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Sahai N, LaRowe D, Senko JM. Bioenergetics of iron snow fueling life on Europa. Proc Natl Acad Sci U S A 2024; 121:e2316452121. [PMID: 38621125 PMCID: PMC11047109 DOI: 10.1073/pnas.2316452121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 03/11/2024] [Indexed: 04/17/2024] Open
Abstract
The main sources of redox gradients supporting high-productivity life in the Europan and other icy ocean world oceans were proposed to be photolytically derived oxidants, such as reactive oxygen species (ROS) from the icy shell, and reductants (Fe(II), S(-II), CH4, H2) from bottom waters reacting with a (ultra)mafic seafloor. Important roadblocks to maintaining life, however, are that the degree of ocean mixing to combine redox species is unknown, and ROS damage biomolecules. Here, we envisage a unique solution using an acid mine drainage (AMD)-filled pit lakes analog system for the Europan ocean, which previous models predicted to be acidic. We hypothesize that surface-generated ROS oxidize dissolved Fe(II) resulting in Fe(III) (hydr)oxide precipitates, that settle to the seafloor as "iron snow." The iron snow provides a respiratory substrate for anaerobic microorganisms ("breathing iron"), and limits harmful ROS exposure since they are now neutralized at the ice-water interface. Based on this scenario, we calculated Gibbs energies and maximal biomass productivities of various anaerobic metabolisms for a range of pH, temperatures, and H2 fluxes. Productivity by iron reducers was greater for most environmental conditions considered, whereas sulfate reducers and methanogens were more favored at high pH. Participation of Fe in the metabolic redox processes is largely neglected in most models of Europan biogeochemistry. Our model overcomes important conceptual roadblocks to life in icy ocean worlds and broadens the potential metabolic diversity, thus increasing total primary productivity, the diversity and volume of habitable environmental niches and, ultimately, the probability of biosignature detection.
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Affiliation(s)
- Nita Sahai
- School of Polymer Science and Polymer Engineering, The University of Akron, Akron, OH44325
- Department of Geosciences, The University of Akron, Akron, OH44325
- Department of Biology, The University of Akron, Akron, OH44325
- Integrated Biosciences Program, The University of Akron, Akron, OH44325
| | - Doug LaRowe
- Department of Earth Sciences, University of Southern California, Los Angeles, CA90089
| | - John M. Senko
- Department of Geosciences, The University of Akron, Akron, OH44325
- Department of Biology, The University of Akron, Akron, OH44325
- Integrated Biosciences Program, The University of Akron, Akron, OH44325
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Demin KA, Prazdnova EV, Minkina TM, Gorovtsov AV. Sulfate-reducing bacteria unearthed: ecological functions of the diverse prokaryotic group in terrestrial environments. Appl Environ Microbiol 2024; 90:e0139023. [PMID: 38551370 PMCID: PMC11022543 DOI: 10.1128/aem.01390-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/18/2024] Open
Abstract
Sulfate-reducing prokaryotes (SRPs) are essential microorganisms that play crucial roles in various ecological processes. Even though SRPs have been studied for over a century, there are still gaps in our understanding of their biology. In the past two decades, a significant amount of data on SRP ecology has been accumulated. This review aims to consolidate that information, focusing on SRPs in soils, their relation to the rare biosphere, uncultured sulfate reducers, and their interactions with other organisms in terrestrial ecosystems. SRPs in soils form part of the rare biosphere and contribute to various processes as a low-density population. The data reveal a diverse range of sulfate-reducing taxa intricately involved in terrestrial carbon and sulfur cycles. While some taxa like Desulfitobacterium and Desulfosporosinus are well studied, others are more enigmatic. For example, members of the Acidobacteriota phylum appear to hold significant importance for the terrestrial sulfur cycle. Many aspects of SRP ecology remain mysterious, including sulfate reduction in different bacterial phyla, interactions with bacteria and fungi in soils, and the existence of soil sulfate-reducing archaea. Utilizing metagenomic, metatranscriptomic, and culture-dependent approaches will help uncover the diversity, functional potential, and adaptations of SRPs in the global environment.
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Rolland C, Burzan N, Leupin OX, Boylan AA, Frutschi M, Wang S, Jacquemin N, Bernier-Latmani R. Microbial hydrogen sinks in the sand-bentonite backfill material for the deep geological disposal of radioactive waste. Front Microbiol 2024; 15:1359677. [PMID: 38690357 PMCID: PMC11060177 DOI: 10.3389/fmicb.2024.1359677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Accepted: 03/19/2024] [Indexed: 05/02/2024] Open
Abstract
The activity of subsurface microorganisms can be harnessed for engineering projects. For instance, the Swiss radioactive waste repository design can take advantage of indigenous microorganisms to tackle the issue of a hydrogen gas (H2) phase pressure build-up. After repository closure, it is expected that anoxic steel corrosion of waste canisters will lead to an H2 accumulation. This occurrence should be avoided to preclude damage to the structural integrity of the host rock. In the Swiss design, the repository access galleries will be back-filled, and the choice of this material provides an opportunity to select conditions for the microbially-mediated removal of excess gas. Here, we investigate the microbial sinks for H2. Four reactors containing an 80/20 (w/w) mixture of quartz sand and Wyoming bentonite were supplied with natural sulfate-rich Opalinus Clay rock porewater and with pure H2 gas for up to 108 days. Within 14 days, a decrease in the sulfate concentration was observed, indicating the activity of the sulfate-reducing bacteria detected in the reactor, e.g., from Desulfocurvibacter genus. Additionally, starting at day 28, methane was detected in the gas phase, suggesting the activity of methanogens present in the solid phase, such as the Methanosarcina genus. This work evidences the development, under in-situ relevant conditions, of a backfill microbiome capable of consuming H2 and demonstrates its potential to contribute positively to the long-term safety of a radioactive waste repository.
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Affiliation(s)
- Camille Rolland
- Environmental Microbiology Laboratory, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Niels Burzan
- Environmental Microbiology Laboratory, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Olivier X. Leupin
- National Cooperative for the Disposal of Radioactive Waste, Wettingen, Switzerland
| | - Aislinn A. Boylan
- Environmental Microbiology Laboratory, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Manon Frutschi
- Environmental Microbiology Laboratory, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Simiao Wang
- Environmental Microbiology Laboratory, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Nicolas Jacquemin
- Environmental Microbiology Laboratory, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Rizlan Bernier-Latmani
- Environmental Microbiology Laboratory, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
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Kato M, Sugitani R, Niiyama S, Kamiya T, Matsuura N. Microbial diversity in shallow-sea sediment from Tsukumo Bay, Japan, determined by 16S rRNA gene amplicon sequencing. Microbiol Resour Announc 2024; 13:e0106123. [PMID: 38497622 PMCID: PMC11008114 DOI: 10.1128/mra.01061-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 03/06/2024] [Indexed: 03/19/2024] Open
Abstract
Information about the microbiota in marine sediments is important because the microbiota and their activities in sediments affect the surrounding marine environment. To evaluate the microbial diversity, we performed 16S rRNA gene amplicon sequencing on sediment samples from 19 stations in Tsukumo Bay, the northern area of Noto Peninsula, Japan.
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Affiliation(s)
- Moe Kato
- Faculty of Geosciences and Civil Engineering, Kanazawa University, Ishikawa, Japan
| | - Reina Sugitani
- School of Geosciences and Civil Engineering, Kanazawa University, Ishikawa, Japan
| | - Sota Niiyama
- Faculty of Geosciences and Civil Engineering, Kanazawa University, Ishikawa, Japan
- Okinawa Prefectural Museum and Art Museum, Okinawa, Japan
| | - Takahiro Kamiya
- Faculty of Geosciences and Civil Engineering, Kanazawa University, Ishikawa, Japan
| | - Norihisa Matsuura
- Faculty of Geosciences and Civil Engineering, Kanazawa University, Ishikawa, Japan
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Lindsay MR, D’Angelo T, Munson-McGee JH, Saidi-Mehrabad A, Devlin M, McGonigle J, Goodell E, Herring M, Lubelczyk LC, Mascena C, Brown JM, Gavelis G, Liu J, Yousavich DJ, Hamilton-Brehm SD, Hedlund BP, Lang S, Treude T, Poulton NJ, Stepanauskas R, Moser DP, Emerson D, Orcutt BN. Species-resolved, single-cell respiration rates reveal dominance of sulfate reduction in a deep continental subsurface ecosystem. Proc Natl Acad Sci U S A 2024; 121:e2309636121. [PMID: 38573964 PMCID: PMC11009646 DOI: 10.1073/pnas.2309636121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 02/23/2024] [Indexed: 04/06/2024] Open
Abstract
Rates of microbial processes are fundamental to understanding the significance of microbial impacts on environmental chemical cycling. However, it is often difficult to quantify rates or to link processes to specific taxa or individual cells, especially in environments where there are few cultured representatives with known physiology. Here, we describe the use of the redox-enzyme-sensitive molecular probe RedoxSensor™ Green to measure rates of anaerobic electron transfer physiology (i.e., sulfate reduction and methanogenesis) in individual cells and link those measurements to genomic sequencing of the same single cells. We used this method to investigate microbial activity in hot, anoxic, low-biomass (~103 cells mL-1) groundwater of the Death Valley Regional Flow System, California. Combining this method with electron donor amendment experiments and metatranscriptomics confirmed that the abundant spore formers including Candidatus Desulforudis audaxviator were actively reducing sulfate in this environment, most likely with acetate and hydrogen as electron donors. Using this approach, we measured environmental sulfate reduction rates at 0.14 to 26.9 fmol cell-1 h-1. Scaled to volume, this equates to a bulk environmental rate of ~103 pmol sulfate L-1 d-1, similar to potential rates determined with radiotracer methods. Despite methane in the system, there was no evidence for active microbial methanogenesis at the time of sampling. Overall, this method is a powerful tool for estimating species-resolved, single-cell rates of anaerobic metabolism in low-biomass environments while simultaneously linking genomes to phenomes at the single-cell level. We reveal active elemental cycling conducted by several species, with a large portion attributable to Ca. Desulforudis audaxviator.
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Affiliation(s)
| | | | | | | | - Molly Devlin
- Division of Hydrologic Sciences, Desert Research Institute, Las Vegas, NV89119
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV89154
| | - Julia McGonigle
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME04544
| | - Elizabeth Goodell
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME04544
- Department of Geology, Oberlin College, Oberlin, OH44074
| | - Melissa Herring
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME04544
- Department of Marine and Environmental Sciences, Northeastern University, Boston, MA02115
| | | | | | - Julia M. Brown
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME04544
| | - Greg Gavelis
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME04544
| | - Jiarui Liu
- Department of Earth, Planetary, and Space Sciences, University of California Los Angeles, Los Angeles, CA90095
| | - D. J. Yousavich
- Department of Earth, Planetary, and Space Sciences, University of California Los Angeles, Los Angeles, CA90095
| | | | - Brian P. Hedlund
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV89154
| | - Susan Lang
- School of the Earth, Ocean and Environment, University of South Carolina, Columbia, SC29208
| | - Tina Treude
- Department of Earth, Planetary, and Space Sciences, University of California Los Angeles, Los Angeles, CA90095
- Department of Atmospheric and Oceanic Sciences, University of California Los Angeles, Los Angeles, CA90095
| | | | | | - Duane P. Moser
- Division of Hydrologic Sciences, Desert Research Institute, Las Vegas, NV89119
| | - David Emerson
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME04544
| | - Beth N. Orcutt
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME04544
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Gao S, Chen Z, Zhu S, Yu J, Wen X. Enhancement of medium-chain fatty acids production from sludge anaerobic fermentation liquid under moderate sulfate reduction. J Environ Manage 2024; 354:120459. [PMID: 38402788 DOI: 10.1016/j.jenvman.2024.120459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 01/10/2024] [Accepted: 02/20/2024] [Indexed: 02/27/2024]
Abstract
In recent years, there has been a marked increase in the production of excess sludge. Chain-elongation (CE) fermentation presents a promising approach for carbon resource recovery from sludge, enabling the transformation of carbon into medium-chain fatty acids (MCFAs). However, the impact of sulfate, commonly presents in sludge, on the CE process remains largely unexplored. In this study, batch tests for CE process of sludge anaerobic fermentation liquid (SAFL) under different SCOD/SO42- ratios were performed. The moderate sulfate reduction under the optimum SCOD/SO42- of 20:1 enhanced the n-caproate production, giving the maximum n-caproate concentration, selectivity and production rate of 5.49 g COD/L, 21.4% and 4.87 g COD/L/d, respectively. The excessive sulfate reduction under SCOD/SO42- ≤ 5 completely inhibited the CE process, resulting in almost no n-caproate generation. The variations in n-caproate production under different conditions of SCOD/SO42- were all well fitted with the modified Gompertz kinetic model. Alcaligenes and Ruminococcaceae_UCG-014 were the dominant genus-level biomarkers under moderate sulfate reduction (SCOD/SO42- = 20), which enhanced the n-caproate production by increasing the generation of acetyl-CoA and the hydrolysis of difficult biodegradable substances in SAFL. The findings presented in this work elucidate a strategy and provide a theoretical framework for the further enhancement of MCFAs production from excess sludge.
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Affiliation(s)
- Shan Gao
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China
| | - Zhan Chen
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China.
| | - Shihui Zhu
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China
| | - Jinlan Yu
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China
| | - Xianghua Wen
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China.
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Claypool DJ, Zhang YG, Xia Y, Sun J. Conditional Vitamin D Receptor Deletion Induces Fungal and Archaeal Dysbiosis and Altered Metabolites. Metabolites 2024; 14:32. [PMID: 38248835 PMCID: PMC10819266 DOI: 10.3390/metabo14010032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2023] [Revised: 12/24/2023] [Accepted: 12/28/2023] [Indexed: 01/23/2024] Open
Abstract
A vitamin D receptor (VDR) deficiency leads to the dysbiosis of intestinal bacteria and is associated with various diseases, including cancer, infections, and inflammatory bowel disease. However, the impact of a VDR deficiency on fungi and archaea is unknown. We conditionally deleted the VDR in Paneth cells (VDRΔPC), intestinal epithelial cells (VDRΔIEC), or myeloid cells (VDRΔLyz) in mice and collected feces for shotgun metagenomic sequencing and untargeted metabolomics. We found that fungi were significantly altered in each knockout (KO) group compared to the VDRLoxp control. The VDRΔLyz mice had the most altered fungi species (three depleted and seven enriched), followed by the VDRΔPC mice (six depleted and two enriched), and the VDRΔIEC mice (one depleted and one enriched). The methanogen Methanofollis liminatans was enriched in the VDRΔPC and VDRΔLyz mice and two further archaeal species (Thermococcus piezophilus and Sulfolobus acidocaldarius) were enriched in the VDRΔLyz mice compared to the Loxp group. Significant correlations existed among altered fungi, archaea, bacteria, and viruses in the KO mice. Functional metagenomics showed changes in several biologic functions, including decreased sulfate reduction and increased biosynthesis of cobalamin (vitamin B12) in VDRΔLyz mice relative to VDRLoxp mice. Fecal metabolites were analyzed to examine the involvement of sulfate reduction and other pathways. In conclusion, a VDR deficiency caused the formation of altered fungi and archaea in a tissue- and sex-dependent manner. These results provide a foundation about the impact of a host factor (e.g., VDR deficiency) on fungi and archaea. It opens the door for further studies to determine how mycobiome and cross-kingdom interactions in the microbiome community and metabolites contribute to the risk of certain diseases.
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Affiliation(s)
- Duncan J. Claypool
- Department of Medicine, University of Illinois Chicago, Chicago, IL 60612, USA; (D.J.C.); (Y.-G.Z.)
- Department of Bioengineering, University of Illinois Chicago, Chicago, IL 60607, USA
| | - Yong-Guo Zhang
- Department of Medicine, University of Illinois Chicago, Chicago, IL 60612, USA; (D.J.C.); (Y.-G.Z.)
| | - Yinglin Xia
- Department of Medicine, University of Illinois Chicago, Chicago, IL 60612, USA; (D.J.C.); (Y.-G.Z.)
- Jesse Brown VA Medical Center, Chicago, IL 60612, USA
| | - Jun Sun
- Department of Medicine, University of Illinois Chicago, Chicago, IL 60612, USA; (D.J.C.); (Y.-G.Z.)
- Department of Bioengineering, University of Illinois Chicago, Chicago, IL 60607, USA
- Jesse Brown VA Medical Center, Chicago, IL 60612, USA
- Department of Microbiology and Immunology, University of Illinois Chicago, Chicago, IL 60612, USA
- UIC Cancer Center, University of Illinois Chicago, Chicago, IL 60612, USA
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Long M, Zhou C, Zheng X, Rittmann BE. Reduction of Chromate via Biotic and Abiotic Pathways in the Presence of Three Co-contaminating Electron Acceptors. Environ Sci Technol 2023; 57:21190-21199. [PMID: 38051765 DOI: 10.1021/acs.est.3c04812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/07/2023]
Abstract
Bioreduction of Cr(VI) to Cr(III) is a promising technology for removing Cr(VI), but Cr(VI) reduction alone cannot support microbial growth. This study investigated the reduction of Cr(VI) in the presence of three electron acceptors that typically coexist with Cr(VI): NO3-, SO42-, and Fe(III). All three systems could reduce Cr(VI) to Cr(III), but the fate of Cr, its impacts on reduction of the other acceptors, and its impact on the microbial community differed. Although Cr(VI) was continuously removed in the NO3--reduction systems, batch tests showed that denitrification was inhibited primarily through impeding nitrite reduction. The SO42- and Fe(III) reduction systems reduced Cr(VI) using a combination of biotic and abiotic processes. Across all three systems, the abundance of genera capable of reducing Cr(VI) increased following the introduction of Cr(VI). Conversely, the abundance of genera that cannot reduce or resist Cr(VI) decreased, leading to restructuring of the microbial community. Furthermore, the abundance of sulfide oxidizers and Fe(II) oxidizers substantially increased after the introduction of chromate. This study provides fundamental knowledge about how Cr(VI) bioreduction interacts with bioreductions of three other co-contaminating electron acceptors.
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Affiliation(s)
- Min Long
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China
- Biodesign Swette Center for Environmental Biotechnology, Arizona State University, Tempe, Arizona 85287, United States
| | - Chen Zhou
- Biodesign Swette Center for Environmental Biotechnology, Arizona State University, Tempe, Arizona 85287, United States
| | - Xiong Zheng
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China
| | - Bruce E Rittmann
- Biodesign Swette Center for Environmental Biotechnology, Arizona State University, Tempe, Arizona 85287, United States
- School of Sustainable Engineering and the Built Environment, Arizona State University, Tempe, Arizona 85287, United States
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Zhang PX, Yao JF, Liu YL, Zhang WY, Yin XF, Tie BQ. [Effect of Combined Application of an Enterobacter and Sulfur Fertilizer on Cadmium and Arsenic Accumulation in Rice]. Huan Jing Ke Xue 2023; 44:7036-7044. [PMID: 38098426 DOI: 10.13227/j.hjkx.202211110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 12/18/2023]
Abstract
The aim of this study was to explore the effects of different sulfur fertilizers combined with sulfate-reducing bacteria on the accumulation of cadmium and arsenic in rice and the formation of iron plaque under long-term flooding conditions and to provide a reference for the safe production of rice fields polluted by moderate and mild cadmium and arsenic. We adopted a pot experiment, selecting two sulfur fertilizers, sulfur and calcium sulfate, and Enterobacter M5 with sulfate-reducing ability, and designed six treatments of single application and combined application of different sulfur fertilizers and M5. The results showed that the combined application of calcium sulfate and M5(CM5) had the best effect on reducing available cadmium and arsenic in rice rhizosphere soil. The combined application of sulfur fertilizer or M5 could reduce the content of cadmium and inorganic arsenic in early season rice grains by 8%-51% and 42%-61%, respectively, under flooding conditions. The content of cadmium and inorganic arsenic in late rice grains decreased by 81%-92% and 41%-62%, respectively. The treatment of the combined application of sulfur and M5(SM5) and CM5 had the best effect on reducing cadmium and arsenic content in both early and late season rice grains. SM5 and CM5 could promote the adsorption of cadmium and arsenic by iron plaque, and the extracted cadmium and arsenic content of ACA in both treatments was significantly higher than that of CK. The extracted iron content of ACA in the CM5 treatment was also significantly higher than that of CK, which indicates that the combined application of calcium sulfate and M5 would promote the formation of iron plaque. The results showed that the combined application of sulfur fertilizer and M5 was better than single application in reducing the content of cadmium and arsenic in grains, whereas the combined application of calcium sulfate and M5 was the best and most stable method.
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Affiliation(s)
- Pu-Xin Zhang
- College of Resources and Environment, Hunan Agricultural University, Changsha 410128, China
- Hunan Engineering & Technology Research Center for Irrigation Water Purification, Changsha 410128, China
- Key Laboratory of Southern Farmland Pollution Prevention and Control, Ministry of Agriculture and Rural Affairs, Changsha 410128, China
| | - Jun-Fan Yao
- College of Resources and Environment, Hunan Agricultural University, Changsha 410128, China
- Hunan Engineering & Technology Research Center for Irrigation Water Purification, Changsha 410128, China
- Key Laboratory of Southern Farmland Pollution Prevention and Control, Ministry of Agriculture and Rural Affairs, Changsha 410128, China
| | - Yu-Ling Liu
- College of Resources and Environment, Hunan Agricultural University, Changsha 410128, China
- Hunan Engineering & Technology Research Center for Irrigation Water Purification, Changsha 410128, China
- Key Laboratory of Southern Farmland Pollution Prevention and Control, Ministry of Agriculture and Rural Affairs, Changsha 410128, China
| | - Wei-Yu Zhang
- College of Resources and Environment, Hunan Agricultural University, Changsha 410128, China
- Hunan Engineering & Technology Research Center for Irrigation Water Purification, Changsha 410128, China
- Key Laboratory of Southern Farmland Pollution Prevention and Control, Ministry of Agriculture and Rural Affairs, Changsha 410128, China
| | - Xue-Fei Yin
- College of Resources and Environment, Hunan Agricultural University, Changsha 410128, China
- Hunan Engineering & Technology Research Center for Irrigation Water Purification, Changsha 410128, China
- Key Laboratory of Southern Farmland Pollution Prevention and Control, Ministry of Agriculture and Rural Affairs, Changsha 410128, China
| | - Bo-Qing Tie
- College of Resources and Environment, Hunan Agricultural University, Changsha 410128, China
- Hunan Engineering & Technology Research Center for Irrigation Water Purification, Changsha 410128, China
- Key Laboratory of Southern Farmland Pollution Prevention and Control, Ministry of Agriculture and Rural Affairs, Changsha 410128, China
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Coon GR, Duesing PD, Paul R, Baily JA, Lloyd KG. Biological methane production and accumulation under sulfate-rich conditions at Cape Lookout Bight, NC. Front Microbiol 2023; 14:1268361. [PMID: 37869653 PMCID: PMC10587565 DOI: 10.3389/fmicb.2023.1268361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 09/14/2023] [Indexed: 10/24/2023] Open
Abstract
Introduction Anaerobic oxidation of methane (AOM) is hypothesized to occur through reverse hydrogenotrophic methanogenesis in marine sediments because sulfate reducers pull hydrogen concentrations so low that reverse hydrogenotrophic methanogenesis is exergonic. If true, hydrogenotrophic methanogenesis can theoretically co-occur with sulfate reduction if the organic matter is so labile that fermenters produce more hydrogen than sulfate reducers can consume, causing hydrogen concentrations to rise. Finding accumulation of biologically-produced methane in sulfate-containing organic-rich sediments would therefore support the theory that AOM occurs through reverse hydrogenotrophic methanogenesis since it would signal the absence of net AOM in the presence of sulfate. Methods 16S rRNA gene libraries were compared to geochemistry and incubations in high depth-resolution sediment cores collected from organic-rich Cape Lookout Bight, North Carolina. Results We found that methane began to accumulate while sulfate is still abundant (6-8 mM). Methane-cycling archaea ANME-1, Methanosarciniales, and Methanomicrobiales also increased at these depths. Incubations showed that methane production in the upper 16 cm in sulfate-rich sediments was biotic since it could be inhibited by 2-bromoethanosulfonoic acid (BES). Discussion We conclude that methanogens mediate biological methane production in these organic-rich sediments at sulfate concentrations that inhibit methanogenesis in sediments with less labile organic matter, and that methane accumulation and growth of methanogens can occur under these conditions as well. Our data supports the theory that H2 concentrations, rather than the co-occurrence of sulfate and methane, control whether methanogenesis or AOM via reverse hydrogenotrophic methanogenesis occurs. We hypothesize that the high amount of labile organic matter at this site prevents AOM, allowing methane accumulation when sulfate is low but still present in mM concentrations.
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Karnachuk OV, Rusanov II, Panova IA, Kadnikov VV, Avakyan MR, Ikkert OP, Lukina AP, Beletsky AV, Mardanov AV, Knyazev YV, Volochaev MN, Pimenov NV, Ravin NV. The low-temperature germinating spores of the thermophilic Desulfofundulus contribute to an extremely high sulfate reduction in burning coal seams. Front Microbiol 2023; 14:1204102. [PMID: 37779687 PMCID: PMC10540450 DOI: 10.3389/fmicb.2023.1204102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 08/31/2023] [Indexed: 10/03/2023] Open
Abstract
Burning coal seams, characterized by massive carbon monoxide (CO) emissions, the presence of secondary sulfates, and high temperatures, represent suitable environments for thermophilic sulfate reduction. The diversity and activity of dissimilatory sulfate reducers in these environments remain unexplored. In this study, using metagenomic approaches, in situ activity measurements with a radioactive tracer, and cultivation we have shown that members of the genus Desulfofundulus are responsible for the extremely high sulfate reduction rate (SRR) in burning lignite seams in the Altai Mountains. The maximum SRR reached 564 ± 21.9 nmol S cm-3 day-1 at 60°C and was of the same order of magnitude for both thermophilic (60°C) and mesophilic (23°C) incubations. The 16S rRNA profiles and the search for dsr gene sequences in the metagenome revealed members of the genus Desulfofundulus as the main sulfate reducers. The thermophilic Desulfofundulus sp. strain Al36 isolated in pure culture, did not grow at temperatures below 50°C, but produced spores that germinated into metabolically active cells at 20 and 15°C. Vegetative cells germinating from spores produced up to 0.738 ± 0.026 mM H2S at 20°C and up to 0.629 ± 0.007 mM H2S at 15°C when CO was used as the sole electron donor. The Al36 strain maintains significant production of H2S from sulfate over a wide temperature range from 15°C to 65°C, which is important in variable temperature biotopes such as lignite burning seams. Burning coal seams producing CO are ubiquitous throughout the world, and biogenic H2S may represent an overlooked significant flux to the atmosphere. The thermophilic spore outgrowth and their metabolic activity at temperatures below the growth minimum may be important for other spore-forming bacteria of environmental, industrial and clinical importance.
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Affiliation(s)
- Olga V. Karnachuk
- Laboratory of Biochemistry and Molecular Biology, Tomsk State University, Tomsk, Russia
| | - Igor I. Rusanov
- Institute of Microbiology, Research Centre of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | - Inna A. Panova
- Laboratory of Biochemistry and Molecular Biology, Tomsk State University, Tomsk, Russia
| | - Vitaly V. Kadnikov
- Institute of Bioengineering, Research Centre of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | - Marat R. Avakyan
- Laboratory of Biochemistry and Molecular Biology, Tomsk State University, Tomsk, Russia
| | - Olga P. Ikkert
- Laboratory of Biochemistry and Molecular Biology, Tomsk State University, Tomsk, Russia
| | - Anastasia P. Lukina
- Laboratory of Biochemistry and Molecular Biology, Tomsk State University, Tomsk, Russia
| | - Alexey V. Beletsky
- Institute of Bioengineering, Research Centre of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | - Andrey V. Mardanov
- Institute of Bioengineering, Research Centre of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | | | | | - Nikolai V. Pimenov
- Institute of Microbiology, Research Centre of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | - Nikolai V. Ravin
- Institute of Bioengineering, Research Centre of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
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12
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Diao M, Dyksma S, Koeksoy E, Ngugi DK, Anantharaman K, Loy A, Pester M. Global diversity and inferred ecophysiology of microorganisms with the potential for dissimilatory sulfate/sulfite reduction. FEMS Microbiol Rev 2023; 47:fuad058. [PMID: 37796897 PMCID: PMC10591310 DOI: 10.1093/femsre/fuad058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 10/01/2023] [Accepted: 10/03/2023] [Indexed: 10/07/2023] Open
Abstract
Sulfate/sulfite-reducing microorganisms (SRM) are ubiquitous in nature, driving the global sulfur cycle. A hallmark of SRM is the dissimilatory sulfite reductase encoded by the genes dsrAB. Based on analysis of 950 mainly metagenome-derived dsrAB-carrying genomes, we redefine the global diversity of microorganisms with the potential for dissimilatory sulfate/sulfite reduction and uncover genetic repertoires that challenge earlier generalizations regarding their mode of energy metabolism. We show: (i) 19 out of 23 bacterial and 2 out of 4 archaeal phyla harbor uncharacterized SRM, (ii) four phyla including the Desulfobacterota harbor microorganisms with the genetic potential to switch between sulfate/sulfite reduction and sulfur oxidation, and (iii) the combination as well as presence/absence of different dsrAB-types, dsrL-types and dsrD provides guidance on the inferred direction of dissimilatory sulfur metabolism. We further provide an updated dsrAB database including > 60% taxonomically resolved, uncultured family-level lineages and recommendations on existing dsrAB-targeted primers for environmental surveys. Our work summarizes insights into the inferred ecophysiology of newly discovered SRM, puts SRM diversity into context of the major recent changes in bacterial and archaeal taxonomy, and provides an up-to-date framework to study SRM in a global context.
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Affiliation(s)
- Muhe Diao
- Department of Microorganisms, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig D-38124, Germany
| | - Stefan Dyksma
- Department of Microorganisms, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig D-38124, Germany
| | - Elif Koeksoy
- Department of Microorganisms, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig D-38124, Germany
| | - David Kamanda Ngugi
- Department of Microorganisms, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig D-38124, Germany
| | - Karthik Anantharaman
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Alexander Loy
- Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna A-1030, Austria
| | - Michael Pester
- Department of Microorganisms, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig D-38124, Germany
- Technical University of Braunschweig, Institute of Microbiology, Braunschweig D-38106, Germany
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13
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Kieu TQH, Nguyen TY, Do CL. Treatment of Organic and Sulfate/Sulfide Contaminated Wastewater and Bioelectricity Generation by Sulfate-Reducing Bioreactor Coupling with Sulfide-Oxidizing Fuel Cell. Molecules 2023; 28:6197. [PMID: 37687026 PMCID: PMC10488401 DOI: 10.3390/molecules28176197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Revised: 08/19/2023] [Accepted: 08/19/2023] [Indexed: 09/10/2023] Open
Abstract
A wastewater treatment system has been established based on sulfate-reducing and sulfide-oxidizing processes for treating organic wastewater containing high sulfate/sulfide. The influence of COD/SO42- ratio and hydraulic retention time (HRT) on removal efficiencies of sulfate, COD, sulfide and electricity generation was investigated. The continuous operation of the treatment system was carried out for 63 days with the optimum COD/SO42- ratio and HRT. The result showed that the COD and sulfate removal efficiencies were stable, reaching 94.8 ± 0.6 and 93.0 ± 1.3% during the operation. A power density level of 18.0 ± 1.6 mW/m2 was obtained with a sulfide removal efficiency of 93.0 ± 1.2%. However, the sulfide removal efficiency and power density decreased gradually after 45 days. The results from scanning electron microscopy (SEM) with an energy dispersive X-ray (EDX) show that sulfur accumulated on the anode, which could explain the decline in sulfide oxidation and electricity generation. This study provides a promising treatment system to scale up for its actual applications in this type of wastewater.
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Affiliation(s)
- Thi Quynh Hoa Kieu
- Institute of Biotechnology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi 100000, Vietnam
- Faculty of Biotechnology, Graduate University of Science and Technology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet Str., Cau Giay, Hanoi 100000, Vietnam
| | - Thi Yen Nguyen
- Institute of Biotechnology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi 100000, Vietnam
| | - Chi Linh Do
- Institute of Material Sciences, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi 100000, Vietnam
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14
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Yang S, Tang R, Han S, Xie CJ, Liu GH, Zhou SG. A novel strictly anaerobic sulfate-reducing diazotrophic bacterium Fundidesulfovibrio terrae sp. nov., isolated from paddy soil. Int J Syst Evol Microbiol 2023; 73. [PMID: 37185059 DOI: 10.1099/ijsem.0.005880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/17/2023] Open
Abstract
A strictly anaerobic sulfate-reducing strain, designated SG127T, was isolated from paddy soil. SG127T showed the highest 16S rRNA gene sequence similarity to the type strain of Fundidesulfovibrio magnetotacticus (98.2 %). A phylogenetic tree based on 16S rRNA gene sequences indicated that SG127T clustered with members of the genus Fundidesulfovibrio. Growth of SG127T was observed at 20-37 °C (optimum, 30 °C), pH 5.5-9.0 (optimum, 7.0-8.0) and with 0-0.2 % (w/v) NaCl (optimally without NaCl). SG127T contained MK-7 as the only menaquinone and anteiso-C15 : 0, anteiso-C17 : 1ω9c, C18 : 0, iso-C14 : 0, iso-C15 : 0, iso-C16:0, iso-C16 : 1H, iso-C18 : 1H and summed feature nine as the major fatty acids. The genomic DNA G+C content of SG127T was 64.6 %. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between SG127T and the closely related Fundidesulfovibrio magnetotacticus were 78.5% and 23.2 %, respectively, which were lower than the cut-off values (ANI 95-96% and dDDH 70 %) for prokaryotic species delineation. SG127T had desulfoviridin, possessed nitrogen fixation genes (nifHDK) and actively fixed nitrogen according to the acetylene reduction assay. On the basis of these results, strain SG127T represents a novel species of the genus Fundidesulfovibrio, for which the name Fundidesulfovibrio terrae sp. nov. is proposed. The type strain is SG127T (= GDMCC 1.3137T = JCM 35589T).
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Affiliation(s)
- Shang Yang
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou City, 350002, PR China
| | - Rong Tang
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou City, 350002, PR China
| | - Shuang Han
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou City, 350002, PR China
| | - Cheng-Jie Xie
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou City, 350002, PR China
| | - Guo-Hong Liu
- Agricultural Bio-resources Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou City, 350003, PR China
| | - Shun-Gui Zhou
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou City, 350002, PR China
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15
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Yang S, Anthony SE, Jenrich M, In 't Zandt MH, Strauss J, Overduin PP, Grosse G, Angelopoulos M, Biskaborn BK, Grigoriev MN, Wagner D, Knoblauch C, Jaeschke A, Rethemeyer J, Kallmeyer J, Liebner S. Microbial methane cycling in sediments of Arctic thermokarst lagoons. Glob Chang Biol 2023; 29:2714-2731. [PMID: 36811358 DOI: 10.1111/gcb.16649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 01/27/2023] [Indexed: 05/31/2023]
Abstract
Thermokarst lagoons represent the transition state from a freshwater lacustrine to a marine environment, and receive little attention regarding their role for greenhouse gas production and release in Arctic permafrost landscapes. We studied the fate of methane (CH4 ) in sediments of a thermokarst lagoon in comparison to two thermokarst lakes on the Bykovsky Peninsula in northeastern Siberia through the analysis of sediment CH4 concentrations and isotopic signature, methane-cycling microbial taxa, sediment geochemistry, lipid biomarkers, and network analysis. We assessed how differences in geochemistry between thermokarst lakes and thermokarst lagoons, caused by the infiltration of sulfate-rich marine water, altered the microbial methane-cycling community. Anaerobic sulfate-reducing ANME-2a/2b methanotrophs dominated the sulfate-rich sediments of the lagoon despite its known seasonal alternation between brackish and freshwater inflow and low sulfate concentrations compared to the usual marine ANME habitat. Non-competitive methylotrophic methanogens dominated the methanogenic community of the lakes and the lagoon, independent of differences in porewater chemistry and depth. This potentially contributed to the high CH4 concentrations observed in all sulfate-poor sediments. CH4 concentrations in the freshwater-influenced sediments averaged 1.34 ± 0.98 μmol g-1 , with highly depleted δ13 C-CH4 values ranging from -89‰ to -70‰. In contrast, the sulfate-affected upper 300 cm of the lagoon exhibited low average CH4 concentrations of 0.011 ± 0.005 μmol g-1 with comparatively enriched δ13 C-CH4 values of -54‰ to -37‰ pointing to substantial methane oxidation. Our study shows that lagoon formation specifically supports methane oxidizers and methane oxidation through changes in pore water chemistry, especially sulfate, while methanogens are similar to lake conditions.
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Affiliation(s)
- Sizhong Yang
- GFZ German Research Center for Geosciences, Helmholtz Centre Potsdam, Section Geomicrobiology, Potsdam, Germany
- Cryosphere Research Station on the Qinghai-Tibet Plateau, State Key Laboratory of Cryospheric Science, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, China
| | - Sara E Anthony
- Institute of Geology and Mineralogy, University of Cologne, Cologne, Germany
| | - Maren Jenrich
- Permafrost Research Section, Alfred Wegener Institute Helmholtz Center for Polar and Marine Research, Potsdam, Germany
- Institute of Geosciences, University of Potsdam, Potsdam, Germany
| | - Michiel H In 't Zandt
- Department of Microbiology, RIBES, Radboud University, Nijmegen, the Netherlands
- Netherlands Earth System Science Center, Utrecht University, Utrecht, the Netherlands
| | - Jens Strauss
- Permafrost Research Section, Alfred Wegener Institute Helmholtz Center for Polar and Marine Research, Potsdam, Germany
| | - Pier Paul Overduin
- Permafrost Research Section, Alfred Wegener Institute Helmholtz Center for Polar and Marine Research, Potsdam, Germany
| | - Guido Grosse
- Permafrost Research Section, Alfred Wegener Institute Helmholtz Center for Polar and Marine Research, Potsdam, Germany
- Institute of Geosciences, University of Potsdam, Potsdam, Germany
| | - Michael Angelopoulos
- Permafrost Research Section, Alfred Wegener Institute Helmholtz Center for Polar and Marine Research, Potsdam, Germany
| | - Boris K Biskaborn
- Polar Terrestrial Environmental Systems Section, Alfred Wegener Institute Helmholtz Center for Polar and Marine Research, Potsdam, Germany
| | - Mikhail N Grigoriev
- Laboratory of General Geocryology, Melnikov Permafrost Institute, Siberian Branch of the Russian Academy of Sciences, Yakutsk, Russia
| | - Dirk Wagner
- GFZ German Research Center for Geosciences, Helmholtz Centre Potsdam, Section Geomicrobiology, Potsdam, Germany
- Institute of Geosciences, University of Potsdam, Potsdam, Germany
| | - Christian Knoblauch
- Institute of Soil Science, Universität Hamburg, Hamburg, Germany
- Center for Earth System Research and Sustainability, Universität Hamburg, Hamburg, Germany
| | - Andrea Jaeschke
- Institute of Geology and Mineralogy, University of Cologne, Cologne, Germany
| | - Janet Rethemeyer
- Institute of Geology and Mineralogy, University of Cologne, Cologne, Germany
| | - Jens Kallmeyer
- GFZ German Research Center for Geosciences, Helmholtz Centre Potsdam, Section Geomicrobiology, Potsdam, Germany
| | - Susanne Liebner
- GFZ German Research Center for Geosciences, Helmholtz Centre Potsdam, Section Geomicrobiology, Potsdam, Germany
- Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
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16
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Zhang L, Yin Y, Sun Y, Liang X, Graham DE, Pierce EM, Löffler FE, Gu B. Inhibition of Methylmercury and Methane Formation by Nitrous Oxide in Arctic Tundra Soil Microcosms. Environ Sci Technol 2023; 57:5655-5665. [PMID: 36976621 PMCID: PMC10100821 DOI: 10.1021/acs.est.2c09457] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 03/03/2023] [Accepted: 03/16/2023] [Indexed: 06/18/2023]
Abstract
Climate warming causes permafrost thaw predicted to increase toxic methylmercury (MeHg) and greenhouse gas [i.e., methane (CH4), carbon dioxide (CO2), and nitrous oxide (N2O)] formation. A microcosm incubation study with Arctic tundra soil over 145 days demonstrates that N2O at 0.1 and 1 mM markedly inhibited microbial MeHg formation, methanogenesis, and sulfate reduction, while it slightly promoted CO2 production. Microbial community analyses indicate that N2O decreased the relative abundances of methanogenic archaea and microbial clades implicated in sulfate reduction and MeHg formation. Following depletion of N2O, both MeHg formation and sulfate reduction rapidly resumed, whereas CH4 production remained low, suggesting that N2O affected susceptible microbial guilds differently. MeHg formation strongly coincided with sulfate reduction, supporting prior reports linking sulfate-reducing bacteria to MeHg formation in the Arctic soil. This research highlights complex biogeochemical interactions in governing MeHg and CH4 formation and lays the foundation for future mechanistic studies for improved predictive understanding of MeHg and greenhouse gas fluxes from thawing permafrost ecosystems.
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Affiliation(s)
- Lijie Zhang
- Environmental
Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
- Department
of Chemistry and Environmental Science, New Jersey Institute of Technology, Newark, New Jersey 07102, United States
| | - Yongchao Yin
- Biosciences
Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
- Center
for Environmental Biotechnology, University
of Tennessee, Knoxville, Tennessee 37996, United States
- Department
of Microbiology, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Yanchen Sun
- Center
for Environmental Biotechnology, University
of Tennessee, Knoxville, Tennessee 37996, United States
- Department
of Civil and Environmental Engineering, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Xujun Liang
- Environmental
Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - David E. Graham
- Biosciences
Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Eric M. Pierce
- Environmental
Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Frank E. Löffler
- Biosciences
Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
- Center
for Environmental Biotechnology, University
of Tennessee, Knoxville, Tennessee 37996, United States
- Department
of Microbiology, University of Tennessee, Knoxville, Tennessee 37996, United States
- Department
of Civil and Environmental Engineering, University of Tennessee, Knoxville, Tennessee 37996, United States
- Department
of Biosystems Engineering and Soil Science, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Baohua Gu
- Environmental
Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
- Department
of Biosystems Engineering and Soil Science, University of Tennessee, Knoxville, Tennessee 37996, United States
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17
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Woodard TL, Ueki T, Lovley DR. H(2) Is a Major Intermediate in Desulfovibrio vulgaris Corrosion of Iron. mBio 2023;:e0007623. [PMID: 36786581 DOI: 10.1128/mbio.00076-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023] Open
Abstract
Desulfovibrio vulgaris has been a primary pure culture sulfate reducer for developing microbial corrosion concepts. Multiple mechanisms for how it accepts electrons from Fe0 have been proposed. We investigated Fe0 oxidation with a mutant of D. vulgaris in which hydrogenase genes were deleted. The hydrogenase mutant grew as well as the parental strain with lactate as the electron donor, but unlike the parental strain, it was not able to grow on H2. The parental strain reduced sulfate with Fe0 as the sole electron donor, but the hydrogenase mutant did not. H2 accumulated over time in Fe0 cultures of the hydrogenase mutant and sterile controls but not in parental strain cultures. Sulfide stimulated H2 production in uninoculated controls apparently by both reacting with Fe0 to generate H2 and facilitating electron transfer from Fe0 to H+. Parental strain supernatants did not accelerate H2 production from Fe0, ruling out a role for extracellular hydrogenases. Previously proposed electron transfer between Fe0 and D. vulgaris via soluble electron shuttles was not evident. The hydrogenase mutant did not reduce sulfate in the presence of Fe0 and either riboflavin or anthraquinone-2,6-disulfonate, and these potential electron shuttles did not stimulate parental strain sulfate reduction with Fe0 as the electron donor. The results demonstrate that D. vulgaris primarily accepts electrons from Fe0 via H2 as an intermediary electron carrier. These findings clarify the interpretation of previous D. vulgaris corrosion studies and suggest that H2-mediated electron transfer is an important mechanism for iron corrosion under sulfate-reducing conditions. IMPORTANCE Microbial corrosion of iron in the presence of sulfate-reducing microorganisms is economically significant. There is substantial debate over how microbes accelerate iron corrosion. Tools for genetic manipulation have only been developed for a few Fe(III)-reducing and methanogenic microorganisms known to corrode iron and in each case those microbes were found to accept electrons from Fe0 via direct electron transfer. However, iron corrosion is often most intense in the presence of sulfate-reducing microbes. The finding that Desulfovibrio vulgaris relies on H2 to shuttle electrons between Fe0 and cells revives the concept, developed in some of the earliest studies on microbial corrosion, that sulfate reducers consumption of H2 is a major microbial corrosion mechanism. The results further emphasize that direct Fe0-to-microbe electron transfer has yet to be rigorously demonstrated in sulfate-reducing microbes.
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18
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Dohrmann AB, Krüger M. Microbial H 2 Consumption by a Formation Fluid from a Natural Gas Field at High-Pressure Conditions Relevant for Underground H 2 Storage. Environ Sci Technol 2023; 57:1092-1102. [PMID: 36599497 DOI: 10.1021/acs.est.2c07303] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Underground hydrogen storage (UHS) has been proposed as one option for storage of excess energy from renewable sources. Depleted gas reservoirs appear suitable, but at the same time, they may be environments with potentially high microbial abundances and activities. Hydrogen (H2) is one of the most energetic substrates in such environments, and many microorganisms are able to oxidize H2, potentially leading to loss of H2 or other unwanted reactions like production of, e.g., H2S, clogging, or corrosion. This study addressed the potential of H2 consumption by naturally abundant microorganisms in formation fluid from a gas field at near in situ pressure and temperature conditions. Microbial H2 consumption was evident at ambient and 100 bar and tolerated pressure variations reflecting cycles of H2 storage. Temperature strongly influenced the activity with higher activity at 30 °C but lower activity at 60 °C. The activity was sulfate-dependent, and sulfide was produced. The microbial community composition changed during H2 consumption with an increase in sulfate-reducing prokaryotes (SRP). Thus, the presence of an SRP-containing, H2-consuming microbial community with activity at UHS-relevant pressure and temperature conditions was shown and should be taken into account when planning UHS at this and other sites.
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Affiliation(s)
- Anja B Dohrmann
- Federal Institute for Geosciences and Natural Resources (BGR), Stilleweg 2, 30655Hannover, Germany
| | - Martin Krüger
- Federal Institute for Geosciences and Natural Resources (BGR), Stilleweg 2, 30655Hannover, Germany
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19
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Yin XF, Liu YL, Wu D, Huang XM, Zhang PX, Tie BQ. [Inactivation of Cd and As by an Enterobacter Isolated from Cd and As Contaminated Farmland Soil]. Huan Jing Ke Xue 2023; 44:436-443. [PMID: 36635831 DOI: 10.13227/j.hjkx.202202152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
A strain of Enterobacter was screened from cadmium and arsenic contaminated farmland soil and its passivation mechanism of cadmium and arsenic were explored through removing performance and characterization experiments. The results showed that the screened strain M5 was identified as Enterobacter sp. with a sulfate-reduction function, and its maximum resistance concentration was approximately 1 mmol·L-1 to cadmium and arsenic. In the simulation system, the maximum removal efficiencies of cadmium and arsenic were 94.13% and 27.26% by strain M5, respectively. The results of SEM-EDS and XRD confirmed that Cd and As were fixed to CdS and As2S3, and XPS results showed that carboxyl groups, hydroxyl groups, and amide groups on the surface of the bacteria were mainly involved in biological adsorption. These results can provide new ideas and a theoretical basis for microbial applications to soil remediations for heavy metal pollution.
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Affiliation(s)
- Xue-Fei Yin
- College of Resources and Environment, Hunan Agricultural University, Changsha 410128, China.,Hunan Engineering & Technology Research Center for Irrigation Water Purification, Changsha 410128, China.,Key Laboratory of Southern Farmland Pollution Prevention and Control, Ministry of Agriculture and Rural Affairs, Changsha 410128, China
| | - Yu-Ling Liu
- College of Resources and Environment, Hunan Agricultural University, Changsha 410128, China.,Hunan Engineering & Technology Research Center for Irrigation Water Purification, Changsha 410128, China.,Key Laboratory of Southern Farmland Pollution Prevention and Control, Ministry of Agriculture and Rural Affairs, Changsha 410128, China
| | - De Wu
- College of Resources and Environment, Hunan Agricultural University, Changsha 410128, China.,Hunan Engineering & Technology Research Center for Irrigation Water Purification, Changsha 410128, China.,Key Laboratory of Southern Farmland Pollution Prevention and Control, Ministry of Agriculture and Rural Affairs, Changsha 410128, China
| | - Xin-Ming Huang
- College of Resources and Environment, Hunan Agricultural University, Changsha 410128, China.,Hunan Engineering & Technology Research Center for Irrigation Water Purification, Changsha 410128, China.,Key Laboratory of Southern Farmland Pollution Prevention and Control, Ministry of Agriculture and Rural Affairs, Changsha 410128, China
| | - Pu-Xin Zhang
- College of Resources and Environment, Hunan Agricultural University, Changsha 410128, China.,Hunan Engineering & Technology Research Center for Irrigation Water Purification, Changsha 410128, China.,Key Laboratory of Southern Farmland Pollution Prevention and Control, Ministry of Agriculture and Rural Affairs, Changsha 410128, China
| | - Bo-Qing Tie
- College of Resources and Environment, Hunan Agricultural University, Changsha 410128, China.,Hunan Engineering & Technology Research Center for Irrigation Water Purification, Changsha 410128, China.,Key Laboratory of Southern Farmland Pollution Prevention and Control, Ministry of Agriculture and Rural Affairs, Changsha 410128, China
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McGlynn SE, Perkins G, Sim MS, Mackey M, Deerinck TJ, Thor A, Phan S, Ballard D, Ellisman MH, Orphan VJ. A Cristae-Like Microcompartment in Desulfobacterota. mBio 2022; 13:e0161322. [PMID: 36321837 DOI: 10.1128/mbio.01613-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Some Alphaproteobacteria contain intracytoplasmic membranes (ICMs) and proteins homologous to those responsible for the mitochondrial cristae, an observation which has given rise to the hypothesis that the Alphaproteobacteria endosymbiont had already evolved cristae-like structures and functions. However, our knowledge of microbial fine structure is still limited, leaving open the possibility of structurally homologous ICMs outside the Alphaproteobacteria. Here, we report on the detailed characterization of lamellar cristae-like ICMs in environmental sulfate-reducing Desulfobacterota that form syntrophic partnerships with anaerobic methane-oxidizing (ANME) archaea. These structures are junction-bound to the cytoplasmic membrane and resemble the form seen in the lamellar cristae of opisthokont mitochondria. Extending these observations, we also characterized similar structures in Desulfovibrio carbinolicus, a close relative of the magnetotactic D. magneticus, which does not contain magnetosomes. Despite a remarkable structural similarity, the key proteins involved in cristae formation have not yet been identified in Desulfobacterota, suggesting that an analogous, but not a homologous, protein organization system developed during the evolution of some members of Desulfobacterota. IMPORTANCE Working with anaerobic consortia of methane oxidizing ANME archaea and their sulfate-reducing bacterial partners recovered from deep sea sediments and with the related sulfate-reducing bacterial isolate D. carbinolicus, we discovered that their intracytoplasmic membranes (ICMs) appear remarkably similar to lamellar cristae. Three-dimensional electron microscopy allowed for the novel analysis of the nanoscale attachment of ICMs to the cytoplasmic membrane, and these ICMs are structurally nearly identical to the crista junction architecture seen in metazoan mitochondria. However, the core junction-forming proteins must be different. The outer membrane vesicles were observed to bud from syntrophic Desulfobacterota, and darkly stained granules were prominent in both Desulfobacterota and D. carbinolicus. These findings expand the taxonomic breadth of ICM-producing microorganisms and add to our understanding of three-dimensional microbial fine structure in environmental microorganisms.
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Brazelton WJ, McGonigle JM, Motamedi S, Pendleton HL, Twing KI, Miller BC, Lowe WJ, Hoffman AM, Prator CA, Chadwick GL, Anderson RE, Thomas E, Butterfield DA, Aquino KA, Früh-Green GL, Schrenk MO, Lang SQ. Metabolic Strategies Shared by Basement Residents of the Lost City Hydrothermal Field. Appl Environ Microbiol 2022;:e0092922. [PMID: 35950875 DOI: 10.1128/aem.00929-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Alkaline fluids venting from chimneys of the Lost City hydrothermal field flow from a potentially vast microbial habitat within the seafloor where energy and organic molecules are released by chemical reactions within rocks uplifted from Earth's mantle. In this study, we investigated hydrothermal fluids venting from Lost City chimneys as windows into subseafloor environments where the products of geochemical reactions, such as molecular hydrogen (H2), formate, and methane, may be the only available sources of energy for biological activity. Our deep sequencing of metagenomes and metatranscriptomes from these hydrothermal fluids revealed a few key species of archaea and bacteria that are likely to play critical roles in the subseafloor microbial ecosystem. We identified a population of Thermodesulfovibrionales (belonging to phylum Nitrospirota) as a prevalent sulfate-reducing bacterium that may be responsible for much of the consumption of H2 and sulfate in Lost City fluids. Metagenome-assembled genomes (MAGs) classified as Methanosarcinaceae and Candidatus Bipolaricaulota were also recovered from venting fluids and represent potential methanogenic and acetogenic members of the subseafloor ecosystem. These genomes share novel hydrogenases and formate dehydrogenase-like sequences that may be unique to hydrothermal environments where H2 and formate are much more abundant than carbon dioxide. The results of this study include multiple examples of metabolic strategies that appear to be advantageous in hydrothermal and subsurface alkaline environments where energy and carbon are provided by geochemical reactions. IMPORTANCE The Lost City hydrothermal field is an iconic example of a microbial ecosystem fueled by energy and carbon from Earth's mantle. Uplift of mantle rocks into the seafloor can trigger a process known as serpentinization that releases molecular hydrogen (H2) and creates unusual environmental conditions where simple organic carbon molecules are more stable than dissolved inorganic carbon. This study provides an initial glimpse into the kinds of microbes that live deep within the seafloor where serpentinization takes place, by sampling hydrothermal fluids exiting from the Lost City chimneys. The metabolic strategies that these microbes appear to be using are also shared by microbes that inhabit other sites of serpentinization, including continental subsurface environments and natural springs. Therefore, the results of this study contribute to a broader, interdisciplinary effort to understand the general principles and mechanisms by which serpentinization-associated processes can support life on Earth and perhaps other worlds.
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22
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Hunt KA, von Netzer F, Gorman-Lewis D, Stahl DA. Microbial maintenance energy quantified and modeled with microcalorimetry. Biotechnol Bioeng 2022; 119:2413-2422. [PMID: 35680566 DOI: 10.1002/bit.28155] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 06/06/2022] [Accepted: 06/08/2022] [Indexed: 11/08/2022]
Abstract
Refining the energetic costs of cellular maintenance is essential for predicting microbial growth and survival in the environment. Here, we evaluate a simple batch culture method to quantify energy partitioning between growth and maintenance using microcalorimetry and thermodynamic modeling. The constants derived from the batch culture system were comparable to those that have been reported from meta-analyses of data derived from chemostat studies. The model accurately predicted temperature-dependent biomass yield and the upper temperature limit of growth for Desulfovibrio alaskensis G20, suggesting the method may have broad application. An Arrhenius temperature dependence for the specific energy consumption rate, inferred from substrate consumption and heat evolution, was observed over the entire viable temperature range. By combining this relationship for specific energy consumption rates and observed specific growth rates, the model describes an increase in nongrowth associated maintenance at higher temperatures and the corresponding decrease in energy available for growth. This analytical and thermodynamic formulation suggests that simply monitoring heat evolution in batch culture could be a useful complement to the recognized limitations of estimating maintenance using extrapolation to zero growth in chemostats.
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Affiliation(s)
- Kristopher A Hunt
- Department of Civil and Environmental Engineering, University of Washington, Seattle, Washington, USA
| | - Frederick von Netzer
- Department of Civil and Environmental Engineering, University of Washington, Seattle, Washington, USA
| | - Drew Gorman-Lewis
- Department of Earth and Space Sciences, University of Washington, Seattle, Washington, USA
| | - David A Stahl
- Department of Civil and Environmental Engineering, University of Washington, Seattle, Washington, USA
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Barnes RJ, Voegtlin SP, Naik SR, Gomes R, Hubert CRJ, Larter SR, Bryant SL. Inhibition of Sulfate Reduction and Cell Division by Desulfovibrio desulfuricans Coated in Palladium Metal. Appl Environ Microbiol 2022;:e0058022. [PMID: 35638843 DOI: 10.1128/aem.00580-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The growth of sulfate-reducing bacteria (SRB) and associated hydrogen sulfide production can be problematic in a range of industries such that inhibition strategies are needed. A range of SRB can reduce metal ions, a strategy that has been utilized for bioremediation, metal recovery, and synthesis of precious metal catalysts. In some instances, the metal remains bound to the cell surface, and the impact of this coating on bacterial cell division and metabolism has not previously been reported. In this study, Desulfovibrio desulfuricans cells (1g dry weight) enabled the reduction of up to 1500 mmol (157.5 g) palladium (Pd) ions, resulting in cells being coated in approximately 1 μm of metal. Thickly coated cells were no longer able to metabolize or divide, ultimately leading to the death of the population. Increasing Pd coating led to prolonged inhibition of sulfate reduction, which ceased completely after cells had been coated with 1200 mmol Pd g-1 dry cells. Less Pd nanoparticle coating permitted cells to carry out sulfate reduction and divide, allowing the population to recover over time as surface-associated Pd diminished. Overcoming inhibition in this way was more rapid using lactate as the electron donor, compared to formate. When using formate as an electron donor, preferential Pd(II) reduction took place in the presence of 100 mM sulfate. The inhibition of important metabolic pathways using a biologically enabled casing in metal highlights a new mechanism for the development of microbial control strategies. IMPORTANCE Microbial reduction of sulfate to hydrogen sulfide is highly undesirable in several industrial settings. Some sulfate-reducing bacteria are also able to transform metal ions in their environment into metal phases that remain attached to their outer cell surface. This study demonstrates the remarkable extent to which Desulfovibrio desulfuricans can be coated with locally generated metal nanoparticles, with individual cells carrying more than 100 times their mass of palladium metal. Moreover, it reveals the effect of metal coating on metabolism and replication for a wide range of metal loadings, with bacteria unable to reduce sulfate to sulfide beyond a specific threshold. These findings present a foundation for a novel means of modulating the activity of sulfate-reducing bacteria.
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Nuppunen-Puputti M, Kietäväinen R, Raulio M, Soro A, Purkamo L, Kukkonen I, Bomberg M. Epilithic Microbial Community Functionality in Deep Oligotrophic Continental Bedrock. Front Microbiol 2022; 13:826048. [PMID: 35300483 PMCID: PMC8921683 DOI: 10.3389/fmicb.2022.826048] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 01/12/2022] [Indexed: 01/03/2023] Open
Abstract
The deep terrestrial biosphere hosts vast sessile rock surface communities and biofilms, but thus far, mostly planktic communities have been studied. We enriched deep subsurface microbial communities on mica schist in microcosms containing bedrock groundwater from the depth of 500 m from Outokumpu, Finland. The biofilms were visualized using scanning electron microscopy, revealing numerous different microbial cell morphologies and attachment strategies on the mica schist surface, e.g., bacteria with outer membrane vesicle-like structures, hair-like extracellular extensions, and long tubular cell structures expanding over hundreds of micrometers over mica schist surfaces. Bacterial communities were analyzed with amplicon sequencing showing that Pseudomonas, Desulfosporosinus, Hydrogenophaga, and Brevundimonas genera dominated communities after 8–40 months of incubation. A total of 21 metagenome assembled genomes from sessile rock surface metagenomes identified genes involved in biofilm formation, as well as a wide variety of metabolic traits indicating a high degree of environmental adaptivity to oligotrophic environment and potential for shifting between multiple energy or carbon sources. In addition, we detected ubiquitous organic carbon oxidation and capacity for arsenate and selenate reduction within our rocky MAGs. Our results agree with the previously suggested interaction between the deep subsurface microbial communities and the rock surfaces, and that this interaction could be crucial for sustaining life in the harsh anoxic and oligotrophic deep subsurface of crystalline bedrock environment.
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Affiliation(s)
| | | | - Mari Raulio
- European Chemicals Agency (ECHA), Helsinki, Finland
| | - Aino Soro
- VTT Technical Research Centre of Finland Ltd., Espoo, Finland
| | | | - Ilmo Kukkonen
- Department of Physics, University of Helsinki, Helsinki, Finland
| | - Malin Bomberg
- VTT Technical Research Centre of Finland Ltd., Espoo, Finland
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25
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St James AR, Richardson RE. Stimulation of dissimilatory sulfate reduction in response to sulfate in microcosm incubations from two contrasting temperate peatlands near Ithaca, NY, USA. FEMS Microbiol Lett 2021; 368:6455309. [PMID: 34875060 DOI: 10.1093/femsle/fnab153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 12/03/2021] [Indexed: 11/12/2022] Open
Abstract
Peatlands are responsible for over half of wetland methane emissions, yet major uncertainties remain regarding carbon flow, especially when increased availability of electron acceptors stimulates competing physiologies. We used microcosm incubations to study the effects of sulfate on microorganisms in two temperate peatlands, one bog and one fen. Three different electron donor treatments were used (13C-acetate, 13C-formate and a mixture of 12C short-chain fatty acids) to elucidate the responses of sulfate-reducing bacteria (SRB) and methanogens to sulfate stimulation. Methane production was measured and metagenomic sequencing was performed, with only the heavy DNA fraction sequenced from treatments receiving 13C electron donors. Our data demonstrate stimulation of dissimilatory sulfate reduction in both sites, with contrasting community responses. In McLean Bog (MB), hydrogenotrophic Deltaproteobacteria and acetotrophic Peptococcaceae lineages of SRB were stimulated, as were lineages with unclassified dissimilatory sulfite reductases. In Michigan Hollow Fen (MHF), there was little stimulation of Peptococcaceae populations, and a small stimulation of Deltaproteobacteria SRB populations only in the presence of formate as electron donor. Sulfate stimulated an increase in relative abundance of reads for both oxidative and reductive sulfite reductases, suggesting stimulation of an internal sulfur cycle. Together, these data indicate a stimulation of SRB activity in response to sulfate in both sites, with a stronger growth response in MB than MHF. This study provides valuable insights into microbial community responses to sulfate in temperate peatlands and is an important first step to understanding how SRB and methanogens compete to regulate carbon flow in these systems.
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Affiliation(s)
- Andrew R St James
- School of Civil and Environmental Engineering, Cornell University, Ithaca, NY 14853, USA
| | - Ruth E Richardson
- School of Civil and Environmental Engineering, Cornell University, Ithaca, NY 14853, USA
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26
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Qi Q, Angermayr SA, Bollenbach T. Uncovering Key Metabolic Determinants of the Drug Interactions Between Trimethoprim and Erythromycin in Escherichia coli. Front Microbiol 2021; 12:760017. [PMID: 34745067 PMCID: PMC8564399 DOI: 10.3389/fmicb.2021.760017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 09/30/2021] [Indexed: 11/16/2022] Open
Abstract
Understanding interactions between antibiotics used in combination is an important theme in microbiology. Using the interactions between the antifolate drug trimethoprim and the ribosome-targeting antibiotic erythromycin in Escherichia coli as a model, we applied a transcriptomic approach for dissecting interactions between two antibiotics with different modes of action. When trimethoprim and erythromycin were combined, the transcriptional response of genes from the sulfate reduction pathway deviated from the dominant effect of trimethoprim on the transcriptome. We successfully altered the drug interaction from additivity to suppression by increasing the sulfate level in the growth environment and identified sulfate reduction as an important metabolic determinant that shapes the interaction between the two drugs. Our work highlights the potential of using prioritization of gene expression patterns as a tool for identifying key metabolic determinants that shape drug-drug interactions. We further demonstrated that the sigma factor-binding protein gene crl shapes the interactions between the two antibiotics, which provides a rare example of how naturally occurring variations between strains of the same bacterial species can sometimes generate very different drug interactions.
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Affiliation(s)
- Qin Qi
- Institute of Science and Technology Austria, Klosterneuburg, Austria.,Institute for Biological Physics, University of Cologne, Cologne, Germany
| | | | - Tobias Bollenbach
- Institute for Biological Physics, University of Cologne, Cologne, Germany.,Center for Data and Simulation Science, University of Cologne, Cologne, Germany
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27
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Adam N, Han Y, Laufer-Meiser K, Bährle R, Schwarz-Schampera U, Schippers A, Perner M. Deltaproteobacterium Strain KaireiS1, a Mesophilic, Hydrogen-Oxidizing and Sulfate-Reducing Bacterium From an Inactive Deep-Sea Hydrothermal Chimney. Front Microbiol 2021; 12:686276. [PMID: 34630341 PMCID: PMC8494109 DOI: 10.3389/fmicb.2021.686276] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 08/24/2021] [Indexed: 11/13/2022] Open
Abstract
A novel deltaproteobacterial, mesophilic, hydrogen-oxidizing, and sulfate-reducing bacterium (strain KaireiS1) was highly enriched from an inactive chimney located in the active zone of the Kairei hydrothermal vent field (Central Indian Ridge) in the Indian Ocean. Based on 16S rRNA gene analyses, strain KaireiS1 is the currently only cultured representative of a cluster of uncultured Deltaproteobacteria, positioned within the Desulfobulbaceae family, between the Desulfobulbus genus and the “Cable Bacteria.” A facultative autotrophic lifestyle of KaireiS1 is indicated by its growth in the absence of organic compounds, measurements of CO2-fixation rates, and activity measurements of carbon monoxide dehydrogenase, the key enzyme of the reductive Acetyl-CoA pathway. Apart from hydrogen, strain KaireiS1 can also use propionate, lactate, and pentadecane as electron donors. However, the highest cell numbers were reached when grown autotrophically with molecular hydrogen. Hydrogen uptake activity was found in membrane and soluble fractions of cell-free extracts and reached up to 2,981±129 nmol H2*min−1*mg−1 of partially purified protein. Commonly, autotrophic sulfate-reducing bacteria from the Deltaproteobacteria class, thriving in hydrothermal vent habitats are described as thermophiles. Given its physiological characteristics and specific isolation source, strain KaireiS1 demonstrates a previously unnoticed potential for microbial sulfate reduction by autotrophs taking place at moderate temperatures in hydrothermal vent fields.
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Affiliation(s)
- Nicole Adam
- GEOMAR and Molecular Biology of Microbial Consortia, GEOMAR Helmholtz Center for Ocean Research Kiel, Kiel, Germany
| | - Yuchen Han
- GEOMAR and Molecular Biology of Microbial Consortia, Biocenter Klein Flottbek, University of Hamburg, Hamburg, Germany.,Microbiology and Biotechnology, Biocenter Klein Flottbek, University of Hamburg, Hamburg, Germany
| | - Katja Laufer-Meiser
- GEOMAR and Molecular Biology of Microbial Consortia, GEOMAR Helmholtz Center for Ocean Research Kiel, Kiel, Germany
| | - Rebecca Bährle
- GEOMAR and Molecular Biology of Microbial Consortia, GEOMAR Helmholtz Center for Ocean Research Kiel, Kiel, Germany
| | - Ulrich Schwarz-Schampera
- Federal Institute for Geosciences and Natural Resources (BGR), Hannover, Germany.,International Seabed Authority, Kingston, Jamaica
| | - Axel Schippers
- Federal Institute for Geosciences and Natural Resources (BGR), Hannover, Germany
| | - Mirjam Perner
- GEOMAR and Molecular Biology of Microbial Consortia, GEOMAR Helmholtz Center for Ocean Research Kiel, Kiel, Germany.,GEOMAR and Molecular Biology of Microbial Consortia, Biocenter Klein Flottbek, University of Hamburg, Hamburg, Germany
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28
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Yadav A, Borrelli JC, Elshahed MS, Youssef NH. Genomic Analysis of Family UBA6911 (Group 18 Acidobacteria) Expands the Metabolic Capacities of the Phylum and Highlights Adaptations to Terrestrial Habitats. Appl Environ Microbiol 2021; 87:e0094721. [PMID: 34160232 PMCID: PMC8357285 DOI: 10.1128/aem.00947-21] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 06/14/2021] [Indexed: 12/19/2022] Open
Abstract
Approaches for recovering and analyzing genomes belonging to novel, hitherto-unexplored bacterial lineages have provided invaluable insights into the metabolic capabilities and ecological roles of yet-uncultured taxa. The phylum Acidobacteria is one of the most prevalent and ecologically successful lineages on Earth, yet currently, multiple lineages within this phylum remain unexplored. Here, we utilize genomes recovered from Zodletone Spring, an anaerobic sulfide and sulfur-rich spring in southwestern Oklahoma, as well as from multiple disparate soil and nonsoil habitats, to examine the metabolic capabilities and ecological role of members of family UBA6911 (group 18) Acidobacteria. The analyzed genomes clustered into five distinct genera, with genera Gp18_AA60 and QHZH01 recovered from soils, genus Ga0209509 from anaerobic digestors, and genera Ga0212092 and UBA6911 from freshwater habitats. All genomes analyzed suggested that members of Acidobacteria group 18 are metabolically versatile heterotrophs capable of utilizing a wide range of proteins, amino acids, and sugars as carbon sources, possess respiratory and fermentative capacities, and display few auxotrophies. Soil-dwelling genera were characterized by larger genome sizes, higher numbers of CRISPR loci, an expanded carbohydrate active enzyme (CAZyme) machinery enabling debranching of specific sugars from polymers, possession of a C1 (methanol and methylamine) degradation machinery, and a sole dependence on aerobic respiration. In contrast, nonsoil genomes encoded a more versatile respiratory capacity for oxygen, nitrite, sulfate, and trimethylamine N-oxide (TMAO) respiration, as well as the potential for utilizing the Wood-Ljungdahl (WL) pathway as an electron sink during heterotrophic growth. Our results not only expand our knowledge of the metabolism of a yet-uncultured bacterial lineage but also provide interesting clues on how terrestrialization and niche adaptation drive metabolic specialization within the Acidobacteria. IMPORTANCE Members of the Acidobacteria are important players in global biogeochemical cycles, especially in soils. A wide range of acidobacterial lineages remain currently unexplored. We present a detailed genomic characterization of genomes belonging to family UBA6911 (also known as group 18) within the phylum Acidobacteria. The genomes belong to different genera and were obtained from soil (genera Gp18_AA60 and QHZH01), freshwater habitats (genera Ga0212092 and UBA6911), and an anaerobic digestor (genus Ga0209509). While all members of the family shared common metabolic features, e.g., heterotrophic respiratory abilities, broad substrate utilization capacities, and few auxotrophies, distinct differences between soil and nonsoil genera were observed. Soil genera were characterized by expanded genomes, higher numbers of CRISPR loci, a larger carbohydrate active enzyme (CAZyme) repertoire enabling monomer extractions from polymer side chains, and methylotrophic (methanol and methylamine) degradation capacities. In contrast, nonsoil genera encoded more versatile respiratory capacities for utilizing nitrite, sulfate, TMAO, and the WL pathway, in addition to oxygen as electron acceptors. Our results not only broaden our understanding of the metabolic capacities within the Acidobacteria but also provide interesting clues on how terrestrialization shaped Acidobacteria evolution and niche adaptation.
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Affiliation(s)
- Archana Yadav
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Jenna C. Borrelli
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Mostafa S. Elshahed
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Noha H. Youssef
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, USA
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Shi X, Oliveira DAF, Holsten L, Steinhauer K, de Rezende JR. Long-Term Biocide Efficacy and Its Effect on a Souring Microbial Community. Appl Environ Microbiol 2021; 87:e0084221. [PMID: 34160245 DOI: 10.1128/AEM.00842-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Reservoir souring, which is the production of H2S mainly by sulfate-reducing microorganisms (SRM) in oil reservoirs, has been a long-standing issue for the oil industry. While biocides have been frequently applied to control biogenic souring, the effects of biocide treatment are usually temporary, and biocides eventually fail. The reasons for biocide failure and the long-term response of the microbial community remain poorly understood. In this study, one-time biocide treatments with glutaraldehyde (GA) and an aldehyde-releasing biocide (ARB) at low (100 ppm) and high (750 ppm) doses were individually applied to a complex SRM community, followed by 1 year of monitoring of the chemical responses and the microbial community succession. The chemical results showed that souring control failed after 7 days at a dose of 100 ppm regardless of the biocide type and lasting souring control for the entire 1-year period was achieved only with ARB at 750 ppm. Microbial community analyses suggested that the high-dose biocide treatments resulted in 1 order of magnitude lower average total microbial abundance and average SRM abundance, compared to the low-dose treatments. The recurrence of souring was associated with reduction of alpha diversity and with long-term microbial community structure changes; therefore, monitoring changes in microbial community metrics may provide early warnings of the failure of a biocide-based souring control program in the field. Furthermore, spore-forming sulfate reducers (Desulfotomaculum and Desulfurispora) were enriched and became dominant in both GA-treated groups, which could cause challenges for the design of long-lasting remedial souring control strategies. IMPORTANCE Reservoir souring is a problem for the oil and gas industry, because H2S corrodes the steel infrastructure, downgrades oil quality, and poses substantial risks to field personnel and the environment. Biocides have been widely applied to remedy souring, but the long-term performance of biocide treatments is hard to predict or to optimize due to limited understanding of the microbial ecology affected by biocide treatment. This study investigates the long-term biocide performance and associated changes in the abundance, diversity, and structure of the souring microbial community, thus advancing the knowledge toward a deeper understanding of the microbial ecology of biocide-treated systems and contributing to the improvement of current biocide-based souring control practices. The study showcases the potential application of incorporating microbial community analyses to forecast souring, and it highlights the long-term consequences of biocide treatment in the microbial communities, with relevance to both operators and regulators.
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30
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Slobodkina G, Allioux M, Merkel A, Cambon-Bonavita MA, Alain K, Jebbar M, Slobodkin A. Physiological and Genomic Characterization of a Hyperthermophilic Archaeon Archaeoglobus neptunius sp. nov. Isolated From a Deep-Sea Hydrothermal Vent Warrants the Reclassification of the Genus Archaeoglobus. Front Microbiol 2021; 12:679245. [PMID: 34335500 PMCID: PMC8322695 DOI: 10.3389/fmicb.2021.679245] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 06/30/2021] [Indexed: 11/28/2022] Open
Abstract
Hyperthermophilic archaea of the genus Archaeoglobus are the subject of many fundamental and biotechnological researches. Despite their significance, the class Archaeoglobi is currently represented by only eight species obtained as axenic cultures and taxonomically characterized. Here, we report the isolation and characterization of a new species of Archaeoglobus from a deep-sea hydrothermal vent (Mid-Atlantic Ridge, TAG) for which the name Archaeoglobus neptunius sp. nov. is proposed. The type strain is SE56T (=DSM 110954T = VKM B-3474T). The cells of the novel isolate are motile irregular cocci growing at 50–85°C, pH 5.5–7.5, and NaCl concentrations of 1.5–4.5% (w/v). Strain SE56T grows lithoautotrophically with H2 as an electron donor, sulfite or thiosulfate as an electron acceptor, and CO2/HCO3− as a carbon source. It is also capable of chemoorganotrophic growth by reduction of sulfate, sulfite, or thiosulfate. The genome of the new isolate consists of a 2,115,826 bp chromosome with an overall G + C content of 46.0 mol%. The whole-genome annotation confirms the key metabolic features of the novel isolate demonstrated experimentally. Genome contains a complete set of genes involved in CO2 fixation via reductive acetyl-CoA pathway, gluconeogenesis, hydrogen and fatty acids oxidation, sulfate reduction, and flagellar motility. The phylogenomic reconstruction based on 122 conserved single-copy archaeal proteins supported by average nucleotide identity (ANI), average amino acid identity (AAI), and alignment fraction (AF) values, indicates a polyphyletic origin of the species currently included into the genus Archaeoglobus, warranting its reclassification.
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Affiliation(s)
- Galina Slobodkina
- Winogradsky Institute of Microbiology, Federal Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | - Maxime Allioux
- Laboratoire de Microbiologie des Environnements Extrêmes LM2E, Univ Brest, CNRS, IFREMER, IRP 1211 MicrobSea, UMR 6197, Plouzané, France
| | - Alexander Merkel
- Winogradsky Institute of Microbiology, Federal Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | - Marie-Anne Cambon-Bonavita
- Laboratoire de Microbiologie des Environnements Extrêmes LM2E, Univ Brest, CNRS, IFREMER, IRP 1211 MicrobSea, UMR 6197, Plouzané, France
| | - Karine Alain
- Laboratoire de Microbiologie des Environnements Extrêmes LM2E, Univ Brest, CNRS, IFREMER, IRP 1211 MicrobSea, UMR 6197, Plouzané, France
| | - Mohamed Jebbar
- Laboratoire de Microbiologie des Environnements Extrêmes LM2E, Univ Brest, CNRS, IFREMER, IRP 1211 MicrobSea, UMR 6197, Plouzané, France
| | - Alexander Slobodkin
- Winogradsky Institute of Microbiology, Federal Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
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Paper JM, Flynn TM, Boyanov MI, Kemner KM, Haller BR, Crank K, Lower A, Jin Q, Kirk MF. Influences of pH and substrate supply on the ratio of iron to sulfate reduction. Geobiology 2021; 19:405-420. [PMID: 33934496 DOI: 10.1111/gbi.12444] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 03/23/2021] [Accepted: 03/28/2021] [Indexed: 06/12/2023]
Abstract
Iron reduction and sulfate reduction often occur simultaneously in anoxic systems, and where that is the case, the molar ratio between the reactions (i.e., Fe/SO42- reduced) influences their impact on water quality and carbon storage. Previous research has shown that pH and the supply of electron donors and acceptors affect that ratio, but it is unclear how their influences compare and affect one another. This study examines impacts of pH and the supply of acetate, sulfate, and goethite on the ratio of iron to sulfate reduction in semi-continuous sediment bioreactors. We examined which parameter had the greatest impact on that ratio and whether the parameter influences depended on the state of each other. Results show that pH had a greater influence than acetate supply on the ratio of iron to sulfate reduction, and that the impact of acetate supply on the ratio depended on pH. In acidic reactors (pH 6.0 media), the ratio of iron to sulfate reduction decreased from 3:1 to 2:1 as acetate supply increased (0-1 mM). In alkaline reactors (pH 7.5 media), iron and sulfate were reduced in equal proportions, regardless of acetate supply. Secondly, a comparison of experiments with and without sulfate shows that the extent of iron reduction was greater if sulfate reduction was occurring and that the effect was larger in alkaline reactors than acidic reactors. Thus, the influence of sulfate supply on iron reduction extent also depended on pH and suggests that iron reduction grows more dependent on sulfate reduction as pH increases. Our results compare well to trends in groundwater geochemistry and provide further evidence that pH is a major control on iron and sulfate reduction in systems with crystalline (oxyhydr)oxides. pH not only affects the ratio between the reactions but also the influences of other parameters on that ratio.
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Affiliation(s)
- Janet M Paper
- Department of Geology, Kansas State University, Manhattan, KS, USA
| | - Theodore M Flynn
- Biosciences Division, Argonne National Laboratory, Argonne, IL, USA
| | - Maxim I Boyanov
- Biosciences Division, Argonne National Laboratory, Argonne, IL, USA
- Institute of Chemical Engineering, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Kenneth M Kemner
- Biosciences Division, Argonne National Laboratory, Argonne, IL, USA
| | - Ben R Haller
- Department of Geology, Kansas State University, Manhattan, KS, USA
| | - Kathleen Crank
- Department of Biology, Benedictine College, Atchison, KS, USA
| | - AnneMarie Lower
- Department of Biology, Benedictine College, Atchison, KS, USA
| | - Qusheng Jin
- Department of Earth Sciences, University of Oregon, Eugene, OR, USA
| | - Matthew F Kirk
- Department of Geology, Kansas State University, Manhattan, KS, USA
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32
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Orellana R, Arancibia A, Badilla L, Acosta J, Arancibia G, Escar R, Ferrada G, Seeger M. Ecophysiological Features Shape the Distribution of Prophages and CRISPR in Sulfate Reducing Prokaryotes. Microorganisms 2021; 9:microorganisms9050931. [PMID: 33925267 PMCID: PMC8146710 DOI: 10.3390/microorganisms9050931] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2021] [Revised: 04/18/2021] [Accepted: 04/23/2021] [Indexed: 12/28/2022] Open
Abstract
Sulfate reducing prokaryotes (SRP) are a phylogenetically and physiologically diverse group of microorganisms that use sulfate as an electron acceptor. SRP have long been recognized as key players of the carbon and sulfur cycles, and more recently, they have been identified to play a relevant role as part of syntrophic and symbiotic relations and the human microbiome. Despite their environmental relevance, there is a poor understanding about the prevalence of prophages and CRISPR arrays and how their distribution and dynamic affect the ecological role of SRP. We addressed this question by analyzing the results of a comprehensive survey of prophages and CRISPR in a total of 91 genomes of SRP with several genotypic, phenotypic, and physiological traits, including genome size, cell volume, minimum doubling time, cell wall, and habitat, among others. Our analysis discovered 81 prophages in 51 strains, representing the 56% of the total evaluated strains. Prophages are non-uniformly distributed across the SRP phylogeny, where prophage-rich lineages belonged to Desulfovibrionaceae and Peptococcaceae. Furthermore, our study found 160 CRISPR arrays in 71 SRP, which is more abundant and widely spread than previously expected. Although there is no correlation between presence and abundance of prophages and CRISPR arrays at the strain level, our analysis showed that there is a directly proportional relation between cellular volumes and number of prophages per cell. This result suggests that there is an additional selective pressure for strains with smaller cells to get rid of foreign DNA, such as prophages, but not CRISPR, due to less availability of cellular resources. Analysis of the prophage genes encoding viral structural proteins reported that 44% of SRP prophages are classified as Myoviridae, and comparative analysis showed high level of homology, but not synteny, among prophages belonging to the Family Desulfovibrionaceae. We further recovered viral-like particles and structures that resemble outer membrane vesicles from D. vulgaris str. Hildenborough. The results of this study improved the current understanding of dynamic interactions between prophages and CRISPR with their hosts in both cultured and hitherto-uncultured SRP strains, and how their distribution affects the microbial community dynamics in several sulfidogenic natural and engineered environments.
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Affiliation(s)
- Roberto Orellana
- Laboratorio de Biología Celular y Ecofisiología Microbiana, Facultad de Ciencias Naturales y Exactas, Universidad de Playa Ancha, Leopoldo Carvallo 270, Valparaíso 2360001, Chile; (A.A.); (L.B.)
- Correspondence:
| | - Alejandra Arancibia
- Laboratorio de Biología Celular y Ecofisiología Microbiana, Facultad de Ciencias Naturales y Exactas, Universidad de Playa Ancha, Leopoldo Carvallo 270, Valparaíso 2360001, Chile; (A.A.); (L.B.)
| | - Leonardo Badilla
- Laboratorio de Biología Celular y Ecofisiología Microbiana, Facultad de Ciencias Naturales y Exactas, Universidad de Playa Ancha, Leopoldo Carvallo 270, Valparaíso 2360001, Chile; (A.A.); (L.B.)
| | - Jonathan Acosta
- Departamento de Estadística, Pontificia Universidad Católica de Chile, Avda. Vicuña Mackenna 4860, Santiago 7820436, Chile;
| | - Gabriela Arancibia
- Laboratorio de Microbiología Molecular y Biotecnología Ambiental, Departamento de Química & Centro de Biotecnología Daniel Alkalay-Lowitt, Universidad Técnica Federico Santa María, Avenida España 1680, Valparaíso 2390123, Chile; (G.A.); (R.E.); (G.F.); (M.S.)
| | - Rodrigo Escar
- Laboratorio de Microbiología Molecular y Biotecnología Ambiental, Departamento de Química & Centro de Biotecnología Daniel Alkalay-Lowitt, Universidad Técnica Federico Santa María, Avenida España 1680, Valparaíso 2390123, Chile; (G.A.); (R.E.); (G.F.); (M.S.)
| | - Gustavo Ferrada
- Laboratorio de Microbiología Molecular y Biotecnología Ambiental, Departamento de Química & Centro de Biotecnología Daniel Alkalay-Lowitt, Universidad Técnica Federico Santa María, Avenida España 1680, Valparaíso 2390123, Chile; (G.A.); (R.E.); (G.F.); (M.S.)
| | - Michael Seeger
- Laboratorio de Microbiología Molecular y Biotecnología Ambiental, Departamento de Química & Centro de Biotecnología Daniel Alkalay-Lowitt, Universidad Técnica Federico Santa María, Avenida España 1680, Valparaíso 2390123, Chile; (G.A.); (R.E.); (G.F.); (M.S.)
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Kushkevych I, Hýžová B, Vítězová M, Rittmann SKMR. Microscopic Methods for Identification of Sulfate-Reducing Bacteria from Various Habitats. Int J Mol Sci 2021; 22:4007. [PMID: 33924516 PMCID: PMC8069399 DOI: 10.3390/ijms22084007] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 03/31/2021] [Accepted: 04/03/2021] [Indexed: 12/01/2022] Open
Abstract
This paper is devoted to microscopic methods for the identification of sulfate-reducing bacteria (SRB). In this context, it describes various habitats, morphology and techniques used for the detection and identification of this very heterogeneous group of anaerobic microorganisms. SRB are present in almost every habitat on Earth, including freshwater and marine water, soils, sediments or animals. In the oil, water and gas industries, they can cause considerable economic losses due to their hydrogen sulfide production; in periodontal lesions and the colon of humans, they can cause health complications. Although the role of these bacteria in inflammatory bowel diseases is not entirely known yet, their presence is increased in patients and produced hydrogen sulfide has a cytotoxic effect. For these reasons, methods for the detection of these microorganisms were described. Apart from selected molecular techniques, including metagenomics, fluorescence microscopy was one of the applied methods. Especially fluorescence in situ hybridization (FISH) in various modifications was described. This method enables visual identification of SRB, determining their abundance and spatial distribution in environmental biofilms and gut samples.
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Affiliation(s)
- Ivan Kushkevych
- Department of Experimental Biology, Faculty of Science, Masaryk University, 62500 Brno, Czech Republic; (B.H.); (M.V.)
| | - Blanka Hýžová
- Department of Experimental Biology, Faculty of Science, Masaryk University, 62500 Brno, Czech Republic; (B.H.); (M.V.)
| | - Monika Vítězová
- Department of Experimental Biology, Faculty of Science, Masaryk University, 62500 Brno, Czech Republic; (B.H.); (M.V.)
| | - Simon K.-M. R. Rittmann
- Archaea Physiology & Biotechnology Group, Department of Functional and Evolutionary Ecology, Universität Wien, 1090 Wien, Austria
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34
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Yang Z, Liu Z, Sklodowska A, Musialowski M, Bajda T, Yin H, Drewniak L. Microbiological Sulfide Removal-From Microorganism Isolation to Treatment of Industrial Effluent. Microorganisms 2021; 9:microorganisms9030611. [PMID: 33809787 PMCID: PMC8002234 DOI: 10.3390/microorganisms9030611] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Revised: 03/13/2021] [Accepted: 03/14/2021] [Indexed: 11/29/2022] Open
Abstract
Management of excessive aqueous sulfide is one of the most significant challenges of treating effluent after biological sulfate reduction for metal recovery from hydrometallurgical leachate. The main objective of this study was to characterize and verify the effectiveness of a sulfide-oxidizing bacterial (SOB) consortium isolated from post-mining wastes for sulfide removal from industrial leachate through elemental sulfur production. The isolated SOB has a complete sulfur-oxidizing metabolic system encoded by sox genes and is dominated by the Arcobacter genus. XRD analysis confirmed the presence of elemental sulfur in the collected sediment during cultivation of the SOB in synthetic medium under controlled physicochemical conditions. The growth yield after three days of cultivation reached ~2.34 gprotein/molsulfid, while approximately 84% of sulfide was transformed into elemental sulfur after 5 days of incubation. Verification of isolated SOB on the industrial effluent confirmed that it can be used for effective sulfide concentration reduction (~100% reduced from the initial 75.3 mg/L), but for complete leachate treatment (acceptable for discharged limits), bioaugmentation with other bacteria is required to ensure adequate reduction of chemical oxygen demand (COD).
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Affiliation(s)
- Zhendong Yang
- Institute of Microbiology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland; (Z.Y.); (A.S.); (M.M.)
| | - Zhenghua Liu
- School of Minerals Processing and Bioengineering, Central South University, No. 932 Lushan South Road, Changsha 410083, China; (Z.L.); (H.Y.)
| | - Aleksandra Sklodowska
- Institute of Microbiology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland; (Z.Y.); (A.S.); (M.M.)
| | - Marcin Musialowski
- Institute of Microbiology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland; (Z.Y.); (A.S.); (M.M.)
| | - Tomasz Bajda
- Faculty of Geology, Geophysics and Environmental Protection, AGH University of Science and Technology in Krakow, A. Mickiewicza 30, 30-059 Krakow, Poland;
| | - Huaqun Yin
- School of Minerals Processing and Bioengineering, Central South University, No. 932 Lushan South Road, Changsha 410083, China; (Z.L.); (H.Y.)
| | - Lukasz Drewniak
- Institute of Microbiology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland; (Z.Y.); (A.S.); (M.M.)
- Correspondence: ; Tel./Fax: +48-22-55-41-219
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35
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Alves JI, Salvador AF, Castro AR, Zheng Y, Nijsse B, Atashgahi S, Sousa DZ, Stams AJM, Alves MM, Cavaleiro AJ. Long-Chain Fatty Acids Degradation by Desulfomonile Species and Proposal of " Candidatus Desulfomonile Palmitatoxidans". Front Microbiol 2021; 11:539604. [PMID: 33391191 PMCID: PMC7773648 DOI: 10.3389/fmicb.2020.539604] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Accepted: 11/24/2020] [Indexed: 11/13/2022] Open
Abstract
Microbial communities with the ability to convert long-chain fatty acids (LCFA) coupled to sulfate reduction can be important in the removal of these compounds from wastewater. In this work, an enrichment culture, able to oxidize the long-chain fatty acid palmitate (C16 : 0) coupled to sulfate reduction, was obtained from anaerobic granular sludge. Microscopic analysis of this culture, designated HP culture, revealed that it was mainly composed of one morphotype with a typical collar-like cell wall invagination, a distinct morphological feature of the Desulfomonile genus. 16S rRNA gene amplicon and metagenome-assembled genome (MAG) indeed confirmed that the abundant phylotype in HP culture belong to Desulfomonile genus [ca. 92% 16S rRNA gene sequences closely related to Desulfomonile spp.; and ca. 82% whole genome shotgun (WGS)]. Based on similar cell morphology and average nucleotide identity (ANI) (77%) between the Desulfomonile sp. in HP culture and the type strain Desulfomonile tiedjei strain DCB-1T, we propose a novel species designated as "Candidatus Desulfomonile palmitatoxidans." This bacterium shares 94.3 and 93.6% 16S rRNA gene identity with Desulfomonile limimaris strain DCB-MT and D. tiedjei strain DCB-1T, respectively. Based on sequence abundance of Desulfomonile-morphotype in HP culture, its predominance in the microscopic observations, and presence of several genes coding for enzymes involved in LCFA degradation, the proposed species "Ca. Desulfomonile palmitatoxidans" most probably plays an important role in palmitate degradation in HP culture. Analysis of the growth of HP culture and D. tiedjei strain DCB-1T with short- (butyrate), medium- (caprylate) and long-chain fatty acids (palmitate, stearate, and oleate) showed that both cultures degraded all fatty acids coupled to sulfate reduction, except oleate that was only utilized by HP culture. In the absence of sulfate, neither HP culture, nor D. tiedjei strain DCB-1T degraded palmitate when incubated with Methanobacterium formicicum as a possible methanogenic syntrophic partner. Unlike D. tiedjei strain DCB-1T, "Ca. Desulfomonile palmitatoxidans" lacks reductive dehalogenase genes in its genome, and HP culture was not able to grow by organohalide respiration. An emended description of the genus Desulfomonile is proposed. Our study reveals an unrecognized LCFA degradation feature of the Desulfomonile genus.
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Affiliation(s)
- Joana I Alves
- Centre of Biological Engineering, University of Minho, Braga, Portugal
| | | | - A Rita Castro
- Centre of Biological Engineering, University of Minho, Braga, Portugal
| | - Ying Zheng
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, Netherlands
| | - Bart Nijsse
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, Netherlands.,Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen, Netherlands
| | - Siavash Atashgahi
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, Netherlands
| | - Diana Z Sousa
- Centre of Biological Engineering, University of Minho, Braga, Portugal.,Laboratory of Microbiology, Wageningen University & Research, Wageningen, Netherlands
| | - Alfons J M Stams
- Centre of Biological Engineering, University of Minho, Braga, Portugal.,Laboratory of Microbiology, Wageningen University & Research, Wageningen, Netherlands
| | - M Madalena Alves
- Centre of Biological Engineering, University of Minho, Braga, Portugal
| | - Ana J Cavaleiro
- Centre of Biological Engineering, University of Minho, Braga, Portugal
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36
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Bin Hudari MS, Vogt C, Richnow HH. Effect of Temperature on Acetate Mineralization Kinetics and Microbial Community Composition in a Hydrocarbon-Affected Microbial Community During a Shift From Oxic to Sulfidogenic Conditions. Front Microbiol 2021; 11:606565. [PMID: 33391229 PMCID: PMC7773710 DOI: 10.3389/fmicb.2020.606565] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 11/23/2020] [Indexed: 01/04/2023] Open
Abstract
Aquifer thermal energy storage (ATES) allows for the seasonal storage and extraction of heat in the subsurface thus reducing reliance on fossil fuels and supporting decarbonization of the heating and cooling sector. However, the impacts of higher temperatures toward biodiversity and ecosystem services in the subsurface environment remain unclear. Here, we conducted a laboratory microcosm study comprising a hydrocarbon-degrading microbial community from a sulfidic hydrocarbon-contaminated aquifer spiked with 13C-labeled acetate and incubated at temperatures between 12 and 80°C to evaluate (i) the extent and rates of acetate mineralization and (ii) the resultant temperature-induced shifts in the microbial community structure. We observed biphasic mineralization curves at 12, 25, 38, and 45°C, arising from immediate and fast aerobic mineralization due to an initial oxygen exposure, followed by slower mineralization at sulfidogenic conditions. At 60°C and several replicates at 45°C, acetate was only aerobically mineralized. At 80°C, no mineralization was observed within 178 days. Rates of acetate mineralization coupled to sulfate reduction at 25 and 38°C were six times faster than at 12°C. Distinct microbial communities developed in oxic and strictly anoxic phases of mineralization as well as at different temperatures. Members of the Alphaproteobacteria were dominant in the oxic mineralization phase at 12–38°C, succeeded by a more diverse community in the anoxic phase composed of Deltaproteobacteria, Clostridia, Spirochaetia, Gammaproteobacteria and Anaerolinea, with varying abundances dependent on the temperature. In the oxic phases at 45 and 60°C, phylotypes affiliated to spore-forming Bacilli developed. In conclusion, temperatures up to 38°C allowed aerobic and anaerobic acetate mineralization albeit at varying rates, while mineralization occurred mainly aerobically between 45 and 60°C; thermophilic sulfate reducers being active at temperatures > 45°C were not detected. Hence, temperature may affect dissolved organic carbon mineralization rates in ATES while the variability in the microbial community composition during the transition from micro-oxic to sulfidogenic conditions highlights the crucial role of electron acceptor availability when combining ATES with bioremediation.
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Affiliation(s)
| | - Carsten Vogt
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research, Leipzig, Germany
| | - Hans Hermann Richnow
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research, Leipzig, Germany
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Xin Y, Gao R, Cui F, Lü C, Liu H, Liu H, Xia Y, Xun L. The Heterotrophic Bacterium Cupriavidus pinatubonensis JMP134 Oxidizes Sulfide to Sulfate with Thiosulfate as a Key Intermediate. Appl Environ Microbiol 2020; 86:e01835-20. [PMID: 32917752 DOI: 10.1128/AEM.01835-20] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 09/02/2020] [Indexed: 12/26/2022] Open
Abstract
Heterotrophic bacteria actively participate in the biogeochemical cycle of sulfur on Earth. The heterotrophic bacterium Cupriavidus pinatubonensis JMP134 contains several enzymes involved in sulfur oxidation, but how these enzymes work together to oxidize sulfide in the bacterium has not been studied. Using gene-deletion and whole-cell assays, we determined that the bacterium uses sulfide:quinone oxidoreductase to oxidize sulfide to polysulfide, which is further oxidized to sulfite by persulfide dioxygenase. Sulfite spontaneously reacts with polysulfide to produce thiosulfate. The sulfur-oxidizing (Sox) system oxidizes thiosulfate to sulfate. Flavocytochrome c sulfide dehydrogenase enhances thiosulfate oxidation by the Sox system but couples with the Sox system for sulfide oxidation to sulfate in the absence of sulfide:quinone oxidoreductase. Thus, C. pinatubonensis JMP134 contains a main pathway and a contingent pathway for sulfide oxidation.IMPORTANCE We establish a new pathway of sulfide oxidation with thiosulfate as a key intermediate in Cupriavidus pinatubonensis JMP134. The bacterium mainly oxidizes sulfide by using sulfide:quinone oxidoreductase, persulfide dioxygenase, and the Sox system with thiosulfate as a key intermediate. Although the purified and reconstituted Sox system oxidizes sulfide, its rate of sulfide oxidation in C. pinatubonensis JMP134 is too low to be physiologically relevant. The findings reveal how these sulfur-oxidizing enzymes participate in sulfide oxidation in a single bacterium.
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Smith DA, Fike DA, Johnston DT, Bradley AS. Isotopic Fractionation Associated With Sulfate Import and Activation by Desulfovibrio vulgaris str. Hildenborough. Front Microbiol 2020; 11:529317. [PMID: 33072004 PMCID: PMC7531388 DOI: 10.3389/fmicb.2020.529317] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Accepted: 08/14/2020] [Indexed: 11/13/2022] Open
Abstract
The use of stable isotopes to trace biogeochemical sulfur cycling relies on an understanding of how isotopic fractionation is imposed by metabolic networks. We investigated the effects of the first two enzymatic steps in the dissimilatory sulfate reduction (DSR) network - sulfate permease and sulfate adenylyl transferase (Sat) - on the sulfur and oxygen isotopic composition of residual sulfate. Mutant strains of Desulfovibrio vulgaris str. Hildenborough (DvH) with perturbed expression of these enzymes were grown in batch culture, with a subset grown in continuous culture, to examine the impact of these enzymatic steps on growth rate, cell specific sulfate reduction rate and isotopic fractionations in comparison to the wild type strain. Deletion of several permease genes resulted in only small (∼1‰) changes in sulfur isotope fractionation, a difference that approaches the uncertainties of the measurement. Mutants that perturb Sat expression show higher fractionations than the wild type strain. This increase probably relates to an increased material flux between sulfate and APS, allowing an increase in the expressed fractionation of rate-limiting APS reductase. This work illustrates that flux through the initial steps of the DSR pathway can affect the fractionation imposed by the overall pathway, even though these steps are themselves likely to impose only small fractionations.
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Affiliation(s)
- Derek A Smith
- Department of Earth and Planetary Sciences, Washington University in St. Louis, St. Louis, MO, United States
| | - David A Fike
- Department of Earth and Planetary Sciences, Washington University in St. Louis, St. Louis, MO, United States
| | - David T Johnston
- Department of Earth and Planetary Sciences, Harvard University, Cambridge, MA, United States
| | - Alexander S Bradley
- Department of Earth and Planetary Sciences, Washington University in St. Louis, St. Louis, MO, United States.,Division of Biology and Biomedical Sciences, Washington University in St. Louis, St. Louis, MO, United States
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Xie X, Spiteller D, Huhn T, Schink B, Müller N. Desulfatiglans anilini Initiates Degradation of Aniline With the Production of Phenylphosphoamidate and 4-Aminobenzoate as Intermediates Through Synthases and Carboxylases From Different Gene Clusters. Front Microbiol 2020; 11:2064. [PMID: 33013754 PMCID: PMC7500099 DOI: 10.3389/fmicb.2020.02064] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 08/05/2020] [Indexed: 01/22/2023] Open
Abstract
The anaerobic degradation of aniline was studied in the sulfate-reducing bacterium Desulfatiglans anilini. Our aim was to identify the genes and their proteins that are required for the initial activation of aniline as well as to characterize intermediates of this reaction. Aniline-induced genes were revealed by comparison of the proteomes of D. anilini grown with different substrates (aniline, 4-aminobenzoate, phenol, and benzoate). Most genes encoding proteins that were highly abundant in aniline- or 4-aminobenzoate-grown D. anilini cells but not in phenol- or benzoate-grown cells were located in the putative gene clusters ani (aniline degradation), hcr (4-hydroxybenzoyl-CoA reductase) and phe (phenol degradation). Of these putative gene clusters, only the phe gene cluster has been studied previously. Based on the differential proteome analysis, four candidate genes coding for kinase subunits and carboxylase subunits were suspected to be responsible for the initial conversion of aniline to 4-aminobenzoate. These genes were cloned and overproduced in E. coli. The recombinant proteins were obtained in inclusion bodies but could be refolded successfully. Two subunits of phenylphosphoamidate synthase and two carboxylase subunits converted aniline to 4-aminobenzoate with phenylphosphoamidate as intermediate under consumption of ATP. Only when both carboxylase subunits, one from gene cluster ani and the other from gene cluster phe, were combined, phenylphosphoamidate was converted to 4-aminobenzoate in vitro, with Mn2+, K+, and FMN as co-factors. Thus, aniline is degraded by the anaerobic bacterium D. anilini only by recruiting genes for the enzymatic machinery from different gene clusters. We conclude, that D. anilini carboxylates aniline to 4-aminobenzoate via phenylphosphoamidate as an energy rich intermediate analogous to the degradation of phenol to 4-hydroxybenzoate via phenylphosphate.
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Affiliation(s)
- Xiaoman Xie
- Department of Biology, Universität Konstanz, Konstanz, Germany.,Konstanz Research School Chemical Biology, Konstanz, Germany
| | - Dieter Spiteller
- Department of Biology, Universität Konstanz, Konstanz, Germany.,Konstanz Research School Chemical Biology, Konstanz, Germany
| | - Thomas Huhn
- Konstanz Research School Chemical Biology, Konstanz, Germany.,Department of Chemistry, Universität Konstanz, Konstanz, Germany
| | - Bernhard Schink
- Department of Biology, Universität Konstanz, Konstanz, Germany.,Konstanz Research School Chemical Biology, Konstanz, Germany
| | - Nicolai Müller
- Department of Biology, Universität Konstanz, Konstanz, Germany
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40
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Plugge CM, Sousa JAB, Christel S, Dopson M, Bijmans MFM, Stams AJM, Diender M. Syngas as Electron Donor for Sulfate and Thiosulfate Reducing Haloalkaliphilic Microorganisms in a Gas-Lift Bioreactor. Microorganisms 2020; 8:E1451. [PMID: 32971967 DOI: 10.3390/microorganisms8091451] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 09/17/2020] [Accepted: 09/21/2020] [Indexed: 11/16/2022] Open
Abstract
Biodesulfurization processes remove toxic and corrosive hydrogen sulfide from gas streams (e.g., natural gas, biogas, or syngas). To improve the efficiency of these processes under haloalkaline conditions, a sulfate and thiosulfate reduction step can be included. The use of H2/CO mixtures (as in syngas) instead of pure H2 was tested to investigate the potential cost reduction of the electron donor required. Syngas is produced in the gas-reforming process and consists mainly of H2, carbon monoxide (CO), and carbon dioxide (CO2). Purification of syngas to obtain pure H2 implies higher costs because of additional post-treatment. Therefore, the use of syngas has merit in the biodesulfurization process. Initially, CO inhibited hydrogen-dependent sulfate reduction. However, after 30 days the biomass was adapted and both H2 and CO were used as electron donors. First, formate was produced, followed by sulfate and thiosulfate reduction, and later in the reactor run acetate and methane were detected. Sulfide production rates with sulfate and thiosulfate after adaptation were comparable with previously described rates with only hydrogen. The addition of CO marginally affected the microbial community in which Tindallia sp. was dominant. Over time, acetate production increased and acetogenesis became the dominant process in the bioreactor. Around 50% of H2/CO was converted to acetate. Acetate supported biomass growth and higher biomass concentrations were reached compared to bioreactors without CO feed. Finally, CO addition resulted in the formation of small, compact microbial aggregates. This suggests that CO or syngas can be used to stimulate aggregation in haloalkaline biodesulfurization systems.
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van der Graaf CM, Sánchez-España J, Yusta I, Ilin A, Shetty SA, Bale NJ, Villanueva L, Stams AJM, Sánchez-Andrea I. Biosulfidogenesis Mediates Natural Attenuation in Acidic Mine Pit Lakes. Microorganisms 2020; 8:E1275. [PMID: 32825668 PMCID: PMC7565709 DOI: 10.3390/microorganisms8091275] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 08/10/2020] [Accepted: 08/14/2020] [Indexed: 12/13/2022] Open
Abstract
Acidic pit lakes are abandoned open pit mines filled with acid mine drainage (AMD)-highly acidic, metalliferous waters that pose a severe threat to the environment and are rarely properly remediated. Here, we investigated two meromictic, oligotrophic acidic mine pit lakes in the Iberian Pyrite Belt (IPB), Filón Centro (Tharsis) (FC) and La Zarza (LZ). We observed a natural attenuation of acidity and toxic metal concentrations towards the lake bottom, which was more pronounced in FC. The detection of Cu and Zn sulfides in the monimolimnion of FC suggests precipitation of dissolved metals as metal sulfides, pointing to biogenic sulfide formation. This was supported by microbial diversity analysis via 16S rRNA gene amplicon sequencing of samples from the water column, which showed the presence of sulfidogenic microbial taxa in FC and LZ. In the monimolimnion of FC, sequences affiliated with the putative sulfate-reducing genus Desulfomonile were dominant (58%), whereas in the more acidic and metal-enriched LZ, elemental sulfur-reducing Acidianus and Thermoplasma spp., and disproportionating Desulfocapsa spp. were more abundant. Furthermore, the detection of reads classified as methanogens and Desulfosporosinus spp., although at low relative abundance, represents one of the lowest pH values (2.9 in LZ) at which these taxa have been reported, to our knowledge. Analysis of potential biomarker lipids provided evidence that high levels of phosphocholine lipids with mixed acyl/ether glycerol core structures were associated with Desulfomonile, while ceramide lipids were characteristic of Microbacter in these environments. We propose that FC and LZ function as natural bioremediation reactors where metal sulfide precipitation is mediated by biosulfidogenesis starting from elemental sulfur reduction and disproportionation at an early stage (LZ), followed by sulfate reduction at a later stage (FC).
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Affiliation(s)
- Charlotte M. van der Graaf
- Laboratory of Microbiology, Wageningen University, Stippeneng 4, 6708 WE Wageningen, The Netherlands; (S.A.S.); (A.J.M.S.)
| | - Javier Sánchez-España
- Geochemistry and Sustainable Mining Unit, Dept of Geological Resources, Spanish Geological Survey (IGME), Calera 1, Tres Cantos, 28760 Madrid, Spain;
| | - Iñaki Yusta
- Dept of Mineralogy and Petrology, University of the Basque Country (UPV/EHU), Apdo. 644, 48080 Bilbao, Spain; (I.Y.); (A.I.)
| | - Andrey Ilin
- Dept of Mineralogy and Petrology, University of the Basque Country (UPV/EHU), Apdo. 644, 48080 Bilbao, Spain; (I.Y.); (A.I.)
| | - Sudarshan A. Shetty
- Laboratory of Microbiology, Wageningen University, Stippeneng 4, 6708 WE Wageningen, The Netherlands; (S.A.S.); (A.J.M.S.)
| | - Nicole J. Bale
- NIOZ Royal Netherlands Institute for Sea Research, Department of Marine Microbiology and Biogeochemistry, and Utrecht University, Landsdiep 4, 1797 SZ ‘t Horntje, The Netherlands; (N.J.B.); (L.V.)
| | - Laura Villanueva
- NIOZ Royal Netherlands Institute for Sea Research, Department of Marine Microbiology and Biogeochemistry, and Utrecht University, Landsdiep 4, 1797 SZ ‘t Horntje, The Netherlands; (N.J.B.); (L.V.)
| | - Alfons J. M. Stams
- Laboratory of Microbiology, Wageningen University, Stippeneng 4, 6708 WE Wageningen, The Netherlands; (S.A.S.); (A.J.M.S.)
- Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - Irene Sánchez-Andrea
- Laboratory of Microbiology, Wageningen University, Stippeneng 4, 6708 WE Wageningen, The Netherlands; (S.A.S.); (A.J.M.S.)
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Li H, Yang Q, Zhou H. Niche Differentiation of Sulfate- and Iron-Dependent Anaerobic Methane Oxidation and Methylotrophic Methanogenesis in Deep Sea Methane Seeps. Front Microbiol 2020; 11:1409. [PMID: 32733397 PMCID: PMC7360803 DOI: 10.3389/fmicb.2020.01409] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2020] [Accepted: 05/29/2020] [Indexed: 11/18/2022] Open
Abstract
Methane seeps are widespread seafloor ecosystems shaped by complex physicochemical-biological interactions over geological timescales, and seep microbiomes play a vital role in global biogeochemical cycling of key elements on Earth. However, the mechanisms underlying the coexistence of methane-cycling microbial communities remain largely elusive. Here, high-resolution sediment incubation experiments revealed a cryptic methane cycle in the South China Sea (SCS) methane seep ecosystem, showing the coexistence of sulfate (SO4 2-)- or iron (Fe)-dependent anaerobic oxidation of methane (AOM) and methylotrophic methanogenesis. This previously unrecognized methane cycling is not discernible from geochemical profiles due to high net methane consumption. High-throughput sequencing and Catalyzed Reporter Deposition-Fluorescence in situ Hybridization (CARD-FISH) results suggested that anaerobic methane-oxidizing archaea (ANME)-2 and -3 coupled to sulfate-reducing bacteria (SRB) carried out SO4 2--AOM, and alternative ANME-2 and -3 solely or coupled to iron-reducing bacteria (IRB) might participate in Fe-AOM in sulfate-depleted environments. This finding suggested that ANME could alter AOM metabolic pathways according to geochemical changes. Furthermore, the majority of methylotrophic methanogens belonged to Methanimicrococcus, and hydrogenotrophic and acetoclastic methanogens were likely inhibited by sulfate or iron respiration. Fe-AOM and methylotrophic methanogenesis are overlooked potential sources and sinks of methane in methane seep ecosystems, thus influencing methane budgets and even the global carbon budget in the ocean.
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Affiliation(s)
| | - Qunhui Yang
- State Key Laboratory of Marine Geology, Tongji University, Shanghai, China
| | - Huaiyang Zhou
- State Key Laboratory of Marine Geology, Tongji University, Shanghai, China
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Ward LM, Bertran E, Johnston DT. Genomic sequence analysis of Dissulfurirhabdus thermomarina SH388 and proposed reassignment to Dissulfurirhabdaceae fam. nov. Microb Genom 2020; 6:mgen000390. [PMID: 32553052 PMCID: PMC7478628 DOI: 10.1099/mgen.0.000390] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Accepted: 05/20/2020] [Indexed: 11/18/2022] Open
Abstract
Here, we report the draft genome sequence of Dissulfurirhabdus thermomarina SH388. Improved phylogenetic and taxonomic analysis of this organism using genome-level analyses supports assignment of this organism to a novel family within the phylum Desulfobacterota. Additionally, comparative genomic and phylogenetic analyses contextualize the convergent evolution of sulfur disproportionation and potential extracellular electron transfer in this organism relative to other members of the Desulfobacterota.
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Affiliation(s)
- Lewis M. Ward
- Department of Earth and Planetary Sciences, Harvard University, Cambridge, MA, USA
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, Japan
| | - Emma Bertran
- Department of Earth and Planetary Sciences, Harvard University, Cambridge, MA, USA
- Department of Geosciences, Princeton University, Princeton, NJ, USA
| | - David T. Johnston
- Department of Earth and Planetary Sciences, Harvard University, Cambridge, MA, USA
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Kushkevych I, Castro Sangrador J, Dordević D, Rozehnalová M, Černý M, Fafula R, Vítězová M, Rittmann SKMR. Evaluation of Physiological Parameters of Intestinal Sulfate-Reducing Bacteria Isolated from Patients Suffering from IBD and Healthy People. J Clin Med 2020; 9:E1920. [PMID: 32575467 PMCID: PMC7357025 DOI: 10.3390/jcm9061920] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 06/15/2020] [Accepted: 06/16/2020] [Indexed: 01/26/2023] Open
Abstract
BACKGROUND Inflammatory bowel diseases (IBDs) are multifactorial illnesses of the intestine, to which microorganisms are contributing. Among the contributing microorganisms, sulfate-reducing bacteria (SRB) are suggested to be involved in the process of bowel inflammation due to the production of hydrogen sulfide (H2S) by dissimilatory sulfate reduction. The aims of our research were to physiologically examine SRB in fecal samples of patients with IBD and a control group, their identification, the study of the process of dissimilatory sulfate reduction (sulfate consumption and H2S production) and biomass accumulation. Determination of biogenic elements of the SRB and evaluation of obtained parameters by using statistical methods were also included in the research. The material for the research consisted of 14 fecal samples, which was obtained from patients and control subjects. METHODS Microscopic techniques, microbiological, biochemical, biophysical methods and statistical analysis were included. RESULTS Colonies of SRB were isolated from all the fecal samples, and subsequently, 35 strains were obtained. Vibrio-shaped cells stained Gram-negative were dominant in all purified studied strains. All strains had a high percentage of similarity by the 16S rRNA gene with deposited sequences in GenBank of Desulfovibrio vulgaris. Cluster analysis of sulfate reduction parameters allowed the grouping of SRB strains. Significant (p < 0.05) differences were not observed between healthy individuals and patients with IBD with regard to sulfate reduction parameters (sulfate consumption, H2S and biomass accumulation). Moreover, we found that manganese and iron contents in the cell extracts are higher among healthy individuals in comparison to unhealthy individuals that have an intestinal bowel disease, especially ulcerative colitis. CONCLUSIONS The observations obtained from studying SRB emphasize differences in the intestinal microbial processes of healthy and unhealthy people.
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Affiliation(s)
- Ivan Kushkevych
- Department of Experimental Biology, Faculty of Science, Masaryk University, Kamenice 753/5, 62500 Brno, Czech Republic; (J.C.S.); (M.C.); (M.V.)
| | - Jorge Castro Sangrador
- Department of Experimental Biology, Faculty of Science, Masaryk University, Kamenice 753/5, 62500 Brno, Czech Republic; (J.C.S.); (M.C.); (M.V.)
- Faculty of Biology, University of Salamanca, Campus Miguel de Unamuno C/Donantes de sangre, s/n 37007 Salamanca, Spain
| | - Dani Dordević
- Department of Plant Origin Foodstuffs Hygiene and Technology, Faculty of Veterinary Hygiene and Ecology, University of Veterinary and Pharmaceutical Sciences, 61242 Brno, Czech Republic;
| | - Monika Rozehnalová
- Centre of Region Hana for Biotechnological an Agricultural Research, Central Laboratories and Research Support, Faculty of Science, Palacky University Olomouc, 77900 Olomouc, Czech Republic;
| | - Martin Černý
- Department of Experimental Biology, Faculty of Science, Masaryk University, Kamenice 753/5, 62500 Brno, Czech Republic; (J.C.S.); (M.C.); (M.V.)
| | - Roman Fafula
- Department of Medical Biophysics, Danylo Halytsky Lviv National Medical University, 69 Pekarska St., 79010 Lviv, Ukraine;
| | - Monika Vítězová
- Department of Experimental Biology, Faculty of Science, Masaryk University, Kamenice 753/5, 62500 Brno, Czech Republic; (J.C.S.); (M.C.); (M.V.)
| | - Simon K.-M. R. Rittmann
- Archaea Physiology & Biotechnology Group, Department of Functional and Evolutionary Ecology, Universität Wien, Althanstraße 14, 1090 Vienna, Austria
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Liu Y, Luo M, Ye R, Huang J, Xiao L, Hu Q, Zhu A, Tong C. Impacts of the rhizosphere effect and plant species on organic carbon mineralization rates and pathways, and bacterial community composition in a tidal marsh. FEMS Microbiol Ecol 2020; 95:5538758. [PMID: 31344237 DOI: 10.1093/femsec/fiz120] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Accepted: 07/18/2019] [Indexed: 11/13/2022] Open
Abstract
Despite the growing recognition regarding the carbon cycle in the rhizosphere of upland ecosystems, little is known regarding the rhizosphere effect on soil organic carbon (SOC) mineralization in tidal marsh soils. In the current study, in situ rhizobox experiments (including rhizosphere and inner and outer bulk soil) were conducted in an estuarine tidal marsh. Our results showed that a higher abundance of total bacteria, Geobacter, dsrA and mcrA and lower α-diversity were observed in the rhizosphere relative to the bulk soil. Rhizosphere effects shifted the partition of terminal metabolic pathways from sulfate reduction in the bulk soil to the co-dominance of microbial Fe(III) and sulfate reduction in the rhizosphere. Although the rhizosphere effect promoted the rates of three terminal metabolic pathways, it showed greater preference towards microbial Fe(III) reduction in the tidal marsh soils. Plant species had little impact on the partitioning of terminal metabolic pathways, but did affect the potential of total SOC mineralization together with the abundance and diversity of total bacteria. Both the rhizosphere effect and plant species influenced the bacterial community composition in the tidal marsh soils; however, plant species had a less pronounced impact on the bacterial community compared with that of the rhizosphere effect.
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Affiliation(s)
- Yuxiu Liu
- Key Laboratory of Humid Subtropical Eco-Geographical Process, Ministry of Education, Fujian Normal University, Fuzhou 350007, China
| | - Min Luo
- Key Laboratory of Humid Subtropical Eco-Geographical Process, Ministry of Education, Fujian Normal University, Fuzhou 350007, China.,School of Environment and Resource, Fuzhou University, Fuzhou 350116, China
| | - Rongzhong Ye
- Pee Dee Research & Education Centers, Clemson University, Florence, SC 29506, USA
| | - Jiafang Huang
- Key Laboratory of Humid Subtropical Eco-Geographical Process, Ministry of Education, Fujian Normal University, Fuzhou 350007, China
| | - Leilei Xiao
- Key Laboratory of Coastal Biology and Biological Resources Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, China
| | - Qikai Hu
- Key Laboratory of Humid Subtropical Eco-Geographical Process, Ministry of Education, Fujian Normal University, Fuzhou 350007, China.,School of Environment and Resource, Fuzhou University, Fuzhou 350116, China
| | - Aijv Zhu
- Key Laboratory of Humid Subtropical Eco-Geographical Process, Ministry of Education, Fujian Normal University, Fuzhou 350007, China
| | - Chuan Tong
- Key Laboratory of Humid Subtropical Eco-Geographical Process, Ministry of Education, Fujian Normal University, Fuzhou 350007, China
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46
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Pellerin A, Antler G, Marietou A, Turchyn AV, Jørgensen BB. The effect of temperature on sulfur and oxygen isotope fractionation by sulfate reducing bacteria (Desulfococcus multivorans). FEMS Microbiol Lett 2020; 367:5817845. [PMID: 32267916 DOI: 10.1093/femsle/fnaa061] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Accepted: 04/04/2020] [Indexed: 11/14/2022] Open
Abstract
Temperature influences microbiological growth and catabolic rates. Between 15 and 35 °C the growth rate and cell specific sulfate reduction rate of the sulfate reducing bacterium Desulfococcus multivorans increased with temperature. Sulfur isotope fractionation during sulfate reduction decreased with increasing temperature from 27.2 ‰ at 15 °C to 18.8 ‰ at 35 °C which is consistent with a decreasing reversibility of the metabolic pathway as the catabolic rate increases. Oxygen isotope fractionation, in contrast, decreased between 15 and 25 °C and then increased again between 25 and 35 °C, suggesting increasing reversibility in the first steps of the sulfate reducing pathway at higher temperatures. This points to a decoupling in the reversibility of sulfate reduction between the steps from the uptake of sulfate into the cell to the formation of sulfite, relative to the whole pathway from sulfate to sulfide. This observation is consistent with observations of increasing sulfur isotope fractionation when sulfate reducing bacteria are living near their upper temperature limit. The oxygen isotope decoupling may be a first signal of changing physiology as the bacteria cope with higher temperatures.
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Affiliation(s)
- André Pellerin
- Center for Geomicrobiology, Ny Munkegade 116, Aarhus C 8000, Aarhus University, Department of Bioscience, Denmark.,Department of Geological and Environmental Sciences, Ben-Gurion University of the Negev, P. O. Box 653, Beer-Sheva 84105, Israel
| | - Gilad Antler
- Department of Geological and Environmental Sciences, Ben-Gurion University of the Negev, P. O. Box 653, Beer-Sheva 84105, Israel.,The Interuniversity Institute for Marine Sciences of Eilat, PO Box 469, Eilat 88103, Israel
| | - Angeliki Marietou
- Center for Geomicrobiology, Ny Munkegade 116, Aarhus C 8000, Aarhus University, Department of Bioscience, Denmark
| | - Alexandra V Turchyn
- Cambridge University, Downing Street, Cambridge, CB2 3EQ, Departement of Earth Sciences, Cambridge, UK
| | - Bo Barker Jørgensen
- Center for Geomicrobiology, Ny Munkegade 116, Aarhus C 8000, Aarhus University, Department of Bioscience, Denmark
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Pérez-Bernal MF, Brito EMS, Bartoli M, Aubé J, Ollivier B, Guyoneaud R, Hirschler-Réa A. Desulfobotulus mexicanus sp. nov., a novel sulfate-reducing bacterium isolated from the sediment of an alkaline crater lake in Mexico. Int J Syst Evol Microbiol 2020; 70:3219-3225. [PMID: 32271141 DOI: 10.1099/ijsem.0.004159] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel Gram-negative, non-spore-forming, vibrio-shaped, anaerobic, alkaliphilic, sulfate-reducing bacterium, designated strain PAR22NT, was isolated from sediment samples collected at an alkaline crater lake in Guanajuato (Mexico). Strain PAR22NT grew at temperatures between 15 and 37 °C (optimum, 32 °C), at pH between pH 8.3 and 10.1 (optimum, pH 9.0-9.6), and in the presence of NaCl up to 10 %. Pyruvate, 2-methylbutyrate and fatty acids (4-18 carbon atoms) were used as electron donors in the presence of sulfate as a terminal electron acceptor and were incompletely oxidized to acetate and CO2. Besides sulfate, both sulfite and elemental sulfur were also used as terminal electron acceptors and were reduced to sulfide. The predominant fatty acids were summed feature 10 (C18 : 1 ω7c and/or C18 : 1 ω9t and/or C18 : 1 ω12t), C18 : 1 ω9c and C16 : 0. The genome size of strain PAR22NT was 3.8 Mb including 3391 predicted genes. The genomic DNA G+C content was 49.0 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that it belongs to the genus Desulfobotulus within the class Deltaproteobacteria. Its closest phylogenetic relatives are Desulfobotulus alkaliphilus (98.4 % similarity) and Desulfobotulus sapovorans (97.9 % similarity). Based on phylogenetic, phenotypic and chemotaxonomic characteristics, we propose that the isolate represents a novel species of the genus Desulfobotulus with the name Desulfobotulus mexicanus sp. nov. The type strain is PAR22NT (=DSM 105758T=JCM 32146T).
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Affiliation(s)
- Maria Fernanda Pérez-Bernal
- Aix Marseille Univ., Université de Toulon, CNRS, IRD, MIO UM 110, 13288, Marseille, France.,Laboratory of Sanitary and Environmental Engineering, Engineering Division, Campus de Guanajuato, University of Guanajuato, Guanajuato, Mexico.,Environmental Microbiology group, IPREM UMR CNRS 5254, Université de Pau et des Pays de l'Adour, IBEAS, Pau, France
| | - Elcia M S Brito
- Laboratory of Sanitary and Environmental Engineering, Engineering Division, Campus de Guanajuato, University of Guanajuato, Guanajuato, Mexico.,Aix Marseille Univ., Université de Toulon, CNRS, IRD, MIO UM 110, 13288, Marseille, France
| | - Manon Bartoli
- Aix Marseille Univ., Université de Toulon, CNRS, IRD, MIO UM 110, 13288, Marseille, France
| | - Johanne Aubé
- Present address: Univ. Brest, CNRS, IFREMER, Laboratoire de Microbiologie des Environnements Extrêmes, Plouzané, France.,Environmental Microbiology group, IPREM UMR CNRS 5254, Université de Pau et des Pays de l'Adour, IBEAS, Pau, France
| | - Bernard Ollivier
- Aix Marseille Univ., Université de Toulon, CNRS, IRD, MIO UM 110, 13288, Marseille, France
| | - Rémy Guyoneaud
- Environmental Microbiology group, IPREM UMR CNRS 5254, Université de Pau et des Pays de l'Adour, IBEAS, Pau, France
| | - Agnès Hirschler-Réa
- Aix Marseille Univ., Université de Toulon, CNRS, IRD, MIO UM 110, 13288, Marseille, France
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Liu H, Liu X, Ding N. An Innovative in Situ Monitoring of Sulfate Reduction within a Wastewater Biofilm by H 2S and SO 42- Microsensors. Int J Environ Res Public Health 2020; 17:E2023. [PMID: 32204360 DOI: 10.3390/ijerph17062023] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/22/2019] [Revised: 03/07/2020] [Accepted: 03/16/2020] [Indexed: 11/17/2022]
Abstract
Microelectrodes can be used to obtain chemical profiles within biofilm microenvironments. For example, sulfate (SO42-) and hydrogen sulfide (H2S) microelectrodes can be used to study sulfate reduction activity in this context. However, there is no SO42- microelectrode available for studying sulfate reduction in biofilms. In this study, SO42- and H2S microelectrodes were fabricated and applied in the measurement of a wastewater membrane-aerated biofilm (MAB) to investigate the in situ sulfate reduction activity. Both the SO42- and H2S microelectrodes with a tip diameter of around 20 micrometers were successfully developed and displayed satisfying selectivity to SO42- and H2S, respectively. The Nernstian slopes of calibration curves of the fabricated SO42- electrodes were close to -28.1 mV/decade, and the R2 values were greater than 98%. Within the selected concentration range from 10-5 M (0.96 mg/L) to 10-2 M (960 mg/L), the response of the SO42- microelectrode was log-linearly related to its concentration. The successfully fabricated SO42- microelectrode was combined with the existing H2S microelectrode and applied on an environmental wastewater biofilm sample to investigate the sulfate reduction activity within it. The H2S and SO42- microelectrodes showed stable responses and good performance, and the decrease of SO42- with an accompanying increased of H2S within the biofilm indicated the in situ sulfate reduction activity. The application of combined SO42- and H2S microelectrodes in wastewater biofilms could amend the current understanding of sulfate reduction and sulfur oxidation within environmental biofilms based on only H2S microelectrodes.
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Kushkevych I, Cejnar J, Treml J, Dordević D, Kollar P, Vítězová M. Recent Advances in Metabolic Pathways of Sulfate Reduction in Intestinal Bacteria. Cells 2020; 9:E698. [PMID: 32178484 PMCID: PMC7140700 DOI: 10.3390/cells9030698] [Citation(s) in RCA: 78] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 03/06/2020] [Accepted: 03/10/2020] [Indexed: 01/10/2023] Open
Abstract
Sulfate is present in foods, beverages, and drinking water. Its reduction and concentration in the gut depend on the intestinal microbiome activity, especially sulfate-reducing bacteria (SRB), which can be involved in inflammatory bowel disease (IBD). Assimilatory sulfate reduction (ASR) is present in all living organisms. In this process, sulfate is reduced to hydrogen sulfide and then included in cysteine and methionine biosynthesis. In contrast to assimilatory sulfate reduction, the dissimilatory process is typical for SRB. A terminal product of this metabolism pathway is hydrogen sulfide, which can be involved in gut inflammation and also causes problems in industries (due to corrosion effects). The aim of the review was to compare assimilatory and dissimilatory sulfate reduction (DSR). These processes occur in some species of intestinal bacteria (e.g., Escherichia and Desulfovibrio genera). The main attention was focused on the description of genes and their location in selected strains. Their coding expression of the enzymes is associated with anabolic processes in various intestinal bacteria. These analyzed recent advances can be important factors for proposing possibilities of metabolic pathway extension from hydrogen sulfide to cysteine in intestinal SRB. The switch from the DSR metabolic pathway to the ASR metabolic pathway is important since toxic sulfide is not produced as a final product.
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Affiliation(s)
- Ivan Kushkevych
- Department of Experimental Biology, Faculty of Science, Masaryk University, Kamenice 753/5, 62500 Brno, Czech Republic; (J.C.); (M.V.)
- Department of Molecular Biology and Pharmaceutical Biotechnology, University of Veterinary and Pharmaceutical Sciences Brno, 61242 Brno, Czech Republic;
| | - Jiří Cejnar
- Department of Experimental Biology, Faculty of Science, Masaryk University, Kamenice 753/5, 62500 Brno, Czech Republic; (J.C.); (M.V.)
| | - Jakub Treml
- Department of Molecular Biology and Pharmaceutical Biotechnology, University of Veterinary and Pharmaceutical Sciences Brno, 61242 Brno, Czech Republic;
| | - Dani Dordević
- Department of Plant Origin Foodstuffs Hygiene and Technology, Faculty of Veterinary Hygiene and Ecology, University of Veterinary and Pharmaceutical Sciences, 61242 Brno, Czech Republic;
| | - Peter Kollar
- Department of Human Pharmacology and Toxicology, Faculty of Pharmacy, University of Veterinary and Pharmaceutical Sciences, 61242 Brno, Czech Republic;
| | - Monika Vítězová
- Department of Experimental Biology, Faculty of Science, Masaryk University, Kamenice 753/5, 62500 Brno, Czech Republic; (J.C.); (M.V.)
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Liu J, Adrian L, Häggblom MM. Transcriptomic and Proteomic Responses of the Organohalide-Respiring Bacterium Desulfoluna spongiiphila to Growth with 2,6-Dibromophenol as the Electron Acceptor. Appl Environ Microbiol 2020; 86:e02146-19. [PMID: 31836581 PMCID: PMC7028966 DOI: 10.1128/aem.02146-19] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Accepted: 12/10/2019] [Indexed: 01/31/2023] Open
Abstract
Organohalide respiration is an important process in the global halogen cycle and for bioremediation. In this study, we compared the global transcriptomic and proteomic analyses of Desulfoluna spongiiphila strain AA1, an organohalide-respiring member of the Desulfobacterota isolated from a marine sponge, with 2,6-dibromophenol or with sulfate as an electron acceptor. The most significant difference of the transcriptomic analysis was the expression of one reductive dehalogenase gene cluster (rdh16), which was significantly upregulated with the addition of 2,6-dibromophenol. The corresponding protein, reductive dehalogenase RdhA16032, was detected in the proteome under treatment with 2,6-dibromophenol but not with sulfate only. There was no significant difference in corrinoid biosynthesis gene expression levels between the two treatments, indicating that the production of corrinoid in D. spongiiphila is constitutive or not specific for organohalide versus sulfate respiration. Electron-transporting proteins or mediators unique for reductive dehalogenation were not revealed in our analysis, and we hypothesize that reductive dehalogenation may share an electron-transporting system with sulfate reduction. The metabolism of D. spongiiphila, predicted from transcriptomic and proteomic results, demonstrates high metabolic versatility and provides insights into the survival strategies of a marine sponge symbiont in an environment rich in organohalide compounds and other secondary metabolites.IMPORTANCE Respiratory reductive dehalogenation is an important process in the overall cycling of both anthropogenic and natural organohalide compounds. Marine sponges produce a vast array of bioactive compounds as secondary metabolites, including diverse halogenated compounds that may enrich for dehalogenating bacteria. Desulfoluna spongiiphila strain AA1 was originally enriched and isolated from the marine sponge Aplysina aerophoba and can grow with both brominated compounds and sulfate as electron acceptors for respiration. An understanding of the overall gene expression and the protein production profile in response to organohalides is needed to identify the full complement of genes or enzymes involved in organohalide respiration. Elucidating the metabolic capacity of this sponge-associated bacterium lays the foundation for understanding how dehalogenating bacteria may control the fate of organohalide compounds in sponges and their role in a symbiotic organobromine cycle.
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Affiliation(s)
- Jie Liu
- Department of Biochemistry and Microbiology, School of Environmental and Biological Sciences, Rutgers University, New Brunswick, New Jersey, USA
| | - Lorenz Adrian
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
- Fachgebiet Geobiotechnologie, Technische Universität Berlin, Berlin, Germany
| | - Max M Häggblom
- Department of Biochemistry and Microbiology, School of Environmental and Biological Sciences, Rutgers University, New Brunswick, New Jersey, USA
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