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Saghaï A, Hallin S. Diversity and ecology of NrfA-dependent ammonifying microorganisms. Trends Microbiol 2024; 32:602-613. [PMID: 38462391 DOI: 10.1016/j.tim.2024.02.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 02/11/2024] [Accepted: 02/13/2024] [Indexed: 03/12/2024]
Abstract
Nitrate ammonifiers are a taxonomically diverse group of microorganisms that reduce nitrate to ammonium, which is released, and thereby contribute to the retention of nitrogen in ecosystems. Despite their importance for understanding the fate of nitrate, they remain a largely overlooked group in the nitrogen cycle. Here, we present the latest advances on free-living microorganisms using NrfA to reduce nitrite during ammonification. We describe their diversity and ecology in terrestrial and aquatic environments, as well as the environmental factors influencing the competition for nitrate with denitrifiers that reduce nitrate to gaseous nitrogen species, including the greenhouse gas nitrous oxide (N2O). We further review the capacity of ammonifiers for other redox reactions, showing that they likely play multiple roles in the cycling of elements.
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Affiliation(s)
- Aurélien Saghaï
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Sara Hallin
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden.
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2
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Tian H, Gao P, Qi C, Li G, Ma T. Nitrate and oxygen significantly changed the abundance rather than structure of sulphate-reducing and sulphur-oxidising bacteria in water retrieved from petroleum reservoirs. ENVIRONMENTAL MICROBIOLOGY REPORTS 2024; 16:e13248. [PMID: 38581137 PMCID: PMC10997955 DOI: 10.1111/1758-2229.13248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 03/12/2024] [Indexed: 04/08/2024]
Abstract
Sulphate-reducing bacteria (SRB) are the main culprits of microbiologically influenced corrosion in water-flooding petroleum reservoirs, but some sulphur-oxidising bacteria (SOB) are stimulated when nitrate and oxygen are injected, which control the growth of SRB. This study aimed to determine the distributions of SRB and SOB communities in injection-production systems and to analyse the responses of these bacteria to different treatments involving nitrate and oxygen. Desulfovibrio, Desulfobacca, Desulfobulbus, Sulfuricurvum and Dechloromonas were commonly detected via 16S rRNA gene sequencing. Still, no significant differences were observed for either the SRB or SOB communities between injection and production wells. Three groups of water samples collected from different sampling sites were incubated. Statistical analysis of functional gene (dsrB and soxB) clone libraries and quantitative polymerase chain reaction showed that the SOB community structures were more strongly affected by the nitrate and oxygen levels than SRB clustered according to the sampling site; moreover, both the SRB and SOB community abundances significantly changed. Additionally, the highest SRB inhibitory effect and the lowest dsrB/soxB ratio were obtained under high concentrations of nitrate and oxygen in the three groups, suggesting that the synergistic effect of nitrate and oxygen level was strong on the inhibition of SRB by potential SOB.
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Affiliation(s)
- Huimei Tian
- College of ForestryShandong Agricultural UniversityTaianChina
- Ecology Postdoctoral Mobile StationForestry College of Shandong Agricultural UniversityTaianChina
| | - Peike Gao
- College of Life SciencesQufu Normal UniversityJiningChina
| | - Chen Qi
- College of ForestryShandong Agricultural UniversityTaianChina
| | - Guoqiang Li
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life SciencesNankai UniversityTianjinChina
| | - Ting Ma
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life SciencesNankai UniversityTianjinChina
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3
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Egas RA, Kurth JM, Boeren S, Sousa DZ, Welte CU, Sánchez-Andrea I. A novel mechanism for dissimilatory nitrate reduction to ammonium in Acididesulfobacillus acetoxydans. mSystems 2024; 9:e0096723. [PMID: 38323850 PMCID: PMC10949509 DOI: 10.1128/msystems.00967-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2023] [Accepted: 12/25/2023] [Indexed: 02/08/2024] Open
Abstract
The biological route of nitrate reduction has important implications for the bioavailability of nitrogen within ecosystems. Nitrate reduction via nitrite, either to ammonium (ammonification) or to nitrous oxide or dinitrogen (denitrification), determines whether nitrogen is retained within the system or lost as a gas. The acidophilic sulfate-reducing bacterium (aSRB) Acididesulfobacillus acetoxydans can perform dissimilatory nitrate reduction to ammonium (DNRA). While encoding a Nar-type nitrate reductase, A. acetoxydans lacks recognized nitrite reductase genes. In this study, A. acetoxydans was cultivated under conditions conducive to DNRA. During cultivations, we monitored the production of potential nitrogen intermediates (nitrate, nitrite, nitric oxide, hydroxylamine, and ammonium). Resting cell experiments were performed with nitrate, nitrite, and hydroxylamine to confirm their reduction to ammonium, and formed intermediates were tracked. To identify the enzymes involved in DNRA, comparative transcriptomics and proteomics were performed with A. acetoxydans growing under nitrate- and sulfate-reducing conditions. Nitrite is likely reduced to ammonia by the previously undescribed nitrite reductase activity of the NADH-linked sulfite reductase AsrABC, or by a putatively ferredoxin-dependent homolog of the nitrite reductase NirA (DEACI_1836), or both. We identified enzymes and intermediates not previously associated with DNRA and nitrosative stress in aSRB. This increases our knowledge about the metabolism of this type of bacteria and helps the interpretation of (meta)genome data from various ecosystems on their DNRA potential and the nitrogen cycle.IMPORTANCENitrogen is crucial to any ecosystem, and its bioavailability depends on microbial nitrogen-transforming reactions. Over the recent years, various new nitrogen-transforming reactions and pathways have been identified, expanding our view on the nitrogen cycle and metabolic versatility. In this study, we elucidate a novel mechanism employed by Acididesulfobacillus acetoxydans, an acidophilic sulfate-reducing bacterium, to reduce nitrate to ammonium. This finding underscores the diverse physiological nature of dissimilatory reduction to ammonium (DNRA). A. acetoxydans was isolated from acid mine drainage, an extremely acidic environment where nitrogen metabolism is poorly studied. Our findings will contribute to understanding DNRA potential and variations in extremely acidic environments.
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Affiliation(s)
- Reinier A. Egas
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
| | - Julia M. Kurth
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
- Microcosm Earth Centre, Philipps-Universität Marburg & Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Sjef Boeren
- Laboratory of Biochemistry, Wageningen University & Research, Wageningen, The Netherlands
| | - Diana Z. Sousa
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
- Centre for Living Technologies, Alliance TU/e, WUR, UU, UMC Utrecht, Utrecht, The Netherlands
| | - Cornelia U. Welte
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Nijmegen, The Netherlands
| | - Irene Sánchez-Andrea
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
- Department of Environmental Sciences for Sustainability, IE University, Segovia, Spain
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4
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Zeng XC, Xu Y, Lu H, Xiong J, Xu H, Wu W. Contradictory Impacts of Nitrate on the Dissimilatory Arsenate-Respiring Prokaryotes-Induced Reductive Mobilization of Arsenic from Contaminated Sediments: Mechanism Insight from Metagenomic and Functional Analyses. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:13473-13486. [PMID: 37639510 DOI: 10.1021/acs.est.3c02190] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Dissimilatory arsenate-respiring prokaryotes (DARPs) are considered to be a key impetus of the reductive dissolution of solid-phase arsenic. However, little is known about the interaction between nitrate and DARPs so far. In this study, we showed that nitrate either inhibited or promoted the DARP population-catalyzed reductive mobilization of As in sediments. Metagenomic analysis of the microbial communities in the microcosms after seven days of As release assays suggested that microbes mainly consisted of: Type-I DARPs having potential to reduce NO3- into NO2- and Type-II DARPs having potential to reduce NO3- to NH4+. We further isolated two cultivable DARPs, Neobacillus sp. A01 and Paenibacillus sp. A02, which represent Type-I and -II DARPs, respectively. We observed that nitrate suppressed A01-mediated release of As(III) but promoted A02-mediated release of As(III). Furthermore, we demonstrated that this observation was due to the fact that nitrite, the end product of incomplete denitrification by Type-I DARPs, suppressed the arrA gene expression per cell and growth of all DARPs, whereas ammonium, the end product of dissimilatory nitrate reduction to ammonium (DNRA) by Type-II DARPs, enhanced the arrA gene expression per cell and significantly promoted the growth of all DARPs. These findings suggest that the actual effects of nitrate on DARP population-catalyzed reductive mobilization of arsenic, largely depend on the ratio of Type-I to Type-II DARPs in sediments.
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Affiliation(s)
- Xian-Chun Zeng
- State Key Laboratory of Biogeology and Environmental Geology & School of Environmental Studies, China University of Geosciences (Wuhan), Wuhan 430079, People's Republic of China
| | - Yifan Xu
- State Key Laboratory of Biogeology and Environmental Geology & School of Environmental Studies, China University of Geosciences (Wuhan), Wuhan 430079, People's Republic of China
| | - Hongyu Lu
- State Key Laboratory of Biogeology and Environmental Geology & School of Environmental Studies, China University of Geosciences (Wuhan), Wuhan 430079, People's Republic of China
| | - Jianyu Xiong
- State Key Laboratory of Biogeology and Environmental Geology & School of Environmental Studies, China University of Geosciences (Wuhan), Wuhan 430079, People's Republic of China
| | - Hai Xu
- Division of Endocrinology and Rheumatology, HuangPi People's Hospital, the Third Affiliated Hospital of Jianghan University, Wuhan 430300, China
| | - Weiwei Wu
- State Key Laboratory of Biogeology and Environmental Geology & School of Environmental Studies, China University of Geosciences (Wuhan), Wuhan 430079, People's Republic of China
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5
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Lemaire ON, Belhamri M, Wagner T. Structural and biochemical elucidation of class I hybrid cluster protein natively extracted from a marine methanogenic archaeon. Front Microbiol 2023; 14:1179204. [PMID: 37250035 PMCID: PMC10210160 DOI: 10.3389/fmicb.2023.1179204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 04/03/2023] [Indexed: 05/31/2023] Open
Abstract
Whilst widespread in the microbial world, the hybrid cluster protein (HCP) has been paradoxically a long-time riddle for microbiologists. During three decades, numerous studies on a few model organisms unravelled its structure and dissected its metal-containing catalyst, but the physiological function of the enzyme remained elusive. Recent studies on bacteria point towards a nitric oxide reductase activity involved in resistance during nitrate and nitrite reduction as well as host infection. In this study, we isolated and characterised a naturally highly produced HCP class I from a marine methanogenic archaeon grown on ammonia. The crystal structures of the enzyme in a reduced and partially oxidised state, obtained at a resolution of 1.45 and 1.36-Å, respectively, offered a precise picture of the archaeal enzyme intimacy. There are striking similarities with the well-studied enzymes from Desulfovibrio species regarding sequence, kinetic parameters, structure, catalyst conformations, and internal channelling systems. The close phylogenetic relationship between the enzymes from Methanococcales and many Bacteria corroborates this similarity. Indeed, Methanococcales HCPs are closer to these bacterial homologues than to any other archaeal enzymes. The relatively high constitutive production of HCP in M. thermolithotrophicus, in the absence of a notable nitric oxide source, questions the physiological function of the enzyme in these ancient anaerobes.
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Bourceau OM, Ferdelman T, Lavik G, Mussmann M, Kuypers MMM, Marchant HK. Simultaneous sulfate and nitrate reduction in coastal sediments. ISME COMMUNICATIONS 2023; 3:17. [PMID: 36882570 PMCID: PMC9992702 DOI: 10.1038/s43705-023-00222-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 01/30/2023] [Accepted: 02/09/2023] [Indexed: 03/09/2023]
Abstract
The oscillating redox conditions that characterize coastal sandy sediments foster microbial communities capable of respiring oxygen and nitrate simultaneously, thereby increasing the potential for organic matter remineralization, nitrogen (N)-loss and emissions of the greenhouse gas nitrous oxide. It is unknown to what extent these conditions also lead to overlaps between dissimilatory nitrate and sulfate respiration. Here, we show that sulfate and nitrate respiration co-occur in the surface sediments of an intertidal sand flat. Furthermore, we found strong correlations between dissimilatory nitrite reduction to ammonium (DNRA) and sulfate reduction rates. Until now, the nitrogen and sulfur cycles were assumed to be mainly linked in marine sediments by the activity of nitrate-reducing sulfide oxidisers. However, transcriptomic analyses revealed that the functional marker gene for DNRA (nrfA) was more associated with microorganisms known to reduce sulfate rather than oxidise sulfide. Our results suggest that when nitrate is supplied to the sediment community upon tidal inundation, part of the sulfate reducing community may switch respiratory strategy to DNRA. Therefore increases in sulfate reduction rate in-situ may result in enhanced DNRA and reduced denitrification rates. Intriguingly, the shift from denitrification to DNRA did not influence the amount of N2O produced by the denitrifying community. Our results imply that microorganisms classically considered as sulfate reducers control the potential for DNRA within coastal sediments when redox conditions oscillate and therefore retain ammonium that would otherwise be removed by denitrification, exacerbating eutrophication.
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Affiliation(s)
- O M Bourceau
- Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359, Bremen, Germany
| | - T Ferdelman
- Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359, Bremen, Germany
| | - G Lavik
- Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359, Bremen, Germany
| | - M Mussmann
- University of Vienna, Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, Djerassiplatz 1, A-1030, Vienna, Austria
| | - M M M Kuypers
- Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359, Bremen, Germany
| | - H K Marchant
- Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359, Bremen, Germany.
- University of Bremen, Center for Marine Environmental Sciences, MARUM, 28359, Bremen, Germany.
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7
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Cai MH, Luo G, Li J, Li WT, Li Y, Li AM. Substrate competition and microbial function in sulfate-reducing internal circulation anaerobic reactor in the presence of nitrate. CHEMOSPHERE 2021; 280:130937. [PMID: 34162109 DOI: 10.1016/j.chemosphere.2021.130937] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Revised: 04/16/2021] [Accepted: 05/13/2021] [Indexed: 06/13/2023]
Abstract
Nitrate and sulfate often coexist in organic wastewater. In this study, an internal circulation anaerobic reactor was conducted to investigate the impact of nitrate on sulfate reduction. The results showed that sulfate reduction rate dropped from 78.4% to 41.4% at NO3- /SO42- ratios ranging from 0 to 1.03, largely attributed to the inactivity of acetate-utilizing sulfate-reducing bacteria (SRB) and preferential usage of nitrate of propionate-utilizing SRB. Meanwhile, high nitrate removal efficiency was maintained and COD removal efficiency increased with nitrate addition. Enhancement of propionate and butyrate degradation based on Modified Gompertz model and Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt2) analysis. Moreover, nitrate triggered the shift of microbial community and function. Twelve genera affiliated to Firmicutes, Bacteroidetes and Proteobacteria were identified as keystone genera via network analysis, which kept functional stability of the bacterial community responding to nitrate stress. Increased nitrate inhibited Desulfovibrio, but promoted the growth of Desulforhabdus. Both the predicted functional genes associated with assimilatory sulfate reduction pathway (cysC and cysNC) and dissimilatory sulfate reduction pathway (aprA, aprB, dsrA and dsrB) exhibited negative relationship with nitrate addition.
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Affiliation(s)
- Min-Hui Cai
- State Key Laboratory of Pollution Control and Resources Reuse, School of the Environment, Nanjing University, Nanjing, 210023, China
| | - Gan Luo
- State Key Laboratory of Pollution Control and Resources Reuse, School of the Environment, Nanjing University, Nanjing, 210023, China
| | - Jun Li
- State Key Laboratory of Pollution Control and Resources Reuse, School of the Environment, Nanjing University, Nanjing, 210023, China
| | - Wen-Tao Li
- State Key Laboratory of Pollution Control and Resources Reuse, School of the Environment, Nanjing University, Nanjing, 210023, China
| | - Yan Li
- State Key Laboratory of Pollution Control and Resources Reuse, School of the Environment, Nanjing University, Nanjing, 210023, China.
| | - Ai-Min Li
- State Key Laboratory of Pollution Control and Resources Reuse, School of the Environment, Nanjing University, Nanjing, 210023, China
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8
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Zhou J, Xing J. Haloalkaliphilic denitrifiers-dependent sulfate-reducing bacteria thrive in nitrate-enriched environments. WATER RESEARCH 2021; 201:117354. [PMID: 34157573 DOI: 10.1016/j.watres.2021.117354] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 05/17/2021] [Accepted: 06/06/2021] [Indexed: 06/13/2023]
Abstract
As bridge in global cycles of carbon, nitrogen, and sulfur, sulfate-reducing bacteria (SRB) play more and more important role under various environments, especially the saline-alkali environments with significant increase in area caused by human activities. Sulfate reduction can be inhibited by environmental nitrate. However, how SRB cope with environmental nitrate stress in these extreme environments still remain unclear. Here, after a long-term enrichment of sediment from saline-alkali Qinghai Lake of China using anaerobic filter reactors, nitrate was added to evaluate the response of SRB. With the increase in nitrate concentrations, the inhibition on sulfate reduction was gradually observed. Interestingly, extension of hydraulic retention time can relieve the inhibition caused by high nitrate concentration. Mass balance analysis showed that nitrate reduction is prior to sulfate reduction. Further metatranscriptomic analysis shows that, genes of nitrite reductase (periplasmic cytochrome c nitrite reductase gene) and energy metabolisms (lactate dehydrogenase, formate dehydrogenase, pyruvate:ferredoxin-oxidoreductase, and fumarate reductase genes) in SRB was down-regulated, challenging the long-held opinion that up-regulation of these genes can relieve the nitrate inhibition. Most importantly, the nitrate addition activated the denitrification pathway in denitrifying bacteria (DB) via significantly up-regulating the expression of the corresponding genes (nitrite reductase, nitric oxide reductase c subunit, nitric oxide reductase activation protein and nitrous oxide reductase genes), quickly reducing the environmental nitrate and relieving the nitrate inhibition on SRB. Our findings unravel that in response to environmental nitrate stress, haloalkaliphilic SRB show dependency on DB, and expand our knowledge of microbial relationship during sulfur and nitrogen cycles.
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Affiliation(s)
- Jiemin Zhou
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.
| | - Jianmin Xing
- Key Laboratory of Green Process and Engineering, State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, China
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9
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Dordević D, Jančíková S, Vítězová M, Kushkevych I. Hydrogen sulfide toxicity in the gut environment: Meta-analysis of sulfate-reducing and lactic acid bacteria in inflammatory processes. J Adv Res 2021; 27:55-69. [PMID: 33318866 PMCID: PMC7728594 DOI: 10.1016/j.jare.2020.03.003] [Citation(s) in RCA: 88] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 03/13/2020] [Accepted: 03/14/2020] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Hydrogen sulfide is the final product of sulfate-reducing bacteria metabolism. Its high concentration in the gut can affect adversely bowel environment and intestinal microbiota by toxicity and pH lowering. AIM OF REVIEW The aim of the review was to give observations related to the properties of bacterial communities inhabiting the gut, with the emphasis on sulfate-reducing bacteria and lactic acid bacteria. KEY SCIENTIFIC CONCEPTS OF REVIEW The conduction of meta-analysis was another goal, since it gave statistical observation of the relevant studies. The review literature consisted of more than 160 studies, published from 1945 to 2019. Meta-analysis included 16 studies and they were chosen from the Web of Science database. The systematic review gave important information about the development of gut inflammation, with emphasis on sulfate-reducing and lactic acid bacteria. Oppositely from sulfate-reducing bacteria, probiotic properties of lactic acid bacteria are effective inhibitors against inflammatory bowel disease development, including ulcerative colitis. These facts were confirmed by the conducted meta-analysis. The results and observations gained from the systematic review represent the emphasized importance of gut microbiota for bowel inflammation. On the other side, it should be stated that more studies in the future will provide even better confirmations.
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Affiliation(s)
- Dani Dordević
- Department of Plant Origin Foodstuffs Hygiene and Technology, Faculty of Veterinary Hygiene and Ecology, University of Veterinary and Pharmaceutical Sciences Brno, Czech Republic
| | - Simona Jančíková
- Department of Plant Origin Foodstuffs Hygiene and Technology, Faculty of Veterinary Hygiene and Ecology, University of Veterinary and Pharmaceutical Sciences Brno, Czech Republic
| | - Monika Vítězová
- Department of Experimental Biology, Faculty of Science, Masaryk University, Kamenice 753/5, 625 00 Brno, Czech Republic
| | - Ivan Kushkevych
- Department of Experimental Biology, Faculty of Science, Masaryk University, Kamenice 753/5, 625 00 Brno, Czech Republic
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10
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Williamson AJ, Engelbrektson AL, Liu Y, Huang LL, Kumar A, Menon AR, Thieme J, Carlson HK, Coates JD. Tungstate Control of Microbial Sulfidogenesis and Souring of the Engineered Environment. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2020; 54:16119-16127. [PMID: 33253556 DOI: 10.1021/acs.est.0c04682] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Sulfide accumulation in oil reservoir fluids (souring) from the activity of sulfate-reducing microorganisms (SRM) is of grave concern because of the associated health and facility failure risks. Here, we present an assessment of tungstate as a selective and potent inhibitor of SRM. Dose-response inhibitor experiments were conducted with a number of SRM isolates and enrichments at 30-80 °C and an increase in the effectiveness of tungstate treatment at higher temperatures was observed. To explore mixed inhibitor treatment modes, we tested synergy or antagonism between several inhibitors with tungstate, and found synergism between WO42- and NO2-, while additive effects were observed with ClO4- and NO3-. We also evaluated SRM inhibition by tungstate in advective upflow oil-sand-packed columns. Although 2 mM tungstate was initially sufficient to inhibit sulfidogenesis, subsequent temporal CaWO4 precipitation resulted in loss of the bioavailable inhibitor from solution and a concurrent increase in effluent sulfide. Mixing 4 mM sodium carbonate with the 2 mM tungstate was enough to promote tungstate solubility to reach inhibitory concentrations, without precipitation, and completely inhibit SRM activity. Overall, we demonstrate the effectiveness of tungstate as a potent SRM inhibitor, particularly at higher temperatures, and propose a novel carbonate-tungstate formulation for application to soured oil reservoirs.
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Affiliation(s)
- Adam J Williamson
- Energy Biosciences Institute, 2151 Berkeley Way, California 94704, United States
| | - Anna L Engelbrektson
- Energy Biosciences Institute, 2151 Berkeley Way, California 94704, United States
| | - Yi Liu
- Energy Biosciences Institute, 2151 Berkeley Way, California 94704, United States
| | - Leah L Huang
- Energy Biosciences Institute, 2151 Berkeley Way, California 94704, United States
| | - Aarti Kumar
- Energy Biosciences Institute, 2151 Berkeley Way, California 94704, United States
| | - Aruna R Menon
- Energy Biosciences Institute, 2151 Berkeley Way, California 94704, United States
| | - Juergen Thieme
- NSLS-II Brookhaven National Laboratory, Brookhaven, New York 11973, United States
| | - Hans K Carlson
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - John D Coates
- Energy Biosciences Institute, 2151 Berkeley Way, California 94704, United States
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11
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Experimental evolution reveals nitrate tolerance mechanisms in Desulfovibrio vulgaris. ISME JOURNAL 2020; 14:2862-2876. [PMID: 32934357 DOI: 10.1038/s41396-020-00753-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 08/09/2020] [Accepted: 08/17/2020] [Indexed: 11/08/2022]
Abstract
Elevated nitrate in the environment inhibits sulfate reduction by important microorganisms of sulfate-reducing bacteria (SRB). Several SRB may respire nitrate to survive under elevated nitrate, but how SRB that lack nitrate reductase survive to elevated nitrate remains elusive. To understand nitrate adaptation mechanisms, we evolved 12 populations of a model SRB (i.e., Desulfovibrio vulgaris Hildenborough, DvH) under elevated NaNO3 for 1000 generations, analyzed growth and acquired mutations, and linked their genotypes with phenotypes. Nitrate-evolved (EN) populations significantly (p < 0.05) increased nitrate tolerance, and whole-genome resequencing identified 119 new mutations in 44 genes of 12 EN populations, among which six functional gene groups were discovered with high mutation frequencies at the population level. We observed a high frequency of nonsense or frameshift mutations in nitrosative stress response genes (NSR: DVU2543, DVU2547, and DVU2548), nitrogen regulatory protein C family genes (NRC: DVU2394-2396, DVU2402, and DVU2405), and nitrate cluster (DVU0246-0249 and DVU0251). Mutagenesis analysis confirmed that loss-of-functions of NRC and NSR increased nitrate tolerance. Also, functional gene groups involved in fatty acid synthesis, iron regulation, and two-component system (LytR/LytS) known to be responsive to multiple stresses, had a high frequency of missense mutations. Mutations in those gene groups could increase nitrate tolerance through regulating energy metabolism, barring entry of nitrate into cells, altering cell membrane characteristics, or conferring growth advantages at the stationary phase. This study advances our understanding of nitrate tolerance mechanisms and has important implications for linking genotypes with phenotypes in DvH.
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12
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Evaluation of mtr cluster expression in Shewanella RCRI7 during uranium removal. Arch Microbiol 2020; 202:2711-2726. [DOI: 10.1007/s00203-020-01981-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2020] [Revised: 07/03/2020] [Accepted: 07/10/2020] [Indexed: 11/30/2022]
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13
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Li Y, Feng X, Zhang T, Zhou X, Li C. Preparation of magnetic macroporous polymer sphere for biofilm immobilization and biodesulfurization. REACT FUNCT POLYM 2019. [DOI: 10.1016/j.reactfunctpolym.2019.04.016] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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14
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Yang F, Li W, Liu C, Wang M, Li Q, Sun Y. Impact of total carbon/sulfate on methane production and sulfate removal from co-digestion of sulfate-containing wastewater and corn stalk. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2019; 243:411-418. [PMID: 31103687 DOI: 10.1016/j.jenvman.2019.04.129] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Revised: 04/04/2019] [Accepted: 04/30/2019] [Indexed: 06/09/2023]
Abstract
During the process of preparing furfural by straw depolymerization with dilute sulfuric acid, large amounts of high temperature sulfate-rich organic wastewater were produced. It cannot be treated directly by anaerobic digestion and converted to bioenergy due to high concentrations of sulfate. In this study, anaerobic co-digestion of sulfate containing wastewater and corn stalk was performed at thermophilic conditions to investigate the influences of total carbon (TC)/sulfate (6, 16, 35 and 110) on methane production and sulfate removal. The results showed that the highest methane production of 260.14 mL g-1 volatile solid (VS) was achieved at TC/sulfate of 35, which was significantly higher than 12.53 mL g-1 VS obtained at TC/sulfate of 6. Moreover, the results of sulfate balance analysis showed a maximum sulfate removal of 93.43% was achieved at TC/sulfate of 16, and sulfate concentration in biogas slurry was less than 0.1 g/L regardless of TC/sulfate after 28 days of co-digestion. The microbial community was analyzed using 16S rDNA sequencing technology, the results showed that methane was mainly produced by Methanoculleus and Methanosarcina, and sulfate was removed via Desulfotomaculum, and the relative abundance of methanogenic archaea (MA) and sulfate reducing bacteria (SRB) were significantly correlated with methane production and sulfate removal. It can concluded that higher methane production and sulfate removal can be obtained by anaerobic co-digestion of sulfate containing wastewater and corn stalk at properly TC/sulfate.
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Affiliation(s)
- Fuli Yang
- Department of Agriculture Biological Environment and Energy Engineering, Northeast Agriculture University, No. 600 Changjiang Road, Xiangfang District, Harbin, 150030, China
| | - Wenzhe Li
- Department of Agriculture Biological Environment and Energy Engineering, Northeast Agriculture University, No. 600 Changjiang Road, Xiangfang District, Harbin, 150030, China.
| | - Changyu Liu
- Department of Agriculture Biological Environment and Energy Engineering, Northeast Agriculture University, No. 600 Changjiang Road, Xiangfang District, Harbin, 150030, China; College of Architecture and Civil Engineering, Northeast Petroleum University, No. 199 Development Road, High-tech Development District, Daqing, 163318, China
| | - Mengyi Wang
- Department of Agriculture Biological Environment and Energy Engineering, Northeast Agriculture University, No. 600 Changjiang Road, Xiangfang District, Harbin, 150030, China
| | - Qiang Li
- Department of Agriculture Biological Environment and Energy Engineering, Northeast Agriculture University, No. 600 Changjiang Road, Xiangfang District, Harbin, 150030, China
| | - Yong Sun
- Department of Agriculture Biological Environment and Energy Engineering, Northeast Agriculture University, No. 600 Changjiang Road, Xiangfang District, Harbin, 150030, China
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15
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Gao SH, Ho JY, Fan L, Nouwens A, Hoelzle RD, Schulz B, Guo J, Zhou J, Yuan Z, Bond PL. A comparative proteomic analysis of Desulfovibrio vulgaris Hildenborough in response to the antimicrobial agent free nitrous acid. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 672:625-633. [PMID: 30974354 DOI: 10.1016/j.scitotenv.2019.03.442] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Revised: 03/12/2019] [Accepted: 03/28/2019] [Indexed: 06/09/2023]
Abstract
Sulfate reducing bacteria (SRB) can contribute to facilitating serious concrete corrosion through the production of hydrogen sulfide in sewers. Recently, free nitrous acid (FNA) was discovered as a promising antimicrobial agent to inhibit SRB activities thereby limiting hydrogen sulfide production in sewers. However, knowledge of the bacterial response to increasing levels of the antimicrobial agent is unknown. Here we report the proteomic response of Desulfovibrio vulgaris Hildenborough and reveal that the antimicrobial effect of FNA is multi-targeted and dependent on the FNA levels. This was achieved using a sequential window acquisition of all theoretical mass spectrometry analysis to determine protein abundance variations in D. vulgaris during exposure to different FNA concentrations. When exposed to 1.0 μg N/L FNA, nitrite reduction (nitrite reductase) related proteins and nitrosative stress related proteins, including the hybrid cluster protein, showed distinct increased abundances. When exposed to 4.0 and 8.0 μg N/L FNA, increased abundance was detected for proteins putatively involved in nitrite reduction. Abundance of proteins involved in the sulfate reduction pathway (from adenylylphophosulfate to sulfite) and lactate oxidation pathway (from pyruvate to acetate) were initially inhibited in response to FNA at 8 h incubation, and then recovered at 12 h incubation. Lowered ribosomal protein abundance in D. vulgaris was detected, however, total cellular protein levels were mostly constant in the presence or absence of FNA. In addition, this study indicates that proteins coded by genes DVU2543, DVU0772, and DVU3212 potentially participate in resisting oxidative stress with FNA exposure. These findings share new insights for understanding the dynamic responses of D. vulgaris to FNA and could be useful to guide and improve the practical applications of FNA-based technologies for control of sewer corrosion.
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Affiliation(s)
- Shu-Hong Gao
- Advanced Water Management Centre, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia; Institute for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK 73019, USA
| | - Jun Yuan Ho
- Advanced Water Management Centre, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia
| | - Lu Fan
- Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen 518055, China
| | - Amanda Nouwens
- School of Chemistry & Molecular Biosciences, The University of Queensland, St Lucia, Brisbane, QLD 4072, Australia
| | - Robert D Hoelzle
- Advanced Water Management Centre, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia; Australian Centre for Ecogenomics, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia
| | - Benjamin Schulz
- School of Chemistry & Molecular Biosciences, The University of Queensland, St Lucia, Brisbane, QLD 4072, Australia
| | - Jianhua Guo
- Advanced Water Management Centre, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia
| | - Jizhong Zhou
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK 73019, USA
| | - Zhiguo Yuan
- Advanced Water Management Centre, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia
| | - Philip L Bond
- Advanced Water Management Centre, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia.
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16
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Chen Z, Gao SH, Jin M, Sun S, Lu J, Yang P, Bond PL, Yuan Z, Guo J. Physiological and transcriptomic analyses reveal CuO nanoparticle inhibition of anabolic and catabolic activities of sulfate-reducing bacterium. ENVIRONMENT INTERNATIONAL 2019; 125:65-74. [PMID: 30710801 DOI: 10.1016/j.envint.2019.01.058] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2018] [Revised: 01/21/2019] [Accepted: 01/22/2019] [Indexed: 06/09/2023]
Abstract
The widespread use of CuO nanoparticles (NPs) results in their continuous release into the environment, which could pose risks to public health and to microbial ecosystems. Following consumption, NPs will initially enter into sewer systems and interact with and potentially influence sewer microbial communities. An understanding of the response of microbes in sewers, particularly sulfate-reducing bacteria (SRB), to the CuO NPs induced stress is important as hydrogen sulfide produced by SRB can cause sewer corrosion and odour emissions. In this study, we elucidated how the anabolic and catabolic processes of a model SRB, Desulfovibrio vulgaris Hidenborough (D. vulgaris), respond to CuO NPs. Physiological analyses indicated that the exposure of the culture to CuO NPs at elevated concentrations (>50 mg/L) inhibited both its anabolic and catabolic activities, as revealed by lowered cell proliferation and sulfate reduction rate. The antibacterial effects of CuO NPs were mainly attributed to the overproduction of reactive oxygen species. Transcriptomic analysis indicated that genes encoding for flagellar assembly and some genes involved in electron transfer and respiration were down-regulated, while genes for the ferric uptake regulator (Fur) were up-regulated. Moreover, the CuO NPs exposure significantly up-regulated genes involved in protein synthesis and ATP synthesis. These results suggest that CuO NPs inhibited energy conversion, cell mobility, and iron starvation to D. vulgaris. Meanwhile, D. vulgaris attempted to respond to the stress of CuO NPs by increasing protein and ATP synthesis. These findings offer new insights into the bacterial-nanoparticles interaction at the transcriptional level, and advance our understanding of impacts of CuO NPs on SRB in the environment.
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Affiliation(s)
- Zhaoyu Chen
- Advanced Water Management Centre, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia; Department of Environmental Science & Engineering, Sichuan University, Chengdu, Sichuan 610065, China
| | - Shu-Hong Gao
- Advanced Water Management Centre, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia
| | - Min Jin
- Advanced Water Management Centre, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia
| | - Shengjie Sun
- Advanced Water Management Centre, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia
| | - Ji Lu
- Advanced Water Management Centre, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia
| | - Ping Yang
- Department of Environmental Science & Engineering, Sichuan University, Chengdu, Sichuan 610065, China
| | - Philip L Bond
- Advanced Water Management Centre, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia
| | - Zhiguo Yuan
- Advanced Water Management Centre, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia
| | - Jianhua Guo
- Advanced Water Management Centre, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia.
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17
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Stoeva MK, Coates JD. Specific inhibitors of respiratory sulfate reduction: towards a mechanistic understanding. MICROBIOLOGY-SGM 2018; 165:254-269. [PMID: 30556806 DOI: 10.1099/mic.0.000750] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Microbial sulfate reduction (SR) by sulfate-reducing micro-organisms (SRM) is a primary environmental mechanism of anaerobic organic matter mineralization, and as such influences carbon and sulfur cycling in many natural and engineered environments. In industrial systems, SR results in the generation of hydrogen sulfide, a toxic, corrosive gas with adverse human health effects and significant economic and environmental consequences. Therefore, there has been considerable interest in developing strategies for mitigating hydrogen sulfide production, and several specific inhibitors of SRM have been identified and characterized. Specific inhibitors are compounds that disrupt the metabolism of one group of organisms, with little or no effect on the rest of the community. Putative specific inhibitors of SRM have been used to control sulfidogenesis in industrial and engineered systems. Despite the value of these inhibitors, mechanistic and quantitative studies into the molecular mechanisms of their inhibition have been sparse and unsystematic. The insight garnered by such studies is essential if we are to have a more complete understanding of SR, including the past and current selective pressures acting upon it. Furthermore, the ability to reliably control sulfidogenesis - and potentially assimilatory sulfate pathways - relies on a thorough molecular understanding of inhibition. The scope of this review is to summarize the current state of the field: how we measure and understand inhibition, the targets of specific SR inhibitors and how SRM acclimatize and/or adapt to these stressors.
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Affiliation(s)
- Magdalena K Stoeva
- 1Energy Biosciences Institute, University of California - Berkeley, Berkeley, CA, USA
- 2Department of Plant and Microbial Biology, University of California - Berkeley, Berkeley, CA, USA
| | - John D Coates
- 2Department of Plant and Microbial Biology, University of California - Berkeley, Berkeley, CA, USA
- 1Energy Biosciences Institute, University of California - Berkeley, Berkeley, CA, USA
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18
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Jiang Y, Zhang B, He C, Shi J, Borthwick AGL, Huang X. Synchronous microbial vanadium (V) reduction and denitrification in groundwater using hydrogen as the sole electron donor. WATER RESEARCH 2018; 141:289-296. [PMID: 29803094 DOI: 10.1016/j.watres.2018.05.033] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Revised: 05/18/2018] [Accepted: 05/18/2018] [Indexed: 06/08/2023]
Abstract
Groundwater co-contaminated by vanadium (V) (V(V)) and nitrate requires efficient remediation to prevent adverse environmental impacts. However, little is known about simultaneous bio-reductions of V(V) and nitrate supported by gaseous electron donors in aquifers. This study is among the first to examine microbial V(V) reduction and denitrification with hydrogen as the sole electron donor. V(V) removal efficiency of 91.0 ± 3.2% was achieved in test bioreactors within 7 d, with synchronous, complete removal of nitrate. V(V) was reduced to V(IV), which precipitated naturally under near-neutral conditions, and nitrate tended to be converted to nitrogen, both of which processes helped to purify the groundwater. Volatile fatty acids (VFAs) were produced from hydrogen oxidation. High-throughput 16S rRNA gene sequencing and metagenomic analyses revealed the evolutionary behavior of microbial communities and functional genes. The genera Dechloromonas and Hydrogenophaga promoted bio-reductions of V(V) and nitrate directly coupled to hydrogen oxidation. Enriched Geobacter and denitrifiers also indicated synergistic mechanism, with VFAs acting as organic carbon sources for heterotrophically functional bacteria while reducing V(V) and nitrate. These findings are likely to be useful in revealing biogeochemical fates of V(V) and nitrate in aquifer and developing technology for removing them simultaneously from groundwater.
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Affiliation(s)
- Yufeng Jiang
- School of Water Resources and Environment, MOE Key Laboratory of Groundwater Circulation and Environmental Evolution, China University of Geosciences (Beijing), Beijing, 100083, PR China
| | - Baogang Zhang
- School of Water Resources and Environment, MOE Key Laboratory of Groundwater Circulation and Environmental Evolution, China University of Geosciences (Beijing), Beijing, 100083, PR China.
| | - Chao He
- School of Water Resources and Environment, MOE Key Laboratory of Groundwater Circulation and Environmental Evolution, China University of Geosciences (Beijing), Beijing, 100083, PR China
| | - Jiaxin Shi
- School of Water Resources and Environment, MOE Key Laboratory of Groundwater Circulation and Environmental Evolution, China University of Geosciences (Beijing), Beijing, 100083, PR China
| | - Alistair G L Borthwick
- School of Engineering, The University of Edinburgh, The King's Buildings, Edinburgh, EH9 3JL, UK
| | - Xueyang Huang
- School of Water Resources and Environment, MOE Key Laboratory of Groundwater Circulation and Environmental Evolution, China University of Geosciences (Beijing), Beijing, 100083, PR China
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19
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Improved Buffering Capacity and Methane Production by Anaerobic Co-Digestion of Corn Stalk and Straw Depolymerization Wastewater. ENERGIES 2018. [DOI: 10.3390/en11071751] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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20
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Fida TT, Voordouw J, Ataeian M, Kleiner M, Okpala G, Mand J, Voordouw G. Synergy of Sodium Nitroprusside and Nitrate in Inhibiting the Activity of Sulfate Reducing Bacteria in Oil-Containing Bioreactors. Front Microbiol 2018; 9:981. [PMID: 29867883 PMCID: PMC5965020 DOI: 10.3389/fmicb.2018.00981] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Accepted: 04/26/2018] [Indexed: 11/13/2022] Open
Abstract
Sodium nitroprusside (SNP) disrupts microbial biofilms through the release of nitric oxide (NO). The actions of SNP on bacteria have been mostly limited to the genera Pseudomonas, Clostridium, and Bacillus. There are no reports of its biocidal action on sulfate-reducing bacteria (SRB), which couple the reduction of sulfate to sulfide with the oxidation of organic electron donors. Here, we report the inhibition and kill of SRB by low SNP concentrations [0.05 mM (15 ppm)] depending on biomass concentration. Chemical reaction of SNP with sulfide did not compromise its efficacy. SNP was more effective than five biocides commonly used to control SRB. Souring, the SRB activity in oil reservoirs, is often controlled by injection of nitrate. Control of SRB-mediated souring in oil-containing bioreactors was inhibited by 4 mM (340 ppm) of sodium nitrate, but required only 0.05 mM (15 ppm) of SNP. Interestingly, nitrate and SNP were found to be highly synergistic with 0.003 mM (1 ppm) of SNP and 1 mM (85 ppm) of sodium nitrate being sufficient in inhibiting souring. Hence, using SNP as an additive may greatly increase the efficacy of nitrate injection in oil reservoirs.
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Affiliation(s)
- Tekle T Fida
- Petroleum Microbiology Research Group, Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Johanna Voordouw
- Petroleum Microbiology Research Group, Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Maryam Ataeian
- Department of Geosciences, University of Calgary, Calgary, AB, Canada
| | - Manuel Kleiner
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, United States
| | - Gloria Okpala
- Petroleum Microbiology Research Group, Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Jaspreet Mand
- Petroleum Microbiology Research Group, Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Gerrit Voordouw
- Petroleum Microbiology Research Group, Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
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21
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Keller AH, Kleinsteuber S, Vogt C. Anaerobic Benzene Mineralization by Nitrate-Reducing and Sulfate-Reducing Microbial Consortia Enriched From the Same Site: Comparison of Community Composition and Degradation Characteristics. MICROBIAL ECOLOGY 2018; 75:941-953. [PMID: 29124312 DOI: 10.1007/s00248-017-1100-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Accepted: 10/26/2017] [Indexed: 05/22/2023]
Abstract
Benzene mineralization under nitrate-reducing conditions was successfully established in an on-site reactor continuously fed with nitrate and sulfidic, benzene-containing groundwater extracted from a contaminated aquifer. Filling material from the reactor columns was used to set up anoxic enrichment cultures in mineral medium with benzene as electron donor and sole organic carbon source and nitrate as electron acceptor. Benzene degradation characteristics and community composition under nitrate-reducing conditions were monitored and compared to those of a well-investigated benzene-mineralizing consortium enriched from the same column system under sulfate-reducing conditions. The nitrate-reducing cultures degraded benzene at a rate of 10.1 ± 1.7 μM d-1, accompanied by simultaneous reduction of nitrate to nitrite. The previously studied sulfate-reducing culture degraded benzene at similar rates. Carbon and hydrogen stable isotope enrichment factors determined for nitrate-dependent benzene degradation differed significantly from those of the sulfate-reducing culture (ΛH/C nitrate = 12 ± 3 compared to ΛH/C sulfate = 28 ± 3), indicating different benzene activation mechanisms under the two conditions. The nitrate-reducing community was mainly composed of Betaproteobacteria, Ignavibacteria, and Anaerolineae. Azoarcus and a phylotype related to clone Dok59 (Rhodocyclaceae) were the dominant genera, indicating an involvement in nitrate-dependent benzene degradation. The primary benzene degrader of the sulfate-reducing consortium, a phylotype belonging to the Peptococcaceae, was absent in the nitrate-reducing consortium.
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Affiliation(s)
- Andreas H Keller
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research-UFZ, Permoserstraße 15, 04318, Leipzig, Germany
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, Permoserstraße 15, 04318, Leipzig, Germany
| | - Sabine Kleinsteuber
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, Permoserstraße 15, 04318, Leipzig, Germany
| | - Carsten Vogt
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research-UFZ, Permoserstraße 15, 04318, Leipzig, Germany.
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22
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Narenkumar J, Ramesh N, Rajasekar A. Control of corrosive bacterial community by bronopol in industrial water system. 3 Biotech 2018; 8:55. [PMID: 29354366 PMCID: PMC5756150 DOI: 10.1007/s13205-017-1071-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Accepted: 12/26/2017] [Indexed: 10/18/2022] Open
Abstract
ABSTRACT Ten aerobic corrosive bacterial strains were isolated from a cooling tower water system (CWS) which were identified based on the biochemical characterization and 16S rRNA gene sequencing. Out of them, dominant corrosion-causing bacteria, namely, Bacillus thuringiensis EN2, Terribacillus aidingensis EN3, and Bacillus oleronius EN9, were selected for biocorrosion studies on mild steel 1010 (MS) in a CWS. The biocorrosion behaviour of EN2, EN3, and EN9 strains was studied using immersion test (weight loss method), electrochemical analysis, and surface analysis. To address the corrosion problems, an anti-corrosive study using a biocide, bronopol was also demonstrated. Scanning electron microscopy and Fourier-transform infrared spectroscopy analyses of the MS coupons with biofilm developed after exposure to CWS confirmed the accumulation of extracellular polymeric substances and revealed that biofilms was formed as microcolonies, which subsequently cause pitting corrosion. In contrast, the biocide system, no pitting type of corrosion, was observed and weight loss was reduced about 32 ± 2 mg over biotic system (286 ± 2 mg). FTIR results confirmed the adsorption of bronopol on the MS metal surface as protective layer (co-ordination of NH2-Fe3+) to prevent the biofilm formation and inhibit the corrosive chemical compounds and thus led to reduction of corrosion rate (10 ± 1 mm/year). Overall, the results from WL, EIS, SEM, XRD, and FTIR concluded that bronopol was identified as effective biocide and corrosion inhibitor which controls the both chemical and biocorrosion of MS in CWS. GRAPHICAL ABSTRACT
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Affiliation(s)
- Jayaraman Narenkumar
- Environmental Molecular Microbiology Research Laboratory, Department of Biotechnology, Thiruvalluvar University, Serkkadu, Vellore, Tamilnadu 632115 India
| | - Nachimuthu Ramesh
- School of Bio Sciences and Technology, VIT University, Vellore, Tamilnadu 632 014 India
| | - Aruliah Rajasekar
- Environmental Molecular Microbiology Research Laboratory, Department of Biotechnology, Thiruvalluvar University, Serkkadu, Vellore, Tamilnadu 632115 India
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23
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Sousa JR, Silveira CM, Fontes P, Roma-Rodrigues C, Fernandes AR, Van Driessche G, Devreese B, Moura I, Moura JJ, Almeida MG. Understanding the response of Desulfovibrio desulfuricans ATCC 27774 to the electron acceptors nitrate and sulfate - biosynthetic costs modulate substrate selection. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2017; 1865:1455-1469. [DOI: 10.1016/j.bbapap.2017.07.021] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Revised: 07/12/2017] [Accepted: 07/21/2017] [Indexed: 11/27/2022]
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24
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Okpala GN, Chen C, Fida T, Voordouw G. Effect of Thermophilic Nitrate Reduction on Sulfide Production in High Temperature Oil Reservoir Samples. Front Microbiol 2017; 8:1573. [PMID: 28900416 PMCID: PMC5581841 DOI: 10.3389/fmicb.2017.01573] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Accepted: 08/03/2017] [Indexed: 01/25/2023] Open
Abstract
Oil fields can experience souring, the reduction of sulfate to sulfide by sulfate-reducing microorganisms. At the Terra Nova oil field near Canada's east coast, with a reservoir temperature of 95°C, souring was indicated by increased hydrogen sulfide in produced waters (PW). Microbial community analysis by 16S rRNA gene sequencing showed the hyperthermophilic sulfate-reducing archaeon Archaeoglobus in Terra Nova PWs. Growth enrichments in sulfate-containing media at 55-70°C with lactate or volatile fatty acids yielded the thermophilic sulfate-reducing bacterium (SRB) Desulfotomaculum. Enrichments at 30-45°C in nitrate-containing media indicated the presence of mesophilic nitrate-reducing bacteria (NRB), which reduce nitrate without accumulation of nitrite, likely to N2. Thermophilic NRB (tNRB) of the genera Marinobacter and Geobacillus were detected and isolated at 30-50°C and 40-65°C, respectively, and only reduced nitrate to nitrite. Added nitrite strongly inhibited the isolated thermophilic SRB (tSRB) and tNRB and SRB could not be maintained in co-culture. Inhibition of tSRB by nitrate in batch and continuous cultures required inoculation with tNRB. The results suggest that nitrate injected into Terra Nova is reduced to N2 at temperatures up to 45°C but to nitrite only in zones from 45 to 65°C. Since the hotter zones of the reservoir (65-80°C) are inhabited by thermophilic and hyperthermophilic sulfate reducers, souring at these temperatures might be prevented by nitrite production if nitrate-reducing zones of the system could be maintained at 45-65°C.
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Affiliation(s)
- Gloria N. Okpala
- Petroleum Microbiology Research Group, Department of Biological Sciences, University of Calgary, CalgaryAB, Canada
| | - Chuan Chen
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of TechnologyHarbin, China
| | - Tekle Fida
- Petroleum Microbiology Research Group, Department of Biological Sciences, University of Calgary, CalgaryAB, Canada
| | - Gerrit Voordouw
- Petroleum Microbiology Research Group, Department of Biological Sciences, University of Calgary, CalgaryAB, Canada
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25
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Suri N, Voordouw J, Voordouw G. The Effectiveness of Nitrate-Mediated Control of the Oil Field Sulfur Cycle Depends on the Toluene Content of the Oil. Front Microbiol 2017; 8:956. [PMID: 28620357 PMCID: PMC5450463 DOI: 10.3389/fmicb.2017.00956] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Accepted: 05/12/2017] [Indexed: 11/13/2022] Open
Abstract
The injection of nitrate is one of the most commonly used technologies to impact the sulfur cycle in subsurface oil fields. Nitrate injection enhances the activity of nitrate-reducing bacteria, which produce nitrite inhibiting sulfate-reducing bacteria (SRB). Subsequent reduction of nitrate to di-nitrogen (N2) alleviates the inhibition of SRB by nitrite. It has been shown for the Medicine Hat Glauconitic C (MHGC) field, that alkylbenzenes especially toluene are important electron donors for the reduction of nitrate to nitrite and N2. However, the rate and extent of reduction of nitrate to nitrite and of nitrite to nitrogen have not been studied for multiple oil fields. Samples of light oil (PNG, CPM, and Tundra), light/heavy oil (Gryphon and Obigbo), and of heavy oil (MHGC) were collected from locations around the world. The maximum concentration of nitrate in the aqueous phase, which could be reduced in microcosms inoculated with MHGC produced water, increased with the toluene concentration in the oil phase. PNG, Gryphon, CPM, Obigbo, MHGC, and Tundra oils had 77, 17, 5.9, 4.0, 2.6, and 0.8 mM toluene, respectively. In incubations with 49 ml of aqueous phase and 1 ml of oil these were able to reduce 22.2, 12.3, 7.9, 4.6, 4.0, and 1.4 mM of nitrate, respectively. Nitrate reduced increased to 35 ± 4 mM upon amendment of all these oils with 570 mM toluene prior to incubation. Souring control by nitrate injection requires that the nitrate is directed toward oxidation of sulfide, not toluene. Hence, the success of nitrate injections will be inversely proportional to the toluene content of the oil. Oil composition is therefore an important determinant of the success of nitrate injection to control souring in a particular field.
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Affiliation(s)
- Navreet Suri
- Petroleum Microbiology Research Group, Department of Biological Sciences, University of Calgary, CalgaryAB, Canada
| | - Johanna Voordouw
- Petroleum Microbiology Research Group, Department of Biological Sciences, University of Calgary, CalgaryAB, Canada
| | - Gerrit Voordouw
- Petroleum Microbiology Research Group, Department of Biological Sciences, University of Calgary, CalgaryAB, Canada
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Sharrar AM, Flood BE, Bailey JV, Jones DS, Biddanda BA, Ruberg SA, Marcus DN, Dick GJ. Novel Large Sulfur Bacteria in the Metagenomes of Groundwater-Fed Chemosynthetic Microbial Mats in the Lake Huron Basin. Front Microbiol 2017; 8:791. [PMID: 28533768 PMCID: PMC5421297 DOI: 10.3389/fmicb.2017.00791] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Accepted: 04/18/2017] [Indexed: 11/25/2022] Open
Abstract
Little is known about large sulfur bacteria (LSB) that inhabit sulfidic groundwater seeps in large lakes. To examine how geochemically relevant microbial metabolisms are partitioned among community members, we conducted metagenomic analysis of a chemosynthetic microbial mat in the Isolated Sinkhole, which is in a deep, aphotic environment of Lake Huron. For comparison, we also analyzed a white mat in an artesian fountain that is fed by groundwater similar to Isolated Sinkhole, but that sits in shallow water and is exposed to sunlight. De novo assembly and binning of metagenomic data from these two communities yielded near complete genomes and revealed representatives of two families of LSB. The Isolated Sinkhole community was dominated by novel members of the Beggiatoaceae that are phylogenetically intermediate between known freshwater and marine groups. Several of these Beggiatoaceae had 16S rRNA genes that contained introns previously observed only in marine taxa. The Alpena fountain was dominated by populations closely related to Thiothrix lacustris and an SM1 euryarchaeon known to live symbiotically with Thiothrix spp. The SM1 genomic bin contained evidence of H2-based lithoautotrophy. Genomic bins of both the Thiothrix and Beggiatoaceae contained genes for sulfur oxidation via the rDsr pathway, H2 oxidation via Ni-Fe hydrogenases, and the use of O2 and nitrate as electron acceptors. Mats at both sites also contained Deltaproteobacteria with genes for dissimilatory sulfate reduction (sat, apr, and dsr) and hydrogen oxidation (Ni-Fe hydrogenases). Overall, the microbial mats at the two sites held low-diversity microbial communities, displayed evidence of coupled sulfur cycling, and did not differ largely in their metabolic potentials, despite the environmental differences. These results show that groundwater-fed communities in an artesian fountain and in submerged sinkholes of Lake Huron are a rich source of novel LSB, associated heterotrophic and sulfate-reducing bacteria, and archaea.
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Affiliation(s)
- Allison M Sharrar
- Department of Earth and Environmental Sciences, University of Michigan, Ann ArborMI, USA
| | - Beverly E Flood
- Department of Earth Sciences, University of Minnesota, MinneapolisMN, USA
| | - Jake V Bailey
- Department of Earth Sciences, University of Minnesota, MinneapolisMN, USA
| | - Daniel S Jones
- Department of Earth Sciences, University of Minnesota, MinneapolisMN, USA.,BioTechnology Institute, University of Minnesota, MinneapolisMN, USA
| | - Bopaiah A Biddanda
- Annis Water Resources Institute, Grand Valley State University, MuskegonMI, USA
| | - Steven A Ruberg
- NOAA-Great Lakes Environmental Research Laboratory, Ann ArborMI, USA
| | - Daniel N Marcus
- Department of Earth and Environmental Sciences, University of Michigan, Ann ArborMI, USA
| | - Gregory J Dick
- Department of Earth and Environmental Sciences, University of Michigan, Ann ArborMI, USA
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Bonifay V, Wawrik B, Sunner J, Snodgrass EC, Aydin E, Duncan KE, Callaghan AV, Oldham A, Liengen T, Beech I. Metabolomic and Metagenomic Analysis of Two Crude Oil Production Pipelines Experiencing Differential Rates of Corrosion. Front Microbiol 2017; 8:99. [PMID: 28197141 PMCID: PMC5281625 DOI: 10.3389/fmicb.2017.00099] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Accepted: 01/13/2017] [Indexed: 01/06/2023] Open
Abstract
Corrosion processes in two North Sea oil production pipelines were studied by analyzing pig envelope samples via metagenomic and metabolomic techniques. Both production systems have similar physico-chemical properties and injection waters are treated with nitrate, but one pipeline experiences severe corrosion and the other does not. Early and late pigging material was collected to gain insight into the potential causes for differential corrosion rates. Metabolites were extracted and analyzed via ultra-high performance liquid chromatography/high-resolution mass spectrometry with electrospray ionization (ESI) in both positive and negative ion modes. Metabolites were analyzed by comparison with standards indicative of aerobic and anaerobic hydrocarbon metabolism and by comparison to predicted masses for KEGG metabolites. Microbial community structure was analyzed via 16S rRNA gene qPCR, sequencing of 16S PCR products, and MySeq Illumina shotgun sequencing of community DNA. Metagenomic data were used to reconstruct the full length 16S rRNA genes and genomes of dominant microorganisms. Sequence data were also interrogated via KEGG annotation and for the presence of genes related to terminal electron accepting (TEA) processes as well as aerobic and anaerobic hydrocarbon degradation. Significant and distinct differences were observed when comparing the ‘high corrosion’ (HC) and the ‘low corrosion’ (LC) pipeline systems, especially with respect to the TEA utilization potential. The HC samples were dominated by sulfate-reducing bacteria (SRB) and archaea known for their ability to utilize simple carbon substrates, whereas LC samples were dominated by pseudomonads with the genetic potential for denitrification and aerobic hydrocarbon degradation. The frequency of aerobic hydrocarbon degradation genes was low in the HC system, and anaerobic hydrocarbon degradation genes were not detected in either pipeline. This is in contrast with metabolite analysis, which demonstrated the presence of several succinic acids in HC samples that are diagnostic of anaerobic hydrocarbon metabolism. Identifiable aerobic metabolites were confined to the LC samples, consistent with the metagenomic data. Overall, these data suggest that corrosion management might benefit from a more refined understanding of microbial community resilience in the face of disturbances such as nitrate treatment or pigging, which frequently prove insufficient to alter community structure toward a stable, less-corrosive assemblage.
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Affiliation(s)
- Vincent Bonifay
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman OK, USA
| | - Boris Wawrik
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman OK, USA
| | - Jan Sunner
- Department of Microbiology and Plant Biology, University of Oklahoma, NormanOK, USA; Institute for Energy and the Environment, University of Oklahoma, NormanOK, USA
| | - Emily C Snodgrass
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman OK, USA
| | - Egemen Aydin
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman OK, USA
| | - Kathleen E Duncan
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman OK, USA
| | - Amy V Callaghan
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman OK, USA
| | - Athenia Oldham
- Department of Biology, University of Texas of the Permian Basin, Odessa TX, USA
| | - Turid Liengen
- Research Centre Porsgrunn, Statoil ASA, Herøya Industripark Porsgrunn, Norway
| | - Iwona Beech
- Department of Microbiology and Plant Biology, University of Oklahoma, NormanOK, USA; Institute for Energy and the Environment, University of Oklahoma, NormanOK, USA
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Antimicrobial Effects of Free Nitrous Acid on Desulfovibrio vulgaris: Implications for Sulfide-Induced Corrosion of Concrete. Appl Environ Microbiol 2016; 82:5563-75. [PMID: 27371588 DOI: 10.1128/aem.01655-16] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Accepted: 06/28/2016] [Indexed: 01/04/2023] Open
Abstract
Hydrogen sulfide produced by sulfate-reducing bacteria (SRB) in sewers causes odor problems and asset deterioration due to the sulfide-induced concrete corrosion. Free nitrous acid (FNA) was recently demonstrated as a promising antimicrobial agent to alleviate hydrogen sulfide production in sewers. However, details of the antimicrobial mechanisms of FNA are largely unknown. Here, we report the multiple-targeted antimicrobial effects of FNA on the SRB Desulfovibrio vulgaris Hildenborough by determining the growth, physiological, and gene expression responses to FNA exposure. The activities of growth, respiration, and ATP generation were inhibited when exposed to FNA. These changes were reflected in the transcript levels detected during exposure. The removal of FNA was evident by nitrite reduction that likely involved nitrite reductase and the poorly characterized hybrid cluster protein, and the genes coding for these proteins were highly expressed. During FNA exposure, lowered ribosome activity and protein production were detected. Additionally, conditions within the cells were more oxidizing, and there was evidence of oxidative stress. Based on an interpretation of the measured responses, we present a model depicting the antimicrobial effects of FNA on D. vulgaris These findings provide new insight for understanding the responses of D. vulgaris to FNA and will provide a foundation for optimal application of this antimicrobial agent for improved control of sewer corrosion and odor management.IMPORTANCE Hydrogen sulfide produced by SRB in sewers causes odor problems and results in serious deterioration of sewer assets that requires very costly and demanding rehabilitation. Currently, there is successful application of the antimicrobial agent free nitrous acid (FNA), the protonated form of nitrite, for the control of sulfide levels in sewers (G. Jiang et al., Water Res 47:4331-4339, 2013, http://dx.doi.org/10.1016/j.watres.2013.05.024). However, the details of the antimicrobial mechanisms of FNA are largely unknown. In this study, we identified the key responses (decreased anaerobic respiration, reducing FNA, combating oxidative stress, and shutting down protein synthesis) of Desulfovibrio vulgaris Hildenborough, a model sewer corrosion bacterium, to FNA exposure by examining the growth, physiological, and gene expression changes. These findings provide new insight and underpinning knowledge for understanding the responses of D. vulgaris to FNA exposure, thereby benefiting the practical application of FNA for improved control of sewer corrosion and odor.
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Villahermosa D, Corzo A, Garcia-Robledo E, González JM, Papaspyrou S. Kinetics of Indigenous Nitrate Reducing Sulfide Oxidizing Activity in Microaerophilic Wastewater Biofilms. PLoS One 2016; 11:e0149096. [PMID: 26872267 PMCID: PMC4752510 DOI: 10.1371/journal.pone.0149096] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Accepted: 01/27/2016] [Indexed: 11/18/2022] Open
Abstract
Nitrate decreases sulfide release in wastewater treatment plants (WWTP), but little is known on how it affects the microzonation and kinetics of related microbial processes within the biofilm. The effect of nitrate addition on these properties for sulfate reduction, sulfide oxidation, and oxygen respiration were studied with the use of microelectrodes in microaerophilic wastewater biofilms. Mass balance calaculations and community composition analysis were also performed. At basal WWTP conditions, the biofilm presented a double-layer system. The upper microaerophilic layer (~300 μm) showed low sulfide production (0.31 μmol cm-3 h-1) and oxygen consumption rates (0.01 μmol cm-3 h-1). The anoxic lower layer showed high sulfide production (2.7 μmol cm-3 h-1). Nitrate addition decreased net sulfide production rates, caused by an increase in sulfide oxidation rates (SOR) in the upper layer, rather than an inhibition of sulfate reducing bacteria (SRB). This suggests that the indigenous nitrate reducing-sulfide oxidizing bacteria (NR-SOB) were immediately activated by nitrate. The functional vertical structure of the biofilm changed to a triple-layer system, where the previously upper sulfide-producing layer in the absence of nitrate split into two new layers: 1) an upper sulfide-consuming layer, whose thickness is probably determined by the nitrate penetration depth within the biofilm, and 2) a middle layer producing sulfide at an even higher rate than in the absence of nitrate in some cases. Below these layers, the lower net sulfide-producing layer remained unaffected. Net SOR varied from 0.05 to 0.72 μmol cm-3 h-1 depending on nitrate and sulfate availability. Addition of low nitrate concentrations likely increased sulfate availability within the biofilm and resulted in an increase of both net sulfate reduction and net sulfide oxidation by overcoming sulfate diffusional limitation from the water phase and the strong coupling between SRB and NR-SOB syntrophic relationship.
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Affiliation(s)
- Desirée Villahermosa
- Departamento de Biología, Facultad de Ciencias del Mar y Ambientales, Universidad de Cádiz, Pol. Río San Pedro s/n, 11510-Puerto Real, Cádiz, Spain
| | - Alfonso Corzo
- Departamento de Biología, Facultad de Ciencias del Mar y Ambientales, Universidad de Cádiz, Pol. Río San Pedro s/n, 11510-Puerto Real, Cádiz, Spain
- * E-mail:
| | - Emilio Garcia-Robledo
- Departamento de Biología, Facultad de Ciencias del Mar y Ambientales, Universidad de Cádiz, Pol. Río San Pedro s/n, 11510-Puerto Real, Cádiz, Spain
| | - Juan M. González
- Instituto de Recursos Naturales y Agrobiología, IRNAS-CSIC, Avda. Reina Mercedes 10, 41012-Sevilla, Spain
| | - Sokratis Papaspyrou
- Departamento de Biología, Facultad de Ciencias del Mar y Ambientales, Universidad de Cádiz, Pol. Río San Pedro s/n, 11510-Puerto Real, Cádiz, Spain
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Xue Y, Voordouw G. Control of Microbial Sulfide Production with Biocides and Nitrate in Oil Reservoir Simulating Bioreactors. Front Microbiol 2015; 6:1387. [PMID: 26696994 PMCID: PMC4672050 DOI: 10.3389/fmicb.2015.01387] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Accepted: 11/20/2015] [Indexed: 12/02/2022] Open
Abstract
Oil reservoir souring by the microbial reduction of sulfate to sulfide is unwanted, because it enhances corrosion of metal infrastructure used for oil production and processing. Reservoir souring can be prevented or remediated by the injection of nitrate or biocides, although injection of biocides into reservoirs is not commonly done. Whether combined application of these agents may give synergistic reservoir souring control is unknown. In order to address this we have used up-flow sand-packed bioreactors injected with 2 mM sulfate and volatile fatty acids (VFA, 3 mM each of acetate, propionate and butyrate) at a flow rate of 3 or 6 pore volumes (PV) per day. Pulsed injection of the biocides glutaraldehyde (Glut), benzalkonium chloride (BAC) and cocodiamine was used to control souring. Souring control was determined as the recovery time (RT) needed to re-establish an aqueous sulfide concentration of 0.8–1 mM (of the 1.7–2 mM before the pulse). Pulses were either for a long time (120 h) at low concentration (long-low) or for a short time (1 h) at high concentration (short-high). The short-high strategy gave better souring control with Glut, whereas the long-low strategy was better with cocodiamine. Continuous injection of 2 mM nitrate alone was not effective, because 3 mM VFA can fully reduce both 2 mM nitrate to nitrite and N2 and, subsequently, 2 mM sulfate to sulfide. No synergy was observed for short-high pulsed biocides and continuously injected nitrate. However, use of continuous nitrate and long-low pulsed biocide gave synergistic souring control with BAC and Glut, as indicated by increased RTs in the presence, as compared to the absence of nitrate. Increased production of nitrite, which increases the effectiveness of souring control by biocides, is the most likely cause for this synergy.
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Affiliation(s)
- Yuan Xue
- Petroleum Microbiology Research Group, Department of Biological Sciences, University of Calgary Calgary, AB, Canada
| | - Gerrit Voordouw
- Petroleum Microbiology Research Group, Department of Biological Sciences, University of Calgary Calgary, AB, Canada
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31
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Suitability of different growth substrates as source of nitrogen for sulfate reducing bacteria. Biodegradation 2015; 26:415-30. [DOI: 10.1007/s10532-015-9745-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Accepted: 09/05/2015] [Indexed: 11/26/2022]
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32
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Regulation of Nitrite Stress Response in Desulfovibrio vulgaris Hildenborough, a Model Sulfate-Reducing Bacterium. J Bacteriol 2015; 197:3400-8. [PMID: 26283774 DOI: 10.1128/jb.00319-15] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2015] [Accepted: 08/12/2015] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED Sulfate-reducing bacteria (SRB) are sensitive to low concentrations of nitrite, and nitrite has been used to control SRB-related biofouling in oil fields. Desulfovibrio vulgaris Hildenborough, a model SRB, carries a cytochrome c-type nitrite reductase (nrfHA) that confers resistance to low concentrations of nitrite. The regulation of this nitrite reductase has not been directly examined to date. In this study, we show that DVU0621 (NrfR), a sigma54-dependent two-component system response regulator, is the positive regulator for this operon. NrfR activates the expression of the nrfHA operon in response to nitrite stress. We also show that nrfR is needed for fitness at low cell densities in the presence of nitrite because inactivation of nrfR affects the rate of nitrite reduction. We also predict and validate the binding sites for NrfR upstream of the nrfHA operon using purified NrfR in gel shift assays. We discuss possible roles for NrfR in regulating nitrate reductase genes in nitrate-utilizing Desulfovibrio spp. IMPORTANCE The NrfA nitrite reductase is prevalent across several bacterial phyla and required for dissimilatory nitrite reduction. However, regulation of the nrfA gene has been studied in only a few nitrate-utilizing bacteria. Here, we show that in D. vulgaris, a bacterium that does not respire nitrate, the expression of nrfHA is induced by NrfR upon nitrite stress. This is the first report of regulation of nrfA by a sigma54-dependent two-component system. Our study increases our knowledge of nitrite stress responses and possibly of the regulation of nitrate reduction in SRB.
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Mansor M, Hamilton TL, Fantle MS, Macalady JL. Metabolic diversity and ecological niches of Achromatium populations revealed with single-cell genomic sequencing. Front Microbiol 2015; 6:822. [PMID: 26322031 PMCID: PMC4530308 DOI: 10.3389/fmicb.2015.00822] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2015] [Accepted: 07/27/2015] [Indexed: 11/13/2022] Open
Abstract
Large, sulfur-cycling, calcite-precipitating bacteria in the genus Achromatium represent a significant proportion of bacterial communities near sediment-water interfaces at sites throughout the world. Our understanding of their potentially crucial roles in calcium, carbon, sulfur, nitrogen, and iron cycling is limited because they have not been cultured or sequenced using environmental genomics approaches to date. We utilized single-cell genomic sequencing to obtain one incomplete and two nearly complete draft genomes for Achromatium collected at Warm Mineral Springs (WMS), FL. Based on 16S rRNA gene sequences, the three cells represent distinct and relatively distant Achromatium populations (91-92% identity). The draft genomes encode key genes involved in sulfur and hydrogen oxidation; oxygen, nitrogen and polysulfide respiration; carbon and nitrogen fixation; organic carbon assimilation and storage; chemotaxis; twitching motility; antibiotic resistance; and membrane transport. Known genes for iron and manganese energy metabolism were not detected. The presence of pyrophosphatase and vacuolar (V)-type ATPases, which are generally rare in bacterial genomes, suggests a role for these enzymes in calcium transport, proton pumping, and/or energy generation in the membranes of calcite-containing inclusions.
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Affiliation(s)
- Muammar Mansor
- Geosciences Department, Pennsylvania State University University Park, PA, USA
| | - Trinity L Hamilton
- Department of Biological Sciences, University of Cincinnati Cincinnati, OH, USA
| | - Matthew S Fantle
- Geosciences Department, Pennsylvania State University University Park, PA, USA
| | - Jennifer L Macalady
- Geosciences Department, Pennsylvania State University University Park, PA, USA
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da Silva SM, Amaral C, Neves SS, Santos C, Pimentel C, Rodrigues-Pousada C. An HcpR paralog of Desulfovibrio gigas provides protection against nitrosative stress. FEBS Open Bio 2015; 5:594-604. [PMID: 26273559 PMCID: PMC4534486 DOI: 10.1016/j.fob.2015.07.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Accepted: 07/01/2015] [Indexed: 01/12/2023] Open
Abstract
Desulfovibrio gigas genome encodes two HcpR paralogs, HcpR1 and HcpR2. Cells lacking HcpR1 are less tolerant to NO. HcpR1 regulates the expression of several genes related to nitrogen metabolism. Phylogenetic analyses indicate that the presence of HcpR paralogs is a common finding among Desulfovibrio species.
Desulfovibrio gigas belongs to the group of sulfate reducing bacteria (SRB). These ubiquitous and metabolically versatile microorganisms are often exposed to reactive nitrogen species (RNS). Nonetheless, the mechanisms and regulatory elements involved in nitrosative stress protection are still poorly understood. The transcription factor HcpR has emerged as a putative regulator of nitrosative stress response among anaerobic bacteria. HcpR is known to orchestrate the expression of the hybrid cluster protein gene, hcp, proposed to be involved in cellular defense against RNS. According to phylogenetic analyses, the occurrence of hcpR paralog genes is a common feature among several Desulfovibrio species. Within the D. gigas genome we have identified two HcpR-related sequences. One of these sequences, hcpR1, was found in the close vicinity of the hcp gene and this finding prompted us to proceed with its functional characterization. We observed that the growth of a D. gigas strain lacking hcpR1 is severely impaired under nitrosative stress. An in silico search revealed several putative targets of HcpR1 that were experimentally validated. The fact that HcpR1 regulates several genes encoding proteins involved in nitrite and nitrate metabolism, together with the sensitive growth phenotype to NO displayed by an hcpR1 mutant strain, strongly supports a relevant role of this factor under nitrosative stress. Moreover, the finding that several Desulfovibrio species possess HcpR paralogs, which have been transmitted vertically in the evolution and diversification of the genus, suggests that these sequences may confer adaptive or survival advantage to these organisms, possibly by increasing their tolerance to nitrosative stress.
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Key Words
- BI, Bayesian inference
- BS, bootstrap
- CRP/FNR, cAMP receptor protein/fumarate and nitrate reductase regulatory protein
- Desulfovibrio
- Frdx, ferredoxin
- GSNO, S-nitrosoglutathione
- HGT, horizontal gene transfer
- Hcp, hybrid cluster protein
- HcpR
- ML, maximum likelihood
- MP, maximum parsimony
- Molecular phylogeny
- NO, nitric oxide
- Nitrosative stress
- PP, posterior probability
- RNS, reactive nitrogen species
- ROO, rubredoxin oxygen reductase
- SRB, sulfate reducing bacteria
- Sulfate reducing bacteria
- Transcription regulation
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Affiliation(s)
- Sofia M da Silva
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Catarina Amaral
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Susana S Neves
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Cátia Santos
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Catarina Pimentel
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Claudina Rodrigues-Pousada
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
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A Post-Genomic View of the Ecophysiology, Catabolism and Biotechnological Relevance of Sulphate-Reducing Prokaryotes. Adv Microb Physiol 2015. [PMID: 26210106 DOI: 10.1016/bs.ampbs.2015.05.002] [Citation(s) in RCA: 173] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Dissimilatory sulphate reduction is the unifying and defining trait of sulphate-reducing prokaryotes (SRP). In their predominant habitats, sulphate-rich marine sediments, SRP have long been recognized to be major players in the carbon and sulphur cycles. Other, more recently appreciated, ecophysiological roles include activity in the deep biosphere, symbiotic relations, syntrophic associations, human microbiome/health and long-distance electron transfer. SRP include a high diversity of organisms, with large nutritional versatility and broad metabolic capacities, including anaerobic degradation of aromatic compounds and hydrocarbons. Elucidation of novel catabolic capacities as well as progress in the understanding of metabolic and regulatory networks, energy metabolism, evolutionary processes and adaptation to changing environmental conditions has greatly benefited from genomics, functional OMICS approaches and advances in genetic accessibility and biochemical studies. Important biotechnological roles of SRP range from (i) wastewater and off gas treatment, (ii) bioremediation of metals and hydrocarbons and (iii) bioelectrochemistry, to undesired impacts such as (iv) souring in oil reservoirs and other environments, and (v) corrosion of iron and concrete. Here we review recent advances in our understanding of SRPs focusing mainly on works published after 2000. The wealth of publications in this period, covering many diverse areas, is a testimony to the large environmental, biogeochemical and technological relevance of these organisms and how much the field has progressed in these years, although many important questions and applications remain to be explored.
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Yuan C, Mosley LM, Fitzpatrick R, Marschner P. Amount of organic matter required to induce sulfate reduction in sulfuric material after re-flooding is affected by soil nitrate concentration. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2015; 151:437-442. [PMID: 25600239 DOI: 10.1016/j.jenvman.2015.01.016] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2014] [Revised: 01/07/2015] [Accepted: 01/10/2015] [Indexed: 06/04/2023]
Abstract
Acid sulfate soils (ASS) with sulfuric material can be remediated through microbial sulfate reduction stimulated by adding organic matter (OM) and increasing the soil pH to >4.5, but the effectiveness of this treatment is influenced by soil properties. Two experiments were conducted using ASS with sulfuric material. In the first experiment with four ASS, OM (finely ground mature wheat straw) was added at 2-6% (w/w) and the pH adjusted to 5.5. After 36 weeks under flooded conditions, the concentration of reduced inorganic sulfur (RIS) and pore water pH were greater in all treatments with added OM than in the control without OM addition. The RIS concentration increased with OM addition rate. The increase in RIS concentration between 4% and 6% OM was significant but smaller than that between 2% and 4%, suggesting other factors limited sulfate reduction. In the second experiment, the effect of nitrate addition on sulfate reduction at different OM addition rates was investigated in one ASS. Organic matter was added at 2 and 4% and nitrate at 0, 100, and 200 mg nitrate-N kg(-1). After 2 weeks under flooded conditions, soil pH and the concentration of FeS measured as acid volatile sulfur (AVS) were lower with nitrate added at both OM addition rates. At a given nitrate addition rate, pH and AVS concentration were higher at 4% OM than at 2%. It can be concluded that sulfate reduction in ASS at pH 5.5 can be limited by low OM availability and high nitrate concentrations. Further, the inhibitory effect of nitrate can be overcome by high OM addition rates.
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Affiliation(s)
- Chaolei Yuan
- School of Agriculture, Food & Wine, The University of Adelaide, Adelaide, SA 5005, Australia
| | - Luke M Mosley
- Water Quality Science, PO Box 310, Belair, SA 5052, Australia; Acid Sulfate Soils Centre, The University of Adelaide, Adelaide, SA 5005, Australia
| | - Rob Fitzpatrick
- Acid Sulfate Soils Centre, The University of Adelaide, Adelaide, SA 5005, Australia
| | - Petra Marschner
- School of Agriculture, Food & Wine, The University of Adelaide, Adelaide, SA 5005, Australia.
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Chen M, Zhou J, Zhang Y, Wang X, Shi Z, Wang X. Fe(III)EDTA and Fe(II)EDTA-NO reduction by a sulfate reducing bacterium in NO and SO₂ scrubbing liquor. World J Microbiol Biotechnol 2015; 31:527-34. [PMID: 25649204 DOI: 10.1007/s11274-015-1813-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Accepted: 01/30/2015] [Indexed: 10/24/2022]
Abstract
A viable process concept, based on NO and SO2 absorption into an alkaline Fe(II)EDTA (EDTA: ethylenediaminetetraacetic acid) solution in a scrubber combined with biological reduction of the absorbed SO2 utilizing sulfate reducing bacteria (SRB) and regeneration of the scrubbing liquor in a single bioreactor, was developed. The SRB, Desulfovibrio sp. CMX, was used and its sulfate reduction performances in FeEDTA solutions and Fe(II)EDTA-NO had been investigated. In this study, the detailed regeneration process of Fe(II)EDTA solution, which contained Fe(III)EDTA and Fe(II)EDTA-NO reduction processes in presence of D. sp. CMX and sulfate, was evaluated. Fe(III)EDTA and Fe(II)EDTA-NO reduction processes were primarily biological, even if Fe(III)EDTA and Fe(II)EDTA-NO could also be chemically convert to Fe(II)EDTA by biogenic sulfide. Regardless presence or absence of sulfate, more than 87 % Fe(III)EDTA and 98 % Fe(II)EDTA-NO were reduced in 46 h, respectively. Sulfate and Fe(III)EDTA had no affection on Fe(II)EDTA-NO reduction. Sulfate enhanced final Fe(III)EDTA reduction. Effect of Fe(III)EDTA on Fe(II)EDTA-NO reduction rate was more obvious than effect of sulfate on Fe(II)EDTA-NO reduction rate before 8 h. To overcome toxicity of Fe(II)EDTA-NO on SRB, Fe(II)EDTA-NO was reduced first and the reduction of Fe(III)EDTA and sulfate occurred after 2 h. First-order Fe(II)EDTA-NO reduction rate and zero-order Fe(III)EDTA reduction rate were detected respectively before 8 h.
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Affiliation(s)
- Mingxiang Chen
- Key Laboratory of Industrial Ecology and Environmental Engineering (MOE), School of Environmental Science and Technology, Dalian University of Technology, Linggong Road 2, Dalian, 116024, People's Republic of China
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Korte HL, Saini A, Trotter VV, Butland GP, Arkin AP, Wall JD. Independence of nitrate and nitrite inhibition of Desulfovibrio vulgaris Hildenborough and use of nitrite as a substrate for growth. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2015; 49:924-931. [PMID: 25534748 DOI: 10.1021/es504484m] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Sulfate-reducing microbes, such as Desulfovibrio vulgaris Hildenborough, cause “souring” of petroleum reservoirs through produced sulfide and precipitate heavy metals, either as sulfides or by alteration of the metal reduction state. Thus, inhibitors of these microbes, including nitrate and nitrite ions, are studied in order to limit their impact. Nitrite is a potent inhibitor of sulfate reducers, and it has been suggested that nitrate does not inhibit these microbes directly but by reduction to nitrite, which serves as the ultimate inhibitor. Here we provide evidence that nitrate inhibition of D. vulgaris can be independent of nitrite production. We also show that D. vulgaris can use nitrite as a nitrogen source or terminal electron acceptor for growth. Moreover, we report that use of nitrite as a terminal electron acceptor requires nitrite reductase (nrfA) as a D. vulgaris nrfA mutant cannot respire nitrite but remains capable of utilizing nitrite as a nitrogen source. These results illuminate previously uncharacterized metabolic abilities of D. vulgaris that may allow niche expansion in low-sulfate environments. Understanding these abilities may lead to better control of sulfate-reducing bacteria in industrial settings and more accurate prediction of their interactions in the environment.
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Chen Y, Wen Y, Zhou J, Tang Z, Li L, Zhou Q, Vymazal J. Effects of cattail biomass on sulfate removal and carbon sources competition in subsurface-flow constructed wetlands treating secondary effluent. WATER RESEARCH 2014; 59:1-10. [PMID: 24768761 DOI: 10.1016/j.watres.2014.03.077] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2013] [Revised: 03/11/2014] [Accepted: 03/28/2014] [Indexed: 06/03/2023]
Abstract
Sulfate is frequently found in the influent of subsurface-flow constructed wetlands (SSF CWs) used as tertiary treatments. To reveal the effects of plants and litters on sulfate removal, as well as the competition for organic carbon among microorganisms in SSF CWs, five laboratory-scale SSF CW microcosms were set up and were operated as a batch system with HRT 5 d. The results showed that the presence of Typha latifolia had little effect on sulfate removal in CWs, with or without additional carbon sources. Cattail litter addition greatly improved sulfate removal in SSF CWs. This improvement was linked to the continuous input of labile organic carbon, which lowers the redox level and supplies a habitat for sulfate reducing bacteria (SRB). The presence of SRB in cattail litter indicated the possibility of sulfate removal around the carbon supplier, but the quantity of microbes in cattail litter was much lower than that in gravel. Stoichiometry calculations showed that the contribution of SRB to COD removal (21-26%) was less than that of methane-producing bacteria (MPB) (47-61%) during the initial stage but dominated COD removal (42-65%) during the terminal stage. The contributions of aerobic bacteria (AB) and denitrification bacteria (DB) to COD removal were always lower than that of SRB. It was also observed that the variations in COD: S ratio had a great influence on the relative abundance of genes between SRB and MPB and both of them could be used as good predictors of carbon competition between SRB and MPB in CWs.
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Affiliation(s)
- Yi Chen
- Key Laboratory of Yangtze Water Environment of Ministry of the State Education, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, PR China; Department of Landscape Ecology, Faculty of Environmental Sciences, Czech University of Life Sciences Prague 16521, Czech Republic
| | - Yue Wen
- Key Laboratory of Yangtze Water Environment of Ministry of the State Education, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, PR China.
| | - Junwei Zhou
- Key Laboratory of Yangtze Water Environment of Ministry of the State Education, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, PR China
| | - Zhiru Tang
- Key Laboratory of Yangtze Water Environment of Ministry of the State Education, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, PR China
| | - Ling Li
- Key Laboratory of Yangtze Water Environment of Ministry of the State Education, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, PR China
| | - Qi Zhou
- Key Laboratory of Yangtze Water Environment of Ministry of the State Education, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, PR China
| | - Jan Vymazal
- Department of Landscape Ecology, Faculty of Environmental Sciences, Czech University of Life Sciences Prague 16521, Czech Republic
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Drønen K, Roalkvam I, Beeder J, Torsvik T, Steen IH, Skauge A, Liengen T. Modeling of heavy nitrate corrosion in anaerobe aquifer injection water biofilm: a case study in a flow rig. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2014; 48:8627-8635. [PMID: 25020005 DOI: 10.1021/es500839u] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Heavy carbon steel corrosion developed during nitrate mitigation of a flow rig connected to a water injection pipeline flowing anaerobe saline aquifer water. Genera-specific QPCR primers quantified 74% of the microbial biofilm community, and further 87% of the community of the nonamended parallel rig. The nonamended biofilm hosted 6.3 × 10(6) SRB cells/cm(2) and the S(35)-sulfate-reduction rate was 1.1 μmol SO4(2-)/cm(2)/day, being congruent with the estimated SRB biomass formation and the sulfate areal flux. Nitrate amendment caused an 18-fold smaller SRB population, but up to 44 times higher sulfate reduction rates. This H2S formation was insufficient to form the observed Fe3S4 layer. Additional H2S was provided by microbial disproportionation of sulfur, also explaining the increased accessibility of sulfate. The reduced nitrate specie nitrite inhibited the dominating H2-scavenging Desulfovibrio population, and sustained the formation of polysulfide and Fe3S4, herby also dissolved sulfur. This terminated the availability of acetate in the inner biofilm and caused cell starvation that initiated growth upon metallic electrons, probably by the sulfur-reducing Desulfuromonas population. On the basis of these observations we propose a model of heavy nitrate corrosion where three microbiological processes of nitrate reduction, disproportionation of sulfur, and metallic electron growth are nicely woven into each other.
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Affiliation(s)
- Karine Drønen
- Uni Research CIPR , Allégaten 41, 5007 Bergen, Norway
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Korte HL, Fels SR, Christensen GA, Price MN, Kuehl JV, Zane GM, Deutschbauer AM, Arkin AP, Wall JD. Genetic basis for nitrate resistance in Desulfovibrio strains. Front Microbiol 2014; 5:153. [PMID: 24795702 PMCID: PMC4001038 DOI: 10.3389/fmicb.2014.00153] [Citation(s) in RCA: 162] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2014] [Accepted: 03/21/2014] [Indexed: 12/31/2022] Open
Abstract
Nitrate is an inhibitor of sulfate-reducing bacteria (SRB). In petroleum production sites, amendments of nitrate and nitrite are used to prevent SRB production of sulfide that causes souring of oil wells. A better understanding of nitrate stress responses in the model SRB, Desulfovibrio vulgaris Hildenborough and Desulfovibrio alaskensis G20, will strengthen predictions of environmental outcomes of nitrate application. Nitrate inhibition of SRB has historically been considered to result from the generation of small amounts of nitrite, to which SRB are quite sensitive. Here we explored the possibility that nitrate might inhibit SRB by a mechanism other than through nitrite inhibition. We found that nitrate-stressed D. vulgaris cultures grown in lactate-sulfate conditions eventually grew in the presence of high concentrations of nitrate, and their resistance continued through several subcultures. Nitrate consumption was not detected over the course of the experiment, suggesting adaptation to nitrate. With high-throughput genetic approaches employing TnLE-seq for D. vulgaris and a pooled mutant library of D. alaskensis, we determined the fitness of many transposon mutants of both organisms in nitrate stress conditions. We found that several mutants, including homologs present in both strains, had a greatly increased ability to grow in the presence of nitrate but not nitrite. The mutated genes conferring nitrate resistance included the gene encoding the putative Rex transcriptional regulator (DVU0916/Dde_2702), as well as a cluster of genes (DVU0251-DVU0245/Dde_0597-Dde_0605) that is poorly annotated. Follow-up studies with individual D. vulgaris transposon and deletion mutants confirmed high-throughput results. We conclude that, in D. vulgaris and D. alaskensis, nitrate resistance in wild-type cultures is likely conferred by spontaneous mutations. Furthermore, the mechanisms that confer nitrate resistance may be different from those that confer nitrite resistance.
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Affiliation(s)
- Hannah L Korte
- Department of Biochemistry, University of Missouri Columbia, MO, USA ; Ecosystems and Networks Integrated with Genes and Molecular Assemblies Berkeley, CA, USA
| | - Samuel R Fels
- Ecosystems and Networks Integrated with Genes and Molecular Assemblies Berkeley, CA, USA ; Department of Molecular Microbiology and Immunology, University of Missouri Columbia, MO, USA
| | - Geoff A Christensen
- Department of Biochemistry, University of Missouri Columbia, MO, USA ; Ecosystems and Networks Integrated with Genes and Molecular Assemblies Berkeley, CA, USA
| | - Morgan N Price
- Ecosystems and Networks Integrated with Genes and Molecular Assemblies Berkeley, CA, USA ; Physical Biosciences Division, Lawrence Berkeley National Laboratory Berkeley, CA, USA
| | - Jennifer V Kuehl
- Ecosystems and Networks Integrated with Genes and Molecular Assemblies Berkeley, CA, USA ; Physical Biosciences Division, Lawrence Berkeley National Laboratory Berkeley, CA, USA
| | - Grant M Zane
- Department of Biochemistry, University of Missouri Columbia, MO, USA ; Ecosystems and Networks Integrated with Genes and Molecular Assemblies Berkeley, CA, USA
| | - Adam M Deutschbauer
- Ecosystems and Networks Integrated with Genes and Molecular Assemblies Berkeley, CA, USA ; Physical Biosciences Division, Lawrence Berkeley National Laboratory Berkeley, CA, USA
| | - Adam P Arkin
- Ecosystems and Networks Integrated with Genes and Molecular Assemblies Berkeley, CA, USA ; Physical Biosciences Division, Lawrence Berkeley National Laboratory Berkeley, CA, USA
| | - Judy D Wall
- Department of Biochemistry, University of Missouri Columbia, MO, USA ; Ecosystems and Networks Integrated with Genes and Molecular Assemblies Berkeley, CA, USA ; Department of Molecular Microbiology and Immunology, University of Missouri Columbia, MO, USA
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Welsh A, Chee-Sanford JC, Connor LM, Löffler FE, Sanford RA. Refined NrfA phylogeny improves PCR-based nrfA gene detection. Appl Environ Microbiol 2014; 80:2110-9. [PMID: 24463965 PMCID: PMC3993153 DOI: 10.1128/aem.03443-13] [Citation(s) in RCA: 111] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2013] [Accepted: 01/16/2014] [Indexed: 11/20/2022] Open
Abstract
Dissimilatory nitrate reduction to ammonium (DNRA) and denitrification are contrasting microbial processes in the terrestrial nitrogen (N) cycle, in that the former promotes N retention and the latter leads to N loss (i.e., the formation of gaseous products). The nitrite reductase NrfA catalyzes nitrite reduction to ammonium, the enzyme associated with respiratory nitrite ammonification and the key step in DNRA. Although well studied biochemically, the diversity and phylogeny of this enzyme had not been rigorously analyzed. A phylogenetic analysis of 272 full-length NrfA protein sequences distinguished 18 NrfA clades with robust statistical support (>90% Bayesian posterior probabilities). Three clades possessed a CXXCH motif in the first heme-binding domain, whereas all other clades had a CXXCK motif in this location. The analysis further identified a KXRH or KXQH motif between the third and fourth heme-binding motifs as a conserved and diagnostic feature of all pentaheme NrfA proteins. PCR primers targeting a portion of the heme-binding motifs that flank this diagnostic region yielded the expected 250-bp-long amplicons with template DNA from eight pure cultures and 16 new nrfA-containing isolates. nrfA amplicons obtained with template DNA from two geomorphically distinct agricultural soils could be assigned to one of the 18 NrfA clades, providing support for this expanded classification. The extended NrfA phylogeny revealed novel diagnostic features of DNRA populations and will be useful to assess nitrate/nitrite fate in natural and engineered ecosystems.
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Affiliation(s)
- Allana Welsh
- University of Illinois at Urbana Champaign, Urbana, Illinois, USA
| | - Joanne C. Chee-Sanford
- University of Illinois at Urbana Champaign, Urbana, Illinois, USA
- USDA-ARS, Urbana, Illinois, USA
| | | | - Frank E. Löffler
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, USA
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, Tennessee, USA
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, Tennessee, USA
- University of Tennessee and Oak Ridge National Laboratory (UT-ORNL) Joint Institute for Biological Sciences (JIBS) and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
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Liao R, Li Y, Yu X, Shi P, Wang Z, Shen K, Shi Q, Miao Y, Li W, Li A. Performance and microbial diversity of an expanded granular sludge bed reactor for high sulfate and nitrate waste brine treatment. J Environ Sci (China) 2014; 26:717-725. [PMID: 25079401 DOI: 10.1016/s1001-0742(13)60479-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2013] [Revised: 08/27/2013] [Accepted: 08/29/2013] [Indexed: 06/03/2023]
Abstract
The disposal of waste brines has become a major challenge that hinders the wide application of ion-exchange resins in the water industry in recent decades. In this study, high sulfate removal efficiency (80%-90%) was achieved at the influent sulfate concentration of 3600 mg/L and 3% NaCl after 145 days in an expanded granular sludge bed (EGSB) reactor. Furthermore, the feasibility of treating synthetic waste brine containing high levels of sulfate and nitrate was investigated in a single EGSB reactor during an operation period of 261 days. The highest nitrate and sulfate loading rate reached 6.38 and 5.78 kg/(m(3)·day) at SO(2-)4-S/NO(-)3-N mass ratio of 4/3, and the corresponding removal efficiency was 99.97% and 82.26% at 3% NaCl, respectively. Meanwhile, 454-pyrosequencing technology was used to analyze the bacterial diversity of the sludge on the 240th day for stable operation of phase X. Results showed that a total of 9194 sequences were obtained, which could be affiliated to 14 phyla, including Proteobacteria, Firmicutes, Chlorobi, Bacteroidetes, Synergistetes and so on. Proteobacteria (77.66%) was the dominant microbial population, followed by Firmicutes (12.23%) and Chlorobi (2.71%).
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Affiliation(s)
- Runhua Liao
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China; School of Materials Science and Engineering, Jingdezhen Ceramic Institute, Jingdezhen 333403, China.
| | - Yan Li
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China
| | - Xuemin Yu
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China
| | - Peng Shi
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China
| | - Zhu Wang
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China
| | - Ke Shen
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China
| | - Qianqian Shi
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China
| | - Yu Miao
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China
| | - Wentao Li
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China
| | - Aimin Li
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China.
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Characterization of Corrosive Bacterial Consortia Isolated from Water in a Cooling Tower. ACTA ACUST UNITED AC 2014. [DOI: 10.1155/2014/803219] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
An analysis of a culturable corrosive bacterial community in water samples from a cooling tower was performed using traditional cultivation techniques and its identification based on 16S rRNA gene sequence. Seven aerobic bacterial species were identified: Pseudomonas putida ARTYP1, Pseudomonas aeruginosa ARTYP2, Massilia timonae ARTYP3, Massilia albidiflava ARTYP4, Pseudomonas mosselii ARTYP5, Massilia sp. ARTYP6, and Pseudomonas sp. ARTYP7. Although some of these species have commonly been observed and reported in biocorrosion studies, the genus Massilia is identified for the first time in water from a cooling tower. The biocorrosion behaviour of copper metal by the new species Massilia timonae ARTYP3 was selected for further investigation using a weight loss method, as well as electrochemical and surface analysis techniques (SEM, AFM, and FTIR). In contrast with an uninoculated system, thin bacterial biofilms and pitting corrosion were observed on the copper metal surface in the presence of M. timonae. The use of a biocide, bronopol, inhibited the formation of biofilm and pitting corrosion on the copper metal surface.
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Green-Saxena A, Dekas AE, Dalleska NF, Orphan VJ. Nitrate-based niche differentiation by distinct sulfate-reducing bacteria involved in the anaerobic oxidation of methane. ISME JOURNAL 2013; 8:150-63. [PMID: 24008326 DOI: 10.1038/ismej.2013.147] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2013] [Revised: 07/19/2013] [Accepted: 07/22/2013] [Indexed: 11/09/2022]
Abstract
Diverse associations between methanotrophic archaea (ANME) and sulfate-reducing bacterial groups (SRB) often co-occur in marine methane seeps; however, the ecophysiology of these different symbiotic associations has not been examined. Here, we applied a combination of molecular, geochemical and Fluorescence in situ hybridization (FISH) coupled to nanoscale secondary ion mass spectrometry (FISH-NanoSIMS) analyses of in situ seep sediments and methane-amended sediment incubations from diverse locations (Eel River Basin, Hydrate Ridge and Costa Rican Margin seeps) to investigate the distribution and physiology of a newly identified subgroup of the Desulfobulbaceae (seepDBB) found in consortia with ANME-2c archaea, and compared these with the more commonly observed associations between the same ANME partner and the Desulfobacteraceae (DSS). FISH analyses revealed aggregates of seepDBB cells in association with ANME-2 from both environmental samples and laboratory incubations that are distinct in their structure relative to co-occurring ANME/DSS consortia. ANME/seepDBB aggregates were most abundant in shallow sediment depths below sulfide-oxidizing microbial mats. Depth profiles of ANME/seepDBB aggregate abundance revealed a positive correlation with elevated porewater nitrate relative to ANME/DSS aggregates in all seep sites examined. This relationship with nitrate was supported by sediment microcosm experiments, in which the abundance of ANME/seepDBB was greater in nitrate-amended incubations relative to the unamended control. FISH-NanoSIMS additionally revealed significantly higher (15)N-nitrate incorporation levels in individual aggregates of ANME/seepDBB relative to ANME/DSS aggregates from the same incubation. These combined results suggest that nitrate is a geochemical effector of ANME/seepDBB aggregate distribution, and provides a unique niche for these consortia through their utilization of a greater range of nitrogen substrates than the ANME/DSS.
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Affiliation(s)
- A Green-Saxena
- Division of Biology, California Institute of Technology, Pasadena, CA, USA
| | - A E Dekas
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, USA
| | - N F Dalleska
- Global Environmental Center, California Institute of Technology, Pasadena, CA, USA
| | - V J Orphan
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, USA
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Chen M, Zhang Y, Zhou J, Dong X, Wang X, Shi Z. Sulfate removal by Desulfovibrio sp. CMX in chelate scrubbing solutions for NO removal. BIORESOURCE TECHNOLOGY 2013; 143:455-460. [PMID: 23831744 DOI: 10.1016/j.biortech.2013.06.037] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2013] [Revised: 06/08/2013] [Accepted: 06/11/2013] [Indexed: 06/02/2023]
Abstract
To study the effects of Fe chelate solution and nitrosyl-complex (Fe(II)EDTA-NO), which might be introduced in the simultaneous biodesulfurization and denitrification process, on the sulfate removal process, a sulfate reducing bacteria Desulfovibrio sp. CMX was investigated for its sulfate removal capacity in the presence of Fe chelate additives and Fe(II)EDTA-NO. Meanwhile, Fe(II)EDTA-NO reduction was also investigated. The addition of Fe(II)EDTA and Fe(III)EDTA could stimulate the sulfate reduction performance. Although Fe(II)EDTA-NO could inhibit the strain, CMX could survive by consuming lactate and recover its sulfate reducing activity after Fe(II)EDTA-NO removed. Sulfate reduction could be enhanced in higher Fe(II)EDTA-NO concentrations (2 and 4 mM) by lactate applied at the middle stage of the experiment, and 72.2% and 62.6% sulfate were removed in 182 h, respectively. In this study, above 90% Fe(II)EDTA-NO (0.25-4 mM) was removed less than 60 h, which was much faster than sulfate reduction.
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Affiliation(s)
- Mingxiang Chen
- Key Laboratory of Industrial Ecology and Environmental Engineering (MOE), School of Environmental Science and Technology, Dalian University of Technology, Linggong Road 2, Dalian 116024, PR China
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Abstract
Despite its reactivity and hence toxicity to living cells, sulfite is readily converted by various microorganisms using distinct assimilatory and dissimilatory metabolic routes. In respiratory pathways, sulfite either serves as a primary electron donor or terminal electron acceptor (yielding sulfate or sulfide, respectively), and its conversion drives electron transport chains that are coupled to chemiosmotic ATP synthesis. Notably, such processes are also seen to play a general role in sulfite detoxification, which is assumed to have an evolutionary ancient origin. The diversity of sulfite conversion is reflected by the fact that the range of microbial sulfite-converting enzymes displays different cofactors such as siroheme, heme c, or molybdopterin. This chapter aims to summarize the current knowledge of microbial sulfite metabolism and focuses on sulfite catabolism. The structure and function of sulfite-converting enzymes and the emerging picture of the modular architecture of the corresponding respiratory/detoxifying electron transport chains is emphasized.
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Affiliation(s)
- Jörg Simon
- Department of Biology, Microbial Energy Conversion and Biotechnology, Technische Universität Darmstadt, Schnittspahnstrasse 10, 64287 Darmstadt, Germany.
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Hybrid cluster proteins and flavodiiron proteins afford protection to Desulfovibrio vulgaris upon macrophage infection. J Bacteriol 2013; 195:2684-90. [PMID: 23564166 DOI: 10.1128/jb.00074-13] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Desulfovibrio species are Gram-negative anaerobic sulfate-reducing bacteria that colonize the human gut. Recently, Desulfovibrio spp. have been implicated in gastrointestinal diseases and shown to stimulate the epithelial immune response, leading to increased production of inflammatory cytokines by macrophages. Activated macrophages are key cells of the immune system that impose nitrosative stress during phagocytosis. Hence, we have analyzed the in vitro and in vivo responses of Desulfovibrio vulgaris Hildenborough to nitric oxide (NO) and the role of the hybrid cluster proteins (HCP1 and HCP2) and rubredoxin oxygen oxidoreductases (ROO1 and ROO2) in NO protection. Among the four genes, hcp2 was the gene most highly induced by NO, and the hcp2 transposon mutant exhibited the lowest viability under conditions of NO stress. Studies in murine macrophages revealed that D. vulgaris survives incubation with these phagocytes and triggers NO production at levels similar to those stimulated by the cytokine gamma interferon (IFN-γ). Furthermore, D. vulgaris hcp and roo mutants exhibited reduced viability when incubated with macrophages, revealing that these gene products contribute to the survival of D. vulgaris during macrophage infection.
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Hsieh YC, Chia TS, Fun HK, Chen CJ. Crystal structure of dimeric flavodoxin from Desulfovibrio gigas suggests a potential binding region for the electron-transferring partner. Int J Mol Sci 2013; 14:1667-83. [PMID: 23322018 PMCID: PMC3565340 DOI: 10.3390/ijms14011667] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2012] [Revised: 12/03/2012] [Accepted: 12/25/2012] [Indexed: 11/16/2022] Open
Abstract
Flavodoxins, which exist widely in microorganisms, have been found in various pathways with multiple physiological functions. The flavodoxin (Fld) containing the cofactor flavin mononucleotide (FMN) from sulfur-reducing bacteria Desulfovibrio gigas (D. gigas) is a short-chain enzyme that comprises 146 residues with a molecular mass of 15 kDa and plays important roles in the electron-transfer chain. To investigate its structure, we purified this Fld directly from anaerobically grown D. gigas cells. The crystal structure of Fld, determined at resolution 1.3 Å, is a dimer with two FMN packing in an orientation head to head at a distance of 17 Å, which generates a long and connected negatively charged region. Two loops, Thr59-Asp63 and Asp95-Tyr100, are located in the negatively charged region and between two FMN, and are structurally dynamic. An analysis of each monomer shows that the structure of Fld is in a semiquinone state; the positions of FMN and the surrounding residues in the active site deviate. The crystal structure of Fld from D. gigas agrees with a dimeric form in the solution state. The dimerization area, dynamic characteristics and structure variations between monomers enable us to identify a possible binding area for its functional partners.
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Affiliation(s)
- Yin-Cheng Hsieh
- Life Science Group, Scientific Research Division, National Synchrotron Radiation Research Center, Hsinchu 30076, Taiwan; E-Mail:
| | - Tze Shyang Chia
- X-ray Crystallography Unit, School of Physics, Universiti Sains Malaysia, 11800 USM, Penang, Malaysia; E-Mails: (T.S.C.); (H.-K.F.)
| | - Hoong-Kun Fun
- X-ray Crystallography Unit, School of Physics, Universiti Sains Malaysia, 11800 USM, Penang, Malaysia; E-Mails: (T.S.C.); (H.-K.F.)
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia; E-Mail:
| | - Chun-Jung Chen
- Life Science Group, Scientific Research Division, National Synchrotron Radiation Research Center, Hsinchu 30076, Taiwan; E-Mail:
- Department of Physics, National Tsing Hua University, Hsinchu 30043, Taiwan
- Institute of Biotechnology, National Cheng Kung University, Tainan City 70101, Taiwan
- University Center for Bioscience and Biotechnology, National Cheng Kung University, Tainan City 70101, Taiwan
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +886-3-5780281 (ext. 7330); Fax: +886-3-5783813
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Giacomucci L, Purdy KJ, Zanardini E, Polo A, Cappitelli F. A new non-degenerate primer pair for the specific detection of the nitrite reductase gene nrfA in the genus Desulfovibrio. J Mol Microbiol Biotechnol 2012; 22:345-51. [PMID: 23295220 DOI: 10.1159/000345768] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Dissimilatory nitrate reduction to ammonia (DNRA) is the process in which nitrate is reduced, via nitrite, to ammonia. Bacteria known to carry out DNRA mainly originate from wastewater treatment plants, where DNRA is a relevant process. The ability to carry out DNRA is phylogenetically widespread, and the gene nrfA, encoding for the key enzyme of the second step of the pathway, could be used as a marker for this process. In this study we developed a new primer pair specific for nrfA in the genus Desulfovibrio. The specificity of the primer pair was tested on DNA from thirteen species of Desulfovibrio and DNA from two wastewater samples. PCR amplifications yielded products of the expected size (850 bp), and sequences obtained from Desulfovibrio strains and environmental sample clone libraries matched the Desulfovibrio nrfA gene. Nevertheless, we found nrfA gene sequences in the environmental samples that are not present in the databases. The new primer set can be used to obtain more sequences of the nrfA gene and improve our knowledge of the DNRA pathway in this genus, e.g. with the aim to improve the wastewater treatment process.
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Affiliation(s)
- L Giacomucci
- Dipartimento di Scienze per gli Alimenti, la Nutrizione e l'Ambiente, Università degli Studi di Milano, Milan, Italy
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