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Huang-Lin E, Tamarit D, Lebrero R, Cantera S. Guyparkeria halophila: Novel cell platform for the efficient valorization of carbon dioxide and thiosulfate into ectoine. BIORESOURCE TECHNOLOGY 2024; 408:131152. [PMID: 39053597 DOI: 10.1016/j.biortech.2024.131152] [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: 05/28/2024] [Revised: 07/18/2024] [Accepted: 07/22/2024] [Indexed: 07/27/2024]
Abstract
Utilizing carbon dioxide (CO2) for valuable chemical production is key to a circular economy. Current processes are costly due to limited microorganism use, low-value products, and the need for affordable energy. This study addresses these challenges by using industrial contaminants like thiosulfate (S2O32-) for CO2 conversion into ectoines. Ectoines, are important ingredients as pharmaceuticals and cosmetics. Here, six microbial genomes were identified as potential candidates to valorize CO2 and S2O32- into ectoine. After laboratory validation at 3 % NaCl, the fastest-growing strain, Guyparkeria halophila, was optimized at 6 %, 9 %, and 15 % NaCl, showing the highest specific ectoine contents (mgEct gbiomass-1) at 15 %. Batch bioreactors, combining optimal conditions, achieved maximum specific ectoine contents of 47 %. These results not only constitute the highest ectoine content so far reported by autotrophs and most of heterotrophs, but also the first proof of a novel valorization platform for CO2 and S2O32-, focused on pharmaceuticals production.
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Affiliation(s)
- E Huang-Lin
- Department of Chemical Engineering and Environmental Technology, University of Valladolid, Dr. Mergelina s/n., Valladolid 47011, Spain; Institute of Sustainable Processes, University of Valladolid, Dr. Mergelina s/n., Valladolid 47011, Spain
| | - D Tamarit
- Theoretical Biology and Bioinformatics, Utrecht University, 3584CH Utrecht, The Netherlands
| | - R Lebrero
- Department of Chemical Engineering and Environmental Technology, University of Valladolid, Dr. Mergelina s/n., Valladolid 47011, Spain; Institute of Sustainable Processes, University of Valladolid, Dr. Mergelina s/n., Valladolid 47011, Spain
| | - S Cantera
- Department of Chemical Engineering and Environmental Technology, University of Valladolid, Dr. Mergelina s/n., Valladolid 47011, Spain; Institute of Sustainable Processes, University of Valladolid, Dr. Mergelina s/n., Valladolid 47011, Spain.
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2
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Twible LE, Whaley-Martin K, Chen LX, Colenbrander Nelson T, Arrey JL, Jarolimek CV, King JJ, Ramilo L, Sonnenberg H, Banfield JF, Apte SC, Warren LA. pH and thiosulfate dependent microbial sulfur oxidation strategies across diverse environments. Front Microbiol 2024; 15:1426584. [PMID: 39101034 PMCID: PMC11294248 DOI: 10.3389/fmicb.2024.1426584] [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: 05/01/2024] [Accepted: 06/18/2024] [Indexed: 08/06/2024] Open
Abstract
Sulfur oxidizing bacteria (SOB) play a key role in sulfur cycling in mine tailings impoundment (TI) waters, where sulfur concentrations are typically high. However, our understanding of SOB sulfur cycling via potential S oxidation pathways (sox, rdsr, and S4I) in these globally ubiquitous contexts, remains limited. Here, we identified TI water column SOB community composition, metagenomics derived metabolic repertoires, physicochemistry, and aqueous sulfur concentration and speciation in four Canadian base metal mine, circumneutral-alkaline TIs over four years (2016 - 2019). Identification and examination of genomes from nine SOB genera occurring in these TI waters revealed two pH partitioned, metabolically distinct groups, which differentially influenced acid generation and sulfur speciation. Complete sox (csox) dominant SOB (e.g., Halothiobacillus spp., Thiomonas spp.) drove acidity generation and S2O3 2- consumption via the csox pathway at lower pH (pH ~5 to ~6.5). At circumneutral pH conditions (pH ~6.5 to ~8.5), the presence of non-csox dominant SOB (hosting the incomplete sox, rdsr, and/or other S oxidation reactions; e.g. Thiobacillus spp., Sulfuriferula spp.) were associated with higher [S2O3 2-] and limited acidity generation. The S4I pathway part 1 (tsdA; S2O3 2- to S4O6 2-), was not constrained by pH, while S4I pathway part 2 (S4O6 2- disproportionation via tetH) was limited to Thiobacillus spp. and thus circumneutral pH values. Comparative analysis of low, natural (e.g., hydrothermal vents and sulfur hot springs) and high (e.g., Zn, Cu, Pb/Zn, and Ni tailings) sulfur systems literature data with these TI results, reveals a distinct TI SOB mining microbiome, characterized by elevated abundances of csox dominant SOB, likely sustained by continuous replenishment of sulfur species through tailings or mining impacted water additions. Our results indicate that under the primarily oxic conditions in these systems, S2O3 2- availability plays a key role in determining the dominant sulfur oxidation pathways and associated geochemical and physicochemical outcomes, highlighting the potential for biological management of mining impacted waters via pH and [S2O3 2-] manipulation.
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Affiliation(s)
- Lauren E. Twible
- Department of Civil and Mineral Engineering, University of Toronto, Toronto, ON, Canada
| | - Kelly Whaley-Martin
- Department of Civil and Mineral Engineering, University of Toronto, Toronto, ON, Canada
| | - Lin-Xing Chen
- Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, CA, United States
| | | | - James L.S. Arrey
- Department of Civil and Mineral Engineering, University of Toronto, Toronto, ON, Canada
| | - Chad V. Jarolimek
- School of Mathematical and Physical Sciences, University of Technology Sydney, Ultimo, NSW, Australia
| | - Josh J. King
- Commonwealth Scientific Industrial and Research Organization, Black Mountain, ACT, Australia
| | | | | | - Jillian F. Banfield
- Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, CA, United States
| | - Simon C. Apte
- Commonwealth Scientific Industrial and Research Organization, Clayton, VIC, Australia
| | - Lesley A. Warren
- Department of Civil and Mineral Engineering, University of Toronto, Toronto, ON, Canada
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3
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Wang Q, Zhang C, Song J, Bamanu B, Zhao Y. Inhibitory mechanism of Cr(VI) on sulfur-based denitrification: Bio-toxicity, bio-electron characteristics, and microbial evolution. JOURNAL OF HAZARDOUS MATERIALS 2024; 472:134447. [PMID: 38692000 DOI: 10.1016/j.jhazmat.2024.134447] [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: 02/09/2024] [Revised: 03/24/2024] [Accepted: 04/25/2024] [Indexed: 05/03/2024]
Abstract
Sulfur-based denitrification is a promising technology for efficient nitrogen removal in low-carbon wastewater, while it is easily affected by toxic substances. This study revealed the inhibitory mechanism of Cr(VI) on thiosulfate-based denitrification, including bio-toxicity and bio-electron characteristics response. The activity of nitrite reductase (NIR) was more sensitive to Cr(VI) than that of nitrate reductase (NAR), and NIR was inhibited by 21.32 % and 19.86 % under 5 and 10 mg/L Cr(VI), resulting in 10.12 and 15.62 mg/L of NO2--N accumulation. The biofilm intercepted 36.57 % of chromium extracellularly by increasing 25.78 % of extracellular polymeric substances, thereby protecting microbes from bio-toxicity under 5 mg/L Cr(VI). However, it was unable to resist 20-30 mg/L of Cr(VI) bio-toxicity as 19.95 and 14.29 mg Cr/(g volatile suspended solids) invaded intracellularly, inducing the accumulation of reactive oxygen species by 165.98 % and 169.12 %, which triggered microbial oxidative-stress and damaged the cells. In terms of electron transfer, S2O32- oxidation was inhibited, and parts of electrons were redirected intracellularly to maintain microbial activity, resulting in insufficient electron donors. Meanwhile, the contents of flavin adenine dinucleotide and cytochrome c decreased under 5-30 mg/L Cr(VI), reducing the electron acquisition rate of denitrification. Thermomonas (the dominant genus) possessed denitrification and Cr(VI) resistance abilities, playing an important role in antioxidant stress and biofilm formation. ENVIRONMENTAL IMPLICATION: Sulfur-based denitrification (SBD) is a promising method for nitrate removal in low-carbon wastewater, while toxic heavy metals such as Cr(VI) negatively impair denitrification. This study elucidated Cr(VI) inhibitory mechanisms on SBD, including bio-toxicity response, bio-electron characteristics, and microbial community structure. Higher concentrations Cr(VI) led to intracellular invasion and oxidative stress, evidenced by ROS accumulation. Moreover, Cr(VI) disrupted electron flow by inhibiting thiosulfate oxidation and affecting electron acquisition by denitrifying enzymes. This study provided valuable insights into Cr(VI) toxicity, which is of great significance for improving wastewater treatment technologies and maintaining efficient and stable operation of SBD in the face of complex environmental challenges.
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Affiliation(s)
- Qian Wang
- School of Environmental Science and Engineering, Tianjin University, Tianjin 300350, China
| | - Chenggong Zhang
- School of Environmental Science and Engineering, Tianjin University, Tianjin 300350, China
| | - Jinxin Song
- School of Environmental Science and Engineering, Tianjin University, Tianjin 300350, China
| | - Bibek Bamanu
- School of Environmental Science and Engineering, Tianjin University, Tianjin 300350, China
| | - Yingxin Zhao
- School of Environmental Science and Engineering, Tianjin University, Tianjin 300350, China.
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Wang Q, Zhang C, Song J, Bamanu B, Zhao Y. Enhancement of bio-promoters on hexavalent chromium inhibited sulfur-driven denitrification: repairing damage, accelerating electron transfer, and reshaping microbial collaboration. BIORESOURCE TECHNOLOGY 2024; 400:130699. [PMID: 38615966 DOI: 10.1016/j.biortech.2024.130699] [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: 01/27/2024] [Revised: 03/13/2024] [Accepted: 04/12/2024] [Indexed: 04/16/2024]
Abstract
Proposing recovery strategies to recover heavy-metal-inhibited sulfur-driven denitrification, as well as disclosing recovery mechanisms, can provide technical support for the stable operation of bio-systems. This study proposed an effective bio-promoter (mediator-promoter composed of L-cysteine, biotin, cytokinin, and anthraquinone-2,6-disulfonate) to recover Cr(VI) inhibited sulfur-driven denitrification, which effectively reduced the recovery time of NO3--N reduction (18-21 cycles) and NO2--N reduction (27-42 cycles) compared with self-recovery. The mediator-promoter repaired microbial damage by promoting intracellular chromium efflux. Moreover, the mediator-promoter reduced the accumulated reactive oxygen species by stimulating the secretion of antioxidant enzymes, reaching equilibrium in the oxidative-antioxidant system. To improve electron transmission, the mediator-promoter restored S2O32- oxidation to provide adequate electron donors and increased electron transfer rate by increasing cytochrome c levels. Mediator-promoter boosted the abundance of Thiobacillus (sulfur-oxidizing bacterium) and Simplicispira (denitrifying bacterium), which were positively correlated, facilitating the rapid denitrification recovery and the long-term stable operation of recovered systems.
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Affiliation(s)
- Qian Wang
- School of Environmental Science and Engineering, Tianjin University, Tianjin 300350, China
| | - Chenggong Zhang
- School of Environmental Science and Engineering, Tianjin University, Tianjin 300350, China
| | - Jinxin Song
- School of Environmental Science and Engineering, Tianjin University, Tianjin 300350, China
| | - Bibek Bamanu
- School of Environmental Science and Engineering, Tianjin University, Tianjin 300350, China
| | - Yingxin Zhao
- School of Environmental Science and Engineering, Tianjin University, Tianjin 300350, China.
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5
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Deng T, He Z, Xu M, Dong M, Guo J, Sun G, Huang H. Species' functional traits and interactions drive nitrate-mediated sulfur-oxidizing community structure and functioning. mBio 2023; 14:e0156723. [PMID: 37702500 PMCID: PMC10653917 DOI: 10.1128/mbio.01567-23] [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: 06/22/2023] [Accepted: 07/18/2023] [Indexed: 09/14/2023] Open
Abstract
IMPORTANCE Understanding the processes and mechanisms governing microbial community assembly and their linkages to ecosystem functioning has long been a core issue in microbial ecology. An in-depth insight still requires combining with analyses of species' functional traits and microbial interactions. Our study showed how species' functional traits and interactions determined microbial community structure and functions by a well-controlled laboratory experiment with nitrate-mediated sulfur oxidation systems using high-throughput sequencing and culture-dependent technologies. The results provided solid evidences that species' functional traits and interactions were the intrinsic factors determining community structure and function. More importantly, our study established quantitative links between community structure and function based on species' functional traits and interactions, which would have important implications for the design and synthesis of microbiomes with expected functions.
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Affiliation(s)
- Tongchu Deng
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Institute of Microbiology, Guangdong Academy of Science, Guangzhou, China
- Guangdong Provincial Key Laboratory of Environmental Protection Microbiology and Regional Ecological Security, Guangzhou, Guangdong, China
| | - Zhili He
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
| | - Meiying Xu
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Institute of Microbiology, Guangdong Academy of Science, Guangzhou, China
- Guangdong Provincial Key Laboratory of Environmental Protection Microbiology and Regional Ecological Security, Guangzhou, Guangdong, China
| | - Meijun Dong
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Institute of Microbiology, Guangdong Academy of Science, Guangzhou, China
- Guangdong Provincial Key Laboratory of Environmental Protection Microbiology and Regional Ecological Security, Guangzhou, Guangdong, China
| | - Jun Guo
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Institute of Microbiology, Guangdong Academy of Science, Guangzhou, China
- Guangdong Provincial Key Laboratory of Environmental Protection Microbiology and Regional Ecological Security, Guangzhou, Guangdong, China
| | - Guoping Sun
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Institute of Microbiology, Guangdong Academy of Science, Guangzhou, China
- Guangdong Provincial Key Laboratory of Environmental Protection Microbiology and Regional Ecological Security, Guangzhou, Guangdong, China
| | - Haobin Huang
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Institute of Microbiology, Guangdong Academy of Science, Guangzhou, China
- Guangdong Provincial Key Laboratory of Environmental Protection Microbiology and Regional Ecological Security, Guangzhou, Guangdong, China
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6
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Sun W, Xu Y, Liang Y, Yu Q, Gao H. A novel bacterial sulfite dehydrogenase that requires three c-type cytochromes for electron transfer. Appl Environ Microbiol 2023; 89:e0110823. [PMID: 37732808 PMCID: PMC10617556 DOI: 10.1128/aem.01108-23] [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: 07/17/2023] [Accepted: 07/27/2023] [Indexed: 09/22/2023] Open
Abstract
c-type Cytochromes (c-Cyts), primarily as electron carriers and oxidoreductases, play a key role in energy transduction processes in virtually all living organisms. Many bacteria, such as Shewanella oneidensis, are particularly rich in c-Cyts, supporting respiratory versatility not seen in eukaryotes. Unfortunately, a large number of c-Cyts are underexplored, and their biological functions remain unknown. In this study, we identify SorCABD of S. oneidensis as a novel sulfite dehydrogenase (SDH), which catalyzes the oxidation of sulfite to sulfate. In addition to catalytic subunit SorA, this enzymatic complex includes three c-Cyt subunits, which all together carry out electron transfer. The electrons extracted from sulfite oxidation are ultimately delivered to oxygen, leading to oxygen reduction, a process relying on terminal oxidase cyt cbb3. Genomic analysis suggests that the homologs of this SDH are present in a small number of bacterial genera, Shewanella and Vibrio in particular. Because these bacteria are generally capable of reducing sulfite under anaerobic conditions, the co-existence of a sulfite oxidation system implies that they may play especially important roles in the transformation of sulfur species in natural environments.Importancec-type Cytochromes (c-Cyts) endow bacteria with high flexibility in their oxidative/respiratory systems, allowing them to extracellularly transform diverse inorganic and organic compounds for survival and growth. However, a large portion of the bacterial c-Cyts remain functionally unknown. Here, we identify three c-Cyts that work together as essential electron transfer partners for the catalytic subunit of a novel SDH in sulfite oxidation in Shewanella oneidensis. This characteristic makes S. oneidensis the first organism known to be capable of oxidizing and reducing sulfite. The findings suggest that Shewanella, along with a small number of other aquatic bacteria, would serve as a particular driving force in the biogeochemical sulfur cycle in nature.
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Affiliation(s)
- Weining Sun
- Key Laboratory of Aging and Cancer Biology of Zhejiang Province, Department of Immunology and Pathogen Biology, School of Basic Medical Sciences, Hangzhou Normal University, Hangzhou, China
- Institute of Microbiology and College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Yuanyou Xu
- Institute of Microbiology and College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Yawen Liang
- Institute of Microbiology and College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Qingzi Yu
- Institute of Microbiology and College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Haichun Gao
- Institute of Microbiology and College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
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7
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Gao Y, Zhu H, Wang J, Shao Z, Wei S, Wang R, Cheng R, Jiang L. Physiological and Genomic Characterization of a Novel Obligately Chemolithoautotrophic, Sulfur-Oxidizing Bacterium of Genus Thiomicrorhabdus Isolated from a Coastal Sediment. Microorganisms 2023; 11:2569. [PMID: 37894227 PMCID: PMC10608990 DOI: 10.3390/microorganisms11102569] [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: 09/13/2023] [Revised: 10/08/2023] [Accepted: 10/13/2023] [Indexed: 10/29/2023] Open
Abstract
Thiomicrorhabdus species, belonging to the family Piscirickettsiaceae in the phylum Pseudomonadotav are usually detected in various sulfur-rich marine environments. However, only a few bacteria of Thiomicrorhabdus have been isolated, and their ecological roles and environmental adaptations still require further understanding. Here, we report a novel strain, XGS-01T, isolated from a coastal sediment, which belongs to genus Thiomicrorhabdus and is most closely related to Thiomicrorhabdus hydrogeniphila MAS2T, with a sequence similarity of 97.8%. Phenotypic characterization showed that XGS-01T is a mesophilic, sulfur-oxidizing, obligate chemolithoautotrophy, with carbon dioxide as its sole carbon source and oxygen as its sole electron acceptor. During thiosulfate oxidation, strain XGS-01T can produce extracellular sulfur of elemental α-S8, as confirmed via scanning electron microscopy and Raman spectromicroscopy. Polyphasic taxonomy results indicate that strain XGS-01T represents a novel species of the genus Thiomicrorhabdus, named Thiomicrorhabdus lithotrophica sp. nov. Genomic analysis confirmed that XGS-01T performed thiosulfate oxidation through a sox multienzyme complex, and harbored fcc and sqr genes for sulfide oxidation. Comparative genomics analysis among five available genomes from Thiomicrorhabdus species revealed that carbon fixation via the oxidation of reduced-sulfur compounds coupled with oxygen reduction is conserved metabolic pathways among members of genus Thiomicrorhabdus.
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Affiliation(s)
- Yu Gao
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China (J.W.); (R.W.)
- State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen 361005, China
- School of Marine Sciences, China University of Geosciences, Beijing 100083, China
| | - Han Zhu
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China (J.W.); (R.W.)
- State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen 361005, China
| | - Jun Wang
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China (J.W.); (R.W.)
- State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen 361005, China
| | - Zongze Shao
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China (J.W.); (R.W.)
- State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen 361005, China
| | - Shiping Wei
- School of Marine Sciences, China University of Geosciences, Beijing 100083, China
| | - Ruicheng Wang
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China (J.W.); (R.W.)
- State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen 361005, China
| | - Ruolin Cheng
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China (J.W.); (R.W.)
- State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen 361005, China
| | - Lijing Jiang
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China (J.W.); (R.W.)
- State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen 361005, China
- School of Marine Biology, Xiamen Ocean Vocational College, Xiamen 361005, China
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8
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Wang S, Lu Q, Liang Z, Yu X, Lin M, Mai B, Qiu R, Shu W, He Z, Wall JD. Generation of zero-valent sulfur from dissimilatory sulfate reduction in sulfate-reducing microorganisms. Proc Natl Acad Sci U S A 2023; 120:e2220725120. [PMID: 37155857 PMCID: PMC10194018 DOI: 10.1073/pnas.2220725120] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 04/14/2023] [Indexed: 05/10/2023] Open
Abstract
Dissimilatory sulfate reduction (DSR) mediated by sulfate-reducing microorganisms (SRMs) plays a pivotal role in global sulfur, carbon, oxygen, and iron cycles since at least 3.5 billion y ago. The canonical DSR pathway is believed to be sulfate reduction to sulfide. Herein, we report a DSR pathway in phylogenetically diverse SRMs through which zero-valent sulfur (ZVS) is directly generated. We identified that approximately 9% of sulfate reduction was directed toward ZVS with S8 as a predominant product, and the ratio of sulfate-to-ZVS could be changed with SRMs' growth conditions, particularly the medium salinity. Further coculturing experiments and metadata analyses revealed that DSR-derived ZVS supported the growth of various ZVS-metabolizing microorganisms, highlighting this pathway as an essential component of the sulfur biogeochemical cycle.
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Affiliation(s)
- Shanquan Wang
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, Guangzhou510006, China
| | - Qihong Lu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, Guangzhou510006, China
| | - Zhiwei Liang
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, Guangzhou510006, China
| | - Xiaoxiao Yu
- State Key Laboratory of Isotope Geochemistry and CAS Center for Excellence in Deep Earth Science, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou510640, China
- Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou511458, China
- University of Chinese Academy of Sciences, Beijing100039, China
| | - Mang Lin
- State Key Laboratory of Isotope Geochemistry and CAS Center for Excellence in Deep Earth Science, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou510640, China
- Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou511458, China
- University of Chinese Academy of Sciences, Beijing100039, China
| | - Bixian Mai
- State Key Laboratory of Isotope Geochemistry and CAS Center for Excellence in Deep Earth Science, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou510640, China
- University of Chinese Academy of Sciences, Beijing100039, China
| | - Rongliang Qiu
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Natural Resources and Environment, South China Agricultural University, Guangzhou510642, China
| | - Wensheng Shu
- Institute of Ecological Science, School of Life Sciences, South China Normal University, Guangzhou510631, China
| | - Zhili He
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, Guangzhou510006, China
| | - Judy D. Wall
- Department of Biochemistry, University of Missouri-Columbia, Columbia, MO65211
- Department of Molecular Microbiology & Immunology, University of Missouri-Columbia, Columbia, MO65211
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9
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Liu R, Shan Y, Xi S, Zhang X, Sun C. A deep-sea sulfate-reducing bacterium generates zero-valent sulfur via metabolizing thiosulfate. MLIFE 2022; 1:257-271. [PMID: 38818226 PMCID: PMC10989961 DOI: 10.1002/mlf2.12038] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 08/04/2022] [Accepted: 08/08/2022] [Indexed: 06/01/2024]
Abstract
Zero-valent sulfur (ZVS) is a crucial intermediate in the sulfur geobiochemical circulation and is widespread in deep-sea cold seeps. Sulfur-oxidizing bacteria are thought to be the major contributors to the formation of ZVS. However, ZVS production mediated by sulfate-reducing bacteria (SRB) has rarely been reported. In this study, we isolated and cultured a typical SRB designated Oceanidesulfovibrio marinus CS1 from deep-sea cold seep sediment in the South China Sea. We show that O. marinus CS1 forms ZVS in the medium supplemented with thiosulfate. Proteomic and protein activity assays revealed that thiosulfate reductase (PhsA) and the sulfide:quinone oxidoreductase (SQR) played key roles in driving ZVS formation in O. marinus CS1. During this process, thiosulfate firstly was reduced by PhsA to form sulfide, then sulfide was oxidized by SQR to produce ZVS. The expressions of PhsA and SQR were significantly upregulated when O. marinus CS1 was cultured in a deep-sea cold seep, strongly indicating that strain CS1 might form ZVS in the deep-sea environment. Notably, homologs of phsA and sqr were widely identified from microbes living in sediments of deep-sea cold seep in the South China Sea by the metagenomic analysis. We thus propose that SRB containing phsA and sqr genes potentially contribute to the formation of ZVS in deep-sea cold seep environments.
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Affiliation(s)
- Rui Liu
- CAS and Shandong Province Key Laboratory of Experimental Marine BiologyCenter of Deep Sea Research, Institute of Oceanology, Chinese Academy of SciencesQingdaoChina
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and TechnologyQingdaoChina
- Center of Ocean Mega‐Science, Chinese Academy of SciencesQingdaoChina
| | - Yeqi Shan
- CAS and Shandong Province Key Laboratory of Experimental Marine BiologyCenter of Deep Sea Research, Institute of Oceanology, Chinese Academy of SciencesQingdaoChina
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and TechnologyQingdaoChina
- Center of Ocean Mega‐Science, Chinese Academy of SciencesQingdaoChina
- College of Earth Science, University of Chinese Academy of SciencesBeijingChina
| | - Shichuan Xi
- Center of Ocean Mega‐Science, Chinese Academy of SciencesQingdaoChina
- College of Earth Science, University of Chinese Academy of SciencesBeijingChina
- CAS Key Laboratory of Marine Geology and EnvironmentCenter of Deep Sea Research, Institute of Oceanology, Chinese Academy of SciencesQingdaoChina
| | - Xin Zhang
- Center of Ocean Mega‐Science, Chinese Academy of SciencesQingdaoChina
- CAS Key Laboratory of Marine Geology and EnvironmentCenter of Deep Sea Research, Institute of Oceanology, Chinese Academy of SciencesQingdaoChina
| | - Chaomin Sun
- CAS and Shandong Province Key Laboratory of Experimental Marine BiologyCenter of Deep Sea Research, Institute of Oceanology, Chinese Academy of SciencesQingdaoChina
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and TechnologyQingdaoChina
- Center of Ocean Mega‐Science, Chinese Academy of SciencesQingdaoChina
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10
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Deep-Sea
In Situ
Insights into the Formation of Zero-Valent Sulfur Driven by a Bacterial Thiosulfate Oxidation Pathway. mBio 2022; 13:e0014322. [PMID: 35852328 PMCID: PMC9426585 DOI: 10.1128/mbio.00143-22] [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] [Indexed: 11/20/2022] Open
Abstract
The contribution of microbes to the deep-sea cold seep sulfur cycle has received considerable attention in recent years. In the previous study, we isolated
E. flavus
21-3 from deep-sea cold seep sediments and described a novel thiosulfate oxidation pathway in the laboratorial condition.
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11
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Metabolism of the Genus Guyparkeria Revealed by Pangenome Analysis. Microorganisms 2022; 10:microorganisms10040724. [PMID: 35456775 PMCID: PMC9032823 DOI: 10.3390/microorganisms10040724] [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: 01/31/2022] [Revised: 03/12/2022] [Accepted: 03/14/2022] [Indexed: 02/04/2023] Open
Abstract
Halophilic sulfur-oxidizing bacteria belonging to the genus Guyparkeria occur at both marine and terrestrial habitats. Common physiological characteristics displayed by Guyparkeria isolates have not yet been linked to the metabolic potential encoded in their genetic inventory. To provide a genetic basis for understanding the metabolism of Guyparkeria, nine genomes were compared to reveal the metabolic capabilities and adaptations. A detailed account is given on Guyparkeria’s ability to assimilate carbon by fixation, to oxidize reduced sulfur, to oxidize thiocyanate, and to cope with salinity stress.
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12
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Patin NV, Dietrich ZA, Stancil A, Quinan M, Beckler JS, Hall ER, Culter J, Smith CG, Taillefert M, Stewart FJ. Gulf of Mexico blue hole harbors high levels of novel microbial lineages. THE ISME JOURNAL 2021; 15:2206-2232. [PMID: 33612832 PMCID: PMC8319197 DOI: 10.1038/s41396-021-00917-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Revised: 01/14/2021] [Accepted: 01/27/2021] [Indexed: 01/31/2023]
Abstract
Exploration of oxygen-depleted marine environments has consistently revealed novel microbial taxa and metabolic capabilities that expand our understanding of microbial evolution and ecology. Marine blue holes are shallow karst formations characterized by low oxygen and high organic matter content. They are logistically challenging to sample, and thus our understanding of their biogeochemistry and microbial ecology is limited. We present a metagenomic and geochemical characterization of Amberjack Hole on the Florida continental shelf (Gulf of Mexico). Dissolved oxygen became depleted at the hole's rim (32 m water depth), remained low but detectable in an intermediate hypoxic zone (40-75 m), and then increased to a secondary peak before falling below detection in the bottom layer (80-110 m), concomitant with increases in nutrients, dissolved iron, and a series of sequentially more reduced sulfur species. Microbial communities in the bottom layer contained heretofore undocumented levels of the recently discovered phylum Woesearchaeota (up to 58% of the community), along with lineages in the bacterial Candidate Phyla Radiation (CPR). Thirty-one high-quality metagenome-assembled genomes (MAGs) showed extensive biochemical capabilities for sulfur and nitrogen cycling, as well as for resisting and respiring arsenic. One uncharacterized gene associated with a CPR lineage differentiated hypoxic from anoxic zone communities. Overall, microbial communities and geochemical profiles were stable across two sampling dates in the spring and fall of 2019. The blue hole habitat is a natural marine laboratory that provides opportunities for sampling taxa with under-characterized but potentially important roles in redox-stratified microbial processes.
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Affiliation(s)
- N V Patin
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA.
- Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA, USA.
- Ocean Chemistry and Ecosystems Division, Atlantic Oceanographic and Meteorological Laboratory, National Oceanic and Atmospheric Administration, Miami, FL, USA.
- Cooperative Institute for Marine and Atmospheric Studies, Rosenstiel School of Marine and Atmospheric Science, University of Miami, Miami, FL, USA.
- Stationed at Southwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, La Jolla, CA, USA.
| | | | - A Stancil
- Harbor Branch Oceanographic Institute, Florida Atlantic University, Ft. Pierce, FL, USA
| | - M Quinan
- Harbor Branch Oceanographic Institute, Florida Atlantic University, Ft. Pierce, FL, USA
| | - J S Beckler
- Harbor Branch Oceanographic Institute, Florida Atlantic University, Ft. Pierce, FL, USA
| | - E R Hall
- Mote Marine Laboratory, Sarasota, FL, USA
| | - J Culter
- Mote Marine Laboratory, Sarasota, FL, USA
| | - C G Smith
- U.S. Geological Survey, St. Petersburg Coastal and Marine Science Center, St. Petersburg, FL, USA
| | - M Taillefert
- School of Earth & Atmospheric Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - F J Stewart
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
- Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA, USA
- Department of Microbiology & Immunology, Montana State University, Bozeman, MT, USA
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13
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Chen Z, Xia Y, Liu H, Liu H, Xun L. The Mechanisms of Thiosulfate Toxicity against Saccharomyces cerevisiae. Antioxidants (Basel) 2021; 10:antiox10050646. [PMID: 33922196 PMCID: PMC8146336 DOI: 10.3390/antiox10050646] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Revised: 04/09/2021] [Accepted: 04/16/2021] [Indexed: 11/16/2022] Open
Abstract
Elemental sulfur and sulfite have been used to inhibit the growth of yeasts, but thiosulfate has not been reported to be toxic to yeasts. We observed that thiosulfate was more inhibitory than sulfite to Saccharomyces cerevisiae growing in a common yeast medium. At pH < 4, thiosulfate was a source of elemental sulfur and sulfurous acid, and both were highly toxic to the yeast. At pH 6, thiosulfate directly inhibited the electron transport chain in yeast mitochondria, leading to reductions in oxygen consumption, mitochondrial membrane potential and cellular ATP. Although thiosulfate was converted to sulfite and H2S by the mitochondrial rhodanese Rdl1, its toxicity was not due to H2S as the rdl1-deletion mutant that produced significantly less H2S was more sensitive to thiosulfate than the wild type. Evidence suggests that thiosulfate inhibits cytochrome c oxidase of the electron transport chain in yeast mitochondria. Thus, thiosulfate is a potential agent against yeasts.
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Affiliation(s)
- Zhigang Chen
- State Key Laboratory of Microbial Technology, Shandong University, 72 Binhai Road, Qingdao 266237, China; (Z.C.); (Y.X.); (H.L.)
| | - Yongzhen Xia
- State Key Laboratory of Microbial Technology, Shandong University, 72 Binhai Road, Qingdao 266237, China; (Z.C.); (Y.X.); (H.L.)
| | - Huaiwei Liu
- State Key Laboratory of Microbial Technology, Shandong University, 72 Binhai Road, Qingdao 266237, China; (Z.C.); (Y.X.); (H.L.)
| | - Honglei Liu
- State Key Laboratory of Microbial Technology, Shandong University, 72 Binhai Road, Qingdao 266237, China; (Z.C.); (Y.X.); (H.L.)
- Correspondence: (H.L.); (L.X.); Tel.: +86-15966642788 (H.L.); +1-509-335-2787 (L.X.)
| | - Luying Xun
- State Key Laboratory of Microbial Technology, Shandong University, 72 Binhai Road, Qingdao 266237, China; (Z.C.); (Y.X.); (H.L.)
- School of Molecular Biosciences, Washington State University, Pullman, WA 991647520, USA
- Correspondence: (H.L.); (L.X.); Tel.: +86-15966642788 (H.L.); +1-509-335-2787 (L.X.)
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14
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Osman JR, Cardon H, Montagnac G, Picard A, Daniel I. Pressure effects on sulfur-oxidizing activity of Thiobacillus thioparus. ENVIRONMENTAL MICROBIOLOGY REPORTS 2021; 13:169-175. [PMID: 33421329 PMCID: PMC7986089 DOI: 10.1111/1758-2229.12922] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 12/16/2020] [Indexed: 06/12/2023]
Abstract
Carbon capture and storage technologies are crucial for reducing carbon emission from power plants as a response to global climate change. The CarbFix project (Iceland) aims at examining the geochemical response of injected CO2 into subsurface reservoirs. The potential role of the subsurface biosphere has been little investigated up to now. Here, we used Thiobacillus thioparus that became abundant at the CarbFix1 pilot site after injection of CO2 and purified geothermal gases in basaltic aquifer at 400-800 m depth (4-8 MPa). The capacity of T. thioparus to produce sulfate, through oxidation of thiosulfate, was measured by Raman spectroscopy as a function of pressure up to 10 MPa. The results show that the growth and metabolic activity of T. thioparus are influenced by the initial concentration of the electron donor thiosulfate. It grows best at low initial concentration of thiosulfate (here 5 g.l-1 or 31.6 mM) and best oxidizes thiosulfate into sulfate at 0.1 MPa with a yield of 14.7 ± 0.5%. Sulfur oxidation stops at 4.3 ± 0.1 MPa (43 bar). This autotrophic specie can thereby react to CO2 and H2 S injection down to 430 m depth and may contribute to induced biogeochemical cycles during subsurface energy operations.
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Affiliation(s)
- Jorge R. Osman
- Univ Lyon, Université Lyon 1, Ens de Lyon, CNRS, UMR 5276 LGL‐TPEVilleurbanneF‐69622France
| | - Hervé Cardon
- Univ Lyon, Université Lyon 1, Ens de Lyon, CNRS, UMR 5276 LGL‐TPEVilleurbanneF‐69622France
| | - Gilles Montagnac
- Univ Lyon, Université Lyon 1, Ens de Lyon, CNRS, UMR 5276 LGL‐TPEVilleurbanneF‐69622France
| | - Aude Picard
- Univ Lyon, Université Lyon 1, Ens de Lyon, CNRS, UMR 5276 LGL‐TPEVilleurbanneF‐69622France
- School of Life SciencesUniversity of Nevada, Las Vegas, 4505 S. Maryland ParkwayLas VegasNV89154‐4004USA
| | - Isabelle Daniel
- Univ Lyon, Université Lyon 1, Ens de Lyon, CNRS, UMR 5276 LGL‐TPEVilleurbanneF‐69622France
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15
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Wang S, Jiang L, Hu Q, Cui L, Zhu B, Fu X, Lai Q, Shao Z, Yang S. Characterization of Sulfurimonas hydrogeniphila sp. nov., a Novel Bacterium Predominant in Deep-Sea Hydrothermal Vents and Comparative Genomic Analyses of the Genus Sulfurimonas. Front Microbiol 2021; 12:626705. [PMID: 33717015 PMCID: PMC7952632 DOI: 10.3389/fmicb.2021.626705] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 02/11/2021] [Indexed: 11/13/2022] Open
Abstract
Bacteria of the genus Sulfurimonas within the class Campylobacteria are predominant in global deep-sea hydrothermal environments and widespread in global oceans. However, only few bacteria of this group have been isolated, and their adaptations for these extreme environments remain poorly understood. Here, we report a novel mesophilic, hydrogen- and sulfur-oxidizing bacterium, strain NW10T, isolated from a deep-sea sulfide chimney of Northwest Indian Ocean.16S rRNA gene sequence analysis showed that strain NW10T was most closely related to the vent species Sulfurimonas paralvinellae GO25T with 95.8% similarity, but ANI and DDH values between two strains were only 19.20 and 24.70%, respectively, indicating that strain NW10 represents a novel species. Phenotypic characterization showed strain NW10T is an obligate chemolithoautotroph utilizing thiosulfate, sulfide, elemental sulfur, or molecular hydrogen as energy sources, and molecular oxygen, nitrate, or elemental sulfur as electron acceptors. Moreover, hydrogen supported a better growth than reduced sulfur compounds. During thiosulfate oxidation, the strain can produce extracellular sulfur of elemental α-S8 with an unknown mechanism. Polyphasic taxonomy results support that strain NW10T represents a novel species of the genus Sulfurimonas, and named as Sulfurimonas hydrogeniphila sp. nov. Genome analyses revealed its diverse energy metabolisms driving carbon fixation via rTCA cycling, including pathways of sulfur/hydrogen oxidation, coupled oxygen/sulfur respiration and denitrification. Comparative analysis of the 11 available genomes from Sulfurimonas species revealed that vent bacteria, compared to marine non-vent strains, possess unique genes encoding Type V Sqr, Group II, and Coo hydrogenase, and are selectively enriched in genes related to signal transduction and inorganic ion transporters. These phenotypic and genotypic features of vent Sulfurimonas may explain their thriving in hydrothermal environments and help to understand the ecological role of Sulfurimonas bacteria in hydrothermal ecosystems.
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Affiliation(s)
- Shasha Wang
- Department of Bioengineering and Biotechnology, Huaqiao University, Xiamen, China
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
- State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen, China
- Fujian Key Laboratory of Marine Genetic Resources, Xiamen, China
| | - Lijing Jiang
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
- State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen, China
- Fujian Key Laboratory of Marine Genetic Resources, Xiamen, China
| | - Qitao Hu
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
- State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen, China
- Fujian Key Laboratory of Marine Genetic Resources, Xiamen, China
| | - Liang Cui
- Department of Bioengineering and Biotechnology, Huaqiao University, Xiamen, China
| | - Bitong Zhu
- Department of Bioengineering and Biotechnology, Huaqiao University, Xiamen, China
| | - Xiaoteng Fu
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
- State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen, China
- Fujian Key Laboratory of Marine Genetic Resources, Xiamen, China
| | - Qiliang Lai
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
- State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen, China
- Fujian Key Laboratory of Marine Genetic Resources, Xiamen, China
| | - Zongze Shao
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
- State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen, China
- Fujian Key Laboratory of Marine Genetic Resources, Xiamen, China
- Southern Marine Science and Engineering Guangdong Laboratory, Zhuhai, China
| | - Suping Yang
- Department of Bioengineering and Biotechnology, Huaqiao University, Xiamen, China
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16
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Leprich DJ, Flood BE, Schroedl PR, Ricci E, Marlow JJ, Girguis PR, Bailey JV. Sulfur bacteria promote dissolution of authigenic carbonates at marine methane seeps. ISME JOURNAL 2021; 15:2043-2056. [PMID: 33574572 PMCID: PMC8245480 DOI: 10.1038/s41396-021-00903-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 12/21/2020] [Accepted: 01/20/2021] [Indexed: 01/04/2023]
Abstract
Carbonate rocks at marine methane seeps are commonly colonized by sulfur-oxidizing bacteria that co-occur with etch pits that suggest active dissolution. We show that sulfur-oxidizing bacteria are abundant on the surface of an exemplar seep carbonate collected from Del Mar East Methane Seep Field, USA. We then used bioreactors containing aragonite mineral coupons that simulate certain seep conditions to investigate plausible in situ rates of carbonate dissolution associated with sulfur-oxidizing bacteria. Bioreactors inoculated with a sulfur-oxidizing bacterial strain, Celeribacter baekdonensis LH4, growing on aragonite coupons induced dissolution rates in sulfidic, heterotrophic, and abiotic conditions of 1773.97 (±324.35), 152.81 (±123.27), and 272.99 (±249.96) μmol CaCO3 • cm−2 • yr−1, respectively. Steep gradients in pH were also measured within carbonate-attached biofilms using pH-sensitive fluorophores. Together, these results show that the production of acidic microenvironments in biofilms of sulfur-oxidizing bacteria are capable of dissolving carbonate rocks, even under well-buffered marine conditions. Our results support the hypothesis that authigenic carbonate rock dissolution driven by lithotrophic sulfur-oxidation constitutes a previously unknown carbon flux from the rock reservoir to the ocean and atmosphere.
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Affiliation(s)
- Dalton J Leprich
- Department of Earth and Environmental Sciences, University of Minnesota Twin-Cities, Minneapolis, MN, 55455, USA.
| | - Beverly E Flood
- Department of Earth and Environmental Sciences, University of Minnesota Twin-Cities, Minneapolis, MN, 55455, USA
| | - Peter R Schroedl
- Department of Earth and Environmental Sciences, University of Minnesota Twin-Cities, Minneapolis, MN, 55455, USA
| | - Elizabeth Ricci
- Department of Earth and Environmental Sciences, University of Minnesota Twin-Cities, Minneapolis, MN, 55455, USA
| | - Jeffery J Marlow
- Department of Biology, Boston University, Boston, MA, 02215, USA
| | - Peter R Girguis
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Jake V Bailey
- Department of Earth and Environmental Sciences, University of Minnesota Twin-Cities, Minneapolis, MN, 55455, USA.
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17
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Xue Y, Jonassen I, Øvreås L, Taş N. Metagenome-assembled genome distribution and key functionality highlight importance of aerobic metabolism in Svalbard permafrost. FEMS Microbiol Ecol 2020; 96:5821278. [PMID: 32301987 PMCID: PMC7174036 DOI: 10.1093/femsec/fiaa057] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 04/09/2020] [Indexed: 12/17/2022] Open
Abstract
Permafrost underlies a large portion of the land in the Northern Hemisphere. It is proposed to be an extreme habitat and home for cold-adaptive microbial communities. Upon thaw permafrost is predicted to exacerbate increasing global temperature trend, where awakening microbes decompose millennia old carbon stocks. Yet our knowledge on composition, functional potential and variance of permafrost microbiome remains limited. In this study, we conducted a deep comparative metagenomic analysis through a 2 m permafrost core from Svalbard, Norway to determine key permafrost microbiome in this climate sensitive island ecosystem. To do so, we developed comparative metagenomics methods on metagenomic-assembled genomes (MAG). We found that community composition in Svalbard soil horizons shifted markedly with depth: the dominant phylum switched from Acidobacteria and Proteobacteria in top soils (active layer) to Actinobacteria, Bacteroidetes, Chloroflexi and Proteobacteria in permafrost layers. Key metabolic potential propagated through permafrost depths revealed aerobic respiration and soil organic matter decomposition as key metabolic traits. We also found that Svalbard MAGs were enriched in genes involved in regulation of ammonium, sulfur and phosphate. Here, we provide a new perspective on how permafrost microbiome is shaped to acquire resources in competitive and limited resource conditions of deep Svalbard soils.
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Affiliation(s)
- Yaxin Xue
- Computational Biology Unit, Department of Informatics, University of Bergen,Thormøhlensgt 55 N-5008, Bergen, Norway
| | - Inge Jonassen
- Computational Biology Unit, Department of Informatics, University of Bergen,Thormøhlensgt 55 N-5008, Bergen, Norway
| | - Lise Øvreås
- Department of Biological Sciences, University of Bergen, Thormøhlensgt 53 N-5020, Bergen, Norway.,University Center in Svalbard, UNIS, N-9171, Longyearbyen, Norway
| | - Neslihan Taş
- Ecology Department, Earth and Environmental Sciences Area, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA.,Environmental Genomics and Systems Biology, Biosciences Area, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
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18
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Zhang J, Liu R, Xi S, Cai R, Zhang X, Sun C. A novel bacterial thiosulfate oxidation pathway provides a new clue about the formation of zero-valent sulfur in deep sea. ISME JOURNAL 2020; 14:2261-2274. [PMID: 32457501 PMCID: PMC7608252 DOI: 10.1038/s41396-020-0684-5] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 05/06/2020] [Accepted: 05/12/2020] [Indexed: 11/09/2022]
Abstract
Zero-valent sulfur (ZVS) has been shown to be a major sulfur intermediate in the deep-sea cold seep of the South China Sea based on our previous work, however, the microbial contribution to the formation of ZVS in cold seep has remained unclear. Here, we describe a novel thiosulfate oxidation pathway discovered in the deep-sea cold seep bacterium Erythrobacter flavus 21–3, which provides a new clue about the formation of ZVS. Electronic microscopy, energy-dispersive, and Raman spectra were used to confirm that E. flavus 21–3 effectively converts thiosulfate to ZVS. We next used a combined proteomic and genetic method to identify thiosulfate dehydrogenase (TsdA) and thiosulfohydrolase (SoxB) playing key roles in the conversion of thiosulfate to ZVS. Stoichiometric results of different sulfur intermediates further clarify the function of TsdA in converting thiosulfate to tetrathionate (−O3S–S–S–SO3−), SoxB in liberating sulfone from tetrathionate to form ZVS and sulfur dioxygenases (SdoA/SdoB) in oxidizing ZVS to sulfite under some conditions. Notably, homologs of TsdA, SoxB, and SdoA/SdoB widely exist across the bacteria including in Erythrobacter species derived from different environments. This strongly indicates that this novel thiosulfate oxidation pathway might be frequently used by microbes and plays an important role in the biogeochemical sulfur cycle in nature.
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Affiliation(s)
- Jing Zhang
- CAS Key Laboratory of Experimental Marine Biology & Center of Deep Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,College of Earth Science, University of Chinese Academy of Sciences, Beijing, China.,Center of Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Rui Liu
- CAS Key Laboratory of Experimental Marine Biology & Center of Deep Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Center of Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Shichuan Xi
- College of Earth Science, University of Chinese Academy of Sciences, Beijing, China.,Center of Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China.,CAS Key Laboratory of Marine Geology and Environment & Center of Deep Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | - Ruining Cai
- CAS Key Laboratory of Experimental Marine Biology & Center of Deep Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,College of Earth Science, University of Chinese Academy of Sciences, Beijing, China.,Center of Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Xin Zhang
- Center of Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China.,CAS Key Laboratory of Marine Geology and Environment & Center of Deep Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | - Chaomin Sun
- CAS Key Laboratory of Experimental Marine Biology & Center of Deep Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China. .,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China. .,Center of Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China.
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19
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Camacho D, Frazao R, Fouillen A, Nanci A, Lang BF, Apte SC, Baron C, Warren LA. New Insights Into Acidithiobacillus thiooxidans Sulfur Metabolism Through Coupled Gene Expression, Solution Chemistry, Microscopy, and Spectroscopy Analyses. Front Microbiol 2020; 11:411. [PMID: 32231653 PMCID: PMC7082400 DOI: 10.3389/fmicb.2020.00411] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Accepted: 02/27/2020] [Indexed: 01/23/2023] Open
Abstract
Here, we experimentally expand understanding of the reactions and enzymes involved in Acidithiobacillus thiooxidans ATCC 19377 S0 andS 2 O 3 2 - metabolism by developing models that integrate gene expression analyzed by RNA-Seq, solution sulfur speciation, electron microscopy and spectroscopy. The A. thiooxidansS 2 O 3 2 - metabolism model involves the conversion ofS 2 O 3 2 - to SO 4 2 - , S0 andS 4 O 6 2 - , mediated by the sulfur oxidase complex (Sox), tetrathionate hydrolase (TetH), sulfide quinone reductase (Sqr), and heterodisulfate reductase (Hdr) proteins. These same proteins, with the addition of rhodanese (Rhd), were identified to convert S0 to SO 3 2 - ,S 2 O 3 2 - and polythionates in the A. thiooxidans S0 metabolism model. Our combined results shed light onto the important role specifically of TetH inS 2 O 3 2 - metabolism. Also, we show that activity of Hdr proteins rather than Sdo are likely associated with S0 oxidation. Finally, our data suggest that formation of intracellularS 2 O 3 2 - is a critical step in S0 metabolism, and that recycling of internally generated SO 3 2 - occurs, through comproportionating reactions that result inS 2 O 3 2 - . Electron microscopy and spectroscopy confirmed intracellular production and storage of S0 during growth on both S0 andS 2 O 3 2 - substrates.
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Affiliation(s)
- David Camacho
- School of Geography and Earth Science, Faculty of Science, McMaster University, Hamilton, ON, Canada
| | - Rodolfo Frazao
- Department of Biochemistry and Molecular Medicine, Faculty of Medicine, Université de Montréal, Montreal, QC, Canada
| | - Aurélien Fouillen
- Department of Biochemistry and Molecular Medicine, Faculty of Medicine, Université de Montréal, Montreal, QC, Canada
- Laboratory for the Study of Calcified Tissues and Biomaterials, Faculty of Dentistry, Université de Montréal, Montreal, QC, Canada
| | - Antonio Nanci
- Department of Biochemistry and Molecular Medicine, Faculty of Medicine, Université de Montréal, Montreal, QC, Canada
- Laboratory for the Study of Calcified Tissues and Biomaterials, Faculty of Dentistry, Université de Montréal, Montreal, QC, Canada
| | - B. Franz Lang
- Department of Biochemistry and Molecular Medicine, Faculty of Medicine, Université de Montréal, Montreal, QC, Canada
| | - Simon C. Apte
- CSIRO, Land and Water, Lucas Heights, NSW, Australia
| | - Christian Baron
- Department of Biochemistry and Molecular Medicine, Faculty of Medicine, Université de Montréal, Montreal, QC, Canada
| | - Lesley A. Warren
- School of Geography and Earth Science, Faculty of Science, McMaster University, Hamilton, ON, Canada
- Department of Civil and Mineral Engineering, Faculty of Applied Science and Engineering, University of Toronto, Toronto, ON, Canada
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20
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Magnuson E, Mykytczuk NC, Pellerin A, Goordial J, Twine SM, Wing B, Foote SJ, Fulton K, Whyte LG. Thiomicrorhabdus
streamers and sulfur cycling in perennial hypersaline cold springs in the Canadian high Arctic. Environ Microbiol 2020; 23:3384-3400. [DOI: 10.1111/1462-2920.14916] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Revised: 12/10/2019] [Accepted: 01/08/2020] [Indexed: 11/29/2022]
Affiliation(s)
- Elisse Magnuson
- Natural Resource Sciences McGill University Montreal QC Canada
| | | | - Andre Pellerin
- Centre for Geomicrobiology Aarhus University Aarhus Denmark
| | - Jacqueline Goordial
- Natural Resource Sciences McGill University Montreal QC Canada
- School of Environmental Sciences University of Guelph Guelph, ON Canada
| | - Susan M. Twine
- Institute for Biological Sciences National Research Council Ottawa Ontario
| | - Boswell Wing
- Earth and Planetary Sciences McGill University Montreal QC Canada
| | - Simon J. Foote
- Institute for Biological Sciences National Research Council Ottawa Ontario
| | - Kelly Fulton
- Institute for Biological Sciences National Research Council Ottawa Ontario
| | - Lyle G. Whyte
- Natural Resource Sciences McGill University Montreal QC Canada
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21
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Cron B, Henri P, Chan CS, Macalady JL, Cosmidis J. Elemental Sulfur Formation by Sulfuricurvum kujiense Is Mediated by Extracellular Organic Compounds. Front Microbiol 2019; 10:2710. [PMID: 31827465 PMCID: PMC6890823 DOI: 10.3389/fmicb.2019.02710] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Accepted: 11/08/2019] [Indexed: 11/13/2022] Open
Abstract
Elemental sulfur [S(0)] is a central and ecologically important intermediate in the sulfur cycle, which can be used by a wide diversity of microorganisms that gain energy from its oxidation, reduction, or disproportionation. S(0) is formed by oxidation of reduced sulfur species, which can be chemically or microbially mediated. A variety of sulfur-oxidizing bacteria can biomineralize S(0), either intracellularly or extracellularly. The details and mechanisms of extracellular S(0) formation by bacteria have been in particular understudied so far. An important question in this respect is how extracellular S(0) minerals can be formed and remain stable in the environment outside of their thermodynamic stability domain. It was recently discovered that S(0) minerals could be formed and stabilized by oxidizing sulfide in the presence of dissolved organic compounds, a process called S(0) organomineralization. S(0) particles formed through this mechanism possess specific signatures such as morphologies that differ from that of their inorganically precipitated counterparts, encapsulation within an organic envelope, and metastable crystal structures (presence of the monoclinic β- and γ-S8 allotropes). Here, we investigated S(0) formation by the chemolithoautotrophic sulfur-oxidizing and nitrate-reducing bacterium Sulfuricurvum kujiense (Epsilonproteobacteria). We performed a thorough characterization of the S(0) minerals produced extracellularly in cultures of this microorganism, and showed that they present all the specific signatures (morphology, association with organics, and crystal structures) of organomineralized S(0). Using "spent medium" experiments, we furthermore demonstrated that soluble extracellular compounds produced by S. kujiense are necessary to form and stabilize S(0) minerals outside of the cells. This study provides the first experimental evidence of the importance of organomineralization in microbial S(0) formation. The prevalence of organomineralization in extracellular S(0) precipitation by other sulfur bacteria remains to be investigated, and the biological role of this mechanism is still unclear. However, we propose that sulfur-oxidizing bacteria could use soluble organics to stabilize stores of bioavailable S(0) outside the cells.
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Affiliation(s)
- Brandi Cron
- Department of Geosciences, The Pennsylvania State University, University Park, PA, United States
| | - Pauline Henri
- Department of Earth Sciences, University of Delaware, Newark, DE, United States
| | - Clara S Chan
- Department of Earth Sciences, University of Delaware, Newark, DE, United States
| | - Jennifer L Macalady
- Department of Geosciences, The Pennsylvania State University, University Park, PA, United States
| | - Julie Cosmidis
- Department of Geosciences, The Pennsylvania State University, University Park, PA, United States
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22
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Rameez MJ, Pyne P, Mandal S, Chatterjee S, Alam M, Bhattacharya S, Mondal N, Sarkar J, Ghosh W. Two pathways for thiosulfate oxidation in the alphaproteobacterial chemolithotroph Paracoccus thiocyanatus SST. Microbiol Res 2019; 230:126345. [PMID: 31585234 DOI: 10.1016/j.micres.2019.126345] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 09/08/2019] [Accepted: 09/21/2019] [Indexed: 02/02/2023]
Abstract
Chemolithotrophic bacteria oxidize various sulfur species for energy and electrons, thereby operationalizing biogeochemical sulfur cycles in nature. The best-studied pathway of bacterial sulfur-chemolithotrophy involves direct oxidation of thiosulfate (S2O32-) to sulfate (SO42-) without any free intermediate. This pathway mediated by SoxXAYZBCD is apparently the exclusive mechanism of thiosulfate oxidation in facultatively chemolithotrophic alphaproteobacteria. Here we explore the molecular mechanisms of sulfur oxidation in the thiosulfate- and tetrathionate(S4O62-)-oxidizing alphaproteobacterium Paracoccus thiocyanatus SST, and compare them with the prototypical Sox process of Paracoccus pantotrophus. Our results reveal a unique case where an alphaproteobacterium has Sox as its secondary pathway of thiosulfate oxidation converting ∼10% of the thiosulfate supplied, whilst ∼90% of the substrate is oxidized via a pathway that produces tetrathionate as an intermediate. Sulfur oxidation kinetics of a deletion mutant showed that thiosulfate-to-tetrathionate conversion, in SST, is catalyzed by a thiosulfate dehydrogenase (TsdA) homolog that has far-higher substrate-affinity than the Sox system of this bacterium, which in turn is also less efficient than the P. pantotrophus Sox. Deletion of soxB abolished sulfate-formation from thiosulfate/tetrathionate, while thiosulfate-to-tetrathionate conversion remained unperturbed. Physiological studies revealed the involvement of glutathione in SST tetrathionate oxidation. However, zero impact of the insertional mutation of a thiol dehydrotransferase (thdT) homolog, together with the absence of sulfite as an intermediate, indicated that SST tetrathionate oxidation is mechanistically novel, and distinct from its betaproteobacterial counterpart mediated by glutathione, ThdT, SoxBCD and sulfite:acceptor oxidoreductase. The present findings highlight extensive functional diversification of sulfur-oxidizing enzymes across phylogenetically close, as well as distant, bacteria.
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Affiliation(s)
- Moidu Jameela Rameez
- Department of Microbiology, Bose Institute, P-1/12 CIT Scheme VIIM, Kolkata, 700054, India
| | - Prosenjit Pyne
- Department of Microbiology, Bose Institute, P-1/12 CIT Scheme VIIM, Kolkata, 700054, India
| | - Subhrangshu Mandal
- Department of Microbiology, Bose Institute, P-1/12 CIT Scheme VIIM, Kolkata, 700054, India
| | - Sumit Chatterjee
- Department of Microbiology, Bose Institute, P-1/12 CIT Scheme VIIM, Kolkata, 700054, India
| | - Masrure Alam
- Department of Microbiology, Bose Institute, P-1/12 CIT Scheme VIIM, Kolkata, 700054, India
| | | | - Nibendu Mondal
- Department of Microbiology, Bose Institute, P-1/12 CIT Scheme VIIM, Kolkata, 700054, India
| | - Jagannath Sarkar
- Department of Microbiology, Bose Institute, P-1/12 CIT Scheme VIIM, Kolkata, 700054, India
| | - Wriddhiman Ghosh
- Department of Microbiology, Bose Institute, P-1/12 CIT Scheme VIIM, Kolkata, 700054, India.
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23
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Houghton JL, Foustoukos DI, Fike DA. The effect of O 2 and pressure on thiosulfate oxidation by Thiomicrospira thermophila. GEOBIOLOGY 2019; 17:564-576. [PMID: 31180189 DOI: 10.1111/gbi.12352] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Revised: 05/07/2019] [Accepted: 05/15/2019] [Indexed: 06/09/2023]
Abstract
Microbial sulfur cycling in marine sediments often occurs in environments characterized by transient chemical gradients that affect both the availability of nutrients and the activity of microbes. High turnover rates of intermediate valence sulfur compounds and the intermittent availability of oxygen in these systems greatly impact the activity of sulfur-oxidizing micro-organisms in particular. In this study, the thiosulfate-oxidizing hydrothermal vent bacterium Thiomicrospira thermophila strain EPR85 was grown in continuous culture at a range of dissolved oxygen concentrations (0.04-1.9 mM) and high pressure (5-10 MPa) in medium buffered at pH 8. Thiosulfate oxidation under these conditions produced tetrathionate, sulfate, and elemental sulfur, in contrast to previous closed-system experiments at ambient pressure during which thiosulfate was quantitatively oxidized to sulfate. The maximum observed specific growth rate at 5 MPa pressure under unlimited O2 was 0.25 hr-1 . This is comparable to the μmax (0.28 hr-1 ) observed at low pH (<6) at ambient pressure when T. thermophila produces the same mix of sulfur species. The half-saturation constant for O2 ( KO2 ) estimated from this study was 0.2 mM (at a cell density of 105 cells/ml) and was robust at all pressures tested (0.4-10 MPa), consistent with piezotolerant behavior of this strain. The cell-specific KO2 was determined to be 1.5 pmol O2 /cell. The concentrations of products formed were correlated with oxygen availability, with tetrathionate production in excess of sulfate production at all pressure conditions tested. This study provides evidence for transient sulfur storage during times when substrate concentration exceeds cell-specific KO2 and subsequent consumption when oxygen dropped below that threshold. These results may be common among sulfur oxidizers in a variety of environments (e.g., deep marine sediments to photosynthetic microbial mats).
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Affiliation(s)
- Jennifer L Houghton
- Department of Earth and Planetary Sciences, Washington University, St. Louis, Missouri
| | - Dionysis I Foustoukos
- Geophysical Laboratory, Carnegie Institution of Washington, Washington, District of Columbia
| | - David A Fike
- Department of Earth and Planetary Sciences, Washington University, St. Louis, Missouri
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24
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Patwardhan S, Foustoukos DI, Giovannelli D, Yücel M, Vetriani C. Ecological Succession of Sulfur-Oxidizing Epsilon- and Gammaproteobacteria During Colonization of a Shallow-Water Gas Vent. Front Microbiol 2018; 9:2970. [PMID: 30574130 PMCID: PMC6291522 DOI: 10.3389/fmicb.2018.02970] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2018] [Accepted: 11/18/2018] [Indexed: 02/01/2023] Open
Abstract
In this study, we integrated geochemical measurements, microbial diversity surveys and physiological characterization of laboratory strains to investigate substrate-attached filamentous microbial biofilms at Tor Caldara, a shallow-water gas vent in the Tyrrhenian Sea. At this site, the venting gases are mainly composed of CO2 and H2S and the temperature at the emissions is the same as that of the surrounding water. To investigate the composition of the total and active fraction of the Tor Caldara biofilm communities, we collected established and newly formed filaments and we sequenced the 16S rRNA genes (DNA) and the 16S rRNA transcripts (cDNA). Chemoautotrophic sulfur-oxidizing members of the Gammaproteobacteria (predominantly Thiotrichales) dominate the active fraction of the established microbial filaments, while Epsilonproteobacteria (predominantly Sulfurovum spp.) are more prevalent in the young filaments. This indicates a succession of the two communities, possibly in response to age, sulfide and oxygen concentrations. Growth experiments with representative laboratory strains in sulfide gradient medium revealed that Sulfurovum riftiae (Epsilonproteobacteria) grew closer to the sulfide source than Thiomicrospira sp. (Gammaproteobacteria, Thiotrichales). Overall, our findings show that sulfur-oxidizing Epsilonproteobacteria are the dominant pioneer colonizers of the Tor Caldara biofilm communities and that Gammaproteobacteria become prevalent once the community is established. This succession pattern appears to be driven - among other factors - by the adaptation of Epsilon- and Gammaproteobacteria to different sulfide concentrations.
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Affiliation(s)
- Sushmita Patwardhan
- Department of Marine and Coastal Sciences, Rutgers University, New Brunswick, NJ, United States
| | - Dionysis I Foustoukos
- Geophysical Laboratory, Carnegie Institution of Washington, Washington, DC, United States
| | - Donato Giovannelli
- Department of Marine and Coastal Sciences, Rutgers University, New Brunswick, NJ, United States.,Institute of Marine Science, National Research Council, Ancona, Italy.,Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, Japan
| | - Mustafa Yücel
- Institute of Marine Sciences, Middle East Technical University, Mersin, Turkey
| | - Costantino Vetriani
- Department of Marine and Coastal Sciences, Rutgers University, New Brunswick, NJ, United States.,Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ, United States
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25
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Jiang L, Lyu J, Shao Z. Sulfur Metabolism of Hydrogenovibrio thermophilus Strain S5 and Its Adaptations to Deep-Sea Hydrothermal Vent Environment. Front Microbiol 2017; 8:2513. [PMID: 29312214 PMCID: PMC5733100 DOI: 10.3389/fmicb.2017.02513] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Accepted: 12/04/2017] [Indexed: 11/13/2022] Open
Abstract
Hydrogenovibrio bacteria are ubiquitous in global deep-sea hydrothermal vents. However, their adaptations enabling survival in these harsh environments are not well understood. In this study, we characterized the physiology and metabolic mechanisms of Hydrogenovibrio thermophilus strain S5, which was first isolated from an active hydrothermal vent chimney on the Southwest Indian Ridge. Physiological characterizations showed that it is a microaerobic chemolithomixotroph that can utilize sulfide, thiosulfate, elemental sulfur, tetrathionate, thiocyanate or hydrogen as energy sources and molecular oxygen as the sole electron acceptor. During thiosulfate oxidation, the strain produced extracellular sulfur globules 0.7–6.0 μm in diameter that were mainly composed of elemental sulfur and carbon. Some organic substrates including amino acids, tryptone, yeast extract, casamino acids, casein, acetate, formate, citrate, propionate, tartrate, succinate, glucose and fructose can also serve as carbon sources, but growth is weaker than under CO2 conditions, indicating that strain S5 prefers to be chemolithoautotrophic. None of the tested organic carbons could function as energy sources. Growth tests under various conditions confirmed its adaption to a mesophilic mixing zone of hydrothermal vents in which vent fluid was mixed with cold seawater, preferring moderate temperatures (optimal 37°C), alkaline pH (optimal pH 8.0), microaerobic conditions (optimal 4% O2), and reduced sulfur compounds (e.g., sulfide, optimal 100 μM). Comparative genomics showed that strain S5 possesses more complex sulfur metabolism systems than other members of genus Hydrogenovibrio. The genes encoding the intracellular sulfur oxidation protein (DsrEF) and assimilatory sulfate reduction were first reported in the genus Hydrogenovibrio. In summary, the versatility in energy and carbon sources, and unique physiological properties of this bacterium have facilitated its adaptation to deep-sea hydrothermal vent environments.
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Affiliation(s)
- Lijing Jiang
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, State Oceanic Administration, Xiamen, China.,Fujian Key Laboratory of Marine Genetic Resources, Xiamen, China.,Fujian Collaborative Innovation Center of Marine Biological Resources, Xiamen, China
| | - Jie Lyu
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, State Oceanic Administration, Xiamen, China.,Fujian Key Laboratory of Marine Genetic Resources, Xiamen, China.,Fujian Collaborative Innovation Center of Marine Biological Resources, Xiamen, China
| | - Zongze Shao
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, State Oceanic Administration, Xiamen, China.,Fujian Key Laboratory of Marine Genetic Resources, Xiamen, China.,Fujian Collaborative Innovation Center of Marine Biological Resources, Xiamen, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
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26
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Ren Z, Gao H, Elser JJ, Zhao Q. Microbial functional genes elucidate environmental drivers of biofilm metabolism in glacier-fed streams. Sci Rep 2017; 7:12668. [PMID: 28978929 PMCID: PMC5627277 DOI: 10.1038/s41598-017-13086-9] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Accepted: 09/18/2017] [Indexed: 11/09/2022] Open
Abstract
Benthic biofilms in glacier-fed streams harbor diverse microorganisms driving biogeochemical cycles and, consequently, influencing ecosystem-level processes. Benthic biofilms are vulnerable to glacial retreat induced by climate change. To investigate microbial functions of benthic biofilms in glacier-fed streams, we predicted metagenomes from 16s rRNA gene sequence data using PICRUSt and identified functional genes associated with nitrogen and sulfur metabolisms based on KEGG database and explored the relationships between metabolic pathways and abiotic factors in glacier-fed streams in the Tianshan Mountains in Central Asia. Results showed that the distribution of functional genes was mainly associated with glacier area proportion, glacier source proportion, total nitrogen, dissolved organic carbon, and pH. For nitrogen metabolism, the relative abundance of functional genes associated with dissimilatory pathways was higher than those for assimilatory pathways. The relative abundance of functional genes associated with assimilatory sulfate reduction was higher than those involved with the sulfur oxidation system and dissimilatory sulfate reduction. Hydrological factors had more significant correlations with nitrogen metabolism than physicochemical factors and anammox was the most sensitive nitrogen cycling pathway responding to variation of the abiotic environment in these glacial-fed streams. In contrast, sulfur metabolism pathways were not sensitive to variations of abiotic factors in these systems.
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Affiliation(s)
- Ze Ren
- Flathead Lake Biological Station, University of Montana, Polson, MT, 59860, USA
| | - Hongkai Gao
- State Key Laboratory of Cryosheric Sciences, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, China. .,School of Life Sciences, Arizona State University, Tempe, AZ, 85281, USA. .,School of Geography and Planing, Sun Yat-Sen University, Guangzhou, 510275, China.
| | - James J Elser
- Flathead Lake Biological Station, University of Montana, Polson, MT, 59860, USA
| | - Qiudong Zhao
- State Key Laboratory of Cryosheric Sciences, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, China
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27
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Balci N, Brunner B, Turchyn AV. Tetrathionate and Elemental Sulfur Shape the Isotope Composition of Sulfate in Acid Mine Drainage. Front Microbiol 2017; 8:1564. [PMID: 28861071 PMCID: PMC5562728 DOI: 10.3389/fmicb.2017.01564] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2017] [Accepted: 08/02/2017] [Indexed: 11/13/2022] Open
Abstract
Sulfur compounds in intermediate valence states, for example elemental sulfur, thiosulfate, and tetrathionate, are important players in the biogeochemical sulfur cycle. However, key understanding about the pathways of oxidation involving mixed-valance state sulfur species is still missing. Here we report the sulfur and oxygen isotope fractionation effects during the oxidation of tetrathionate (S4O62-) and elemental sulfur (S°) to sulfate in bacterial cultures in acidic conditions. Oxidation of tetrathionate by Acidithiobacillus thiooxidans produced thiosulfate, elemental sulfur and sulfate. Up to 34% of the tetrathionate consumed by the bacteria could not be accounted for in sulfate or other intermediate-valence state sulfur species over the experiments. The oxidation of tetrathionate yielded sulfate that was initially enriched in 34S (ε34SSO4-S4O6) by +7.9‰, followed by a decrease to +1.4‰ over the experiment duration, with an average ε34SSO4-S4O6 of +3.5 ± 0.2‰ after a month of incubation. We attribute this significant sulfur isotope fractionation to enzymatic disproportionation reactions occurring during tetrathionate decomposition, and to the incomplete transformation of tetrathionate into sulfate. The oxygen isotope composition of sulfate (δ18OSO4) from the tetrathionate oxidation experiments indicate that 62% of the oxygen in the formed sulfate was derived from water. The remaining 38% of the oxygen was either inherited from the supplied tetrathionate, or supplied from dissolved atmospheric oxygen (O2). During the oxidation of elemental sulfur, the product sulfate became depleted in 34S between -1.8 and 0‰ relative to the elemental sulfur with an average for ε34SSO4-S0 of -0.9 ± 0.2‰ and all the oxygen atoms in the sulfate derived from water with an average normal oxygen isotope fractionation (ε18OSO4-H2O) of -4.4‰. The differences observed in δ18OSO4 and the sulfur isotope composition of sulfate (δ34SSO4), acid production, and mixed valence state sulfur species generated by the oxidation of the two different substrates suggests a metabolic flexibility in response to sulfur substrate availability. Our results demonstrate that microbial processing of mixed-valence-state sulfur species generates a significant sulfur isotope fractionation in acidic environments and oxidation of mixed-valence state sulfur species may produce sulfate with characteristic sulfur and oxygen isotope signatures. Elemental sulfur and tetrathionate are not only intermediate-valence state sulfur compounds that play a central role in sulfur oxidation pathways, but also key factors in shaping these isotope patterns.
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Affiliation(s)
- Nurgul Balci
- Geomicrobiolog-Biogeochemistry Lab, Department of Geological Engineering, Istanbul Technical UniversityIstanbul, Turkey
| | - Benjamin Brunner
- Department of Biogeochemistry, Max Planck Institute for Marine MicrobiologyBremen, Germany
- Department of Geological Sciences, University of Texas at El PasoEl Paso, TX, United States
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28
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Frisia S, Weyrich LS, Hellstrom J, Borsato A, Golledge NR, Anesio AM, Bajo P, Drysdale RN, Augustinus PC, Rivard C, Cooper A. The influence of Antarctic subglacial volcanism on the global iron cycle during the Last Glacial Maximum. Nat Commun 2017; 8:15425. [PMID: 28598412 PMCID: PMC5472753 DOI: 10.1038/ncomms15425] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Accepted: 03/27/2017] [Indexed: 11/09/2022] Open
Abstract
Marine sediment records suggest that episodes of major atmospheric CO2 drawdown during the last glacial period were linked to iron (Fe) fertilization of subantarctic surface waters. The principal source of this Fe is thought to be dust transported from southern mid-latitude deserts. However, uncertainty exists over contributions to CO2 sequestration from complementary Fe sources, such as the Antarctic ice sheet, due to the difficulty of locating and interrogating suitable archives that have the potential to preserve such information. Here we present petrographic, geochemical and microbial DNA evidence preserved in precisely dated subglacial calcites from close to the East Antarctic Ice-Sheet margin, which together suggest that volcanically-induced drainage of Fe-rich waters during the Last Glacial Maximum could have reached the Southern Ocean. Our results support a significant contribution of Antarctic volcanism to subglacial transport and delivery of nutrients with implications on ocean productivity at peak glacial conditions.
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Affiliation(s)
- Silvia Frisia
- School of Environmental and Life Sciences, The University of Newcastle, Callaghan, New South Wales 2308, Australia
| | - Laura S. Weyrich
- Australian Centre for Ancient DNA (ACAD), The University of Adelaide, Adelaide, South Australia 5005, Australia
| | - John Hellstrom
- School of Earth Sciences, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Andrea Borsato
- School of Environmental and Life Sciences, The University of Newcastle, Callaghan, New South Wales 2308, Australia
| | - Nicholas R. Golledge
- Antarctic Research Centre, Victoria University of Wellington, Wellington 6140, New Zealand
- GNS Science, Avalon, Lower Hut 5011, New Zealand
| | - Alexandre M. Anesio
- Bristol Glaciology Centre, School of Geographical Sciences, University of Bristol, Bristol BS8 1SS, UK
| | - Petra Bajo
- School of Geography, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Russell N. Drysdale
- School of Geography, The University of Melbourne, Parkville, Victoria 3010, Australia
- Environnements, Dynamiques et Territoires de la Montagne, UMR CNRS, Université de Savoie-Mont Blanc, 73376 Le Bourget du Lac, France
| | - Paul C. Augustinus
- School of Environment, The University of Auckland, Private Bag, Auckland 92019, New Zealand
| | - Camille Rivard
- European Synchrotron Radiation Facility, 38000 Grenoble, France
| | - Alan Cooper
- Australian Centre for Ancient DNA (ACAD), The University of Adelaide, Adelaide, South Australia 5005, Australia
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