sustainable Future Technologies, Fondazione Istituto Italiano di Tecnologia, Turin, Italy
| | - Ruggero Bellini
- Centre for Sustainable Future Technologies, Fondazione Istituto Italiano di Tecnologia, Turin, Italy
| | - Arianna Vizzarro
- Centre for Sustainable Future Technologies, Fondazione Istituto Italiano di Tecnologia, Turin, Italy
| | | | | | | | - Candido Fabrizio Pirri
- Centre for Sustainable Future Technologies, Fondazione Istituto Italiano di Tecnologia, Turin, Italy
- Department of Applied Science and Technology, Politecnico di Torino, Turin, Italy
| | - Francesca Verga
- Department of Applied Science and Technology, Politecnico di Torino, Turin, Italy
| | - Barbara Menin
- Centre for Sustainable Future Technologies, Fondazione Istituto Italiano di Tecnologia, Turin, Italy
- National Research Council, Institute of Agricultural Biology and Biotechnology (CNR-IBBA), Milan, Italy
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3
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Watanabe T, Yabe T, Tsuji JM, Fukui M. Desulfoferula mesophilus gen. nov. sp. nov., a mesophilic sulfate-reducing bacterium isolated from a brackish lake sediment. Arch Microbiol 2023; 205:368. [PMID: 37923857 DOI: 10.1007/s00203-023-03711-9] [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] [Revised: 10/13/2023] [Accepted: 10/14/2023] [Indexed: 11/06/2023]
Abstract
A novel sulfate-reducing bacterium (strain 12FAKT) was isolated from sediment sampled from a brackish lake in Japan. Respiratory growth was observed with formate and pyruvate as an electron donor. Sulfate, thiosulfate, elemental sulfur and dimethyl sulfoxide were utilized as an electron acceptor. The isolate grew over a temperature range of 18-42 °C (optimum 35-37 °C), a NaCl concentration range of 50-450 mM (optimum 150-300 mM) and a pH range of 6.6-7.5. The 12FAKT genome consists of a circular chromosome with a length of 4.5 Mbp and G + C content of 63.6%. Based on 16S rRNA gene sequence similarity, the closest cultured relative was Desulfarculus baarsii 2st14T (92.2%). Genome-based phylogenetic analysis placed strain 12FAKT within the family Desulfarculaceae but did not affiliate the strain with any existing genus. Taken together, we propose a novel species of a novel genus, Desulfoferula mesophilus gen. nov. sp. nov. with the type strain 12FAKT (= DSM 115219T = JCM 39399T).
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Affiliation(s)
- Tomohiro Watanabe
- The Institute of Low Temperature Science, Hokkaido University, Kita-19, Nishi-8, Kita-ku, Sapporo, 060-0819, Japan.
| | - Tatsuya Yabe
- The Institute of Low Temperature Science, Hokkaido University, Kita-19, Nishi-8, Kita-ku, Sapporo, 060-0819, Japan
- Graduate School of Environmental Science, Hokkaido University, Kita-10, Nishi-5, Kita-ku, Sapporo, 060-0810, Japan
| | - Jackson M Tsuji
- The Institute of Low Temperature Science, Hokkaido University, Kita-19, Nishi-8, Kita-ku, Sapporo, 060-0819, Japan
- Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima, Yokosuka, Kanagawa, Japan
| | - Manabu Fukui
- The Institute of Low Temperature Science, Hokkaido University, Kita-19, Nishi-8, Kita-ku, Sapporo, 060-0819, Japan
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Michalska K, Brown RK, Schröder U. Carbon source priority and availability limit bidirectional electron transfer in freshwater mixed culture electrochemically active bacterial biofilms. BIORESOUR BIOPROCESS 2023; 10:64. [PMID: 38647932 PMCID: PMC10991894 DOI: 10.1186/s40643-023-00685-w] [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: 06/19/2023] [Accepted: 09/02/2023] [Indexed: 04/25/2024] Open
Abstract
This study investigated, if a mixed electroactive bacterial (EAB) culture cultivated heterotrophically at a positive applied potential could be adapted from oxidative to reductive or bidirectional extracellular electron transfer (EET). To this end, a periodic potential reversal regime between - 0.5 and 0.2 V vs. Ag/AgCl was applied. This yielded biofilm detachment and mediated electroautotrophic EET in combination with carbonate, i.e., dissolved CO2, as the sole carbon source, whereby the emerged mixed culture (S1) contained previously unknown EAB. Using acetate (S2) as well as a mixture of acetate and carbonate (S3) as the main carbon sources yielded primarily alternating electrogenic organoheterotropic metabolism with the higher maximum oxidation current densities recorded for mixed carbon media, exceeding on average 1 mA cm-2. More frequent periodic polarization reversal resulted in the increase of maximum oxidative current densities by about 50% for S2-BES and 80% for S3-BES, in comparison to half-batch polarization. The EAB mixed cultures developed accordingly, with S1 represented by mostly aerobes (84.8%) and being very different in composition to S2 and S3, dominated by anaerobes (96.9 and 96.5%, respectively). S2 and S3 biofilms remained attached to the electrodes. There was only minor evidence of fully reversible bidirectional EET. In conclusion the three triplicates fed with organic and/or inorganic carbon sources demonstrated two forms of diauxie: Firstly, S1-BES showed a preference for the electrode as the electron donor via mediated EET. Secondly, S2-BES and S3-BES showed a preference for acetate as electron donor and c-source, as long as this was available, switching to CO2 reduction, when acetate was depleted.
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Affiliation(s)
- Karina Michalska
- Institute of Biochemistry, University of Greifswald, Felix-Hausdorff-Str. 4, 17489, Greifswald, Germany
| | - Robert Keith Brown
- Institute of Biochemistry, University of Greifswald, Felix-Hausdorff-Str. 4, 17489, Greifswald, Germany
| | - Uwe Schröder
- Institute of Biochemistry, University of Greifswald, Felix-Hausdorff-Str. 4, 17489, Greifswald, Germany.
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Yun Y, Su T, Gui Z, Tian X, Chen Y, Cao Y, Yang S, Xie J, Anwar N, Li M, Li G, Ma T. Stress-responses of microbes in oil reservoir under high tetracycline exposure and their environmental risks. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 315:120355. [PMID: 36243187 DOI: 10.1016/j.envpol.2022.120355] [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: 06/21/2022] [Revised: 09/10/2022] [Accepted: 10/01/2022] [Indexed: 06/16/2023]
Abstract
As the groundwater ecosystem is connected with surface, antibiotics and antibiotic resistance genes (ARGs) in aquatic environments will gradually infiltrate into the deep environment, posing a potential threat to groundwater ecosystem. However, knowledge on the environmental risk of antibiotics and ARGs in groundwater ecosystem and their ecological process still remains unexplored. In this study, lab-scale oil reservoirs under high tetracycline stress were performed to evaluate the dynamics of microbial communities, ARGs and potential functions by using 16S rRNA gene sequencing and metagenomics analysis. Although the presence of antibiotics remarkably reduced the microbial abundance and diversity in a short term, but remain stable or even increased after a long-term incubation. Antibiotic stress caused a greater diversity and abundance of ARGs, and higher numbers of ARGs-related species with the capacity to transfer ARGs to other microbes through horizontal gene transfer. Thus, a much more frequent associations of microbial community at both node- and network-level and a selective pressure on enrichment of antibiotic resistant bacteria related to "anaerobic n-alkane degradation" and "methylotrophic methanogenesis" were observed. It is important to emphasize that high antibiotic stress could also prevent some microbes related to "Sulfate reduction", "Fe(II) oxidation", "Nitrate reduction", and "Xylene and Toluene degradation". This study provides an insight into the long-term stress-responses of microbial communities and functions in oil reservoir under tetracycline exposure, which may help to elucidate the effect of antibiotic stress on biogeochemical cycling with microbial involvement in groundwater ecosystem.
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Affiliation(s)
- Yuan Yun
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin, China
| | - Tianqi Su
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin, China
| | - Ziyu Gui
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin, China
| | - Xuefeng Tian
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin, China
| | - Yu Chen
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin, China
| | - Yunke Cao
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin, China
| | - Shicheng Yang
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin, China
| | - Jinxia Xie
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin, China
| | - Nusratgul Anwar
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin, China
| | - Mingchang Li
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin, China
| | - Guoqiang Li
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin, China
| | - Ting Ma
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin, China.
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Lv X, Li Y, Cheng Y, Lai XH, Yang J, Lu S, Zhang G, Yang C, Jin D, Liu L, Xu J. Canibacter zhuwentaonis sp. nov. and Canibacter zhoujuaniae sp. nov. , isolated from Marmota himalayana. Int J Syst Evol Microbiol 2022; 72. [PMID: 36748412 DOI: 10.1099/ijsem.0.005633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Four Gram-stain-positive, facultatively anaerobic, non-motile, non-spore-forming and rod-shaped bacteria (lx-72T, lx-45, ZJ784T and ZJ955) were isolated from the respiratory tract or faeces of marmot (Marmota himalayana) from the Qinghai-Tibet Plateau in China. Analysis of the 16S rRNA gene sequences showed that all strains belong to the genus Canibacter and are more related to Canibacter oris CCUG 64069T (95.1-97.4 % similarity) than to the genus Leucobacter. Both strain pairs grew well at pH 6-9 and 15-42°C, and ZJ784T/ZJ955 could tolerate slightly higher NaCl (0.5-4.5 %, w/v) than lx-72T/lx-45(0.5-3.5 %). Based on whole-genome sequences, the average nucleotide identity and digital DNA-DNA hybridization values between our four isolates and their closest relative were below the species delineation thresholds of 70 % and 95-96 %. The common major fatty acids (>10 %) of our four strains were anteiso-C15 : 0 and anteiso-C17 : 0. For both new type strains, MK-8(H4) and MK-9(H4) were the major isoprenoid quinones, and diphosphatidylglycerol and phosphatidylglycerol were the main polar lipids. The genomic DNA G+C content of all strains was 53.9 mol%. Based on results from the genomic comparison, phylogenetic analysis, and physiological and biochemical characteristics, the four isolates represent two novel species in the genus Canibacter, for which the names Canibacter zhuwentaonis sp. nov. (type strain lx-72T=KCTC 49658T=GDMCC 1.2569T) and Canibacter zhoujuaniae sp. nov. (type strain ZJ784T=KCTC 49507T=GDMCC 1.1997T) are proposed.
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Affiliation(s)
- Xianglian Lv
- Department of Epidemiology, Shanxi Medical University School of Public Health, Taiyuan, Shanxi, PR China.,State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, PR China
| | - Yinmei Li
- Department of Epidemiology, Shanxi Medical University School of Public Health, Taiyuan, Shanxi, PR China.,State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, PR China
| | - Yanpeng Cheng
- Department of Epidemiology, Shanxi Medical University School of Public Health, Taiyuan, Shanxi, PR China.,State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, PR China.,Shenzhen Center for Disease Control and Prevention, Shenzhen, PR China
| | - Xin-He Lai
- Henan Key Laboratory of Biomolecular Recognition and Sensing, College of Chemistry and Chemical Engineering, Henan Joint International Research Laboratory of Chemo/Biosensing and Early Diagnosis of Major Diseases, Shangqiu Normal University, Shangqiu 476000, PR China
| | - Jing Yang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, PR China.,Shanghai Institute for Emerging and Re-emerging Infectious Diseases, Shanghai Public Health Clinical Center, Shanghai, PR China.,Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing, PR China
| | - Shan Lu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, PR China.,Shanghai Institute for Emerging and Re-emerging Infectious Diseases, Shanghai Public Health Clinical Center, Shanghai, PR China.,Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing, PR China
| | - Gui Zhang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, PR China
| | - Caixin Yang
- Department of Epidemiology, Shanxi Medical University School of Public Health, Taiyuan, Shanxi, PR China.,State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, PR China
| | - Dong Jin
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, PR China.,Shanghai Institute for Emerging and Re-emerging Infectious Diseases, Shanghai Public Health Clinical Center, Shanghai, PR China.,Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing, PR China
| | - Liyun Liu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, PR China.,Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing, PR China
| | - Jianguo Xu
- Department of Epidemiology, Shanxi Medical University School of Public Health, Taiyuan, Shanxi, PR China.,State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, PR China.,Shanghai Institute for Emerging and Re-emerging Infectious Diseases, Shanghai Public Health Clinical Center, Shanghai, PR China.,Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing, PR China.,Institute of Public Health, Nankai University, Tianjin, PR China
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7
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Rolando JL, Kolton M, Song T, Kostka JE. The core root microbiome of Spartina alterniflora is predominated by sulfur-oxidizing and sulfate-reducing bacteria in Georgia salt marshes, USA. MICROBIOME 2022; 10:37. [PMID: 35227326 PMCID: PMC8886783 DOI: 10.1186/s40168-021-01187-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 10/25/2021] [Indexed: 05/12/2023]
Abstract
BACKGROUND Salt marshes are dominated by the smooth cordgrass Spartina alterniflora on the US Atlantic and Gulf of Mexico coastlines. Although soil microorganisms are well known to mediate important biogeochemical cycles in salt marshes, little is known about the role of root microbiomes in supporting the health and productivity of marsh plant hosts. Leveraging in situ gradients in aboveground plant biomass as a natural laboratory, we investigated the relationships between S. alterniflora primary productivity, sediment redox potential, and the physiological ecology of bulk sediment, rhizosphere, and root microbial communities at two Georgia barrier islands over two growing seasons. RESULTS A marked decrease in prokaryotic alpha diversity with high abundance and increased phylogenetic dispersion was found in the S. alterniflora root microbiome. Significantly higher rates of enzymatic organic matter decomposition, as well as the relative abundances of putative sulfur (S)-oxidizing, sulfate-reducing, and nitrifying prokaryotes correlated with plant productivity. Moreover, these functional guilds were overrepresented in the S. alterniflora rhizosphere and root core microbiomes. Core microbiome bacteria from the Candidatus Thiodiazotropha genus, with the metabolic potential to couple S oxidation with C and N fixation, were shown to be highly abundant in the root and rhizosphere of S. alterniflora. CONCLUSIONS The S. alterniflora root microbiome is dominated by highly active and competitive species taking advantage of available carbon substrates in the oxidized root zone. Two microbially mediated mechanisms are proposed to stimulate S. alterniflora primary productivity: (i) enhanced microbial activity replenishes nutrients and terminal electron acceptors in higher biomass stands, and (ii) coupling of chemolithotrophic S oxidation with carbon (C) and nitrogen (N) fixation by root- and rhizosphere-associated prokaryotes detoxifies sulfide in the root zone while potentially transferring fixed C and N to the host plant. Video Abstract.
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Affiliation(s)
- Jose L Rolando
- Georgia Institute of Technology, School of Biological Sciences, Atlanta, GA, 30332, USA
| | - Max Kolton
- Georgia Institute of Technology, School of Biological Sciences, Atlanta, GA, 30332, USA
- French Associates Institute for Agriculture and Biotechnology of Drylands, Ben-Gurion, University of the Negev, Beer Sheva, Israel
| | - Tianze Song
- Georgia Institute of Technology, School of Biological Sciences, Atlanta, GA, 30332, USA
| | - Joel E Kostka
- Georgia Institute of Technology, School of Biological Sciences, Atlanta, GA, 30332, USA.
- Georgia Institute of Technology, School of Earth and Atmospheric Sciences, Atlanta, GA, 30332, USA.
- Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA, 30332, USA.
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8
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Sim MS, Skennerton CT, Orphan VJ. Physiological, genomic, and sulfur isotopic characterization of methanol metabolism by Desulfovibrio carbinolicus. PLoS One 2021; 16:e0245069. [PMID: 33444327 PMCID: PMC7808614 DOI: 10.1371/journal.pone.0245069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2020] [Accepted: 12/21/2020] [Indexed: 11/25/2022] Open
Abstract
Methanol is often considered as a non-competitive substrate for methanogenic archaea, but an increasing number of sulfate-reducing microorganisms (SRMs) have been reported to be capable of respiring with methanol as an electron donor. A better understanding of the fate of methanol in natural or artificial anaerobic systems thus requires knowledge of the methanol dissimilation by SRMs. In this study, we describe the growth kinetics and sulfur isotope effects of Desulfovibrio carbinolicus, a methanol-oxidizing sulfate-reducing deltaproteobacterium, together with its genome sequence and annotation. D. carbinolicus can grow with a series of alcohols from methanol to butanol. Compared to longer-chain alcohols, however, specific growth and respiration rates decrease by several fold with methanol as an electron donor. Larger sulfur isotope fractionation accompanies slowed growth kinetics, indicating low chemical potential at terminal reductive steps of respiration. In a medium containing both ethanol and methanol, D. carbinolicus does not consume methanol even after the cessation of growth on ethanol. Among the two known methanol dissimilatory systems, the genome of D. carbinolicus contains the genes coding for alcohol dehydrogenase but lacks enzymes analogous to methanol methyltransferase. We analyzed the genomes of 52 additional species of sulfate-reducing bacteria that have been tested for methanol oxidation. There is no apparent relationship between phylogeny and methanol metabolizing capacity, but most gram-negative methanol oxidizers grow poorly, and none carry homologs for methyltransferase (mtaB). Although the amount of available data is limited, it is notable that more than half of the known gram-positive methanol oxidizers have both enzymatic systems, showing enhanced growth relative to the SRMs containing only alcohol dehydrogenase genes. Thus, physiological, genomic, and sulfur isotopic results suggest that D. carbinolicus and close relatives have the ability to metabolize methanol but likely play a limited role in methanol degradation in most natural environments.
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Affiliation(s)
- Min Sub Sim
- School of Earth and Environmental Sciences, Seoul National University, Seoul, South Korea
- * E-mail:
| | - Connor T. Skennerton
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, California, United States of America
| | - Victoria J. Orphan
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, California, United States of America
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9
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Ziegler A, Gilligan AM, Dillon JG, Pernet B. Schizasterid Heart Urchins Host Microorganisms in a Digestive Symbiosis of Mesozoic Origin. Front Microbiol 2020; 11:1697. [PMID: 32793161 PMCID: PMC7387435 DOI: 10.3389/fmicb.2020.01697] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Accepted: 06/29/2020] [Indexed: 01/04/2023] Open
Abstract
Because of their lifestyles, abundance, and feeding habits, infaunal marine deposit feeders have a significant impact on the ocean floor. As these animals also ingest microorganisms associated with their sediment and seawater diet, their digestive tract usually contains a diverse array of bacteria. However, while most of these microorganisms are transients, some may become part of a resident gut microbiome, in particular when sheltered from the main flow of digesta in specialized gut compartments. Here, we provide an in-depth analysis of the structure and contents of the intestinal caecum (IC), a hindgut diverticulum found exclusively in schizasterid heart urchins (Echinoidea: Spatangoida: Schizasteridae). Based on specimens of Brisaster townsendi, in addition to various other schizasterid taxa, our structural characterization of the IC shows that the organ is a highly specialized gut compartment with unique structural properties. Next generation sequencing shows that the IC contains a microbial population composed predominantly of Bacteroidales, Desulfobacterales, and Spirochaetales. The microbiome of this gut compartment is significantly different in composition and lower in diversity than the microbial population in the sediment-filled main digestive tract. Inferences on the function and evolution of the IC and its microbiome suggest that this symbiosis plays a distinct role in host nutrition and that it evolved at least 66 million years ago during the final phase of the Mesozoic.
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Affiliation(s)
- Alexander Ziegler
- Institut für Evolutionsbiologie und Ökologie, Rheinische Friedrich-Wilhelms-Universität, Bonn, Germany
| | - Ariel M. Gilligan
- Department of Biological Sciences, California State University, Long Beach, CA, United States
| | - Jesse G. Dillon
- Department of Biological Sciences, California State University, Long Beach, CA, United States
| | - Bruno Pernet
- Department of Biological Sciences, California State University, Long Beach, CA, United States
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10
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Wang W, Tao J, Liu H, Li P, Chen S, Wang P, Zhang C. Contrasting bacterial and archaeal distributions reflecting different geochemical processes in a sediment core from the Pearl River Estuary. AMB Express 2020; 10:16. [PMID: 31970539 PMCID: PMC6975606 DOI: 10.1186/s13568-020-0950-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Accepted: 01/06/2020] [Indexed: 01/27/2023] Open
Abstract
Microbial community structure and metabolic activities have profound impacts on biogeochemical processes in marine sediments. Functional bacteria such as nitrate- and sulfate-reducing bacteria respond to redox gradients by coupling specific reactions amenable to relevant energy metabolisms. However, similar functional patterns have not been observed for sedimentary archaea (except for anaerobic methanotrophs and methanogens). We coupled taxonomic composition with comprehensive geochemical species to investigate the participation of distinct bacteria and archaea in sedimentary geochemical cycles in a sediment core (300 cm) from Pearl River Estuary (PRE). Geochemical properties (NO3−, dissolved Mn and Fe, SO42+, NH4+; dissolved inorganic carbon (DIC), δ13CDIC, dissolved organic carbon (DOC), total organic carbon (TOC), δ13CTOC, and fluorescent dissolved organic matter (FDOM)) exhibited strong depth variability of different trends. Bacterial 16S rRNA- and dsrB gene abundance decreased sharply with depth while archaeal and bathyarchaeotal 16S rRNA gene copies were relatively constant. This resulted in an increase in relative abundance of archaea from surface (11.6%) to bottom (42.8%). Network analysis showed that bacterial groups of Desulfobacterales, Syntrophobacterales and Gammaproteobacteria were significantly (P < 0.0001) associated with SO42− and dissolved Mn while archaeal groups of Bathyarchaeota, Group C3 and Marine Benthic Group D (MBGD) showed close positive correlations (P < 0.0001) with NH4+, δ13CTOC values and humic-like FDOM. Our study suggested that these bacterial groups dominated in redox processes relevant to sulfate or metal oxides, while the archaeal groups are more like to degrade recalcitrant organic compounds in anaerobic sediments.
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Song W, Lee LY, You H, Shi X, Ng HY. Microbial community succession and its correlation with reactor performance in a sponge membrane bioreactor coupled with fiber-bundle anoxic bio-filter for treating saline mariculture wastewater. BIORESOURCE TECHNOLOGY 2020; 295:122284. [PMID: 31669869 DOI: 10.1016/j.biortech.2019.122284] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 10/13/2019] [Accepted: 10/15/2019] [Indexed: 06/10/2023]
Abstract
The application of MBR in high saline wastewater treatment is mainly constrained by poor nitrogen removal and severe membrane fouling caused by high salinity stress. A novel carriers-enhanced MBR system was successfully developed for treating saline mariculture wastewater, which showed efficient TN removal (93.2%) and fouling control. High-throughput sequencing revealed the enhancement mechanism of bio-carriers under high saline condition. Bio-carriers substantially improved the community structure, representatively, nitrifiers abundance (Nitrosomonas, Nitrospira) increased from 2.18% to 9.57%, abundance of denitrifiers (Sulfurimonas, Thermogutta, etc.) also rose from 3.81% to 14.82%. Thereby, the nitrogen removal process was enhanced. Noteworthy, ammonia oxidizer (Nitrosomonas, 8.26%) was the absolute dominant nitrifiers compared with nitrite oxidizer (Nitrospira, 1.13%). This supported the finding of shortcut nitrification-denitrification process in hybrid system. Moreover, a series of biomacromolecule degraders (Lutibacterium, Cycloclasticus, etc.) were detected in bio-carriers, which could account for the mitigation of membrane fouling as result of EPS and SMP degradation.
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Affiliation(s)
- Weilong Song
- Centre for Water Research, Department of Civil and Environmental Engineering, National University of Singapore, 1 Engineering Drive 2, 117576, Singapore; State Key Laboratory of Urban Water Resource and Environment, School of Municipal and Environmental Engineering, Harbin Institute of Technology, Harbin 150090, PR China
| | - Lai Yoke Lee
- Centre for Water Research, Department of Civil and Environmental Engineering, National University of Singapore, 1 Engineering Drive 2, 117576, Singapore
| | - Hong You
- State Key Laboratory of Urban Water Resource and Environment, School of Municipal and Environmental Engineering, Harbin Institute of Technology, Harbin 150090, PR China
| | - Xueqing Shi
- Centre for Water Research, Department of Civil and Environmental Engineering, National University of Singapore, 1 Engineering Drive 2, 117576, Singapore; School of Environmental and Municipal Engineering, Qingdao University of Technology, 11 Fushun Road, Qingdao 266033, PR China
| | - How Yong Ng
- Centre for Water Research, Department of Civil and Environmental Engineering, National University of Singapore, 1 Engineering Drive 2, 117576, Singapore; NUS Environmental Research Institute, National University of Singapore, 5A Engineering Drive 1, 117411, Singapore.
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Davidova IA, Wawrik B, Callaghan AV, Duncan K, Marks CR, Suflita JM. Dethiosulfatarculus sandiegensis gen. nov., sp. nov., isolated from a methanogenic paraffin-degrading enrichment culture and emended description of the family Desulfarculaceae. Int J Syst Evol Microbiol 2015; 66:1242-1248. [PMID: 26704417 DOI: 10.1099/ijsem.0.000864] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A mesophilic deltaproteobacterium, designated strain SPRT, was isolated from a methanogenic consortium capable of degrading long-chain paraffins. Cells were motile, vibrio-shaped, and occurred singly, in pairs or in clusters. Strain SPRT did not metabolize hydrocarbons but grew fermentatively on pyruvate and oxaloacetate and autotrophically with H2 and CO2. Thiosulfate served as a terminal electron acceptor, but sulfate or sulfite did not. The organism required at least 10 g NaCl l- 1 and a small amount of yeast extract (0.001%) for growth. Optimal growth was observed between 30 and 37 °C and a pH range from 6.0 to 7.2. The DNA G+C content of SPRT's genome was 52.02 mol%. Based on 16S rRNA gene sequence analysis, strain SPRT was distinct from previously described Deltaproteobacteria, exhibiting the closest affiliation to Desulfarculus baarsii DSM 2075T and Desulfocarbo indianensis SCBMT, with only 91% similarity between their respective 16S gene sequences. In silico genome comparison supported the distinctiveness between strain SPRT and both Desulfocarbo indianensis SCBMT and Desulfarculus baarsii DSM 2075T. Based on physiological differences, as well as phylogenetic and genomic comparisons, we propose to classify SPRT as the type strain ( = DSM 100305T = JCM 30857T) of a novel species of a new genus with the name Dethiosulfatarculus sandiegensis gen. nov., sp. nov.
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Affiliation(s)
- Irene A Davidova
- Department of Microbiology and Plant Biology, University of Oklahoma, George Lynn Cross Hall, 770 Van Vleet Oval, Norman, OK 73019, USA.,Institute for Energy and the Environment, The University of Oklahoma, 100 East Boyd Street, Room 1510, Norman, OK 73019-1015, USA
| | - Boris Wawrik
- Department of Microbiology and Plant Biology, University of Oklahoma, George Lynn Cross Hall, 770 Van Vleet Oval, Norman, OK 73019, USA
| | - Amy V Callaghan
- Department of Microbiology and Plant Biology, University of Oklahoma, George Lynn Cross Hall, 770 Van Vleet Oval, Norman, OK 73019, USA
| | - Kathleen Duncan
- Department of Microbiology and Plant Biology, University of Oklahoma, George Lynn Cross Hall, 770 Van Vleet Oval, Norman, OK 73019, USA.,Institute for Energy and the Environment, The University of Oklahoma, 100 East Boyd Street, Room 1510, Norman, OK 73019-1015, USA
| | - Christopher R Marks
- Department of Microbiology and Plant Biology, University of Oklahoma, George Lynn Cross Hall, 770 Van Vleet Oval, Norman, OK 73019, USA.,Institute for Energy and the Environment, The University of Oklahoma, 100 East Boyd Street, Room 1510, Norman, OK 73019-1015, USA
| | - Joseph M Suflita
- Department of Microbiology and Plant Biology, University of Oklahoma, George Lynn Cross Hall, 770 Van Vleet Oval, Norman, OK 73019, USA.,Institute for Energy and the Environment, The University of Oklahoma, 100 East Boyd Street, Room 1510, Norman, OK 73019-1015, USA
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Draft Genome Sequence of Desulfocarbo indianensis SCBM, a New Genus of Sulfate-Reducing Bacteria, Isolated from Water Extracted from an Active Coalbed Methane Gas Well. GENOME ANNOUNCEMENTS 2015; 3:3/5/e00970-15. [PMID: 26337881 PMCID: PMC4559730 DOI: 10.1128/genomea.00970-15] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
We used Illumina MiSeq technology to sequence the whole genome of Desulfocarbo indianensis SCBM, a new genus of sulfate-reducing bacteria isolated from a coal bed in Indiana, USA. This draft genome represents the first sequenced genome of the genus Desulfocarbo and the second known genome of the order Desulfarculales.
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An TT, Picardal FW. Desulfuromonas carbonis sp. nov., an Fe(III)-, S0- and Mn(IV)-reducing bacterium isolated from an active coalbed methane gas well. Int J Syst Evol Microbiol 2015; 65:1686-1693. [PMID: 25736408 DOI: 10.1099/ijs.0.000159] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel, mesophilic, obligately anaerobic, acetate-oxidizing, dissimilatory iron-, sulfur-, and manganese-reducing bacterium, designated strain ICBM(T), was obtained from an active, coalbed methane gas well in Indiana, USA. Strain ICBM(T) was a Gram-stain-negative, non-spore-forming, rod-shaped, non-motile bacterium that was rich in c-type cytochromes and formed red colonies in solid medium. Strain ICBM(T) conserved energy to support growth from the oxidation of acetate, propionate, pyruvate, malate, fumarate, succinate and dl-lactate, concomitant with dissimilatory iron reduction. Strain ICBM(T) fermented fumarate yielding succinate and acetate. Strain ICBM(T) was able to grow in the temperature range of 10 °C to 37 °C, NaCl concentration range of 0 to 1.2 M, and pH range of 6.5 to 8.0. The physiological characteristics of strain ICBM(T) indicated that it belongs to the Desulfuromonas cluster. The G+C content of its genomic DNA was 61.2 mol%. The predominant cellular fatty acids were C16 : 0 (39.3%), C16 : 1ω7c and/or iso-C15 : 0 2-OH (36.6%). The closest cultured phylogenetic relative of strain ICBM(T) was Desulfuromonas michiganensis BB1(T) with only 95% 16S rRNA gene sequence similarity. This confirmed that strain ICBM(T) is affiliated with the genus Desulfuromonas . On the basis of phenotypic and genotypic differences between strain ICBM(T) and other taxa of the genus Desulfuromonas , strain ICBM(T) represents a novel species for which the name Desulfuromonas carbonis sp. nov. is proposed (type strain ICBM(T) = DSM 29759(T) = JCM 30471(T)). Strain ICBM(T) is the first Fe(III)-, S(0)-, and Mn(IV)-reducing bacterium that was isolated from a coal bed.
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Affiliation(s)
- Thuy T An
- School of Public and Environmental Affairs, Indiana University, MSB II, 702 N. Walnut Grove Ave, Bloomington, IN 47405-2204, USA
| | - Flynn W Picardal
- School of Public and Environmental Affairs, Indiana University, MSB II, 702 N. Walnut Grove Ave, Bloomington, IN 47405-2204, USA
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