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Sudo M, Osvatic J, Taylor JD, Dufour SC, Prathep A, Wilkins LGE, Rattei T, Yuen B, Petersen JM. SoxY gene family expansion underpins adaptation to diverse hosts and environments in symbiotic sulfide oxidizers. mSystems 2024; 9:e0113523. [PMID: 38747602 PMCID: PMC11237559 DOI: 10.1128/msystems.01135-23] [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: 10/25/2023] [Accepted: 04/13/2024] [Indexed: 06/19/2024] Open
Abstract
Sulfur-oxidizing bacteria (SOB) have developed distinct ecological strategies to obtain reduced sulfur compounds for growth. These range from specialists that can only use a limited range of reduced sulfur compounds to generalists that can use many different forms as electron donors. Forming intimate symbioses with animal hosts is another highly successful ecological strategy for SOB, as animals, through their behavior and physiology, can enable access to sulfur compounds. Symbioses have evolved multiple times in a range of animal hosts and from several lineages of SOB. They have successfully colonized a wide range of habitats, from seagrass beds to hydrothermal vents, with varying availability of symbiont energy sources. Our extensive analyses of sulfur transformation pathways in 234 genomes of symbiotic and free-living SOB revealed widespread conservation in metabolic pathways for sulfur oxidation in symbionts from different host species and environments, raising the question of how they have adapted to such a wide range of distinct habitats. We discovered a gene family expansion of soxY in these genomes, with up to five distinct copies per genome. Symbionts harboring only the "canonical" soxY were typically ecological "specialists" that are associated with specific host subfamilies or environments (e.g., hydrothermal vents, mangroves). Conversely, symbionts with multiple divergent soxY genes formed versatile associations across diverse hosts in various marine environments. We hypothesize that expansion and diversification of the soxY gene family could be one genomic mechanism supporting the metabolic flexibility of symbiotic SOB enabling them and their hosts to thrive in a range of different and dynamic environments.IMPORTANCESulfur metabolism is thought to be one of the most ancient mechanisms for energy generation in microorganisms. A diverse range of microorganisms today rely on sulfur oxidation for their metabolism. They can be free-living, or they can live in symbiosis with animal hosts, where they power entire ecosystems in the absence of light, such as in the deep sea. In the millions of years since they evolved, sulfur-oxidizing bacteria have adopted several highly successful strategies; some are ecological "specialists," and some are "generalists," but which genetic features underpin these ecological strategies are not well understood. We discovered a gene family that has become expanded in those species that also seem to be "generalists," revealing that duplication, repurposing, and reshuffling existing genes can be a powerful mechanism driving ecological lifestyle shifts.
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Affiliation(s)
- Marta Sudo
- University of Vienna, Centre for Microbiology and Environmental Systems Science, Vienna, Austria
- Doctoral School in Microbiology and Environmental Science, University of Vienna, Vienna, Austria
| | - Jay Osvatic
- Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna, Vienna, Austria
- Department of Laboratory Medicine, Medical University of Vienna, Vienna, Austria
| | - John D. Taylor
- Life Sciences, The Natural History Museum, London, United Kingdom
| | - Suzanne C. Dufour
- Department of Biology, Memorial University of Newfoundland, St. John’s, Newfoundland, Canada
| | - Anchana Prathep
- Department of Biology, Faculty of Science, Prince of Songkla University, HatYai, Thailand
| | - Laetitia G. E. Wilkins
- Eco-Evolutionary Interactions Group, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Thomas Rattei
- University of Vienna, Centre for Microbiology and Environmental Systems Science, Vienna, Austria
| | - Benedict Yuen
- University of Vienna, Centre for Microbiology and Environmental Systems Science, Vienna, Austria
- Eco-Evolutionary Interactions Group, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Jillian M. Petersen
- University of Vienna, Centre for Microbiology and Environmental Systems Science, Vienna, Austria
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2
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Ma WJ, Zhang HM, Ma ZS, You XJ, Wei XY, Li Y, Tian Y. Meta-analyzing the mechanism of pyrogenic biochar strengthens nitrogen removal performance in sulfur-driven autotrophic denitrification system: Evidence from metatranscriptomics. WATER RESEARCH 2024; 253:121296. [PMID: 38367378 DOI: 10.1016/j.watres.2024.121296] [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: 11/21/2023] [Revised: 01/16/2024] [Accepted: 02/08/2024] [Indexed: 02/19/2024]
Abstract
Sulfur-driven autotrophic denitrification (SAD) exhibits significant benefits in treating low carbon/nitrogen wastewater. This study presents an eco-friendly, cost-effective, and highly efficient method for enhancing nitrogen removal performance. The addition of biochar prepared at 300 °C (BC300) notably increased nitrogen removal efficiency by 31.60 %. BC300 concurrently enhanced electron production, the activities of the electron transfer system, and electron acceptors. With BC300, the ratio of NADH/NAD+ rose 2.00±0.11 times compared to without biochar, and the expression of NAD(P)H dehydrogenase genes was markedly up-regulated. In the electron transfer system, BC300 improved the electroactivity of extracellular polymeric substances and the activities of NADH dehydrogenase and complex III in intracellular electron transfer. Subsequently, electrons were directed into denitrification enzymes, where the nar, nir, nor, and nos related genes were highly expressed with BC300 addition. Significantly, BC300 activated the Clp and quorum sensing systems, positively influencing numerous gene expressions and microbial communication. Furthermore, the O%, H%, molar O/C, and aromaticity index in biochar were identified as crucial bioavailable parameters for enhancing nitrogen removal in the SAD process. This study not only confirms the application potential of biochar in SAD, but also advances our comprehension of its underlying mechanisms.
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Affiliation(s)
- Wen-Jie Ma
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education, MOE), School of Environmental Science and Technology, Dalian University of Technology, No.2 Linggong Road, Dalian 116024, PR China
| | - Han-Min Zhang
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education, MOE), School of Environmental Science and Technology, Dalian University of Technology, No.2 Linggong Road, Dalian 116024, PR China.
| | - Zi-Shang Ma
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education, MOE), School of Environmental Science and Technology, Dalian University of Technology, No.2 Linggong Road, Dalian 116024, PR China
| | - Xiu-Jia You
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education, MOE), School of Environmental Science and Technology, Dalian University of Technology, No.2 Linggong Road, Dalian 116024, PR China
| | - Xin-Yue Wei
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education, MOE), School of Environmental Science and Technology, Dalian University of Technology, No.2 Linggong Road, Dalian 116024, PR China
| | - Yue Li
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education, MOE), School of Environmental Science and Technology, Dalian University of Technology, No.2 Linggong Road, Dalian 116024, PR China
| | - Yu Tian
- State Key Laboratory of Urban Water Resource and Environment (SKLUWRE), School of Environment, Harbin Institute of Technology, Harbin 150090, PR China.
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3
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Wang L, Liu J, Li Y, Liu Z, Zhang L, Che H, Cui H, Zhang Y. Elemental sulfur-driven autotrophic denitrification process for effective removal of nitrate in mariculture wastewater: Performance, kinetics and microbial community. CHEMOSPHERE 2023; 337:139354. [PMID: 37394184 DOI: 10.1016/j.chemosphere.2023.139354] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2023] [Revised: 05/29/2023] [Accepted: 06/25/2023] [Indexed: 07/04/2023]
Abstract
To date, there is a lack of systematic investigation on the elemental sulfur-driven autotrophic denitrification (SDAD) process for removing nitrate (NO3--N) from mariculture wastewater deficient in organic carbon sources. Therefore, a packed-bed reactor was established and continuously operated for 230 days to investigate the operation performance, kinetic characteristics and microbial community of SDAD biofilm process. Results indicate that the NO3--N removal efficiencies and rates varied with the operational conditions including HRT (1-4 h), influent concentrations of NO3--N (25-100 mg L-1) and DO (0.2-7.0 mg L-1), and temperature (10oC-30 °C), in the ranges of 51.4%-98.6% and 0.054-0.546 g L-1 d-1, respectively. Limestone could partially neutralize the produced acidity. Small portions of NO3--N were converted to nitrite (<4.5%) and ammonia (<2.8%) in the reactor. Operational conditions also influenced the production of acidity, nitrite and ammonia as well as sulfate. Shortening HRT and increasing influent NO3--N concentration turned the optimal fitting model depicting the NO3--N removal along the reactor from half-order to zero-order. Furthermore, the NO3--N removal was accelerated by a higher temperature and influent NO3--N concentration and a lower HRT and influent DO concentration. Microbial richness, evenness and diversity gradually decreased during the autotrophic denitrifier enrichment cultivation and the reactor start-up and operation. Sulfurimonas constituted the predominate genus and the primary functional bacteria in the reactor. This study highlights the SDAD as a promising way to control the coastal eutrophication associated with mariculture wastewater discharge.
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Affiliation(s)
- Lu Wang
- Laoshan Laboratory, Qingdao, 266237, China
| | - Jun Liu
- Laoshan Laboratory, Qingdao, 266237, China; First Institute of Oceanography, Ministry of Natural Resources, Qingdao, 266061, China
| | - Yongfu Li
- College of Oceanography, Hohai University, Nanjing, 210098, China
| | - Zhihao Liu
- Laoshan Laboratory, Qingdao, 266237, China
| | - Long Zhang
- National Fisheries Technology Extension Center, China Society of Fisheries, Beijing, 100125, China
| | - Hong Che
- Laoshan Laboratory, Qingdao, 266237, China
| | - Hongwu Cui
- Laoshan Laboratory, Qingdao, 266237, China; Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China.
| | - Ying Zhang
- Ocean University of China, Qingdao, 266100, China.
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4
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Gao P, Fan K. Sulfur-oxidizing bacteria (SOB) and sulfate-reducing bacteria (SRB) in oil reservoir and biological control of SRB: a review. Arch Microbiol 2023; 205:162. [PMID: 37010699 DOI: 10.1007/s00203-023-03520-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 03/18/2023] [Accepted: 03/26/2023] [Indexed: 04/04/2023]
Abstract
Sulfur-oxidizing bacteria (SOB) and sulfate-reducing bacteria (SRB) inhabit oilfield production systems. Sulfur oxidation driven by SOB and dissimilatory sulfate reduction driven by SRB play important roles in sulfur cycle of oil reservoirs. More importantly, hydrogen sulfide produced by SRB is an acidic, flammable, and smelly toxic gas associated with reservoir souring, corrosion of oil-production facilities, and personnel safety. Effective control of SRB is urgently needed for the oil industry. This depends on an in-depth understanding of the microbial species that drive sulfur cycle and other related microorganisms in oil reservoir environments. Here, we identified SOB and SRB in produced brines of Qizhong block (Xinjiang Oilfield, China) from metagenome sequencing data based on reported SOB and SRB, reviewed metabolic pathways of sulfur oxidation and dissimilatory sulfate reduction, and ways for SRB control. The existing issues and future research of microbial sulfur cycle and SRB control are also discussed. Knowledge of the distribution of the microbial populations, their metabolic characteristics and interactions can help to develop an effective process to harness these microorganisms for oilfield production.
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Affiliation(s)
- Peike Gao
- College of Life Sciences, Qufu Normal University, Qufu, 273165, Shandong, China.
| | - Keyan Fan
- College of Life Sciences, Qufu Normal University, Qufu, 273165, Shandong, China
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5
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Wang S, Jiang L, Cui L, Alain K, Xie S, Shao Z. Transcriptome Analysis of Cyclooctasulfur Oxidation and Reduction by the Neutrophilic Chemolithoautotrophic Sulfurovum indicum from Deep-Sea Hydrothermal Ecosystems. Antioxidants (Basel) 2023; 12:antiox12030627. [PMID: 36978876 PMCID: PMC10045233 DOI: 10.3390/antiox12030627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 02/28/2023] [Accepted: 03/01/2023] [Indexed: 03/06/2023] Open
Abstract
Chemolithoautotrophic Campylobacterota are widespread and predominant in worldwide hydrothermal vents, and they are key players in the turnover of zero-valence sulfur. However, at present, the mechanism of cyclooctasulfur activation and catabolism in Campylobacterota bacteria is not clearly understood. Here, we investigated these processes in a hydrothermal vent isolate named Sulfurovum indicum ST-419. A transcriptome analysis revealed that multiple genes related to biofilm formation were highly expressed during both sulfur oxidation and reduction. Additionally, biofilms containing cells and EPS coated on sulfur particles were observed by SEM, suggesting that biofilm formation may be involved in S0 activation in Sulfurovum species. Meanwhile, several genes encoding the outer membrane proteins of OprD family were also highly expressed, and among them, gene IMZ28_RS00565 exhibited significantly high expressions by 2.53- and 7.63-fold changes under both conditions, respectively, which may play a role in sulfur uptake. However, other mechanisms could be involved in sulfur activation and uptake, as experiments with dialysis bags showed that direct contact between cells and sulfur particles was not mandatory for sulfur reduction activity, whereas cell growth via sulfur oxidation did require direct contact. This indirect reaction could be ascribed to the role of H2S and/or other thiol-containing compounds, such as cysteine and GSH, which could be produced in the culture medium during sulfur reduction. In the periplasm, the sulfur-oxidation-multienzyme complexes soxABXY1Z1 and soxCDY2Z2 are likely responsible for thiosulfate oxidation and S0 oxidation, respectively. In addition, among the four psr gene clusters encoding polysulfide reductases, only psrA3B3C3 was significantly upregulated under the sulfur reduction condition, implying its essential role in sulfur reduction. These results expand our understanding of the interactions of Campylobacterota with the zero-valence sulfur and their adaptability to deep-sea hydrothermal environments.
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Affiliation(s)
- Shasha Wang
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China
- State Key Laboratory Breeding Base of Marine Genetic Resources, Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen 361005, China
- Sino-French Laboratory of Deep-Sea Microbiology (MicrobSea), Xiamen 361005, China
| | - Lijing Jiang
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China
- State Key Laboratory Breeding Base of Marine Genetic Resources, Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen 361005, China
- Sino-French Laboratory of Deep-Sea Microbiology (MicrobSea), Xiamen 361005, China
- Correspondence: (L.J.); (Z.S.)
| | - Liang Cui
- Department of Bioengineering and Biotechnology, Huaqiao University, Xiamen 361021, China
| | - Karine Alain
- CNRS, Université Brest, Ifremer, Unité Biologie et Ecologie des Ecosystèmes Marins Profonds BEEP, UMR 6197, IRP 1211 MicrobSea, IUEM, Rue Dumont d’Urville, F-29280 Plouzané, France
| | - Shaobin Xie
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China
- State Key Laboratory Breeding Base of Marine Genetic Resources, Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen 361005, China
- Sino-French Laboratory of Deep-Sea Microbiology (MicrobSea), Xiamen 361005, China
| | - Zongze Shao
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China
- State Key Laboratory Breeding Base of Marine Genetic Resources, Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen 361005, China
- Sino-French Laboratory of Deep-Sea Microbiology (MicrobSea), Xiamen 361005, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai 519000, China
- Correspondence: (L.J.); (Z.S.)
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6
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Napieralski SA, Fang Y, Marcon V, Forsythe B, Brantley SL, Xu H, Roden EE. Microbial chemolithotrophic oxidation of pyrite in a subsurface shale weathering environment: Geologic considerations and potential mechanisms. GEOBIOLOGY 2022; 20:271-291. [PMID: 34633148 DOI: 10.1111/gbi.12474] [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: 02/18/2021] [Revised: 09/02/2021] [Accepted: 09/27/2021] [Indexed: 06/13/2023]
Abstract
Oxidative weathering of pyrite plays an important role in the biogeochemical cycling of Fe and S in terrestrial environments. While the mechanism and occurrence of biologically accelerated pyrite oxidation under acidic conditions are well established, much less is known about microbially mediated pyrite oxidation at circumneutral pH. Recent work (Percak-Dennett et al., 2017, Geobiology, 15, 690) has demonstrated the ability of aerobic chemolithotrophic microorganisms to accelerate pyrite oxidation at circumneutral pH and proposed two mechanistic models by which this phenomenon might occur. Here, we assess the potential relevance of aerobic microbially catalyzed circumneutral pH pyrite oxidation in relation to subsurface shale weathering at Susquehanna Shale Hills Critical Zone Observatory (SSHCZO) in Pennsylvania, USA. Specimen pyrite mixed with native shale was incubated in groundwater for 3 months at the inferred depth of in situ pyrite oxidation. The colonized materials were used as an inoculum for pyrite-oxidizing enrichment cultures. Microbial activity accelerated the release of sulfate across all conditions. 16S rRNA gene sequencing and metagenomic analysis revealed the dominance of a putative chemolithoautotrophic sulfur-oxidizing bacterium from the genus Thiobacillus in the enrichment cultures. Previously proposed models for aerobic microbial pyrite oxidation were assessed in terms of physical constraints, enrichment culture geochemistry, and metagenomic analysis. Although we conclude that subsurface pyrite oxidation at SSCHZO is largely abiotic, this work nonetheless yields new insight into the potential pathways by which aerobic microorganisms may accelerate pyrite oxidation at circumneutral pH. We propose a new "direct sulfur oxidation" pathway, whereby sulfhydryl-bearing outer membrane proteins mediate oxidation of pyrite surfaces through a persulfide intermediate, analogous to previously proposed mechanisms for direct microbial oxidation of elemental sulfur. The action of this and other direct microbial pyrite oxidation pathways have major implications for controls on pyrite weathering rates in circumneutral pH sedimentary environments where pore throat sizes permit widespread access of microorganisms to pyrite surfaces.
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Affiliation(s)
| | - Yihang Fang
- Department of Geoscience, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Virginia Marcon
- Earth and Environmental Systems Institute, University Park, Pennsylvania, USA
- The Department of Geosciences, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Brandon Forsythe
- Earth and Environmental Systems Institute, University Park, Pennsylvania, USA
| | - Susan L Brantley
- Earth and Environmental Systems Institute, University Park, Pennsylvania, USA
- The Department of Geosciences, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Huifang Xu
- Department of Geoscience, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Eric E Roden
- Department of Geoscience, University of Wisconsin-Madison, Madison, Wisconsin, USA
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7
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Henkel JV, Schulz-Vogt HN, Dellwig O, Pollehne F, Schott T, Meeske C, Beier S, Jürgens K. Biological manganese-dependent sulfide oxidation impacts elemental gradients in redox-stratified systems: indications from the Black Sea water column. THE ISME JOURNAL 2022; 16:1523-1533. [PMID: 35124702 PMCID: PMC9122950 DOI: 10.1038/s41396-022-01200-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 01/06/2022] [Accepted: 01/19/2022] [Indexed: 11/25/2022]
Abstract
The reduction of manganese oxide with sulfide in aquatic redox-stratified systems was previously considered to be mainly chemical, but recent isolation of the Black Sea isolate Candidatus Sulfurimonas marisnigri strain SoZ1 suggests an important role for biological catalyzation. Here we provide evidence from laboratory experiments, field data, and modeling that the latter process has a strong impact on redox zonation in the Black Sea. High relative abundances of Sulfurimonas spp. across the redoxcline in the central western gyre of the Black Sea coincided with the high-level expression of both the sulfide:quinone oxidoreductase gene (sqr, up to 93% expressed by Sulfurimonas spp.) and other sulfur oxidation genes. The cell-specific rate of manganese-coupled sulfide oxidation by Ca. S. marisnigri SoZ1 determined experimentally was combined with the in situ abundance of Sulfurimonas spp. in a one-dimensional numerical model to calculate the vertical sulfide distribution. Abiotic sulfide oxidation was too slow to counterbalance the sulfide flux from euxinic water. We conclude that microbially catalyzed Mn-dependent sulfide oxidation influences the element cycles of Mn, S, C, and N and therefore the prevalence of other functional groups of prokaryotes (e.g., anammox bacteria) in a sulfide-free, anoxic redox zone.
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Affiliation(s)
- J V Henkel
- Leibniz Institute for Baltic Sea Research Warnemünde, Seestrasse 15, Rostock, 18119, Germany.
| | - H N Schulz-Vogt
- Leibniz Institute for Baltic Sea Research Warnemünde, Seestrasse 15, Rostock, 18119, Germany
| | - O Dellwig
- Leibniz Institute for Baltic Sea Research Warnemünde, Seestrasse 15, Rostock, 18119, Germany
| | - F Pollehne
- Leibniz Institute for Baltic Sea Research Warnemünde, Seestrasse 15, Rostock, 18119, Germany
| | - T Schott
- Leibniz Institute for Baltic Sea Research Warnemünde, Seestrasse 15, Rostock, 18119, Germany
| | - C Meeske
- Leibniz Institute for Baltic Sea Research Warnemünde, Seestrasse 15, Rostock, 18119, Germany
| | - S Beier
- Leibniz Institute for Baltic Sea Research Warnemünde, Seestrasse 15, Rostock, 18119, Germany
| | - K Jürgens
- Leibniz Institute for Baltic Sea Research Warnemünde, Seestrasse 15, Rostock, 18119, Germany
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8
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Flood BE, Louw DC, Van der Plas AK, Bailey JV. Giant sulfur bacteria (Beggiatoaceae) from sediments underlying the Benguela upwelling system host diverse microbiomes. PLoS One 2021; 16:e0258124. [PMID: 34818329 PMCID: PMC8612568 DOI: 10.1371/journal.pone.0258124] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 09/20/2021] [Indexed: 01/04/2023] Open
Abstract
Due to their lithotrophic metabolisms, morphological complexity and conspicuous appearance, members of the Beggiatoaceae have been extensively studied for more than 100 years. These bacteria are known to be primarily sulfur-oxidizing autotrophs that commonly occur in dense mats at redox interfaces. Their large size and the presence of a mucous sheath allows these cells to serve as sites of attachment for communities of other microorganisms. But little is known about their individual niche preferences and attached microbiomes, particularly in marine environments, due to a paucity of cultivars and their prevalence in habitats that are difficult to access and study. Therefore, in this study, we compare Beggiatoaceae strain composition, community composition, and geochemical profiles collected from sulfidic sediments at four marine stations off the coast of Namibia. To elucidate community members that were directly attached and enriched in both filamentous Beggiatoaceae, namely Ca. Marithioploca spp. and Ca. Maribeggiatoa spp., as well as non-filamentous Beggiatoaceae, Ca. Thiomargarita spp., the Beggiatoaceae were pooled by morphotype for community analysis. The Beggiatoaceae samples collected from a highly sulfidic site were enriched in strains of sulfur-oxidizing Campylobacterota, that may promote a more hospitable setting for the Beggiatoaceae, which are known to have a lower tolerance for high sulfide to oxygen ratios. We found just a few host-specific associations with the motile filamentous morphotypes. Conversely, we detected 123 host specific enrichments with non-motile chain forming Beggiatoaceae. Potential metabolisms of the enriched strains include fermentation of host sheath material, syntrophic exchange of H2 and acetate, inorganic sulfur metabolism, and nitrite oxidation. Surprisingly, we did not detect any enrichments of anaerobic ammonium oxidizing bacteria as previously suggested and postulate that less well-studied anaerobic ammonium oxidation pathways may be occurring instead.
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Affiliation(s)
- Beverly E. Flood
- Department of Earth and Environmental Sciences, University of Minnesota, Twin Cities, Minnesota, United States of America
- * E-mail:
| | - Deon C. Louw
- National Marine Information and Research Centre, Swakopmund, Namibia
| | | | - Jake V. Bailey
- Department of Earth and Environmental Sciences, University of Minnesota, Twin Cities, Minnesota, United States of America
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Genus-Specific Carbon Fixation Activity Measurements Reveal Distinct Responses to Oxygen Among Hydrothermal Vent Campylobacteria. Appl Environ Microbiol 2021; 88:e0208321. [PMID: 34788061 DOI: 10.1128/aem.02083-21] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Molecular surveys of low temperature deep-sea hydrothermal vent fluids have shown that Campylobacteria (prev. Epsilonproteobacteria) often dominate the microbial community and that three genera - Arcobacter, Sulfurimonas and Sulfurovum - frequently coexist. In this study, we used replicated radiocarbon incubations of deep-sea hydrothermal fluids to investigate activity of each genus under three experimental conditions. To quantify genus-specific radiocarbon incorporation, we used newly designed oligonucleotide probes for Arcobacter, Sulfurimonas, and Sulfurovum to quantify their activity using catalyzed-reporter deposition fluorescence in-situ hybridization (CARD-FISH) combined with fluorescence-activated cell sorting. All three genera actively fixed CO2 in short-term (∼ 20 h) incubations, but responded differently to the additions of nitrate and oxygen. Oxygen additions had the largest effect on community composition, and caused a pronounced shift in community composition at the amplicon sequence variant (ASV) level after only 20 h of incubation. The effect of oxygen on carbon fixation rates appeared to depend on the initial starting community. The presented results support the hypothesis that these chemoautotrophic genera possess functionally redundant core metabolic capabilities, but also reveal finer-scale differences in growth likely reflecting adaptation of physiologically-distinct phylotypes to varying oxygen concentrations in situ. Overall, our study provides new insights into how oxygen controls community composition and total chemoautotrophic activity, and underscores how quickly deep-sea vent microbial communities respond to disturbances. Importance: Sulfidic environments worldwide are often dominated by sulfur-oxidizing, carbon-fixing Campylobacteria. Environmental factors associated with this group's dominance are now understood, but far less is known about the ecology and physiology of members of subgroups of chemoautotrophic Campylobacteria. In this study, we used a novel method to differentiate the genus-specific chemoautotrophic activity of three subtypes of Campylobacteria. In combination with evidence from microscopic counts, chemical consumption/production during incubations, and DNA-based measurements, our data show that oxygen concentration affects both community composition and chemoautotrophic function in situ. These results help us better understand factors controlling microbial diversity at deep-sea hydrothermal vents, and provide first-order insights into the ecophysiological differences between these distinct microbial taxa.
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10
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van Vliet DM, von Meijenfeldt FB, Dutilh BE, Villanueva L, Sinninghe Damsté JS, Stams AJ, Sánchez‐Andrea I. The bacterial sulfur cycle in expanding dysoxic and euxinic marine waters. Environ Microbiol 2021; 23:2834-2857. [PMID: 33000514 PMCID: PMC8359478 DOI: 10.1111/1462-2920.15265] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 09/03/2020] [Accepted: 09/28/2020] [Indexed: 01/29/2023]
Abstract
Dysoxic marine waters (DMW, < 1 μM oxygen) are currently expanding in volume in the oceans, which has biogeochemical, ecological and societal consequences on a global scale. In these environments, distinct bacteria drive an active sulfur cycle, which has only recently been recognized for open-ocean DMW. This review summarizes the current knowledge on these sulfur-cycling bacteria. Critical bottlenecks and questions for future research are specifically addressed. Sulfate-reducing bacteria (SRB) are core members of DMW. However, their roles are not entirely clear, and they remain largely uncultured. We found support for their remarkable diversity and taxonomic novelty by mining metagenome-assembled genomes from the Black Sea as model ecosystem. We highlight recent insights into the metabolism of key sulfur-oxidizing SUP05 and Sulfurimonas bacteria, and discuss the probable involvement of uncultivated SAR324 and BS-GSO2 bacteria in sulfur oxidation. Uncultivated Marinimicrobia bacteria with a presumed organoheterotrophic metabolism are abundant in DMW. Like SRB, they may use specific molybdoenzymes to conserve energy from the oxidation, reduction or disproportionation of sulfur cycle intermediates such as S0 and thiosulfate, produced from the oxidation of sulfide. We expect that tailored sampling methods and a renewed focus on cultivation will yield deeper insight into sulfur-cycling bacteria in DMW.
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Affiliation(s)
- Daan M. van Vliet
- Laboratory of MicrobiologyWageningen University and Research, Stippeneng 4, 6708WEWageningenNetherlands
| | | | - Bas E. Dutilh
- Theoretical Biology and Bioinformatics, Science for LifeUtrecht University, Padualaan 8, 3584 CHUtrechtNetherlands
| | - Laura Villanueva
- Department of Marine Microbiology and BiogeochemistryRoyal Netherlands Institute for Sea Research (NIOZ), Utrecht University, Landsdiep 4, 1797 SZ, 'tHorntje (Texel)Netherlands
| | - Jaap S. Sinninghe Damsté
- Department of Marine Microbiology and BiogeochemistryRoyal Netherlands Institute for Sea Research (NIOZ), Utrecht University, Landsdiep 4, 1797 SZ, 'tHorntje (Texel)Netherlands
- Department of Earth Sciences, Faculty of GeosciencesUtrecht University, Princetonlaan 8A, 3584 CBUtrechtNetherlands
| | - Alfons J.M. Stams
- Laboratory of MicrobiologyWageningen University and Research, Stippeneng 4, 6708WEWageningenNetherlands
- Centre of Biological EngineeringUniversity of Minho, Campus de Gualtar, 4710‐057BragaPortugal
| | - Irene Sánchez‐Andrea
- Laboratory of MicrobiologyWageningen University and Research, Stippeneng 4, 6708WEWageningenNetherlands
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11
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Liu ZX, Yang MH, Mu TZ, Liu JL, Zhang X, Xing JM. Transcriptional response of Thialkalivibrio versutus D301 to different sulfur sources and identification of the sulfur oxidation pathways. J Biotechnol 2021; 329:160-169. [PMID: 33592216 DOI: 10.1016/j.jbiotec.2021.02.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 01/26/2021] [Accepted: 02/07/2021] [Indexed: 12/27/2022]
Abstract
The genus Thialkalivibrio plays an essential role in the biological desulfurization system. However, to date, the sulfur oxidation pathways of Thialkalivibrio are not clearly understood. Here, we performed transcriptomic analysis on Thialkalivibrio versutus D301 with either thiosulfate or chemical sulfur as the sulfur source to understand it. The results show that T. versutus D301 has a higher growth rate and sulfur oxidation activity when thiosulfate is utilized. The use of chemical sulfur as sulfur source leads to decreased expression of genes involved in carbon metabolism, ribosome synthesis and oxidative phosphorylation in T. versutus D301. Potentially due to the adsorption to sulfur particles, the genes related to flagellum assembly and motivation are significantly induced in T. versutus D301 in the presence of chemical sulfur. In the periplasm, both thiosulfate and polysulfide from the chemical sulfur are oxidized to sulfate via the similar truncated Sox system (SoxAXYZB). Then, part of polysulfide reached to cytoplasm through an unidentified route is oxidized to sulfite by the Dsr-like system. The sulfite in the cytoplasm is further catalyzed to sulfate by SoxB or SoeABC. Overall, the difference in the oxidation rates of D301 can be mainly attributed to the bioavailability of the two sulfur sources, not the sulfur oxidation pathways.
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Affiliation(s)
- Zhi-Xia Liu
- CAS Key Laboratory of Green Process and Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, 100190, China; School of Biology and Engineering, Hebei University of Science and Technology, Shijiazhuang, Hebei Province 050018, China
| | - Mao-Hua Yang
- CAS Key Laboratory of Green Process and Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, 100190, China.
| | - Ting-Zhen Mu
- CAS Key Laboratory of Green Process and Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, 100190, China
| | - Jin-Long Liu
- School of Biology and Engineering, Hebei University of Science and Technology, Shijiazhuang, Hebei Province 050018, China.
| | - Xiang Zhang
- Institute of Agro-Food Science and Technology, Shandong Academy of Agricultural Sciences, 250100, China
| | - Jian-Min Xing
- CAS Key Laboratory of Green Process and Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, 100190, China.
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12
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Wang YN, Kai Y, Wang L, Tsang YF, Fu X, Hu J, Xie Y. Key internal factors leading to the variability in CO 2 fixation efficiency of different sulfur-oxidizing bacteria during autotrophic cultivation. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2020; 271:110957. [PMID: 32579519 DOI: 10.1016/j.jenvman.2020.110957] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Revised: 06/07/2020] [Accepted: 06/11/2020] [Indexed: 06/11/2023]
Abstract
Variability in the apparent CO2 fixation yield of four aerobic sulfur-oxidizing bacteria (Halothiobacillus neapolitanus DSM 15147, Thiobacillus thioparus DSM 505, Thiomonas intermedia DSM 18155, and Starkeya novella DSM 506) in autotrophic culturing was studied, and mutual effects of key intrinsic factors on CO2 fixation were explored. DSM 15147 and DSM 505 exhibited much higher CO2 fixation yields than DSM 18155 and DSM 506. The differences in CO2 fixation yield were determined not only by cbb gene transcription, but also by cell synthesis rate, which was determined by rRNA gene copy number; the rRNA gene copy number had a more significant effect than cbb gene transcription on the apparent CO2 fixation yield. Moreover, accumulation of EDOC was observed in all four strains during chemoautotrophic cultivation, and the proportion of EDOC accounting for total fixed organic carbon (TOC; EDOC/TOC ratio) was much higher in DSM 18155 and DSM 506 than in DSM 15147 and DSM 505. The accumulation of EDOC led to a significant decrease in the cbb gene transcription efficiency during cultivation, and a further feedback inhibitory effect on CO2 fixation.
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Affiliation(s)
- Ya-Nan Wang
- Qingdao Solid Waste Pollution Control and Resource Engineering Research Center, College of Environmental and Municipal Engineering, Qingdao University of Technology, Qingdao, 266033, PR China
| | - Yan Kai
- Qingdao Solid Waste Pollution Control and Resource Engineering Research Center, College of Environmental and Municipal Engineering, Qingdao University of Technology, Qingdao, 266033, PR China
| | - Lei Wang
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai, 200092, China; Research Institute for Shanghai Pollution Control and Ecological Security, 200092, China.
| | - Yiu Fai Tsang
- Department of Science and Environmental Studies, The Education University of Hong Kong, Tai Po, New Territories, SAR, Hong Kong, China.
| | - Xiaohua Fu
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai, 200092, China; Research Institute for Shanghai Pollution Control and Ecological Security, 200092, China
| | - Jiajun Hu
- Shanghai Key Laboratory of Bio-Energy Crops, School of Life Sciences, Shanghai University, Shanghai, 200444, China
| | - Yanjun Xie
- Qingdao Solid Waste Pollution Control and Resource Engineering Research Center, College of Environmental and Municipal Engineering, Qingdao University of Technology, Qingdao, 266033, PR China
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13
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Xu X, Zhang R, Jiang H, Yang F. Sulphur-based autotrophic denitrification of wastewater obtained following graphite production: Long-term performance, microbial communities involved, and functional gene analysis. BIORESOURCE TECHNOLOGY 2020; 306:123117. [PMID: 32169509 DOI: 10.1016/j.biortech.2020.123117] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 02/27/2020] [Accepted: 02/29/2020] [Indexed: 06/10/2023]
Abstract
Sulphur-based autotrophic denitrification is an energy-efficient NO3--N removal process; it does not require carbon and may potentially replace traditional denitrification processes. This process was used to treat graphite production-derived wastewater and achieved almost complete removal of NO3--N (concentration in effluent: 5.2 mg/L; concentration in influent: 606 mg/L) at a salinity of 15 g/L with a 30 h hydraulic retention time. A unique microbial community was established, in which the abundance of Thiobacillus increased with the increase of the NO3--N concentration and salinity. Metagenomic analysis revealed that the denitrification metabolic pathway in the bioreactor was active. It also revealed the increased activation of nhaH, a gene encoding Na+/H+ antiporters; proA, proB, and proC, genes encoding proline; and Trk and Kdp systems during the treatment of graphite production-derived wastewater to maintain cell function, providing valuable information about utilizing the sulphur-based autotrophic denitrification process to treat graphite production-derived wastewater.
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Affiliation(s)
- Xiaochen Xu
- Key Laboratory of Industrial Ecology and Environmental Engineering (MOE), School of Environment Science and Technology, Dalian University of Technology, Linggong Road 2, Dalian 116024, China.
| | - Rao Zhang
- Key Laboratory of Industrial Ecology and Environmental Engineering (MOE), School of Environment Science and Technology, Dalian University of Technology, Linggong Road 2, Dalian 116024, China
| | - Hongbin Jiang
- Key Laboratory of Industrial Ecology and Environmental Engineering (MOE), School of Environment Science and Technology, Dalian University of Technology, Linggong Road 2, Dalian 116024, China
| | - Fenglin Yang
- Key Laboratory of Industrial Ecology and Environmental Engineering (MOE), School of Environment Science and Technology, Dalian University of Technology, Linggong Road 2, Dalian 116024, China
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14
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Transcriptomic Response of Nitrosomonas europaea Transitioned from Ammonia- to Oxygen-Limited Steady-State Growth. mSystems 2020; 5:5/1/e00562-19. [PMID: 31937676 PMCID: PMC6967387 DOI: 10.1128/msystems.00562-19] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Nitrification is a ubiquitous microbially mediated process in the environment and an essential process in engineered systems such as wastewater and drinking water treatment plants. However, nitrification also contributes to fertilizer loss from agricultural environments, increasing the eutrophication of downstream aquatic ecosystems, and produces the greenhouse gas nitrous oxide. As ammonia-oxidizing bacteria are the most dominant ammonia-oxidizing microbes in fertilized agricultural soils, understanding their responses to a variety of environmental conditions is essential for curbing the negative environmental effects of nitrification. Notably, oxygen limitation has been reported to significantly increase nitric oxide and nitrous oxide production during nitrification. Here, we investigate the physiology of the best-characterized ammonia-oxidizing bacterium, Nitrosomonas europaea, growing under oxygen-limited conditions. Ammonia-oxidizing microorganisms perform the first step of nitrification, the oxidation of ammonia to nitrite. The bacterium Nitrosomonas europaea is the best-characterized ammonia oxidizer to date. Exposure to hypoxic conditions has a profound effect on the physiology of N. europaea, e.g., by inducing nitrifier denitrification, resulting in increased nitric and nitrous oxide production. This metabolic shift is of major significance in agricultural soils, as it contributes to fertilizer loss and global climate change. Previous studies investigating the effect of oxygen limitation on N. europaea have focused on the transcriptional regulation of genes involved in nitrification and nitrifier denitrification. Here, we combine steady-state cultivation with whole-genome transcriptomics to investigate the overall effect of oxygen limitation on N. europaea. Under oxygen-limited conditions, growth yield was reduced and ammonia-to-nitrite conversion was not stoichiometric, suggesting the production of nitrogenous gases. However, the transcription of the principal nitric oxide reductase (cNOR) did not change significantly during oxygen-limited growth, while the transcription of the nitrite reductase-encoding gene (nirK) was significantly lower. In contrast, both heme-copper-containing cytochrome c oxidases encoded by N. europaea were upregulated during oxygen-limited growth. Particularly striking was the significant increase in transcription of the B-type heme-copper oxidase, proposed to function as a nitric oxide reductase (sNOR) in ammonia-oxidizing bacteria. In the context of previous physiological studies, as well as the evolutionary placement of N. europaea’s sNOR with regard to other heme-copper oxidases, these results suggest sNOR may function as a high-affinity terminal oxidase in N. europaea and other ammonia-oxidizing bacteria. IMPORTANCE Nitrification is a ubiquitous microbially mediated process in the environment and an essential process in engineered systems such as wastewater and drinking water treatment plants. However, nitrification also contributes to fertilizer loss from agricultural environments, increasing the eutrophication of downstream aquatic ecosystems, and produces the greenhouse gas nitrous oxide. As ammonia-oxidizing bacteria are the most dominant ammonia-oxidizing microbes in fertilized agricultural soils, understanding their responses to a variety of environmental conditions is essential for curbing the negative environmental effects of nitrification. Notably, oxygen limitation has been reported to significantly increase nitric oxide and nitrous oxide production during nitrification. Here, we investigate the physiology of the best-characterized ammonia-oxidizing bacterium, Nitrosomonas europaea, growing under oxygen-limited conditions.
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15
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Lahme S, Callbeck CM, Eland LE, Wipat A, Enning D, Head IM, Hubert CR. Comparison of sulfide‐oxidizing
Sulfurimonas
strains reveals a new mode of thiosulfate formation in subsurface environments. Environ Microbiol 2020; 22:1784-1800. [DOI: 10.1111/1462-2920.14894] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 12/02/2019] [Accepted: 12/11/2019] [Indexed: 01/18/2023]
Affiliation(s)
- Sven Lahme
- School of Natural and Environmental SciencesNewcastle University Devonshire Building (3rd floor) Newcastle upon Tyne NE1 7RU UK
| | | | - Lucy E. Eland
- School of ComputingNewcastle University Newcastle upon Tyne UK
| | - Anil Wipat
- School of ComputingNewcastle University Newcastle upon Tyne UK
| | - Dennis Enning
- ExxonMobil Upstream Research Company Spring Texas USA
| | - Ian M. Head
- School of Natural and Environmental SciencesNewcastle University Devonshire Building (3rd floor) Newcastle upon Tyne NE1 7RU UK
| | - Casey R.J. Hubert
- School of Natural and Environmental SciencesNewcastle University Devonshire Building (3rd floor) Newcastle upon Tyne NE1 7RU UK
- Department of Biological SciencesUniversity of Calgary Calgary Canada
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