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Dyksma S, Pester M. Growth of sulfate-reducing Desulfobacterota and Bacillota at periodic oxygen stress of 50% air-O 2 saturation. MICROBIOME 2024; 12:191. [PMID: 39367500 PMCID: PMC11451228 DOI: 10.1186/s40168-024-01909-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Accepted: 08/16/2024] [Indexed: 10/06/2024]
Abstract
BACKGROUND Sulfate-reducing bacteria (SRB) are frequently encountered in anoxic-to-oxic transition zones, where they are transiently exposed to microoxic or even oxic conditions on a regular basis. This can be marine tidal sediments, microbial mats, and freshwater wetlands like peatlands. In the latter, a cryptic but highly active sulfur cycle supports their anaerobic activity. Here, we aimed for a better understanding of how SRB responds to periodically fluctuating redox regimes. RESULTS To mimic these fluctuating redox conditions, a bioreactor was inoculated with peat soil supporting cryptic sulfur cycling and consecutively exposed to oxic (one week) and anoxic (four weeks) phases over a period of > 200 days. SRB affiliated to the genus Desulfosporosinus (Bacillota) and the families Syntrophobacteraceae, Desulfomonilaceae, Desulfocapsaceae, and Desulfovibrionaceae (Desulfobacterota) successively established growing populations (up to 2.9% relative abundance) despite weekly periods of oxygen exposures at 133 µM (50% air saturation). Adaptation mechanisms were analyzed by genome-centric metatranscriptomics. Despite a global drop in gene expression during oxic phases, the perpetuation of gene expression for energy metabolism was observed for all SRBs. The transcriptional response pattern for oxygen resistance was differentiated across individual SRBs, indicating different adaptation strategies. Most SRB transcribed differing sets of genes for oxygen consumption, reactive oxygen species detoxification, and repair of oxidized proteins as a response to the periodical redox switch from anoxic to oxic conditions. Noteworthy, a Desulfosporosinus, a Desulfovibrionaceaea, and a Desulfocapsaceaea representative maintained high transcript levels of genes encoding oxygen defense proteins even under anoxic conditions, while representing dominant SRB populations after half a year of bioreactor operation. CONCLUSIONS In situ-relevant peatland SRB established large populations despite periodic one-week oxygen levels that are one order of magnitude higher than known to be tolerated by pure cultures of SRB. The observed decrease in gene expression regulation may be key to withstand periodically occurring changes in redox regimes in these otherwise strictly anaerobic microorganisms. Our study provides important insights into the stress response of SRB that drives sulfur cycling at oxic-anoxic interphases. Video Abstract.
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Affiliation(s)
- Stefan Dyksma
- Department of Microorganisms, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany.
| | - Michael Pester
- Department of Microorganisms, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany.
- Technical University of Braunschweig, Institute of Microbiology, Braunschweig, Germany.
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2
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Marshall IPG. Electromicrobiological concentration cells are an overlooked potential energy conservation mechanism for subsurface microorganisms. Front Microbiol 2024; 15:1407868. [PMID: 39234547 PMCID: PMC11371792 DOI: 10.3389/fmicb.2024.1407868] [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: 03/27/2024] [Accepted: 08/05/2024] [Indexed: 09/06/2024] Open
Abstract
Thermodynamics has predicted many different kinds of microbial metabolism by determining which pairs of electron acceptors and donors will react to produce an exergonic reaction (a negative net change in Gibbs free energy). In energy-limited environments, such as the deep subsurface, such an approach can reveal the potential for unexpected or counter-intuitive energy sources for microbial metabolism. Up until recently, these thermodynamic calculations have been carried out with the assumption that chemical species appearing on the reactant and product side of a reaction formula have a constant concentration, and thus do not count towards net concentration changes and the overall direction of the reaction. This assumption is reasonable considering microorganisms are too small (~1 μm) for any significant differences in concentration to overcome diffusion. However, recent discoveries have demonstrated that the reductive and oxidative halves of reactions can be separated by much larger distances, from millimetres to centimetres via conductive filamentous bacteria, mineral conductivity, and biofilm conductivity. This means that the concentrations of reactants and products can indeed be different, and that concentration differences can contribute to the net negative change in Gibbs free energy. It even means that the same redox reaction, simultaneously running in forward and reverse, can drive energy conservation, in an ElectroMicrobiological Concentration Cell (EMCC). This paper presents a model to investigate this phenomenon and predict under which circumstances such concentration-driven metabolism might take place. The specific cases of oxygen concentration cells, sulfide concentration cells, and hydrogen concentration cells are examined in more detail.
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Affiliation(s)
- Ian P G Marshall
- Center for Electromicrobiology, Department of Biology, Aarhus University, Aarhus, Denmark
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3
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Wang Z, Ruan X, Li R, Zhang Y. Microbial interaction patterns and nitrogen cycling regularities in lake sediments under different trophic conditions. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 907:167926. [PMID: 37863216 DOI: 10.1016/j.scitotenv.2023.167926] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 10/05/2023] [Accepted: 10/16/2023] [Indexed: 10/22/2023]
Abstract
Exploring how nitrogen (N) cycling microbes interact in eutrophic lake sediments and how biogenic elements influence the nitrogen cycle is crucial for understanding biogeochemical cycles and nitrogen accumulation mechanisms. In this study, sediment samples were collected from various areas of Taihu Lake with different trophic conditions in all four seasons from 2015 to 2017. Using high-throughput sequencing and molecular ecological network analysis, we investigated the microbial interaction patterns and the role of nitrogen cycling in sediments from lakes with different trophic conditions. The results showed distinct structures of sediment microbial networks between lake areas with different trophic conditions. In the more eutrophic region, network indices indicate higher transfer efficiency of energy, material, and information, more significant competition, and weaker niche differentiation of the microbial community. The sedimentary environment in the moderately eutrophic area exhibited greater potential for denitrification, nitrification, and anammox compared to the mesotrophic area, but the inhibition between N functional microbes and limitations in N removal processes were also more likely to occur. The topological structure of the networks showed that the carbon (C), sulfur (S), and iron (Fe) cycles had a strong influence on the nitrogen cycle in both lake areas. In the moderately eutrophic lake area, C- and S-cycling functional bacteria facilitated a closed cycle of the coupled N fixation-nitrification-DNRA (dissimilatory nitrate reduction to ammonium) process and reduced N removal. In the mesotrophic lake area, C- and S-cycling functional bacteria promoted both N fixation and mineralization, and Fe-cycling functional bacteria coupled with denitrifiers enhanced the nitrogen removal process of products from nitrogen fixation and mineralization. This study improved the understanding of the nitrogen cycling mechanism in lake sediments under different trophic conditions.
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Affiliation(s)
- Ziwei Wang
- Department of Hydrosciences, School of Earth Sciences and Engineering, Nanjing University, Nanjing 210023, China; MOE Key Laboratory of Surficial Geochemistry, Nanjing University, Nanjing 210023, China
| | - Xiaohong Ruan
- Department of Hydrosciences, School of Earth Sciences and Engineering, Nanjing University, Nanjing 210023, China; MOE Key Laboratory of Surficial Geochemistry, Nanjing University, Nanjing 210023, China.
| | - Rongfu Li
- Department of Hydrosciences, School of Earth Sciences and Engineering, Nanjing University, Nanjing 210023, China; MOE Key Laboratory of Surficial Geochemistry, Nanjing University, Nanjing 210023, China
| | - Yaping Zhang
- Department of Hydrosciences, School of Earth Sciences and Engineering, Nanjing University, Nanjing 210023, China; MOE Key Laboratory of Surficial Geochemistry, Nanjing University, Nanjing 210023, China
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4
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Kushkevych I, Dordević D, Alberfkani MI, Gajdács M, Ostorházi E, Vítězová M, Rittmann SKMR. NADH and NADPH peroxidases as antioxidant defense mechanisms in intestinal sulfate-reducing bacteria. Sci Rep 2023; 13:13922. [PMID: 37626119 PMCID: PMC10457377 DOI: 10.1038/s41598-023-41185-3] [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: 03/08/2023] [Accepted: 08/23/2023] [Indexed: 08/27/2023] Open
Abstract
Animal and human feces typically include intestinal sulfate-reducing bacteria (SRB). Hydrogen sulfide and acetate are the end products of their dissimilatory sulfate reduction and may create a synergistic effect. Here, we report NADH and NADPH peroxidase activities from intestinal SRB Desulfomicrobium orale and Desulfovibrio piger. We sought to compare enzymatic activities under the influence of various temperature and pH regimes, as well as to carry out kinetic analyses of enzymatic reaction rates, maximum amounts of the reaction product, reaction times, maximum rates of the enzyme reactions, and Michaelis constants in cell-free extracts of intestinal SRB, D. piger Vib-7, and D. orale Rod-9, collected from exponential and stationary growth phases. The optimal temperature (35 °C) and pH (7.0) for both enzyme's activity were determined. The difference in trends of Michaelis constants (Km) during exponential and stationary phases are noticeable between D. piger Vib-7 and D. orale Rod-9; D. orale Rod-9 showed much higher Km (the exception is NADH peroxidase of D. piger Vib-7: 1.42 ± 0.11 mM) during the both monitored phases. Studies of the NADH and NADPH peroxidases-as putative antioxidant defense systems of intestinal SRB and detailed data on the kinetic properties of this enzyme, as expressed by the decomposition of hydrogen peroxide-could be important for clarifying evolutionary mechanisms of antioxidant defense systems, their etiological role in the process of dissimilatory sulfate reduction, and their possible role in the development of bowel diseases.
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Affiliation(s)
- Ivan Kushkevych
- Department of Experimental Biology, Faculty of Science, Masaryk University, Kamenice 753/5, 62500, Brno, Czech Republic.
| | - Dani Dordević
- Department of Plant Origin Food Sciences, Faculty of Veterinary Hygiene and Ecology, University of Veterinary Sciences Brno, Palackého tř. 1946/1, 612 42, Brno, Czech Republic
| | - Mohammad I Alberfkani
- Department of Medical Laboratory Technology, College of Health and Medical Techniques, Duhok Polytechnic University, Duhok, Kurdistan Region, Iraq
| | - Márió Gajdács
- Department of Oral Biology and Experimental Dental Research, Faculty of Dentistry, University of Szeged, Tisza Lajos Krt. 64-66., 6720, Szeged, Hungary
| | - Eszter Ostorházi
- Faculty of Medicine, Institute of Medical Microbiology, Semmelweis University, Nagyvárad Tér 4, 1089, Budapest, Hungary
| | - Monika Vítězová
- Department of Experimental Biology, Faculty of Science, Masaryk University, Kamenice 753/5, 62500, Brno, Czech Republic
| | - Simon K-M R Rittmann
- Archaea Physiology & Biotechnology Group, Department of Functional and Evolutionary Ecology, Universität Wien, 1090, Wien, Austria.
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Gao P, Zhang X, Huang X, Chen Z, Marietou A, Holmkvist L, Qu L, Finster K, Gong X. Genomic insight of sulfate reducing bacterial genus Desulfofaba reveals their metabolic versatility in biogeochemical cycling. BMC Genomics 2023; 24:209. [PMID: 37076818 PMCID: PMC10116758 DOI: 10.1186/s12864-023-09297-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 04/04/2023] [Indexed: 04/21/2023] Open
Abstract
BACKGROUND Sulfate-reducing bacteria (SRB) drive the ocean sulfur and carbon cycling. They constitute a diverse phylogenetic and physiological group and are widely distributed in anoxic marine environments. From a physiological viewpoint, SRB's can be categorized as complete or incomplete oxidizers, meaning that they either oxidize their carbon substrate completely to CO2 or to a stoichiometric mix of CO2 and acetate. Members of Desulfofabaceae family are incomplete oxidizers, and within that family, Desulfofaba is the only genus with three isolates that are classified into three species. Previous physiological experiments revealed their capability of respiring oxygen. RESULTS Here, we sequenced the genomes of three isolates in Desulfofaba genus and reported on a genomic comparison of the three species to reveal their metabolic potentials. Based on their genomic contents, they all could oxidize propionate to acetate and CO2. We confirmed their phylogenetic position as incomplete oxidizers based on dissimilatory sulfate reductase (DsrAB) phylogeny. We found the complete pathway for dissimilatory sulfate reduction, but also different key genes for nitrogen cycling, including nitrogen fixation, assimilatory nitrate/nitrite reduction, and hydroxylamine reduction to nitrous oxide. Their genomes also contain genes that allow them to cope with oxygen and oxidative stress. They have genes that encode for diverse central metabolisms for utilizing different substrates with the potential for more strains to be isolated in the future, yet their distribution is limited. CONCLUSIONS Results based on marker gene search and curated metagenome assembled genomes search suggest a limited environmental distribution of this genus. Our results reveal a large metabolic versatility within the Desulfofaba genus which establishes their importance in biogeochemical cycling of carbon in their respective habitats, as well as in the support of the entire microbial community through releasing easily degraded organic matters.
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Affiliation(s)
- Ping Gao
- Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources (MNR), 266061, Qingdao, PR China
- Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology, 266237, Qingdao, PR China
| | - Xiaoting Zhang
- Institute of Marine Science and Technology, Shandong University, 266237, Qingdao, PR China
| | - Xiaomei Huang
- Institute of Marine Science and Technology, Shandong University, 266237, Qingdao, PR China
| | - Zhiyi Chen
- Institute of Marine Science and Technology, Shandong University, 266237, Qingdao, PR China
| | - Angeliki Marietou
- Section for Microbiology, Department of Biology, Aarhus University, 8000, Aarhus, Denmark
- Department of Biological and Chemical Engineering, Aarhus University, 8000, Aarhus, Denmark
| | - Lars Holmkvist
- Section for Microbiology, Department of Biology, Aarhus University, 8000, Aarhus, Denmark
| | - Lingyun Qu
- Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources (MNR), 266061, Qingdao, PR China
- Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology, 266237, Qingdao, PR China
| | - Kai Finster
- Section for Microbiology, Department of Biology, Aarhus University, 8000, Aarhus, Denmark
- Stellar Astrophysics Center, Department of Physics and Astronomy, Aarhus University, 8000, Aarhus, Denmark
| | - Xianzhe Gong
- Institute of Marine Science and Technology, Shandong University, 266237, Qingdao, PR China.
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Barton LL, Duarte AG, Staicu LC. Genomic insight into iron acquisition by sulfate-reducing bacteria in microaerophilic environments. Biometals 2023; 36:339-350. [PMID: 35767096 DOI: 10.1007/s10534-022-00410-8] [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: 10/29/2021] [Accepted: 06/08/2022] [Indexed: 11/30/2022]
Abstract
Historically, sulfate-reducing bacteria (SRB) have been considered to be strict anaerobes, but reports in the past couple of decades indicate that SRB tolerate exposure to O2 and can even grow in aerophilic environments. With the transition from anaerobic to microaerophilic conditions, the uptake of Fe(III) from the environment by SRB would become important. In evaluating the metabolic capability for the uptake of iron, the genomes of 26 SRB, representing eight families, were examined. All SRB reviewed carry genes (feoA and feoB) for the ferrous uptake system to transport Fe(II) across the plasma membrane into the cytoplasm. In addition, all of the SRB genomes examined have putative genes for a canonical ABC transporter that may transport ferric siderophore or ferric chelated species from the environment. Gram-negative SRB have additional machinery to import ferric siderophores and ferric chelated species since they have the TonB system that can work alongside any of the outer membrane porins annotated in the genome. Included in this review is the discussion that SRB may use the putative siderophore uptake system to import metals other than iron.
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Affiliation(s)
- Larry L Barton
- Department of Biology, University of New Mexico, MSCO3 2020, Albuquerque, NM, 87131, USA
| | - Americo G Duarte
- Instituto de Tecnologia Química E Biológica António Xavier/Universidade NOVA de Lisboa, Av. República, Estação Agronómica Nacional, 2780-157, Oeiras, Portugal
| | - Lucian C Staicu
- Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096, Warsaw, Poland.
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7
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Deng L, Meile C, Fiskal A, Bölsterli D, Han X, Gajendra N, Dubois N, Bernasconi SM, Lever MA. Deposit-feeding worms control subsurface ecosystem functioning in intertidal sediment with strong physical forcing. PNAS NEXUS 2022; 1:pgac146. [PMID: 36714871 PMCID: PMC9802194 DOI: 10.1093/pnasnexus/pgac146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 07/25/2022] [Indexed: 06/18/2023]
Abstract
Intertidal sands are global hotspots of terrestrial and marine carbon cycling with strong hydrodynamic forcing by waves and tides and high macrofaunal activity. Yet, the relative importance of hydrodynamics and macrofauna in controlling these ecosystems remains unclear. Here, we compare geochemical gradients and bacterial, archaeal, and eukaryotic gene sequences in intertidal sands dominated by subsurface deposit-feeding worms (Abarenicola pacifica) to adjacent worm-free areas. We show that hydrodynamic forcing controls organismal assemblages in surface sediments, while in deeper layers selective feeding by worms on fine, algae-rich particles strongly decreases the abundance and richness of all three domains. In these deeper layers, bacterial and eukaryotic network connectivity decreases, while percentages of clades involved in degradation of refractory organic matter, oxidative nitrogen, and sulfur cycling increase. Our findings reveal macrofaunal activity as the key driver of biological community structure and functioning, that in turn influence carbon cycling in intertidal sands below the mainly physically controlled surface layer.
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Affiliation(s)
| | - Christof Meile
- Department of Marine Sciences, University of Georgia, 325 Sanford Drive, Athens, GA 30602, USA
| | | | - Damian Bölsterli
- Institute of Biogeochemistry and Pollutant Dynamics, Swiss Federal Institute of Technology, Zurich (ETH Zurich), Universitätstrasse 16, 8092 Zurich, Switzerland
| | | | - Niroshan Gajendra
- Institute of Biogeochemistry and Pollutant Dynamics, Swiss Federal Institute of Technology, Zurich (ETH Zurich), Universitätstrasse 16, 8092 Zurich, Switzerland
| | - Nathalie Dubois
- Department of Surface Waters - Research and Management, Swiss Federal Institute of Aquatic Science and Technology (EAWAG), Überlandstrasse 133, 8600 Dübendorf, Switzerland
- Department of Earth Sciences, Swiss Federal Institute of Technology, Zurich (ETH Zurich), Sonneggstrasse 5, 8092 Zürich, Switzerland
| | - Stefano M Bernasconi
- Department of Earth Sciences, Swiss Federal Institute of Technology, Zurich (ETH Zurich), Sonneggstrasse 5, 8092 Zürich, Switzerland
| | - Mark A Lever
- Institute of Biogeochemistry and Pollutant Dynamics, Swiss Federal Institute of Technology, Zurich (ETH Zurich), Universitätstrasse 16, 8092 Zurich, Switzerland
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In Situ Genomics and Transcriptomics of SAR202 Subclusters Revealed Subtle Distinct Activities in Deep-Sea Water. Microorganisms 2022; 10:microorganisms10081629. [PMID: 36014047 PMCID: PMC9416657 DOI: 10.3390/microorganisms10081629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 07/22/2022] [Accepted: 07/27/2022] [Indexed: 11/16/2022] Open
Abstract
Deep-sea water columns are enriched with SAR202 that may conduct detrital matter degradation. There are several subclusters in SAR202, but their subtle differences in geochemical cycles are largely unknown, particularly for their in situ activities in the marine deep zone. Deep-sea DNA/RNA samples obtained from 12 continuous time periods over two days by in situ nucleic acid collection apparatus were used to re-evaluate the ecological functions of each SAR202 subcluster at a depth of ~1000 m in the South China Sea (SCS). Phylogenomics of 32 new SAR202 genomes from the SCS and western Pacific revealed their distribution in five subclusters. Metatranscriptomics analysis showed that the subclusters II and III were the dominant SAR202 groups with higher transcriptional activities in the SCS deep-sea zone than other subclusters. The analyses of functional gene expression further indicated that SAR202 subclusters II and III might be involved in different metabolic pathways in the deep-sea environment. The SAR202 subcluster III might take part in the degradation of deep-sea aromatic compounds. Time-course metagenomics and metatranscriptomics data did not show metabolic correlation of subclusters II and III over two days, suggesting diversified ecological functions of SAR202 subclusters under different organic inputs from the overlying water column. Collectively, our results indicate that the SAR202 subclusters play different roles in organic degradation and have probably undergone subtle and gradual adaptive evolution in the dynamic environment of the deep ocean.
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Huang F, Lin X, Yin K. Effects of marine produced organic matter on the potential estuarine capacity of NO x- removal. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 812:151471. [PMID: 34748840 DOI: 10.1016/j.scitotenv.2021.151471] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2021] [Revised: 11/01/2021] [Accepted: 11/02/2021] [Indexed: 06/13/2023]
Abstract
Dissolved inorganic nitrogen (DIN) is very high in the Pearl River Estuary (PRE) and nitrate (NOx-) removal processes such as denitrification, anaerobic ammonium oxidation (anammox) and dissimilatory nitrate reduction to ammonium (DNRA) are important for determining export of DIN to coastal waters. However, fluxes of NOx- removal and influencing factors in the PRE are still unclear. We conducted 4 cruises at 11 sites in the PRE to investigate potential NOx- removal rates, their contributions, and corresponding gene abundances, and controlling factors in surface sediments (0-5 cm). The results showed that the potential rates of denitrification, anammox, and DNRA as well as their contributions varied spatially and seasonally. Denitrification (1.98 ± 1.7 μg N g-1 d-1) was the major NOx- removal processes (68.43 ± 14.61%) while DNRA (0.45 ± 0.28 μg N g-1 d-1) contributed 22.61 ± 14.89% in NOx- removal. The NOx- removal processes and corresponding gene abundances were correlated with the chlorophyll concentrations in both overlying water and sediment, indicating that marine-produced organic matter was the major driver for benthic NOx- removal processes. In addition, water column turbidity had important effects on primary production, which affects benthic N processes. Our study provides evidences for that the turbidity-regulated primary production in overlying water is the primary driver for benthic NOx- removal processes. The contribution of sediment NOx- removal fluxes to water column NOx- concentration was low in the upper estuary and increased in the lower estuary where marine produced chlorophyll a was higher. However, daily fluxes of NOx- removal were estimated to account for only 0.18-7.22% (mean 1.85 ± 1.62%) of NOx- in the whole overlying water column. This suggests that most riverine NOx- was exported out into the adjacent coastal waters.
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Affiliation(s)
- Fangjuan Huang
- School of Marine Sciences, Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, Sun Yat-sen University, Zhuhai 519082, China; Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai 519080, China
| | - Xianbiao Lin
- School of Marine Sciences, Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, Sun Yat-sen University, Zhuhai 519082, China; Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai 519080, China.
| | - Kedong Yin
- School of Marine Sciences, Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, Sun Yat-sen University, Zhuhai 519082, China; Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai 519080, China.
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10
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Using Oxidative Electrodes to Enrich Novel Members in the Desulfobulbaceae Family from Intertidal Sediments. Microorganisms 2021; 9:microorganisms9112329. [PMID: 34835454 PMCID: PMC8618199 DOI: 10.3390/microorganisms9112329] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Revised: 10/21/2021] [Accepted: 11/08/2021] [Indexed: 01/04/2023] Open
Abstract
Members in the family of Desulfobulbaceae may be influential in various anaerobic microbial communities, including those in anoxic aquatic sediments and water columns, and within wastewater treatment facilities and bioelectrochemical systems (BESs) such as microbial fuel cells (MFCs). However, the diversity and roles of the Desulfobulbaceae in these communities have received little attention, and large portions of this family remain uncultured. Here we expand on findings from an earlier study (Li, Reimers, and Alleau, 2020) to more fully characterize Desulfobulbaceae that became prevalent in biofilms on oxidative electrodes of bioelectrochemical reactors. After incubations, DNA extraction, microbial community analyses, and microscopic examination, we found that a group of uncultured Desulfobulbaceae were greatly enriched on electrode surfaces. These Desulfobulbaceae appeared to form filaments with morphological features ascribed to cable bacteria, but the majority were taxonomically distinct from recognized cable bacteria genera. Thus, the present study provides new information about a group of Desulfobulbaceae that can exhibit filamentous morphologies and respire on the oxidative electrodes. While the phylogeny of cable bacteria is still being defined and updated, further enriching these members can contribute to the overall understanding of cable bacteria and may also lead to identification of successful isolation strategies.
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11
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Baleeiro FCF, Ardila MS, Kleinsteuber S, Sträuber H. Effect of Oxygen Contamination on Propionate and Caproate Formation in Anaerobic Fermentation. Front Bioeng Biotechnol 2021; 9:725443. [PMID: 34568301 PMCID: PMC8460912 DOI: 10.3389/fbioe.2021.725443] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 08/19/2021] [Indexed: 01/19/2023] Open
Abstract
Mixed microbial cultures have become a preferred choice of biocatalyst for chain elongation systems due to their ability to convert complex substrates into medium-chain carboxylates. However, the complexity of the effects of process parameters on the microbial metabolic networks is a drawback that makes the task of optimizing product selectivity challenging. Here, we studied the effects of small air contaminations on the microbial community dynamics and the product formation in anaerobic bioreactors fed with lactate, acetate and H2/CO2. Two stirred tank reactors and two bubble column reactors were operated with H2/CO2 gas recirculation for 139 and 116 days, respectively, at pH 6.0 and 32°C with a hydraulic retention time of 14 days. One reactor of each type had periods with air contamination (between 97 ± 28 and 474 ± 33 mL O2 L−1 d−1, lasting from 4 to 32 days), while the control reactors were kept anoxic. During air contamination, production of n-caproate and CH4 was strongly inhibited, whereas no clear effect on n-butyrate production was observed. In a period with detectable O2 concentrations that went up to 18%, facultative anaerobes of the genus Rummeliibacillus became predominant and only n-butyrate was produced. However, at low air contamination rates and with O2 below the detection level, Coriobacteriia and Actinobacteria gained a competitive advantage over Clostridia and Methanobacteria, and propionate production rates increased to 0.8–1.8 mmol L−1 d−1 depending on the reactor (control reactors 0.1–0.8 mmol L−1 d−1). Moreover, i-butyrate production was observed, but only when Methanobacteria abundances were low and, consequently, H2 availability was high. After air contamination stopped completely, production of n-caproate and CH4 recovered, with n-caproate production rates of 1.4–1.8 mmol L−1 d−1 (control 0.7–2.1 mmol L−1 d−1). The results underline the importance of keeping strictly anaerobic conditions in fermenters when consistent n-caproate production is the goal. Beyond that, micro-aeration should be further tested as a controllable process parameter to shape the reactor microbiome. When odd-chain carboxylates are desired, further studies can develop strategies for their targeted production by applying micro-aerobic conditions.
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Affiliation(s)
- Flávio C F Baleeiro
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany.,Institute of Process Engineering in Life Science 2, Technical Biology, Karlsruhe Institute of Technology - KIT, Karlsruhe, Germany
| | - Magda S Ardila
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany.,Institute of Process Engineering in Life Science 2, Technical Biology, Karlsruhe Institute of Technology - KIT, Karlsruhe, Germany
| | - Sabine Kleinsteuber
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Heike Sträuber
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
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12
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Mori F, Umezawa Y, Kondo R, Nishihara GN, Wada M. Potential oxygen consumption and community composition of sediment bacteria in a seasonally hypoxic enclosed bay. PeerJ 2021; 9:e11836. [PMID: 34434647 PMCID: PMC8362671 DOI: 10.7717/peerj.11836] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 07/01/2021] [Indexed: 01/04/2023] Open
Abstract
The dynamics of potential oxygen consumption at the sediment surface in a seasonally hypoxic bay were monitored monthly by applying a tetrazolium dye (2-(4-iodophenyl)-3-(4-nitrophenyl)-5-phenyl-2H-tetrazolium chloride [INT]) reduction assay to intact sediment core samples for two consecutive years (2012–2013). Based on the empirically determined correlation between INT reduction (INT-formazan formation) and actual oxygen consumption of sediment samples, we inferred the relative contribution of biological and non-biological (chemical) processes to the potential whole oxygen consumption in the collected sediment samples. It was demonstrated that both potentials consistently increased and reached a maximum during summer hypoxia in each year. For samples collected in 2012, amplicon sequence variants (ASVs) of the bacterial 16S rRNA genes derived from the sediment surface revealed a sharp increase in the relative abundance of sulfate reducing bacteria toward hypoxia. In addition, a notable shift in other bacterial compositions was observed before and after the INT assay incubation. It was Arcobacter (Arcobacteraceae, Campylobacteria), a putative sulfur-oxidizing bacterial genus, that increased markedly during the assay period in the summer samples. These findings have implications not only for members of Delta- and Gammaproteobacteria that are consistently responsible for the consumption of dissolved oxygen (DO) year-round in the sediment, but also for those that might grow rapidly in response to episodic DO supply on the sediment surface during midst of seasonal hypoxia.
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Affiliation(s)
- Fumiaki Mori
- Graduate School of Fisheries and Environmental Sciences, Nagasaki University, Nagasaki, Nagasaki, Japan.,Institute for East China Sea Research, Organization for Marine Science and Technology, Nagasaki University, Nagasaki, Nagasaki, Japan.,Kochi Institute for Core Sample Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Kochi, Japan
| | - Yu Umezawa
- Department of Environmental Science on Biosphere, Tokyo University of Agriculture and Technology, Tokyo, Japan
| | - Ryuji Kondo
- Department of Marine Science and Technology, Fukui Prefectural University, Fukui, Japan
| | - Gregory N Nishihara
- Graduate School of Fisheries and Environmental Sciences, Nagasaki University, Nagasaki, Nagasaki, Japan.,Institute for East China Sea Research, Organization for Marine Science and Technology, Nagasaki University, Nagasaki, Nagasaki, Japan
| | - Minoru Wada
- Graduate School of Fisheries and Environmental Sciences, Nagasaki University, Nagasaki, Nagasaki, Japan
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13
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Tomasova L, Grman M, Ondrias K, Ufnal M. The impact of gut microbiota metabolites on cellular bioenergetics and cardiometabolic health. Nutr Metab (Lond) 2021; 18:72. [PMID: 34266472 PMCID: PMC8281717 DOI: 10.1186/s12986-021-00598-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 07/02/2021] [Indexed: 12/20/2022] Open
Abstract
Recent research demonstrates a reciprocal relationship between gut microbiota-derived metabolites and the host in controlling the energy homeostasis in mammals. On the one hand, to thrive, gut bacteria exploit nutrients digested by the host. On the other hand, the host utilizes numerous products of gut bacteria metabolism as a substrate for ATP production in the colon. Finally, bacterial metabolites seep from the gut into the bloodstream and interfere with the host’s cellular bioenergetics machinery. Notably, there is an association between alterations in microbiota composition and the development of metabolic diseases and their cardiovascular complications. Some metabolites, like short-chain fatty acids and trimethylamine, are considered markers of cardiometabolic health. Others, like hydrogen sulfide and nitrite, demonstrate antihypertensive properties. Scientific databases were searched for pre-clinical and clinical studies to summarize current knowledge on the role of gut microbiota metabolites in the regulation of mammalian bioenergetics and discuss their potential involvement in the development of cardiometabolic disorders. Overall, the available data demonstrates that gut bacteria products affect physiological and pathological processes controlling energy and vascular homeostasis. Thus, the modulation of microbiota-derived metabolites may represent a new approach for treating obesity, hypertension and type 2 diabetes.
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Affiliation(s)
- Lenka Tomasova
- Institute of Clinical and Translational Research, Biomedical Research Center, Slovak Academy of Sciences, Dubravska cesta 9, 845 05, Bratislava, Slovak Republic.
| | - Marian Grman
- Institute of Clinical and Translational Research, Biomedical Research Center, Slovak Academy of Sciences, Dubravska cesta 9, 845 05, Bratislava, Slovak Republic
| | - Karol Ondrias
- Institute of Clinical and Translational Research, Biomedical Research Center, Slovak Academy of Sciences, Dubravska cesta 9, 845 05, Bratislava, Slovak Republic
| | - Marcin Ufnal
- Department of Experimental Physiology and Pathophysiology, Laboratory of Centre for Preclinical Research, Medical University of Warsaw, 02-091, Warsaw, Poland.
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14
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Borisov VB, Siletsky SA, Paiardini A, Hoogewijs D, Forte E, Giuffrè A, Poole RK. Bacterial Oxidases of the Cytochrome bd Family: Redox Enzymes of Unique Structure, Function, and Utility As Drug Targets. Antioxid Redox Signal 2021; 34:1280-1318. [PMID: 32924537 PMCID: PMC8112716 DOI: 10.1089/ars.2020.8039] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 09/01/2020] [Accepted: 09/02/2020] [Indexed: 12/23/2022]
Abstract
Significance: Cytochrome bd is a ubiquinol:oxygen oxidoreductase of many prokaryotic respiratory chains with a unique structure and functional characteristics. Its primary role is to couple the reduction of molecular oxygen, even at submicromolar concentrations, to water with the generation of a proton motive force used for adenosine triphosphate production. Cytochrome bd is found in many bacterial pathogens and, surprisingly, in bacteria formally denoted as anaerobes. It endows bacteria with resistance to various stressors and is a potential drug target. Recent Advances: We summarize recent advances in the biochemistry, structure, and physiological functions of cytochrome bd in the light of exciting new three-dimensional structures of the oxidase. The newly discovered roles of cytochrome bd in contributing to bacterial protection against hydrogen peroxide, nitric oxide, peroxynitrite, and hydrogen sulfide are assessed. Critical Issues: Fundamental questions remain regarding the precise delineation of electron flow within this multihaem oxidase and how the extraordinarily high affinity for oxygen is accomplished, while endowing bacteria with resistance to other small ligands. Future Directions: It is clear that cytochrome bd is unique in its ability to confer resistance to toxic small molecules, a property that is significant for understanding the propensity of pathogens to possess this oxidase. Since cytochrome bd is a uniquely bacterial enzyme, future research should focus on harnessing fundamental knowledge of its structure and function to the development of novel and effective antibacterial agents.
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Affiliation(s)
- Vitaliy B. Borisov
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russian Federation
| | - Sergey A. Siletsky
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russian Federation
| | | | - David Hoogewijs
- Department of Medicine/Physiology, University of Fribourg, Fribourg, Switzerland
| | - Elena Forte
- Department of Biochemical Sciences, Sapienza University of Rome, Rome, Italy
| | | | - Robert K. Poole
- Department of Molecular Biology and Biotechnology, The University of Sheffield, Sheffield, United Kingdom
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15
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Sheik CS, Badalamenti JP, Telling J, Hsu D, Alexander SC, Bond DR, Gralnick JA, Lollar BS, Toner BM. Novel Microbial Groups Drive Productivity in an Archean Iron Formation. Front Microbiol 2021; 12:627595. [PMID: 33859627 PMCID: PMC8042283 DOI: 10.3389/fmicb.2021.627595] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 03/01/2021] [Indexed: 12/23/2022] Open
Abstract
Deep subsurface environments are decoupled from Earth's surface processes yet diverse, active, and abundant microbial communities thrive in these isolated environments. Microbes inhabiting the deep biosphere face unique challenges such as electron donor/acceptor limitations, pore space/fracture network limitations, and isolation from other microbes within the formation. Of the few systems that have been characterized, it is apparent that nutrient limitations likely facilitate diverse microbe-microbe interactions (i.e., syntrophic, symbiotic, or parasitic) and that these interactions drive biogeochemical cycling of major elements. Here we describe microbial communities living in low temperature, chemically reduced brines at the Soudan Underground Mine State Park, United States. The Soudan Iron mine intersects a massive hematite formation at the southern extent of the Canadian Shield. Fractured rock aquifer brines continuously flow from exploratory boreholes drilled circa 1960 and are enriched in deuterium compared to the global meteoric values, indicating brines have had little contact with surface derived waters, and continually degas low molecular weight hydrocarbons C1-C4. Microbial enrichments suggest that once brines exit the boreholes, oxidation of the hydrocarbons occur. Amplicon sequencing show these borehole communities are low in diversity and dominated by Firmicute and Proteobacteria phyla. From the metagenome assemblies, we recovered approximately thirty genomes with estimated completion over 50%. Analysis of genome taxonomy generally followed the amplicon data, and highlights that several of the genomes represent novel families and genera. Metabolic reconstruction shows two carbon-fixation pathways were dominant, the Wood-Ljungdahl (acetogenesis) and Calvin-Benson-Bassham (via RuBisCo), indicating that inorganic carbon likely enters into the microbial foodweb with differing carbon fractionation potentials. Interestingly, methanogenesis is likely driven by Methanolobus and suggests cycling of methylated compounds and not H2/CO2 or acetate. Furthermore, the abundance of sulfate in brines suggests cryptic sulfur cycling may occur, as we detect possible sulfate reducing and thiosulfate oxidizing microorganisms. Finally, a majority of the microorganisms identified contain genes that would allow them to participate in several element cycles, highlighting that in these deep isolated systems metabolic flexibility may be an important life history trait.
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Affiliation(s)
- Cody S. Sheik
- Department of Biology and the Large Lakes Observatory, University of Minnesota Duluth, Duluth, MN, United States
| | - Jonathan P. Badalamenti
- University of Minnesota Genomics Center, University of Minnesota Twin Cities, Minneapolis, MN, United States
- Biotechnology Institute, University of Minnesota Twin Cities, Saint Paul, MN, United States
| | - Jon Telling
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - David Hsu
- Biotechnology Institute, University of Minnesota Twin Cities, Saint Paul, MN, United States
- Plant and Microbial Biology, University of Minnesota Twin Cities, Saint Paul, MN, United States
| | - Scott C. Alexander
- Department of Earth and Environmental Sciences, University of Minnesota Twin Cities, Minneapolis, MN, United States
| | - Daniel R. Bond
- Biotechnology Institute, University of Minnesota Twin Cities, Saint Paul, MN, United States
- Plant and Microbial Biology, University of Minnesota Twin Cities, Saint Paul, MN, United States
| | - Jeffrey A. Gralnick
- Biotechnology Institute, University of Minnesota Twin Cities, Saint Paul, MN, United States
- Plant and Microbial Biology, University of Minnesota Twin Cities, Saint Paul, MN, United States
| | | | - Brandy M. Toner
- Department of Earth and Environmental Sciences, University of Minnesota Twin Cities, Minneapolis, MN, United States
- Department of Soil, Water, and Climate, University of Minnesota Twin Cities, Saint Paul, MN, United States
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16
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Microbial Communities and Sulfate-Reducing Microorganisms Abundance and Diversity in Municipal Anaerobic Sewage Sludge Digesters from a Wastewater Treatment Plant (Marrakech, Morocco). Processes (Basel) 2020. [DOI: 10.3390/pr8101284] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Both molecular analyses and culture-dependent isolation were combined to investigate the diversity of sulfate-reducing prokaryotes and explore their role in sulfides production in full-scale anaerobic digesters (Marrakech, Morocco). At global scale, using 16S rRNA gene sequencing, Proteobacteria, Bacteroidetes, Firmicutes, Actinobacteria, Synergistetes, and Euryarchaeota were the most dominant phyla. The abundance of Archaea (3.1–5.7%) was linked with temperature. The mcrA gene ranged from 2.18 × 105 to 1.47 × 107 gene copies.g−1 of sludge. The sulfate-reducing prokaryotes, representing 5% of total sequences, involved in sulfides production were Peptococcaceae, Syntrophaceae, Desulfobulbaceae, Desulfovibrionaceae, Syntrophobacteraceae, Desulfurellaceae, and Desulfobacteraceae. Furthermore, dsrB gene ranged from 2.18 × 105 to 1.92 × 107 gene copies.g−1 of sludge. The results revealed that exploration of diversity and function of sulfate-reducing bacteria may play a key role in decreasing sulfide production, an undesirable by-product, during anaerobic digestion.
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17
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Pandey CB, Kumar U, Kaviraj M, Minick KJ, Mishra AK, Singh JS. DNRA: A short-circuit in biological N-cycling to conserve nitrogen in terrestrial ecosystems. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 738:139710. [PMID: 32544704 DOI: 10.1016/j.scitotenv.2020.139710] [Citation(s) in RCA: 113] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 05/21/2020] [Accepted: 05/23/2020] [Indexed: 06/11/2023]
Abstract
This paper reviews dissimilatory nitrate reduction to ammonium (DNRA) in soils - a newly appreciated pathway of nitrogen (N) cycling in the terrestrial ecosystems. The reduction of NO3- occurs in two steps; in the first step, NO3- is reduced to NO2-; and in the second, unlike denitrification, NO2- is reduced to NH4+ without intermediates. There are two sets of NO3-/NO2- reductase enzymes, i.e., Nap/Nrf and Nar/Nir; the former occurs on the periplasmic-membrane and energy conservation is respiratory via electron-transport-chain, whereas the latter is cytoplasmic and energy conservation is both respiratory and fermentative (Nir, substrate-phosphorylation). Since, Nir catalyzes both assimilatory- and dissimilatory-nitrate reduction, the nrfA gene, which transcribes the NrfA protein, is treated as a molecular-marker of DNRA; and a high nrfA/nosZ (N2O-reductase) ratio favours DNRA. Recently, several crystal structures of NrfA have been presumed to producee N2O as a byproduct of DNRA via the NO (nitric-oxide) pathway. Meta-analyses of about 200 publications have revealed that DNRA is regulated by oxidation state of soils and sediments, carbon (C)/N and NO2-/NO3- ratio, and concentrations of ferrous iron (Fe2+) and sulfide (S2-). Under low-redox conditions, a high C/NO3- ratio selects for DNRA while a low ratio selects for denitrification. When the proportion of both C and NO3- are equal, the NO2-/NO3- ratio modulates partitioning of NO3-, and a high NO2-/NO3- ratio favours DNRA. A high S2-/NO3- ratio also promotes DNRA in coastal-ecosystems and saline sediments. Soil pH, temperature, and fine soil particles are other factors known to influence DNRA. Since, DNRA reduces NO3- to NH4+, it is essential for protecting NO3- from leaching and gaseous (N2O) losses and enriches soils with readily available NH4+-N to primary producers and heterotrophic microorganisms. Therefore, DNRA may be treated as a tool to reduce ground-water NO3- pollution, enhance soil health and improve environmental quality.
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Affiliation(s)
- C B Pandey
- ICAR-Central Arid Zone Research Institute, Jodhpur 342003, Rajasthan, India.
| | - Upendra Kumar
- ICAR-National Rice Research Institute, Cuttack 753006, Odisha, India.
| | - Megha Kaviraj
- ICAR-National Rice Research Institute, Cuttack 753006, Odisha, India
| | - K J Minick
- Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC 27695, USA
| | - A K Mishra
- International Rice Research Institute, New Delhi 110012, India
| | - J S Singh
- Ecosystem Analysis Lab, Centre of Advanced Study in Botany, Banaras Hindu University (BHU), Varanasi 221005, India
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18
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Cojean ANY, Lehmann MF, Robertson EK, Thamdrup B, Zopfi J. Controls of H 2S, Fe 2 +, and Mn 2 + on Microbial NO 3 --Reducing Processes in Sediments of an Eutrophic Lake. Front Microbiol 2020; 11:1158. [PMID: 32612583 PMCID: PMC7308436 DOI: 10.3389/fmicb.2020.01158] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Accepted: 05/06/2020] [Indexed: 11/18/2022] Open
Abstract
Understanding the biogeochemical controls on the partitioning between nitrogen (N) removal through denitrification and anaerobic ammonium oxidation (anammox), and N recycling via dissimilatory nitrate (NO3 -) reduction to ammonium (DNRA) is crucial for constraining lacustrine N budgets. Besides organic carbon, inorganic compounds may serve as electron donors for NO3 - reduction, yet the significance of lithotrophic NO3 - reduction in the environment is still poorly understood. Conducting incubation experiments with additions of 15N-labeled compounds and reduced inorganic substrates (H2S, Fe2+, Mn2+), we assessed the role of alternative electron donors in regulating the partitioning between the different NO3 --reducing processes in ferruginous surface sediments of Lake Lugano, Switzerland. In sediment slurry incubations without added inorganic substrates, denitrification and DNRA were the dominant NO3 --reducing pathways, with DNRA contributing between 31 and 46% to the total NO3 - reduction. The contribution of anammox was less than 1%. Denitrification rates were stimulated by low to moderate additions of ferrous iron (Fe2+ ≤ 258 μM) but almost completely suppressed at higher levels (≥1300 μM). Conversely, DNRA was stimulated only at higher Fe2+ concentrations. Dissolved sulfide (H2S, i.e., sum of H2S, HS- and S2-) concentrations up to ∼80 μM, strongly stimulated denitrification, but did not affect DNRA significantly. At higher H2S levels (≥125 μM), both processes were inhibited. We were unable to find clear evidence for Mn2+-supported lithotrophic NO3 - reduction. However, at high concentrations (∼500 μM), Mn2+ additions inhibited NO3 - reduction, while it did not affect the balance between the two NO3 - reduction pathways. Our results provide experimental evidence for chemolithotrophic denitrification or DNRA with Fe2+ and H2S in the Lake Lugano sediments, and demonstrate that all tested potential electron donors, despite the beneficial effect at low concentrations of some of them, can inhibit NO3 - reduction at high concentration levels. Our findings thus imply that the concentration of inorganic electron donors in lake sediments can act as an important regulator of both benthic denitrification and DNRA rates, and suggest that they can exert an important control on the relative partitioning between microbial N removal and N retention in lakes.
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Affiliation(s)
- Adeline N. Y. Cojean
- Department of Environmental Sciences, Aquatic and Stable Isotope Biogeochemistry, University of Basel, Basel, Switzerland
| | - Moritz F. Lehmann
- Department of Environmental Sciences, Aquatic and Stable Isotope Biogeochemistry, University of Basel, Basel, Switzerland
| | | | - Bo Thamdrup
- Department of Biology and Nordic Center for Earth Evolution, University of Southern Denmark, Odense, Denmark
| | - Jakob Zopfi
- Department of Environmental Sciences, Aquatic and Stable Isotope Biogeochemistry, University of Basel, Basel, Switzerland
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19
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Xu YN, Chen Y. Advances in heavy metal removal by sulfate-reducing bacteria. WATER SCIENCE AND TECHNOLOGY : A JOURNAL OF THE INTERNATIONAL ASSOCIATION ON WATER POLLUTION RESEARCH 2020; 81:1797-1827. [PMID: 32666937 DOI: 10.2166/wst.2020.227] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Industrial development has led to generation of large volumes of wastewater containing heavy metals, which need to be removed before the wastewater is released into the environment. Chemical and electrochemical methods are traditionally applied to treat this type of wastewater. These conventional methods have several shortcomings, such as secondary pollution and cost. Bioprocesses are gradually gaining popularity because of their high selectivities, low costs, and reduced environmental pollution. Removal of heavy metals by sulfate-reducing bacteria (SRB) is an economical and effective alternative to conventional methods. The limitations of and advances in SRB activity have not been comprehensively reviewed. In this paper, recent advances from laboratory studies in heavy metal removal by SRB were reported. Firstly, the mechanism of heavy metal removal by SRB is introduced. Then, the factors affecting microbial activity and metal removal efficiency are elucidated and discussed in detail. In addition, recent advances in selection of an electron donor, enhancement of SRB activity, and improvement of SRB tolerance to heavy metals are reviewed. Furthermore, key points for future studies of the SRB process are proposed.
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Affiliation(s)
- Ya-Nan Xu
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China E-mail:
| | - Yinguang Chen
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China E-mail: ; Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, China
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20
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Li Y, Jing H, Kao SJ, Zhang W, Liu H. Metabolic response of prokaryotic microbes to sporadic hypoxia in a eutrophic subtropical estuary. MARINE POLLUTION BULLETIN 2020; 154:111064. [PMID: 32319898 DOI: 10.1016/j.marpolbul.2020.111064] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 03/08/2020] [Accepted: 03/10/2020] [Indexed: 06/11/2023]
Abstract
Coastal eutrophication and consequent oxygen depletion (hypoxia) occurs worldwide due to increased human activity. The paucity of genomic information of microbes in hypoxia prone coastal waters have hindered our understanding of microorganism related causation and adaption to the environment. Here, using metagenomic approach, we investigated microbial metabolic capability in heavily polluted Pearl River estuary. Our results highlighted the possible roles of microbial metabolic activity in the formation of bottom water hypoxia by revealing enriched organic degradation related microbial genes in the bottom layer beneath surface phytoplankton bloom. Microbial nitrate reduction in hypoxia layer was low, possibly due to the low pH and fluctuating oxygen level. On contrary, high abundance of sulfate-reducing, and antibiotic and metal resistance related genes were detected in bottom and surface layers, respectively, indicating microbial adaptation to oxygen depletion and pollution. Our study provides gene level information on the interactive relations between microbial functions and environmental stress.
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Affiliation(s)
- Yingdong Li
- Department of Ocean Science, Hong Kong University of Science and Technology, Kowloon, China
| | - Hongmei Jing
- CAS Key Laboratory for Experimental Study under Deep-sea Extreme Conditions, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
| | - Shuh-Ji Kao
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China
| | - Weipeng Zhang
- Department of Ocean Science, Hong Kong University of Science and Technology, Kowloon, China
| | - Hongbin Liu
- Department of Ocean Science, Hong Kong University of Science and Technology, Kowloon, China; Hong Kong Branch of Southern Marine Science and Engineering Guangdong Laboratory, The Hong Kong University of Science and Technology, Hong Kong, China.
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21
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Effects of Hydraulic Retention Time and Influent Nitrate-N Concentration on Nitrogen Removal and the Microbial Community of an Aerobic Denitrification Reactor Treating Recirculating Marine Aquaculture System Effluent. WATER 2020. [DOI: 10.3390/w12030650] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The effects of hydraulic retention time (HRT) and influent nitrate-N concentration on nitrogen removal and the microbial community composition of an aerobic denitrification reactor treating recirculating marine aquaculture system effluent were evaluated. Results showed that over 98% of nitrogen was removed and ammonia-N and nitrite-N levels were below 1 mg/L when influent nitrate-N was below 150 mg/L and HRT over 5 h. The maximum nitrogen removal efficiency and nitrogen removal rate were observed at HRT of 6 or 7 h when influent nitrate-N was 150 mg/L. High-throughput DNA sequencing analysis revealed that the microbial phyla Proteobacteria and Bacteroidetes were predominant in the reactor, with an average relative total abundance above 70%. The relative abundance of denitrifying bacteria of genera Halomonas and Denitratisoma within the reactor decreased with increasing influent nitrate-N concentrations. Our results show the presence of an aerobically denitrifying microbial consortium with both expected and unexpected members, many of them relatively new to science. Our findings provide insights into the biological workings and inform the design and operation of denitrifying reactors for marine aquaculture systems.
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22
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Müller H, Marozava S, Probst AJ, Meckenstock RU. Groundwater cable bacteria conserve energy by sulfur disproportionation. ISME JOURNAL 2019; 14:623-634. [PMID: 31728021 PMCID: PMC6976610 DOI: 10.1038/s41396-019-0554-1] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 10/28/2019] [Accepted: 11/04/2019] [Indexed: 11/25/2022]
Abstract
Cable bacteria of the family Desulfobulbaceae couple spatially separated sulfur oxidation and oxygen or nitrate reduction by long-distance electron transfer, which can constitute the dominant sulfur oxidation process in shallow sediments. However, it remains unknown how cells in the anoxic part of the centimeter-long filaments conserve energy. We found 16S rRNA gene sequences similar to groundwater cable bacteria in a 1-methylnaphthalene-degrading culture (1MN). Cultivation with elemental sulfur and thiosulfate with ferrihydrite or nitrate as electron acceptors resulted in a first cable bacteria enrichment culture dominated >90% by 16S rRNA sequences belonging to the Desulfobulbaceae. Desulfobulbaceae-specific fluorescence in situ hybridization (FISH) unveiled single cells and filaments of up to several hundred micrometers length to belong to the same species. The Desulfobulbaceae filaments also showed the distinctive cable bacteria morphology with their continuous ridge pattern as revealed by atomic force microscopy. The cable bacteria grew with nitrate as electron acceptor and elemental sulfur and thiosulfate as electron donor, but also by sulfur disproportionation when Fe(Cl)2 or Fe(OH)3 were present as sulfide scavengers. Metabolic reconstruction based on the first nearly complete genome of groundwater cable bacteria revealed the potential for sulfur disproportionation and a chemo-litho-autotrophic metabolism. The presence of different types of hydrogenases in the genome suggests that they can utilize hydrogen as alternative electron donor. Our results imply that cable bacteria not only use sulfide oxidation coupled to oxygen or nitrate reduction by LDET for energy conservation, but sulfur disproportionation might constitute the energy metabolism for cells in large parts of the cable bacterial filaments.
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Affiliation(s)
- Hubert Müller
- Biofilm Center, University of Duisburg-Essen, Universitätsstr. 5, 45141, Essen, Germany
| | - Sviatlana Marozava
- Institute of Groundwater Ecology, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764, Neuherberg, Germany
| | - Alexander J Probst
- Biofilm Center, University of Duisburg-Essen, Universitätsstr. 5, 45141, Essen, Germany
| | - Rainer U Meckenstock
- Biofilm Center, University of Duisburg-Essen, Universitätsstr. 5, 45141, Essen, Germany.
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23
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Virpiranta H, Taskila S, Leiviskä T, Rämö J, Tanskanen J. Development of a process for microbial sulfate reduction in cold mining waters - Cold acclimation of bacterial consortia from an Arctic mining district. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2019; 252:281-288. [PMID: 31158656 DOI: 10.1016/j.envpol.2019.05.087] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Revised: 05/10/2019] [Accepted: 05/16/2019] [Indexed: 06/09/2023]
Abstract
Biological sulfate removal is challenging in cold climates due to the slower metabolism of mesophilic bacteria; however, cold conditions also offer the possibility to isolate bacteria that have adapted to low temperatures. The present research focused on the cold acclimation and characterization of sulfate-reducing bacterial (SRB) consortia enriched from an Arctic sediment sample from northern Finland. Based on 16S rDNA analysis, the most common sulfate-reducing bacterium in all enriched consortia was Desulfobulbus, which belongs to the δ-Proteobacteria. The majority of the cultivated consortia were able to reduce sulfate at temperatures as low as 6 °C with succinic acid as a carbon source. The sulfate reduction rates at 6 °C varied from 13 to 42 mg/L/d. The cultivation medium used in this research was a Postgate medium supplemented with lactate, ethanol or succinic acid. The obtained consortia were able to grow with lactate and succinic acid but surprisingly not with ethanol. Enriched SRB consortia are useful for the biological treatment of sulfate-containing industrial wastewaters in cold conditions.
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Affiliation(s)
- Hanna Virpiranta
- University of Oulu, Chemical Process Engineering, PO Box 4300, 90014, Oulu, Finland.
| | - Sanna Taskila
- University of Oulu, Chemical Process Engineering, PO Box 4300, 90014, Oulu, Finland.
| | - Tiina Leiviskä
- University of Oulu, Chemical Process Engineering, PO Box 4300, 90014, Oulu, Finland.
| | - Jaakko Rämö
- University of Oulu, Chemical Process Engineering, PO Box 4300, 90014, Oulu, Finland.
| | - Juha Tanskanen
- University of Oulu, Chemical Process Engineering, PO Box 4300, 90014, Oulu, Finland.
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24
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Broman E, Li L, Fridlund J, Svensson F, Legrand C, Dopson M. Spring and Late Summer Phytoplankton Biomass Impact on the Coastal Sediment Microbial Community Structure. MICROBIAL ECOLOGY 2019; 77:288-303. [PMID: 30019110 PMCID: PMC6394492 DOI: 10.1007/s00248-018-1229-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Accepted: 07/06/2018] [Indexed: 06/08/2023]
Abstract
Two annual Baltic Sea phytoplankton blooms occur in spring and summer. The bloom intensity is determined by nutrient concentrations in the water, while the period depends on weather conditions. During the course of the bloom, dead cells sink to the sediment where their degradation consumes oxygen to create hypoxic zones (< 2 mg/L dissolved oxygen). These zones prevent the establishment of benthic communities and may result in fish mortality. The aim of the study was to determine how the spring and autumn sediment chemistry and microbial community composition changed due to degradation of diatom or cyanobacterial biomass, respectively. Results from incubation of sediment cores showed some typical anaerobic microbial processes after biomass addition such as a decrease in NO2- + NO3- in the sediment surface (0-1 cm) and iron in the underlying layer (1-2 cm). In addition, an increase in NO2- + NO3- was observed in the overlying benthic water in all amended and control incubations. The combination of NO2- + NO3- diffusion plus nitrification could not account for this increase. Based on 16S rRNA gene sequences, the addition of cyanobacterial biomass during autumn caused a large increase in ferrous iron-oxidizing archaea while diatom biomass amendment during spring caused minor changes in the microbial community. Considering that OTUs sharing lineages with acidophilic microorganisms had a high relative abundance during autumn, it was suggested that specific niches developed in sediment microenvironments. These findings highlight the importance of nitrogen cycling and early microbial community changes in the sediment due to sinking phytoplankton before potential hypoxia occurs.
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Affiliation(s)
- Elias Broman
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Department of Biology and Environmental Science, Linnaeus University, 39182, Kalmar, Sweden.
| | - Lingni Li
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Department of Biology and Environmental Science, Linnaeus University, 39182, Kalmar, Sweden
| | - Jimmy Fridlund
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Department of Biology and Environmental Science, Linnaeus University, 39182, Kalmar, Sweden
| | - Fredrik Svensson
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Department of Biology and Environmental Science, Linnaeus University, 39182, Kalmar, Sweden
| | - Catherine Legrand
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Department of Biology and Environmental Science, Linnaeus University, 39182, Kalmar, Sweden
| | - Mark Dopson
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Department of Biology and Environmental Science, Linnaeus University, 39182, Kalmar, Sweden
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25
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Schoeffler M, Gaudin AL, Ramel F, Valette O, Denis Y, Hania WB, Hirschler-Réa A, Dolla A. Growth of an anaerobic sulfate-reducing bacterium sustained by oxygen respiratory energy conservation after O 2 -driven experimental evolution. Environ Microbiol 2018; 21:360-373. [PMID: 30394641 DOI: 10.1111/1462-2920.14466] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Revised: 10/25/2018] [Accepted: 10/31/2018] [Indexed: 11/30/2022]
Abstract
Desulfovibrio species are representatives of microorganisms at the boundary between anaerobic and aerobic lifestyles, since they contain the enzymatic systems required for both sulfate and oxygen reduction. However, the latter has been shown to be solely a protective mechanism. By implementing the oxygen-driven experimental evolution of Desulfovibrio vulgaris Hildenborough, we have obtained strains that have evolved to grow with energy derived from oxidative phosphorylation linked to oxygen reduction. We show that a few mutations are sufficient for the emergence of this phenotype and reveal two routes of evolution primarily involving either inactivation or overexpression of the gene encoding heterodisulfide reductase. We propose that the oxygen respiration for energy conservation that sustains the growth of the O2 -evolved strains is associated with a rearrangement of metabolite fluxes, especially NAD+ /NADH, leading to an optimized O2 reduction. These evolved strains are the first sulfate-reducing bacteria that exhibit a demonstrated oxygen respiratory process that enables growth.
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Affiliation(s)
- Marine Schoeffler
- Aix Marseille Université, Université de Toulon, CNRS, IRD, MIO, Marseille, France
| | - Anne-Laure Gaudin
- Aix Marseille Université, CNRS, LCB, Marseille, France.,GERME SA, Technopôle de Château Gombert, Marseille, France
| | - Fanny Ramel
- Aix Marseille Université, CNRS, LCB, Marseille, France
| | - Odile Valette
- Aix Marseille Université, CNRS, LCB, Marseille, France
| | - Yann Denis
- Aix Marseille Université, CNRS, IMM, Marseille, France
| | - Wagdi Ben Hania
- Aix Marseille Université, Université de Toulon, CNRS, IRD, MIO, Marseille, France
| | - Agnès Hirschler-Réa
- Aix Marseille Université, Université de Toulon, CNRS, IRD, MIO, Marseille, France
| | - Alain Dolla
- Aix Marseille Université, Université de Toulon, CNRS, IRD, MIO, Marseille, France
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26
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Monteil CL, Perrière G, Menguy N, Ginet N, Alonso B, Waisbord N, Cruveiller S, Pignol D, Lefèvre CT. Genomic study of a novel magnetotactic Alphaproteobacteria uncovers the multiple ancestry of magnetotaxis. Environ Microbiol 2018; 20:4415-4430. [PMID: 30043533 DOI: 10.1111/1462-2920.14364] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Accepted: 07/19/2018] [Indexed: 01/06/2023]
Abstract
Ecological and evolutionary processes involved in magnetotactic bacteria (MTB) adaptation to their environment have been a matter of debate for many years. Ongoing efforts for their characterization are progressively contributing to understand these processes, including the genetic and molecular mechanisms responsible for biomineralization. Despite numerous culture-independent MTB characterizations, essentially within the Proteobacteria phylum, only few species have been isolated in culture because of their complex growth conditions. Here, we report a newly cultivated magnetotactic, microaerophilic and chemoorganoheterotrophic bacterium isolated from the Mediterranean Sea in Marseille, France: Candidatus Terasakiella magnetica strain PR-1 that belongs to an Alphaproteobacteria genus with no magnetotactic relative. By comparing the morphology and the whole genome shotgun sequence of this MTB with those of closer relatives, we brought further evidence that the apparent vertical ancestry of magnetosome genes suggested by previous studies within Alphaproteobacteria hides a more complex evolutionary history involving horizontal gene transfers and/or duplication events before and after the emergence of Magnetospirillum, Magnetovibrio and Magnetospira genera. A genome-scale comparative genomics analysis identified several additional candidate functions and genes that could be specifically associated to MTB lifestyle in this class of bacteria.
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Affiliation(s)
- Caroline L Monteil
- Institute of Biosciences and Biotechnologies of Aix Marseille (BIAM), UMR7265 CEA - CNRS - Aix Marseille University, CEA Cadarache, 13108, Saint-Paul-lez-Durance, France
| | - Guy Perrière
- Laboratoire de Biométrie et Biologie Evolutive, CNRS, UMR5558, Université Claude Bernard - Lyon 1, 69622, Villeurbanne, France
| | - Nicolas Menguy
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590, IRD - IMPMC, 4 place Jussieu, 75005, Paris, France
| | - Nicolas Ginet
- Laboratoire de Chimie Bactérienne, UMR 7283 CNRS, Aix-Marseille Université, Institut de Microbiologie de la Méditerranée, 13402, Marseille, France
| | - Béatrice Alonso
- Institute of Biosciences and Biotechnologies of Aix Marseille (BIAM), UMR7265 CEA - CNRS - Aix Marseille University, CEA Cadarache, 13108, Saint-Paul-lez-Durance, France
| | - Nicolas Waisbord
- Department of Mechanical Engineering, Tufts University, 200 College Avenue, Medford, MA, 02155, USA
| | - Stéphane Cruveiller
- Commissariat à l'Energie Atomique et aux Energies Alternatives - Institut de Biologie François Jacob - Genoscope - Laboratoire d'Analyses Bioinformatiques pour la Génomique et le Métabolisme, UMR - CNRS 8030 Génomique Métabolique, Université d'Evry, Université Paris-Saclay, 91057 Evry, France
| | - David Pignol
- Institute of Biosciences and Biotechnologies of Aix Marseille (BIAM), UMR7265 CEA - CNRS - Aix Marseille University, CEA Cadarache, 13108, Saint-Paul-lez-Durance, France
| | - Christopher T Lefèvre
- Institute of Biosciences and Biotechnologies of Aix Marseille (BIAM), UMR7265 CEA - CNRS - Aix Marseille University, CEA Cadarache, 13108, Saint-Paul-lez-Durance, France
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27
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Müller AL, Pelikan C, de Rezende JR, Wasmund K, Putz M, Glombitza C, Kjeldsen KU, Jørgensen BB, Loy A. Bacterial interactions during sequential degradation of cyanobacterial necromass in a sulfidic arctic marine sediment. Environ Microbiol 2018; 20:2927-2940. [PMID: 30051650 PMCID: PMC6175234 DOI: 10.1111/1462-2920.14297] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Revised: 05/02/2018] [Accepted: 05/24/2018] [Indexed: 11/26/2022]
Abstract
Seafloor microorganisms impact global carbon cycling by mineralizing vast quantities of organic matter (OM) from pelagic primary production, which is predicted to increase in the Arctic because of diminishing sea ice cover. We studied microbial interspecies-carbon-flow during anaerobic OM degradation in arctic marine sediment using stable isotope probing. We supplemented sediment incubations with 13 C-labeled cyanobacterial necromass (spirulina), mimicking fresh OM input, or acetate, an important OM degradation intermediate and monitored sulfate reduction rates and concentrations of volatile fatty acids (VFAs) during substrate degradation. Sequential 16S rRNA gene and transcript amplicon sequencing and fluorescence in situ hybridization combined with Raman microspectroscopy revealed that only few bacterial species were the main degraders of 13 C-spirulina necromass. Psychrilyobacter, Psychromonas, Marinifilum, Colwellia, Marinilabiaceae and Clostridiales species were likely involved in the primary hydrolysis and fermentation of spirulina. VFAs, mainly acetate, produced from spirulina degradation were mineralized by sulfate-reducing bacteria and an Arcobacter species. Cellular activity of Desulfobacteraceae and Desulfobulbaceae species during acetoclastic sulfate reduction was largely decoupled from relative 16S rRNA gene abundance shifts. Our findings provide new insights into the identities and physiological constraints that determine the population dynamics of key microorganisms during complex OM degradation in arctic marine sediments.© 2018 Society for Applied Microbiology and John Wiley & Sons Ltd.
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Affiliation(s)
- Albert L. Müller
- Division of Microbial Ecology, Department of Microbiology and Ecosystem ScienceResearch Network Chemistry meets Microbiology, University of ViennaViennaAustria
| | - Claus Pelikan
- Division of Microbial Ecology, Department of Microbiology and Ecosystem ScienceResearch Network Chemistry meets Microbiology, University of ViennaViennaAustria
- Austrian Polar Research InstituteViennaAustria
| | - Julia R. de Rezende
- Center for Geomicrobiology, Department of BioscienceAarhus UniversityAarhusDenmark
| | - Kenneth Wasmund
- Division of Microbial Ecology, Department of Microbiology and Ecosystem ScienceResearch Network Chemistry meets Microbiology, University of ViennaViennaAustria
- Austrian Polar Research InstituteViennaAustria
| | - Martina Putz
- Division of Microbial Ecology, Department of Microbiology and Ecosystem ScienceResearch Network Chemistry meets Microbiology, University of ViennaViennaAustria
| | | | - Kasper U. Kjeldsen
- Center for Geomicrobiology, Department of BioscienceAarhus UniversityAarhusDenmark
| | - Bo Barker Jørgensen
- Center for Geomicrobiology, Department of BioscienceAarhus UniversityAarhusDenmark
| | - Alexander Loy
- Division of Microbial Ecology, Department of Microbiology and Ecosystem ScienceResearch Network Chemistry meets Microbiology, University of ViennaViennaAustria
- Austrian Polar Research InstituteViennaAustria
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28
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Giachini AJ, Sulzbach TS, Pinto AL, Armas RD, Cortez DH, Silva EP, Buzanello EB, Soares ÁG, Soares CRFS, Rossi MJ. Microbially-enriched poultry litter-derived biochar for the treatment of acid mine drainage. Arch Microbiol 2018; 200:1227-1237. [PMID: 29947837 DOI: 10.1007/s00203-018-1534-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Revised: 10/03/2017] [Accepted: 05/29/2018] [Indexed: 11/28/2022]
Abstract
Sulfate-reducing bacteria (SRB) and a biochar array were used to reduce sulfate concentrations and the levels of metals in acid mine drainage (AMD) waters. Cow manure SRB-enriched biochar promoted sulfate reductions of 41% compared to original AMD, and 39% compared to other treatments (control, AMD sediment, sludge). Treatments reduced levels of all analyzed metals below Brazilian official standards. DGGE showed a significant relation between SRB-source and SRB-structural community, where cow manure and sludge presented the more cohesive community structure throughout the monitoring (180 days). The study showed that AMD treatment alternatives can be applied and are effective in reducing the contamination of wastewaters.
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Affiliation(s)
- Admir J Giachini
- Department of Microbiology, Immunology and Parasitology, Federal University of Santa Catarina, Florianopolis, Main Campus, Trindade, Florianopolis, SC, 88040-970, Brazil.
| | - Thays S Sulzbach
- Department of Microbiology, Immunology and Parasitology, Federal University of Santa Catarina, Florianopolis, Main Campus, Trindade, Florianopolis, SC, 88040-970, Brazil
| | - Antônio L Pinto
- Department of Microbiology, Immunology and Parasitology, Federal University of Santa Catarina, Florianopolis, Main Campus, Trindade, Florianopolis, SC, 88040-970, Brazil
| | - Rafael D Armas
- Department of Microbiology, Immunology and Parasitology, Federal University of Santa Catarina, Florianopolis, Main Campus, Trindade, Florianopolis, SC, 88040-970, Brazil
| | - Douglas H Cortez
- Department of Microbiology, Immunology and Parasitology, Federal University of Santa Catarina, Florianopolis, Main Campus, Trindade, Florianopolis, SC, 88040-970, Brazil
| | - Emanuela P Silva
- Department of Microbiology, Immunology and Parasitology, Federal University of Santa Catarina, Florianopolis, Main Campus, Trindade, Florianopolis, SC, 88040-970, Brazil
| | - Elizandra B Buzanello
- Department of Microbiology, Immunology and Parasitology, Federal University of Santa Catarina, Florianopolis, Main Campus, Trindade, Florianopolis, SC, 88040-970, Brazil
| | - Álvaro G Soares
- SP Research and Technology-SPPT, Highway Senator Andre Franco Montoro, Km 3.8, Mogi Mirim, SP, 13803-355, Brazil
| | - Cláudio R F S Soares
- Department of Microbiology, Immunology and Parasitology, Federal University of Santa Catarina, Florianopolis, Main Campus, Trindade, Florianopolis, SC, 88040-970, Brazil
| | - Márcio J Rossi
- Department of Microbiology, Immunology and Parasitology, Federal University of Santa Catarina, Florianopolis, Main Campus, Trindade, Florianopolis, SC, 88040-970, Brazil
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29
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Hausmann B, Pelikan C, Herbold CW, Köstlbacher S, Albertsen M, Eichorst SA, Glavina Del Rio T, Huemer M, Nielsen PH, Rattei T, Stingl U, Tringe SG, Trojan D, Wentrup C, Woebken D, Pester M, Loy A. Peatland Acidobacteria with a dissimilatory sulfur metabolism. THE ISME JOURNAL 2018; 12:1729-1742. [PMID: 29476143 PMCID: PMC6018796 DOI: 10.1038/s41396-018-0077-1] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Revised: 12/21/2017] [Accepted: 01/20/2018] [Indexed: 12/25/2022]
Abstract
Sulfur-cycling microorganisms impact organic matter decomposition in wetlands and consequently greenhouse gas emissions from these globally relevant environments. However, their identities and physiological properties are largely unknown. By applying a functional metagenomics approach to an acidic peatland, we recovered draft genomes of seven novel Acidobacteria species with the potential for dissimilatory sulfite (dsrAB, dsrC, dsrD, dsrN, dsrT, dsrMKJOP) or sulfate respiration (sat, aprBA, qmoABC plus dsr genes). Surprisingly, the genomes also encoded DsrL, which so far was only found in sulfur-oxidizing microorganisms. Metatranscriptome analysis demonstrated expression of acidobacterial sulfur-metabolism genes in native peat soil and their upregulation in diverse anoxic microcosms. This indicated an active sulfate respiration pathway, which, however, might also operate in reverse for dissimilatory sulfur oxidation or disproportionation as proposed for the sulfur-oxidizing Desulfurivibrio alkaliphilus. Acidobacteria that only harbored genes for sulfite reduction additionally encoded enzymes that liberate sulfite from organosulfonates, which suggested organic sulfur compounds as complementary energy sources. Further metabolic potentials included polysaccharide hydrolysis and sugar utilization, aerobic respiration, several fermentative capabilities, and hydrogen oxidation. Our findings extend both, the known physiological and genetic properties of Acidobacteria and the known taxonomic diversity of microorganisms with a DsrAB-based sulfur metabolism, and highlight new fundamental niches for facultative anaerobic Acidobacteria in wetlands based on exploitation of inorganic and organic sulfur molecules for energy conservation.
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Affiliation(s)
- Bela Hausmann
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network Chemistry meets Microbiology, University of Vienna, Vienna, Austria
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Claus Pelikan
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network Chemistry meets Microbiology, University of Vienna, Vienna, Austria
| | - Craig W Herbold
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network Chemistry meets Microbiology, University of Vienna, Vienna, Austria
| | - Stephan Köstlbacher
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network Chemistry meets Microbiology, University of Vienna, Vienna, Austria
| | - Mads Albertsen
- Department of Chemistry and Bioscience, Center for Microbial Communities, Aalborg University, Aalborg, Denmark
| | - Stephanie A Eichorst
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network Chemistry meets Microbiology, University of Vienna, Vienna, Austria
| | | | - Martin Huemer
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network Chemistry meets Microbiology, University of Vienna, Vienna, Austria
| | - Per H Nielsen
- Department of Chemistry and Bioscience, Center for Microbial Communities, Aalborg University, Aalborg, Denmark
| | - Thomas Rattei
- Division of Computational Systems Biology, Department of Microbiology and Ecosystem Science, Research Network Chemistry meets Microbiology, University of Vienna, Vienna, Austria
| | - Ulrich Stingl
- Department for Microbiology and Cell Science, Fort Lauderdale Research and Education Center, UF/IFAS, University of Florida, Davie, FL, USA
| | - Susannah G Tringe
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Daniela Trojan
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network Chemistry meets Microbiology, University of Vienna, Vienna, Austria
| | - Cecilia Wentrup
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network Chemistry meets Microbiology, University of Vienna, Vienna, Austria
| | - Dagmar Woebken
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network Chemistry meets Microbiology, University of Vienna, Vienna, Austria
| | - Michael Pester
- Department of Biology, University of Konstanz, Konstanz, Germany.
- Leibniz Institute DSMZ, Braunschweig, Germany.
| | - Alexander Loy
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network Chemistry meets Microbiology, University of Vienna, Vienna, Austria
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30
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Liu ZH, Yin H, Lin Z, Dang Z. Sulfate-reducing bacteria in anaerobic bioprocesses: basic properties of pure isolates, molecular quantification, and controlling strategies. ACTA ACUST UNITED AC 2018. [DOI: 10.1080/21622515.2018.1437783] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Ze-hua Liu
- School of Environment and Energy, South China University of Technology, Guangzhou, People’s Republic of China
- Key Lab Pollution Control and Ecosystem Restoration in Industry Cluster, Ministry of Education, Guangzhou, People’s Republic of China
- Guangdong Environmental Protection Key Laboratory of Solid Waste Treatment and Recycling, Guangzhou, People’s Republic of China
- Guangdong Provincial Engineering and Technology Research Center for Environment Risk Prevention and Emergency Disposal, South China University of Technology, Guangzhou, People’s Republic of China
| | - Hua Yin
- School of Environment and Energy, South China University of Technology, Guangzhou, People’s Republic of China
| | - Zhang Lin
- School of Environment and Energy, South China University of Technology, Guangzhou, People’s Republic of China
| | - Zhi Dang
- School of Environment and Energy, South China University of Technology, Guangzhou, People’s Republic of China
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31
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Rice Paddy Nitrospirae Carry and Express Genes Related to Sulfate Respiration: Proposal of the New Genus "Candidatus Sulfobium". Appl Environ Microbiol 2018; 84:AEM.02224-17. [PMID: 29247059 PMCID: PMC5812927 DOI: 10.1128/aem.02224-17] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2017] [Accepted: 12/08/2017] [Indexed: 01/16/2023] Open
Abstract
Nitrospirae spp. distantly related to thermophilic, sulfate-reducing Thermodesulfovibrio species are regularly observed in environmental surveys of anoxic marine and freshwater habitats. Here we present a metaproteogenomic analysis of Nitrospirae bacterium Nbg-4 as a representative of this clade. Its genome was assembled from replicated metagenomes of rice paddy soil that was used to grow rice in the presence and absence of gypsum (CaSO4·2H2O). Nbg-4 encoded the full pathway of dissimilatory sulfate reduction and showed expression of this pathway in gypsum-amended anoxic bulk soil as revealed by parallel metaproteomics. In addition, Nbg-4 encoded the full pathway of dissimilatory nitrate reduction to ammonia (DNRA), with expression of its first step being detected in bulk soil without gypsum amendment. The relative abundances of Nbg-4 were similar under both treatments, indicating that Nbg-4 maintained stable populations while shifting its energy metabolism. Whether Nbg-4 is a strict sulfate reducer or can couple sulfur oxidation to DNRA by operating the pathway of dissimilatory sulfate reduction in reverse could not be resolved. Further genome reconstruction revealed the potential to utilize butyrate, formate, H2, or acetate as an electron donor; the Wood-Ljungdahl pathway was expressed under both treatments. Comparison to publicly available Nitrospirae genome bins revealed the pathway for dissimilatory sulfate reduction also in related Nitrospirae recovered from groundwater. Subsequent phylogenomics showed that such microorganisms form a novel genus within the Nitrospirae, with Nbg-4 as a representative species. Based on the widespread occurrence of this novel genus, we propose for Nbg-4 the name “Candidatus Sulfobium mesophilum,” gen. nov., sp. nov. IMPORTANCE Rice paddies are indispensable for the food supply but are a major source of the greenhouse gas methane. If it were not counterbalanced by cryptic sulfur cycling, methane emission from rice paddy fields would be even higher. However, the microorganisms involved in this sulfur cycling are little understood. By using an environmental systems biology approach with Italian rice paddy soil, we could retrieve the population genome of a novel member of the phylum Nitrospirae. This microorganism encoded the full pathway of dissimilatory sulfate reduction and expressed it in anoxic paddy soil under sulfate-enriched conditions. Phylogenomics and comparison to the results of environmental surveys showed that such microorganisms are actually widespread in freshwater and marine environments. At the same time, they represent an undiscovered genus within the little-explored phylum Nitrospirae. Our results will be important for the design of enrichment strategies and postgenomic studies to further understanding of the contribution of these novel Nitrospirae spp. to the global sulfur cycle.
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32
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Kato S, Shibuya T, Takaki Y, Hirai M, Nunoura T, Suzuki K. Genome-enabled metabolic reconstruction of dominant chemosynthetic colonizers in deep-sea massive sulfide deposits. Environ Microbiol 2018; 20:862-877. [DOI: 10.1111/1462-2920.14032] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Revised: 11/08/2017] [Accepted: 12/13/2017] [Indexed: 11/26/2022]
Affiliation(s)
- Shingo Kato
- Ore Genesis Research Unit, Project Team for Development of New-generation Research Protocol for Submarine Resources; Japan Agency for Marine-Earth Science and Technology (JAMSTEC); Yokosuka Kanagawa 237-0061 Japan
- Research and Development Center for Submarine Resources; JAMSTEC; Yokosuka Kanagawa 237-0061 Japan
| | - Takazo Shibuya
- Ore Genesis Research Unit, Project Team for Development of New-generation Research Protocol for Submarine Resources; Japan Agency for Marine-Earth Science and Technology (JAMSTEC); Yokosuka Kanagawa 237-0061 Japan
- Research and Development Center for Submarine Resources; JAMSTEC; Yokosuka Kanagawa 237-0061 Japan
- Department of Subsurface Geobiological Analysis and Research; JAMSTEC; Yokosuka Kanagawa 237-0061 Japan
| | - Yoshihiro Takaki
- Department of Subsurface Geobiological Analysis and Research; JAMSTEC; Yokosuka Kanagawa 237-0061 Japan
- Ecosystem Observation and Evaluation Methodology Research Unit, Project Team for Development of New-generation Research Protocol for Submarine Resources; JAMSTEC; Yokosuka Kanagawa 237-0061 Japan
- Research and Development Center for Marine Biosciences; JAMSTEC; Yokosuka Kanagawa 237-0061 Japan
| | - Miho Hirai
- Research and Development Center for Marine Biosciences; JAMSTEC; Yokosuka Kanagawa 237-0061 Japan
| | - Takuro Nunoura
- Ecosystem Observation and Evaluation Methodology Research Unit, Project Team for Development of New-generation Research Protocol for Submarine Resources; JAMSTEC; Yokosuka Kanagawa 237-0061 Japan
- Research and Development Center for Marine Biosciences; JAMSTEC; Yokosuka Kanagawa 237-0061 Japan
| | - Katsuhiko Suzuki
- Ore Genesis Research Unit, Project Team for Development of New-generation Research Protocol for Submarine Resources; Japan Agency for Marine-Earth Science and Technology (JAMSTEC); Yokosuka Kanagawa 237-0061 Japan
- Research and Development Center for Submarine Resources; JAMSTEC; Yokosuka Kanagawa 237-0061 Japan
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33
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Lueder U, Druschel G, Emerson D, Kappler A, Schmidt C. Quantitative analysis of O2 and Fe2+ profiles in gradient tubes for cultivation of microaerophilic Iron(II)-oxidizing bacteria. FEMS Microbiol Ecol 2017; 94:4693834. [DOI: 10.1093/femsec/fix177] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Accepted: 12/04/2017] [Indexed: 11/14/2022] Open
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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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Slobodkina GB, Mardanov AV, Ravin NV, Frolova AA, Chernyh NA, Bonch-Osmolovskaya EA, Slobodkin AI. Respiratory Ammonification of Nitrate Coupled to Anaerobic Oxidation of Elemental Sulfur in Deep-Sea Autotrophic Thermophilic Bacteria. Front Microbiol 2017; 8:87. [PMID: 28194142 PMCID: PMC5276818 DOI: 10.3389/fmicb.2017.00087] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Accepted: 01/12/2017] [Indexed: 02/05/2023] Open
Abstract
Respiratory ammonification of nitrate is the microbial process that determines the retention of nitrogen in an ecosystem. To date, sulfur-dependent dissimilatory nitrate reduction to ammonium has been demonstrated only with sulfide as an electron donor. We detected a novel pathway that couples the sulfur and nitrogen cycles. Thermophilic anaerobic bacteria Thermosulfurimonas dismutans and Dissulfuribacter thermophilus, isolated from deep-sea hydrothermal vents, grew autotrophically with elemental sulfur as an electron donor and nitrate as an electron acceptor producing sulfate and ammonium. The genomes of both bacteria contain a gene cluster that encodes a putative nitrate ammonification enzyme system. Nitrate reduction occurs via a Nap-type complex. The reduction of produced nitrite to ammonium does not proceed via the canonical Nrf system because nitrite reductase NrfA is absent in the genomes of both microorganisms. The genome of D. thermophilus encodes a complete sulfate reduction pathway, while the Sox sulfur oxidation system is missing, as shown previously for T. dismutans. Thus, in high-temperature environments, nitrate ammonification with elemental sulfur may represent an unrecognized route of primary biomass production. Moreover, the anaerobic oxidation of sulfur compounds coupled to growth has not previously been demonstrated for the members of Thermodesulfobacteria or Deltaproteobacteria, which were considered exclusively as participants of the reductive branch of the sulfur cycle.
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Affiliation(s)
- Galina B Slobodkina
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences Moscow, Russia
| | - Andrey V Mardanov
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences Moscow, Russia
| | - Nikolai V Ravin
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences Moscow, Russia
| | - Anastasia A Frolova
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences Moscow, Russia
| | - Nikolay A Chernyh
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences Moscow, Russia
| | - Elizaveta A Bonch-Osmolovskaya
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences Moscow, Russia
| | - Alexander I Slobodkin
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences Moscow, Russia
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Xu XJ, Chen C, Wang AJ, Ni BJ, Guo WQ, Yuan Y, Huang C, Zhou X, Wu DH, Lee DJ, Ren NQ. Mathematical modeling of simultaneous carbon-nitrogen-sulfur removal from industrial wastewater. JOURNAL OF HAZARDOUS MATERIALS 2017; 321:371-381. [PMID: 27669378 DOI: 10.1016/j.jhazmat.2016.08.074] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Revised: 07/08/2016] [Accepted: 08/30/2016] [Indexed: 06/06/2023]
Abstract
A mathematical model of carbon, nitrogen and sulfur removal (C-N-S) from industrial wastewater was constructed considering the interactions of sulfate-reducing bacteria (SRB), sulfide-oxidizing bacteria (SOB), nitrate-reducing bacteria (NRB), facultative bacteria (FB), and methane producing archaea (MPA). For the kinetic network, the bioconversion of C-N by heterotrophic denitrifiers (NO3-→NO2-→N2), and that of C-S by SRB (SO42-→S2-) and SOB (S2-→S0) was proposed and calibrated based on batch experimental data. The model closely predicted the profiles of nitrate, nitrite, sulfate, sulfide, lactate, acetate, methane and oxygen under both anaerobic and micro-aerobic conditions. The best-fit kinetic parameters had small 95% confidence regions with mean values approximately at the center. The model was further validated using independent data sets generated under different operating conditions. This work was the first successful mathematical modeling of simultaneous C-N-S removal from industrial wastewater and more importantly, the proposed model was proven feasible to simulate other relevant processes, such as sulfate-reducing, sulfide-oxidizing process (SR-SO) and denitrifying sulfide removal (DSR) process. The model developed is expected to enhance our ability to predict the treatment of carbon-nitrogen-sulfur contaminated industrial wastewater.
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Affiliation(s)
- Xi-Jun Xu
- State Key Laboratory of Urban Water Resource and Environment, School of Municipal and Environmental Engineering, Harbin Institute of Technology, P.O. Box 2650, 73 Huanghe Road, Nangang, Harbin, Heilongjiang 150090, China
| | - Chuan Chen
- State Key Laboratory of Urban Water Resource and Environment, School of Municipal and Environmental Engineering, Harbin Institute of Technology, P.O. Box 2650, 73 Huanghe Road, Nangang, Harbin, Heilongjiang 150090, China.
| | - Ai-Jie Wang
- State Key Laboratory of Urban Water Resource and Environment, School of Municipal and Environmental Engineering, Harbin Institute of Technology, P.O. Box 2650, 73 Huanghe Road, Nangang, Harbin, Heilongjiang 150090, China
| | - Bing-Jie Ni
- Advanced Water Management Centre (AWMC), The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia
| | - Wan-Qian Guo
- State Key Laboratory of Urban Water Resource and Environment, School of Municipal and Environmental Engineering, Harbin Institute of Technology, P.O. Box 2650, 73 Huanghe Road, Nangang, Harbin, Heilongjiang 150090, China
| | - Ye Yuan
- State Key Laboratory of Urban Water Resource and Environment, School of Municipal and Environmental Engineering, Harbin Institute of Technology, P.O. Box 2650, 73 Huanghe Road, Nangang, Harbin, Heilongjiang 150090, China
| | - Cong Huang
- State Key Laboratory of Urban Water Resource and Environment, School of Municipal and Environmental Engineering, Harbin Institute of Technology, P.O. Box 2650, 73 Huanghe Road, Nangang, Harbin, Heilongjiang 150090, China
| | - Xu Zhou
- State Key Laboratory of Urban Water Resource and Environment, School of Municipal and Environmental Engineering, Harbin Institute of Technology, P.O. Box 2650, 73 Huanghe Road, Nangang, Harbin, Heilongjiang 150090, China
| | - Dong-Hai Wu
- State Key Laboratory of Urban Water Resource and Environment, School of Municipal and Environmental Engineering, Harbin Institute of Technology, P.O. Box 2650, 73 Huanghe Road, Nangang, Harbin, Heilongjiang 150090, China
| | - Duu-Jong Lee
- State Key Laboratory of Urban Water Resource and Environment, School of Municipal and Environmental Engineering, Harbin Institute of Technology, P.O. Box 2650, 73 Huanghe Road, Nangang, Harbin, Heilongjiang 150090, China; Department of Chemical Engineering, National Taiwan University, Taipei 106, Taiwan; Department of Chemical Engineering, National Taiwan University of Science and Technology, Taipei 106, Taiwan
| | - Nan-Qi Ren
- State Key Laboratory of Urban Water Resource and Environment, School of Municipal and Environmental Engineering, Harbin Institute of Technology, P.O. Box 2650, 73 Huanghe Road, Nangang, Harbin, Heilongjiang 150090, China.
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Chu L, Wang J. Denitrification of groundwater using a biodegradable polymer as a carbon source: long-term performance and microbial diversity. RSC Adv 2017. [DOI: 10.1039/c7ra11151g] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Nitrate pollution in groundwater is a worldwide problem.
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Affiliation(s)
- Libing Chu
- Collaborative Innovation Center for Advanced Nuclear Energy Technology
- INET
- Tsinghua University
- Beijing 100084
- P. R. China
| | - Jianlong Wang
- Collaborative Innovation Center for Advanced Nuclear Energy Technology
- INET
- Tsinghua University
- Beijing 100084
- P. R. China
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Bryukhanov AL, Korneeva VA, Dinarieva TY, Karnachuk OV, Netrusov AI, Pimenov NV. Components of antioxidant systems in the cells of aerotolerant sulfate-reducing bacteria of the genus Desulfovibrio (strains A2 and TomC) isolated from metal mining waste. Microbiology (Reading) 2016. [DOI: 10.1134/s0026261716060047] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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Lefèvre CT, Howse PA, Schmidt ML, Sabaty M, Menguy N, Luther GW, Bazylinski DA. Growth of magnetotactic sulfate-reducing bacteria in oxygen concentration gradient medium. ENVIRONMENTAL MICROBIOLOGY REPORTS 2016; 8:1003-1015. [PMID: 27701830 DOI: 10.1111/1758-2229.12479] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Although dissimilatory sulfate-reducing bacteria (SRB) are generally described as strictly anaerobic organisms with regard to growth, several reports have shown that some SRB, particularly Desulfovibrio species, are quite resistant to O2 . For example, SRB remain viable in many aerobic environments while some even reduce O2 to H2 O. However, reproducible aerobic growth of SRB has not been unequivocally documented. Desulfovibrio magneticus is a SRB that is also a magnetotactic bacterium (MTB). MTB biomineralize magnetosomes which are intracellular, membrane-bounded, magnetic iron mineral crystals. The ability of D. magneticus to grow aerobically in several different media under air where an O2 concentration gradient formed, or under O2 -free N2 gas was tested. Under air, cells grew as a microaerophilic band of cells at the oxic-anoxic interface in media lacking sulfate. These results show that D. magneticus is capable of aerobic growth with O2 as a terminal electron acceptor. This is the first report of consistent, reproducible aerobic growth of SRB. This finding is critical in determining important ecological roles SRB play in the environment. Interestingly, the crystal structure of the magnetite crystals of D. magneticus grown under microaerobic conditions showed significant differences compared with those produced anaerobically providing more evidence that environmental parameters influence magnetosome formation.
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Affiliation(s)
- Christopher T Lefèvre
- CNRS/CEA/Aix-Marseille Université UMR7265 Institut de biosciences et biotechnologies Laboratoire de Bioénergétique Cellulaire, Saint Paul lez Durance, 13108, France
| | - Paul A Howse
- School of Life Sciences, University of Nevada at Las Vegas, Las Vegas, NV, 89154-4004, USA
| | - Marian L Schmidt
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA
| | - Monique Sabaty
- CNRS/CEA/Aix-Marseille Université UMR7265 Institut de biosciences et biotechnologies Laboratoire de Bioénergétique Cellulaire, Saint Paul lez Durance, 13108, France
| | - Nicolas Menguy
- Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, Sorbonne Universités, Université Pierre et Marie Curie, UMR 7590 CNRS, Institut de Recherche pour le Développement UMR 206, Museum National d'Histoire Naturelle, Paris Cedex 05, 75252, France
| | - George W Luther
- School of Marine Science and Policy, University of Delaware, 700 Pilottown Rd. Lewes, DE, 19958, USA
| | - Dennis A Bazylinski
- School of Life Sciences, University of Nevada at Las Vegas, Las Vegas, NV, 89154-4004, USA
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Liu H, Tan S, Yu T, Liu Y. Sulfate reducing bacterial community and in situ activity in mature fine tailings analyzed by real time qPCR and microsensor. J Environ Sci (China) 2016; 44:141-147. [PMID: 27266310 DOI: 10.1016/j.jes.2015.08.025] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2015] [Revised: 07/18/2015] [Accepted: 07/18/2015] [Indexed: 06/06/2023]
Abstract
Sulfate reducing bacteria (SRB) play significant roles in anaerobic environments in oil sands mature fine tailings (MFTs). Hydrogen sulfide (H2S) is produced during the biological sulfate reduction process. The production of toxic H2S is one of the concerns because it may hinder the landscape remediation efficiency of oil sands tailing ponds. In present study, the in situ activity and the community structure of SRB in MFT and gypsum amended MFT in two settling columns were investigated. Combined techniques of H2S microsensor and dissimilatory sulfite reductase β-subunit (dsrB) genes-based real time quantitative polymerase chain reaction (qPCR) were applied to detect the in situ H2S and the abundance of SRB. A higher diversity of SRB and more H2S were observed in gypsum amended MFT than that in MFT, indicating a higher sulfate reduction activity in gypsum amended MFT; in addition, the activity of SRB varied as depth in both MFT and gypsum amended MFT: the deeper the more H2S produced. Long-term plans for tailings management can be assessed more wisely with the information provided in this study.
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Affiliation(s)
- Hong Liu
- Department of Civil and Environmental Engineering, University of Alberta, Edmonton, Canada
| | - Shuying Tan
- Department of Civil and Environmental Engineering, University of Alberta, Edmonton, Canada
| | - Tong Yu
- Department of Civil and Environmental Engineering, University of Alberta, Edmonton, Canada.
| | - Yang Liu
- Department of Civil and Environmental Engineering, University of Alberta, Edmonton, Canada.
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41
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Biological denitrification using poly(butanediol succinate) as electron donor. Appl Microbiol Biotechnol 2016; 100:6047-53. [DOI: 10.1007/s00253-016-7435-6] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Revised: 02/28/2016] [Accepted: 03/01/2016] [Indexed: 12/01/2022]
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42
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Saia FT, Souza TSO, Duarte RTD, Pozzi E, Fonseca D, Foresti E. Microbial community in a pilot-scale bioreactor promoting anaerobic digestion and sulfur-driven denitrification for domestic sewage treatment. Bioprocess Biosyst Eng 2015; 39:341-52. [DOI: 10.1007/s00449-015-1520-6] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Accepted: 11/25/2015] [Indexed: 01/30/2023]
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Stauffert M, Cravo-Laureau C, Duran R. Dynamic of sulphate-reducing microorganisms in petroleum-contaminated marine sediments inhabited by the polychaete Hediste diversicolor. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2015; 22:15273-15284. [PMID: 25256587 DOI: 10.1007/s11356-014-3624-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2014] [Accepted: 09/16/2014] [Indexed: 06/03/2023]
Abstract
The behaviour of sulphate-reducing microbial community was investigated at the oxic-anoxic interface (0-2 cm) of marine sediments when submitted to oil and enhanced bioturbation activities by the addition of Hediste diversicolor. Although total hydrocarbon removal was not improved by the addition of H. diversicolor, terminal restriction fragment length polymorphism (T-RFLP) analyses based on dsrAB (dissimilatory sulphite reductase) genes and transcripts showed different patterns according to the presence of H. diversicolor which favoured the abundance of dsrB genes during the early stages of incubation. Complementary DNA (cDNA) dsrAB libraries revealed that in presence of H. diversicolor, most dsrAB sequences belonged to hydrocarbonoclastic Desulfobacteraceae, suggesting that sulphate-reducing microorganisms (SRMs) may play an active role in hydrocarbon biodegradation in sediments where the reworking activity is enhanced. Furthermore, the presence of dsrAB sequences related to sequences found associated to environments with high dinitrogen fixation activity suggested potential N2 fixation by SRMs in bioturbated-polluted sediments.
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Affiliation(s)
- Magalie Stauffert
- Equipe Environnement et Microbiologie, Université de Pau et des Pays de l'Adour, IPREM UMR CNRS 5254, BP 1155, 64013, Pau Cedex, France
| | - Cristiana Cravo-Laureau
- Equipe Environnement et Microbiologie, Université de Pau et des Pays de l'Adour, IPREM UMR CNRS 5254, BP 1155, 64013, Pau Cedex, France.
| | - Robert Duran
- Equipe Environnement et Microbiologie, Université de Pau et des Pays de l'Adour, IPREM UMR CNRS 5254, BP 1155, 64013, Pau Cedex, France
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44
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Nielsen M, Revsbech NP, Kühl M. Microsensor measurements of hydrogen gas dynamics in cyanobacterial microbial mats. Front Microbiol 2015; 6:726. [PMID: 26257714 PMCID: PMC4508582 DOI: 10.3389/fmicb.2015.00726] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Accepted: 07/02/2015] [Indexed: 11/16/2022] Open
Abstract
We used a novel amperometric microsensor for measuring hydrogen gas production and consumption at high spatio-temporal resolution in cyanobacterial biofilms and mats dominated by non-heterocystous filamentous cyanobacteria (Microcoleus chtonoplastes and Oscillatoria sp.). The new microsensor is based on the use of an organic electrolyte and a stable internal reference system and can be equipped with a chemical sulfide trap in the measuring tip; it exhibits very stable and sulfide-insensitive measuring signals and a high sensitivity (1.5–5 pA per μmol L-1 H2). Hydrogen gas measurements were done in combination with microsensor measurements of scalar irradiance, O2, pH, and H2S and showed a pronounced H2 accumulation (of up to 8–10% H2 saturation) within the upper mm of cyanobacterial mats after onset of darkness and O2 depletion. The peak concentration of H2 increased with the irradiance level prior to darkening. After an initial build-up over the first 1–2 h in darkness, H2 was depleted over several hours due to efflux to the overlaying water, and due to biogeochemical processes in the uppermost oxic layers and the anoxic layers of the mats. Depletion could be prevented by addition of molybdate pointing to sulfate reduction as a major sink for H2. Immediately after onset of illumination, a short burst of presumably photo-produced H2 due to direct biophotolysis was observed in the illuminated but anoxic mat layers. As soon as O2 from photosynthesis started to accumulate, the H2 was consumed rapidly and production ceased. Our data give detailed insights into the microscale distribution and dynamics of H2 in cyanobacterial biofilms and mats, and further support that cyanobacterial H2 production can play a significant role in fueling anaerobic processes like e.g., sulfate reduction or anoxygenic photosynthesis in microbial mats.
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Affiliation(s)
- Michael Nielsen
- Section of Microbiology, Department of Bioscience, Aarhus University Aarhus, Denmark
| | - Niels P Revsbech
- Section of Microbiology, Department of Bioscience, Aarhus University Aarhus, Denmark
| | - Michael Kühl
- Marine Biological Section, Department of Biology, University of Copenhagen Helsingør, Denmark ; Plant Functional Biology and Climate Change Cluster, University of Technology, Sydney, Ultimo NSW, Australia
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Kolinko S, Richter M, Glöckner FO, Brachmann A, Schüler D. Single-cell genomics of uncultivated deep-branching magnetotactic bacteria reveals a conserved set of magnetosome genes. Environ Microbiol 2015; 18:21-37. [PMID: 26060021 DOI: 10.1111/1462-2920.12907] [Citation(s) in RCA: 88] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2015] [Revised: 05/10/2015] [Accepted: 05/14/2015] [Indexed: 11/26/2022]
Abstract
While magnetosome biosynthesis within the magnetotactic Proteobacteria is increasingly well understood, much less is known about the genetic control within deep-branching phyla, which have a unique ultrastructure and biosynthesize up to several hundreds of bullet-shaped magnetite magnetosomes arranged in multiple bundles of chains, but have no cultured representatives. Recent metagenomic analysis identified magnetosome genes in the genus 'Candidatus Magnetobacterium' homologous to those in Proteobacteria. However, metagenomic analysis has been limited to highly abundant members of the community, and therefore only little is known about the magnetosome biosynthesis, ecophysiology and metabolic capacity in deep-branching MTB. Here we report the analysis of single-cell derived draft genomes of three deep-branching uncultivated MTB. Single-cell sorting followed by whole genome amplification generated draft genomes of Candidatus Magnetobacterium bavaricum and Candidatus Magnetoovum chiemensis CS-04 of the Nitrospirae phylum. Furthermore, we present the first, nearly complete draft genome of a magnetotactic representative from the candidate phylum Omnitrophica, tentatively named Candidatus Omnitrophus magneticus SKK-01. Besides key metabolic features consistent with a common chemolithoautotrophic lifestyle, we identified numerous, partly novel genes most likely involved in magnetosome biosynthesis of bullet-shaped magnetosomes and their arrangement in multiple bundles of chains.
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Affiliation(s)
- Sebastian Kolinko
- Department of Biology I, LMU Biozentrum, Ludwig-Maximilians University Munich, Großhaderner Str. 2-4, Planegg-Martinsried, 82152, Germany
| | - Michael Richter
- Microbial Genomics and Bioinformatics Research Group, Max Planck Institute for Marine Microbiology, Celsiusstr. 1, Bremen, 28359, Germany
| | - Frank-Oliver Glöckner
- Microbial Genomics and Bioinformatics Research Group, Max Planck Institute for Marine Microbiology, Celsiusstr. 1, Bremen, 28359, Germany.,Department of Life Sciences & Chemistry, Jacobs University Bremen, Campus Ring 1, Bremen, 28759, Germany
| | - Andreas Brachmann
- Department of Biology I, LMU Biozentrum, Ludwig-Maximilians University Munich, Großhaderner Str. 2-4, Planegg-Martinsried, 82152, Germany
| | - Dirk Schüler
- Department of Biology I, LMU Biozentrum, Ludwig-Maximilians University Munich, Großhaderner Str. 2-4, Planegg-Martinsried, 82152, Germany.,Department of Microbiology, University Bayreuth, Bayreuth, Germany
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Ramel F, Brasseur G, Pieulle L, Valette O, Hirschler-Réa A, Fardeau ML, Dolla A. Growth of the obligate anaerobe Desulfovibrio vulgaris Hildenborough under continuous low oxygen concentration sparging: impact of the membrane-bound oxygen reductases. PLoS One 2015; 10:e0123455. [PMID: 25837676 PMCID: PMC4383621 DOI: 10.1371/journal.pone.0123455] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Accepted: 03/04/2015] [Indexed: 11/18/2022] Open
Abstract
Although obligate anaerobe, the sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough (DvH) exhibits high aerotolerance that involves several enzymatic systems, including two membrane-bound oxygen reductases, a bd-quinol oxidase and a cc(b/o)o3 cytochrome oxidase. Effect of constant low oxygen concentration on growth and morphology of the wild-type, single (Δbd, Δcox) and double deletion (Δcoxbd) mutant strains of the genes encoding these oxygen reductases was studied. When both wild-type and deletion mutant strains were cultured in lactate/sulfate medium under constant 0.02% O2 sparging, they were able to grow but the final biomasses and the growth yield were lower than that obtained under anaerobic conditions. At the end of the growth, lactate was not completely consumed and when conditions were then switched to anaerobic, growth resumed. Time-lapse microscopy revealed that a large majority of the cells were then able to divide (over 97%) but the time to recover a complete division event was longer for single deletion mutant Δbd than for the three other strains. Determination of the molar growth yields on lactate suggested that a part of the energy gained from lactate oxidation was derived toward cells protection/repairing against oxidative conditions rather than biosynthesis, and that this part was higher in the single deletion mutant Δbd and, to a lesser extent, Δcox strains. Our data show that when DvH encounters oxidative conditions, it is able to stop growing and to rapidly resume growing when conditions are switched to anaerobic, suggesting that it enters active dormancy sate under oxidative conditions. We propose that the pyruvate-ferredoxin oxidoreductase (PFOR) plays a central role in this phenomenon by reversibly switching from an oxidative-sensitive fully active state to an oxidative-insensitive inactive state. The oxygen reductases, and especially the bd-quinol oxidase, would have a crucial function by maintaining reducing conditions that permit PFOR to stay in its active state.
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Affiliation(s)
- Fanny Ramel
- Aix-Marseille Université, CNRS, LCB-UMR7283, Marseille, France
| | - Gael Brasseur
- Aix-Marseille Université, CNRS, LCB-UMR7283, Marseille, France
| | | | - Odile Valette
- Aix-Marseille Université, CNRS, LCB-UMR7283, Marseille, France
| | - Agnès Hirschler-Réa
- Aix-Marseille Université, Université de Toulon, CNRS, IRD, MIO, UM110, 13288 Marseille, Cedex 09, France
| | - Marie Laure Fardeau
- Aix-Marseille Université, Université de Toulon, CNRS, IRD, MIO, UM110, 13288 Marseille, Cedex 09, France
| | - Alain Dolla
- Aix-Marseille Université, CNRS, LCB-UMR7283, Marseille, France
- * E-mail:
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Shen Z, Zhou Y, Liu J, Xiao Y, Cao R, Wu F. Enhanced removal of nitrate using starch/PCL blends as solid carbon source in a constructed wetland. BIORESOURCE TECHNOLOGY 2015; 175:239-44. [PMID: 25459828 DOI: 10.1016/j.biortech.2014.10.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2014] [Revised: 09/29/2014] [Accepted: 10/01/2014] [Indexed: 05/06/2023]
Abstract
Cornstarch/polycaprolactone (SPCL) blends were prepared and used as external carbon source for biological denitrification in a constructed wetland. The denitrification performances, components of dissolved organic matter (DOM) and microbial diversity were investigated. The results showed that nitrate was removed mainly in the layer filled with SPCL, and the average denitrification rate was 0.069kg/m(3)d (nitrate removal efficiency was 98.23%). The major component of DOM was polysaccharides which mainly consisted of reducing sugar. Besides, the concentrations of polysaccharides and reducing sugar decreased along the height of the constructed wetland. Therefore, the dissolved organic carbon (DOC) of effluent decreased to 6.54mg/L. Denitrifying bacteria Bacillus (24.25%) and Thauera (9.36%) were the most abundant genera in the biofilm attached on the surface of SPCL.
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Affiliation(s)
- Zhiqiang Shen
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, PR China; Research Center of Water Pollution Control Technology, Chinese Research Academy of Environmental Sciences, Beijing 100012, PR China
| | - Yuexi Zhou
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, PR China; Research Center of Water Pollution Control Technology, Chinese Research Academy of Environmental Sciences, Beijing 100012, PR China.
| | - Jia Liu
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, PR China; Research Center of Water Pollution Control Technology, Chinese Research Academy of Environmental Sciences, Beijing 100012, PR China; School of Urban Construction, Hebei University of Engineering, Handan 056038, PR China
| | - Yu Xiao
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, PR China; Research Center of Water Pollution Control Technology, Chinese Research Academy of Environmental Sciences, Beijing 100012, PR China; School of Environmental and Municipal Engineering, LanZhou JiaoTong University, Lanzhou 730070, PR China
| | - Rong Cao
- School of Urban Construction, Hebei University of Engineering, Handan 056038, PR China
| | - Fuping Wu
- School of Environmental and Municipal Engineering, LanZhou JiaoTong University, Lanzhou 730070, PR China
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Hao TW, Xiang PY, Mackey HR, Chi K, Lu H, Chui HK, van Loosdrecht MCM, Chen GH. A review of biological sulfate conversions in wastewater treatment. WATER RESEARCH 2014; 65:1-21. [PMID: 25086411 DOI: 10.1016/j.watres.2014.06.043] [Citation(s) in RCA: 184] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2014] [Revised: 06/26/2014] [Accepted: 06/30/2014] [Indexed: 06/03/2023]
Abstract
Treatment of waters contaminated with sulfur containing compounds (S) resulting from seawater intrusion, the use of seawater (e.g. seawater flushing, cooling) and industrial processes has become a challenging issue since around two thirds of the world's population live within 150 km of the coast. In the past, research has produced a number of bioengineered systems for remediation of industrial sulfate containing sewage and sulfur contaminated groundwater utilizing sulfate reducing bacteria (SRB). The majority of these studies are specific with SRB only or focusing on the microbiology rather than the engineered application. In this review, existing sulfate based biotechnologies and new approaches for sulfate contaminated waters treatment are discussed. The sulfur cycle connects with carbon, nitrogen and phosphorus cycles, thus a new platform of sulfur based biotechnologies incorporating sulfur cycle with other cycles can be developed, for the removal of sulfate and other pollutants (e.g. carbon, nitrogen, phosphorus and metal) from wastewaters. All possible electron donors for sulfate reduction are summarized for further understanding of the S related biotechnologies including rates and benefits/drawbacks of each electron donor. A review of known SRB and their environmental preferences with regard to bioreactor operational parameters (e.g. pH, temperature, salinity etc.) shed light on the optimization of sulfur conversion-based biotechnologies. This review not only summarizes information from the current sulfur conversion-based biotechnologies for further optimization and understanding, but also offers new directions for sulfur related biotechnology development.
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Affiliation(s)
- Tian-wei Hao
- Department of Civil & Environmental Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Peng-yu Xiang
- Department of Civil & Environmental Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Hamish R Mackey
- Department of Civil & Environmental Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Kun Chi
- Department of Civil & Environmental Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Hui Lu
- SYSU-HKUST Joint Research Centre for Innovative Environmental Technology, Sun Yat-sen University, Guangzhou, China
| | - Ho-kwong Chui
- Department of Civil & Environmental Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Mark C M van Loosdrecht
- Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC, Delft, The Netherlands
| | - Guang-Hao Chen
- Department of Civil & Environmental Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong; SYSU-HKUST Joint Research Centre for Innovative Environmental Technology, Sun Yat-sen University, Guangzhou, China.
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Liu H, Tan S, Sheng Z, Liu Y, Yu T. Bacterial community structure and activity of sulfate reducing bacteria in a membrane aerated biofilm analyzed by microsensor and molecular techniques. Biotechnol Bioeng 2014; 111:2155-62. [PMID: 24890472 DOI: 10.1002/bit.25277] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2014] [Revised: 04/23/2014] [Accepted: 04/29/2014] [Indexed: 11/07/2022]
Abstract
The activities and vertical spatial distribution of sulfate reducing bacteria (SRB) in an oxygen (O2 )-based membrane aerated biofilm (MAB) were investigated using microsensor (O2 and H2 S) measurements and molecular techniques (polymerase chain reaction-denaturing gradient gel electrophoresis [PCR-DGGE] and fluorescence in situ hybridization [FISH]). The O2 concentration profile revealed that O2 penetrated from the bottom (substratum) of the gas permeable membrane, and was gradually consumed within the biofilm until it was completely depleted near the biofilm/bulk liquid interface, indicating oxic and anoxic zone in the MAB. The H2 S concentration profile showed that H2 S production was found in the upper 285 µm of the biofilm, indicating a high activity of SRB in this region. The results from DGGE of the PCR-amplified dissimilatory sulfite reductase subunit B (dsrB) gene and FISH showed an uneven spatial distribution of SRB. The maximum SRB biomass was located in the upper biofilm. The information from the molecular analysis can be supplemented with that from microsensor measurements to better understand the microbial community and activity of SRB in the MAB.
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Affiliation(s)
- Hong Liu
- Department of Civil and Environmental Engineering, University of Alberta, Edmonton, Alberta, Canada, T6G 2W2
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A genomic view on syntrophic versus non-syntrophic lifestyle in anaerobic fatty acid degrading communities. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2014; 1837:2004-2016. [PMID: 24973598 DOI: 10.1016/j.bbabio.2014.06.005] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2013] [Revised: 06/05/2014] [Accepted: 06/09/2014] [Indexed: 11/22/2022]
Abstract
In sulfate-reducing and methanogenic environments complex biopolymers are hydrolyzed and degraded by fermentative micro-organisms that produce hydrogen, carbon dioxide and short chain fatty acids. Degradation of short chain fatty acids can be coupled to methanogenesis or to sulfate-reduction. Here we study from a genome perspective why some of these micro-organisms are able to grow in syntrophy with methanogens and others are not. Bacterial strains were selected based on genome availability and upon their ability to grow on short chain fatty acids alone or in syntrophic association with methanogens. Systematic functional domain profiling allowed us to shed light on this fundamental and ecologically important question. Extra-cytoplasmic formate dehydrogenases (InterPro domain number; IPR006443), including their maturation protein FdhE (IPR024064 and IPR006452) is a typical difference between syntrophic and non-syntrophic butyrate and propionate degraders. Furthermore, two domains with a currently unknown function seem to be associated with the ability of syntrophic growth. One is putatively involved in capsule or biofilm production (IPR019079) and a second in cell division, shape-determination or sporulation (IPR018365). The sulfate-reducing bacteria Desulfobacterium autotrophicum HRM2, Desulfomonile tiedjei and Desulfosporosinus meridiei were never tested for syntrophic growth, but all crucial domains were found in their genomes, which suggests their possible ability to grow in syntrophic association with methanogens. In addition, profiling domains involved in electron transfer mechanisms revealed the important role of the Rnf-complex and the formate transporter in syntrophy, and indicate that DUF224 may have a role in electron transfer in bacteria other than Syntrophomonas wolfei as well. This article is a part of a Special Issue entitled: 18th European Bioenergetics Conference (Biochim. Biophys. Acta, Volume 1837, Issue 7, July 2014).
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