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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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2
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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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3
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van Erk MR, Bourceau OM, Moncada C, Basu S, Hansel CM, de Beer D. Reactive oxygen species affect the potential for mineralization processes in permeable intertidal flats. Nat Commun 2023; 14:938. [PMID: 36804536 PMCID: PMC9941506 DOI: 10.1038/s41467-023-35818-4] [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: 12/10/2021] [Accepted: 01/03/2023] [Indexed: 02/22/2023] Open
Abstract
Intertidal permeable sediments are crucial sites of organic matter remineralization. These sediments likely have a large capacity to produce reactive oxygen species (ROS) because of shifting oxic-anoxic interfaces and intense iron-sulfur cycling. Here, we show that high concentrations of the ROS hydrogen peroxide are present in intertidal sediments using microsensors, and chemiluminescent analysis on extracted porewater. We furthermore investigate the effect of ROS on potential rates of microbial degradation processes in intertidal surface sediments after transient oxygenation, using slurries that transitioned from oxic to anoxic conditions. Enzymatic removal of ROS strongly increases rates of aerobic respiration, sulfate reduction and hydrogen accumulation. We conclude that ROS are formed in sediments, and subsequently moderate microbial mineralization process rates. Although sulfate reduction is completely inhibited in the oxic period, it resumes immediately upon anoxia. This study demonstrates the strong effects of ROS and transient oxygenation on the biogeochemistry of intertidal sediments.
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Affiliation(s)
- Marit R van Erk
- Max Planck Institute for Marine Microbiology, Bremen, Germany. .,Department of Earth Sciences, Utrecht University, Utrecht, The Netherlands.
| | | | - Chyrene Moncada
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Subhajit Basu
- Max Planck Institute for Marine Microbiology, Bremen, Germany.,School of Health Sciences and Technology (SoHST), University of Petroleum and Energy Studies (UPES), Dehradun, Uttarakhand, 248007, India
| | - Colleen M Hansel
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
| | - Dirk de Beer
- Max Planck Institute for Marine Microbiology, Bremen, Germany
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4
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Gomes ML, Klatt JM, Dick GJ, Grim SL, Rico KI, Medina M, Ziebis W, Kinsman-Costello L, Sheldon ND, Fike DA. Sedimentary pyrite sulfur isotope compositions preserve signatures of the surface microbial mat environment in sediments underlying low-oxygen cyanobacterial mats. GEOBIOLOGY 2022; 20:60-78. [PMID: 34331395 DOI: 10.1111/gbi.12466] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 07/10/2021] [Indexed: 06/13/2023]
Abstract
The sedimentary pyrite sulfur isotope (δ34 S) record is an archive of ancient microbial sulfur cycling and environmental conditions. Interpretations of pyrite δ34 S signatures in sediments deposited in microbial mat ecosystems are based on studies of modern microbial mat porewater sulfide δ34 S geochemistry. Pyrite δ34 S values often capture δ34 S signatures of porewater sulfide at the location of pyrite formation. However, microbial mats are dynamic environments in which biogeochemical cycling shifts vertically on diurnal cycles. Therefore, there is a need to study how the location of pyrite formation impacts pyrite δ34 S patterns in these dynamic systems. Here, we present diurnal porewater sulfide δ34 S trends and δ34 S values of pyrite and iron monosulfides from Middle Island Sinkhole, Lake Huron. The sediment-water interface of this sinkhole hosts a low-oxygen cyanobacterial mat ecosystem, which serves as a useful location to explore preservation of sedimentary pyrite δ34 S signatures in early Earth environments. Porewater sulfide δ34 S values vary by up to ~25‰ throughout the day due to light-driven changes in surface microbial community activity that propagate downwards, affecting porewater geochemistry as deep as 7.5 cm in the sediment. Progressive consumption of the sulfate reservoir drives δ34 S variability, instead of variations in average cell-specific sulfate reduction rates and/or sulfide oxidation at different depths in the sediment. The δ34 S values of pyrite are similar to porewater sulfide δ34 S values near the mat surface. We suggest that oxidative sulfur cycling and other microbial activity promote pyrite formation in and immediately adjacent to the microbial mat and that iron geochemistry limits further pyrite formation with depth in the sediment. These results imply that primary δ34 S signatures of pyrite deposited in organic-rich, iron-poor microbial mat environments capture information about microbial sulfur cycling and environmental conditions at the mat surface and are only minimally affected by deeper sedimentary processes during early diagenesis.
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Affiliation(s)
- Maya L Gomes
- Department of Earth and Planetary Sciences, Johns Hopkins University, Baltimore, MD, USA
| | - Judith M Klatt
- Microsensor Group, Max Planck Institute for Marine Microbiology, Bremen, Germany
- Department of Earth and Environmental Science, University of Michigan, Ann Arbor, MI, USA
| | - Gregory J Dick
- Department of Earth and Environmental Science, University of Michigan, Ann Arbor, MI, USA
| | - Sharon L Grim
- Department of Earth and Environmental Science, University of Michigan, Ann Arbor, MI, USA
- Exobiology Branch, National Aeronautics and Space Administration Ames Research Center, Mountain View, CA, USA
| | - Kathryn I Rico
- Department of Earth and Environmental Science, University of Michigan, Ann Arbor, MI, USA
- Department of Earth and Planetary Sciences, McGill University, Montreal, QC, Canada
| | - Matthew Medina
- Department of Earth and Environmental Science, University of Michigan, Ann Arbor, MI, USA
| | - Wiebke Ziebis
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | | | - Nathan D Sheldon
- Department of Earth and Environmental Science, University of Michigan, Ann Arbor, MI, USA
| | - David A Fike
- Department of Earth and Planetary Sciences, Washington University, Saint Louis, MO, USA
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5
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Luo H, Zhang D, Taylor M, Nguyen C, Wang ZW. Aeration in sludge holding tanks as an economical means for biosolids odor control-A case study. WATER ENVIRONMENT RESEARCH : A RESEARCH PUBLICATION OF THE WATER ENVIRONMENT FEDERATION 2021; 93:1808-1818. [PMID: 33991150 DOI: 10.1002/wer.1582] [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: 12/17/2020] [Revised: 05/02/2021] [Accepted: 05/07/2021] [Indexed: 06/12/2023]
Abstract
Abnormally high-odor detection threshold (DT) values were detected for biosolids produced at one of the water resource recovery facilities (WRRFs) of Washington Suburban Sanitary Commission. As an inexpensive countermeasure, aeration of thickened sludge holding tanks (SHTs) was tested as a solution for mitigating the subsequent biosolids odor emission. Experimental results indicated that the extremely low-oxidation reduction potential (ORP) in the SHTs and the fermentation of high-rate-activated sludge were primarily contributors to the odor emission from the dewatered cake. Two rounds of bench-scale experiments on different days confirmed that aerating the sludge in holding tanks reduced peak emission concentrations of sulfurous odorous compounds such as hydrogen sulfide (H2 S), methanethiol (MT), and dimethyl sulfide (DMS) from 203, 110, and 20 mg m-3 g-1 dry to 119, 70, and 14 mg m-3 g-1 dry, respectively. Further preliminary full-scale validation study showed that even a slight ORP improvement from -180 mV to -162 mV reduced the peak H2 S concentration from 87 to 48 mg m-3 g-1 dry and decreased the biosolids DT value from 4266 to 1862. It was concluded that lifting ORP in SHTs through aeration can be used by utilities as a simple means for biosolids odor control. PRACTITIONER POINTS: Anaerobic storage of high-rate active sludge was the main reason for the excessive biosolids odor. Aeration of sludge holding tanks can effectively reduce biosolids odor. A slight oxidation reduction potential improvement substantially reduced biosolids odor.
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Affiliation(s)
- Hao Luo
- Department of Civil and Environmental Engineering, Center for Applied Water Research and Innovation, Ashburn, VA, USA
| | - Dian Zhang
- Department of Civil and Environmental Engineering, Center for Applied Water Research and Innovation, Ashburn, VA, USA
| | - Malcolm Taylor
- Washington Suburban Sanitary Commission, Laurel, MD, USA
| | | | - Zhi-Wu Wang
- Department of Civil and Environmental Engineering, Center for Applied Water Research and Innovation, Ashburn, VA, USA
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6
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Carvalho JRS, Amaral FM, Florencio L, Kato MT, Delforno TP, Gavazza S. Microaerated UASB reactor treating textile wastewater: The core microbiome and removal of azo dye Direct Black 22. CHEMOSPHERE 2020; 242:125157. [PMID: 31698213 DOI: 10.1016/j.chemosphere.2019.125157] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 10/08/2019] [Accepted: 10/20/2019] [Indexed: 06/10/2023]
Abstract
Sequential anaerobic and aerobic processes have been recommended to treat textile wastewater reliably. In this work, the focus was on finding an energetically more competitive system to remove tetra-azo dye Direct Black 22 (DB22). We operated two upflow anaerobic sludge blanket (UASB) reactors (R1 and R2) in three phases (PI, PII, and PIII). R1 was operated as a conventional UASB, while R2 was microaerated in the upper part (0.18 ± 0.05 mg O2. L-1), aiming to remove DB22 simultaneously with the aromatic amine byproducts. PI consisted of feeding reactors with synthetic textile wastewater (STW), PII had higher salinity in the STW, and PIII was the same as PII, plus sulfate. The results showed that color and COD removal efficiencies were similar for both reactors (67-72% for R1 and 59-78% for R2) without a substantial influence of oxygen in R2. However, microaeration played a crucial role in R2 by removing the anaerobically formed aromatic amines; during PIII, the effluent was 16 times less toxic than that of R1. The microbial community that developed in the sludge bed of both reactors was quite similar, with the core microbiome represented by Trichococcus, Syntrophus and Methanosaeta genera. The increase in salinity in PII and PIII promoted a shift in the microbial community, excluding salty-sensitive genera from the core microbiome. The putative genera Brevundimonas and Ornatilinea were associated to aromatic amine microaerobic removal. Therefore, there is a potential application of a compact microaerated anaerobic system for textile wastewater treatment.
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Affiliation(s)
- J R S Carvalho
- Laboratório de Saneamento Ambiental, Departamento de Engenharia Civil, Universidade Federal de Pernambuco, Av. Acadêmico Hélio Ramos, S/n. Cidade Universitária, CEP 50740-530, Recife, PE, Brazil.
| | - F M Amaral
- Laboratório de Saneamento Ambiental, Departamento de Engenharia Civil, Universidade Federal de Pernambuco, Av. Acadêmico Hélio Ramos, S/n. Cidade Universitária, CEP 50740-530, Recife, PE, Brazil
| | - L Florencio
- Laboratório de Saneamento Ambiental, Departamento de Engenharia Civil, Universidade Federal de Pernambuco, Av. Acadêmico Hélio Ramos, S/n. Cidade Universitária, CEP 50740-530, Recife, PE, Brazil
| | - M T Kato
- Laboratório de Saneamento Ambiental, Departamento de Engenharia Civil, Universidade Federal de Pernambuco, Av. Acadêmico Hélio Ramos, S/n. Cidade Universitária, CEP 50740-530, Recife, PE, Brazil
| | - T P Delforno
- Divisão de Recursos Microbianos, Centro de Pesquisa em Química, Biologia e Agricultura (CPQBA), Universidade de Campinas - UNICAMP, Campinas, SP, CEP 13081-970, Brazil
| | - S Gavazza
- Laboratório de Saneamento Ambiental, Departamento de Engenharia Civil, Universidade Federal de Pernambuco, Av. Acadêmico Hélio Ramos, S/n. Cidade Universitária, CEP 50740-530, Recife, PE, Brazil.
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7
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Lázaro WL, Díez S, Bravo AG, da Silva CJ, Ignácio ÁRA, Guimaraes JRD. Cyanobacteria as regulators of methylmercury production in periphyton. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 668:723-729. [PMID: 30861408 DOI: 10.1016/j.scitotenv.2019.02.233] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Revised: 01/18/2019] [Accepted: 02/15/2019] [Indexed: 06/09/2023]
Abstract
Biotic mercury (Hg) methylation appears to depend on factors such as microbial activity and the concentration and bioavailability of Hg2+ to the Hg-methylating organisms. Recently, the presence of cyanobacteria has been linked with high methylmercury (MeHg) concentrations. The aim of this work was to test MeHg production in microcosms, in relation to the amount of periphytic cyanobacteria, dissolved organic matter (DOM) and phosphorus concentrations, as well as periphytic primary production rates. Water and periphyton samples were collected for cultivation and isolation of cyanobacteria from the Guaporé River floodplain, Brazil. We cultivated the periphyton in microcosms with different concentrations of cyanobacteria, total phosphorus and DOM. The highest net MeHg production (6.8 to 24.6% of added Hg d-1) occurred in the microcosm with added cyanobacteria, followed by microcosms with added phosphorus (6.1 to 11.4%) and added DOM (6.4 to 9.1%). Positive correlations were found between MeHg production, addition of cyanobacteria, phosphorus and DOM and periphytic primary productivity. Our results bring the first direct experimental evidence of the relevance of cyanobacteria and primary production as regulators of MeHg production in periphyton. These findings have numerous implications for the management of natural and engineered wetlands.
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Affiliation(s)
- Wilkinson L Lázaro
- Centro de Estudos em Limnologia Biodiversidade e Etnobiologia do Pantanal, Universidade do Estado de Mato Grosso (UNEMAT), Brasil. Avenida Santos Dummont, Cidade Universitária, 78200-000 Cáceres, MT, Brazil.
| | - Sergi Díez
- Environmental Chemistry Department, Institute of Environmental Assessment and Water Research (IDAEA-CSIC). C/Jordi Girona, 18-26, 08034 Barcelona, Spain.
| | - Andrea G Bravo
- Environmental Chemistry Department, Institute of Environmental Assessment and Water Research (IDAEA-CSIC). C/Jordi Girona, 18-26, 08034 Barcelona, Spain.
| | - Carolina J da Silva
- Centro de Estudos em Limnologia Biodiversidade e Etnobiologia do Pantanal, Universidade do Estado de Mato Grosso (UNEMAT), Brasil. Avenida Santos Dummont, Cidade Universitária, 78200-000 Cáceres, MT, Brazil; Rede Bionorte, Doutorado em Biodiversidade e Biotecnologia da Amazônia Legal. Avenida Fernando Correa da Costa, 2.367, Boa Esperança, 78060-900, Cuiabá, Brazil.
| | - Áurea R A Ignácio
- Centro de Estudos em Limnologia Biodiversidade e Etnobiologia do Pantanal, Universidade do Estado de Mato Grosso (UNEMAT), Brasil. Avenida Santos Dummont, Cidade Universitária, 78200-000 Cáceres, MT, Brazil.
| | - Jean R D Guimaraes
- Laboratório de Traçadores, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro (UFRJ). Av. Carlos Chagas Filho 373 Bloco G, CCS, Cidade Universitária, 21941-902, Rio de Janeiro, RJ, Brazil.
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8
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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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9
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Louyakis AS, Mobberley JM, Vitek BE, Visscher PT, Hagan PD, Reid RP, Kozdon R, Orland IJ, Valley JW, Planavsky NJ, Casaburi G, Foster JS. A Study of the Microbial Spatial Heterogeneity of Bahamian Thrombolites Using Molecular, Biochemical, and Stable Isotope Analyses. ASTROBIOLOGY 2017; 17:413-430. [PMID: 28520472 PMCID: PMC5767104 DOI: 10.1089/ast.2016.1563] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Thrombolites are buildups of carbonate that exhibit a clotted internal structure formed through the interactions of microbial mats and their environment. Despite recent advances, we are only beginning to understand the microbial and molecular processes associated with their formation. In this study, a spatial profile of the microbial and metabolic diversity of thrombolite-forming mats of Highborne Cay, The Bahamas, was generated by using 16S rRNA gene sequencing and predictive metagenomic analyses. These molecular-based approaches were complemented with microelectrode profiling and in situ stable isotope analysis to examine the dominant taxa and metabolic activities within the thrombolite-forming communities. Analyses revealed three distinctive zones within the thrombolite-forming mats that exhibited stratified populations of bacteria and archaea. Predictive metagenomics also revealed vertical profiles of metabolic capabilities, such as photosynthesis and carboxylic and fatty acid synthesis within the mats that had not been previously observed. The carbonate precipitates within the thrombolite-forming mats exhibited isotopic geochemical signatures suggesting that the precipitation within the Bahamian thrombolites is photosynthetically induced. Together, this study provides the first look at the spatial organization of the microbial populations within Bahamian thrombolites and enables the distribution of microbes to be correlated with their activities within modern thrombolite systems. Key Words: Thrombolites-Microbial diversity-Metagenome-Stable isotopes-Microbialites. Astrobiology 17, 413-430.
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Affiliation(s)
- Artemis S. Louyakis
- Department of Microbiology and Cell Science, University of Florida, Space Life Sciences Lab, Merritt Island, Florida
| | - Jennifer M. Mobberley
- Department of Microbiology and Cell Science, University of Florida, Space Life Sciences Lab, Merritt Island, Florida
| | - Brooke E. Vitek
- Rosenstiel School of Marine and Atmospheric Science, University of Miami, Miami, Florida
| | - Pieter T. Visscher
- Department of Marine Sciences, University of Connecticut, Groton, Connecticut
| | - Paul D. Hagan
- Rosenstiel School of Marine and Atmospheric Science, University of Miami, Miami, Florida
| | - R. Pamela Reid
- Rosenstiel School of Marine and Atmospheric Science, University of Miami, Miami, Florida
| | - Reinhard Kozdon
- Lamont-Doherty Earth Observatory, Columbia University, Palisades, New York
- Department of Geoscience, University of Wisconsin, Madison, Wisconsin
| | - Ian J. Orland
- Department of Geoscience, University of Wisconsin, Madison, Wisconsin
| | - John W. Valley
- Department of Geoscience, University of Wisconsin, Madison, Wisconsin
| | - Noah J. Planavsky
- Department of Geology and Geophysics, Yale University, New Haven, Connecticut
| | - Giorgio Casaburi
- Department of Microbiology and Cell Science, University of Florida, Space Life Sciences Lab, Merritt Island, Florida
| | - Jamie S. Foster
- Department of Microbiology and Cell Science, University of Florida, Space Life Sciences Lab, Merritt Island, Florida
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10
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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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11
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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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12
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Pagès A, Grice K, Welsh DT, Teasdale PT, Van Kranendonk MJ, Greenwood P. Lipid Biomarker and Isotopic Study of Community Distribution and Biomarker Preservation in a Laminated Microbial Mat from Shark Bay, Western Australia. MICROBIAL ECOLOGY 2015; 70:459-472. [PMID: 25812998 DOI: 10.1007/s00248-015-0598-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2014] [Accepted: 03/09/2015] [Indexed: 06/04/2023]
Abstract
Modern microbial mats from Shark Bay present some structural similarities with ancient stromatolites; thus, the functionality of microbial communities and processes of diagenetic preservation of modern mats may provide an insight into ancient microbial assemblages and preservation. In this study, the vertical distribution of microbial communities was investigated in a well-laminated smooth mat from Shark Bay. Biolipid and compound-specific isotopic analyses were performed to investigate the distribution of microbial communities in four distinct layers of the mat. Biomarkers indicative of cyanobacteria were more abundant in the uppermost oxic layer. Diatom markers (e.g. C25 HBI alkene, C20:4ω6 and C20:5ω3 polar lipid fatty acids (PLFAs)) were also detected in high abundance in the uppermost layer, but also in the deepest layer under conditions of permanent darkness and anoxia, where they probably used NO3 (-) for respiration. CycC19:0, an abundant PLFA of purple sulfur bacteria (PSB), was detected in all layers and presented the most (13)C-depleted values of all PLFAs, consistent with photoautotrophic PSB. Sulfur-bound aliphatic and aromatic biomarkers were detected in all layers, highlighting the occurrence of early sulfurisation which may be an important mechanism in the sedimentary preservation of functional biolipids in living and, thus, also ancient mats.
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Affiliation(s)
- Anais Pagès
- WA Organic and Isotope Geochemistry Centre, Department of Chemistry, The Institute for Geoscience Research, Curtin University, GPO Box U1987, Perth, Western Australia, 6845, Australia,
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A Post-Genomic View of the Ecophysiology, Catabolism and Biotechnological Relevance of Sulphate-Reducing Prokaryotes. Adv Microb Physiol 2015. [PMID: 26210106 DOI: 10.1016/bs.ampbs.2015.05.002] [Citation(s) in RCA: 174] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Dissimilatory sulphate reduction is the unifying and defining trait of sulphate-reducing prokaryotes (SRP). In their predominant habitats, sulphate-rich marine sediments, SRP have long been recognized to be major players in the carbon and sulphur cycles. Other, more recently appreciated, ecophysiological roles include activity in the deep biosphere, symbiotic relations, syntrophic associations, human microbiome/health and long-distance electron transfer. SRP include a high diversity of organisms, with large nutritional versatility and broad metabolic capacities, including anaerobic degradation of aromatic compounds and hydrocarbons. Elucidation of novel catabolic capacities as well as progress in the understanding of metabolic and regulatory networks, energy metabolism, evolutionary processes and adaptation to changing environmental conditions has greatly benefited from genomics, functional OMICS approaches and advances in genetic accessibility and biochemical studies. Important biotechnological roles of SRP range from (i) wastewater and off gas treatment, (ii) bioremediation of metals and hydrocarbons and (iii) bioelectrochemistry, to undesired impacts such as (iv) souring in oil reservoirs and other environments, and (v) corrosion of iron and concrete. Here we review recent advances in our understanding of SRPs focusing mainly on works published after 2000. The wealth of publications in this period, covering many diverse areas, is a testimony to the large environmental, biogeochemical and technological relevance of these organisms and how much the field has progressed in these years, although many important questions and applications remain to be explored.
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14
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Korneeva VA, Pimenov NV, Krek AV, Tourova TP, Bryukhanov AL. Sulfate-reducing bacterial communities in the water column of the Gdansk Deep (Baltic Sea). Microbiology (Reading) 2015. [DOI: 10.1134/s002626171502006x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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15
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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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16
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Parsons RJ, Nelson CE, Carlson CA, Denman CC, Andersson AJ, Kledzik AL, Vergin KL, McNally SP, Treusch AH, Giovannoni SJ. Marine bacterioplankton community turnover within seasonally hypoxic waters of a subtropical sound: Devil's Hole, Bermuda. Environ Microbiol 2014; 17:3481-99. [DOI: 10.1111/1462-2920.12445] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2013] [Accepted: 02/23/2014] [Indexed: 12/22/2022]
Affiliation(s)
- Rachel J. Parsons
- Bermuda Institute for Ocean Science (BIOS); St. George's GE 01 Bermuda
| | - Craig E. Nelson
- Department of Ecology, Evolution and Marine Biology; Marine Science Institute; University of California; Santa Barbara CA USA
- Center for Microbial Oceanography: Research and Education; Department of Oceanography; University of Hawai‘i at Mānoa; Honolulu HI USA
| | - Craig A. Carlson
- Bermuda Institute for Ocean Science (BIOS); St. George's GE 01 Bermuda
- Department of Ecology, Evolution and Marine Biology; Marine Science Institute; University of California; Santa Barbara CA USA
| | - Carmen C. Denman
- Department of Microbiology; Oregon State University; Corvallis OR USA
- London School of Hygiene and Tropical Medicine; London UK
| | - Andreas J. Andersson
- Bermuda Institute for Ocean Science (BIOS); St. George's GE 01 Bermuda
- Scripps Institution of Oceanography; University of California San Diego; San Diego CA USA
| | - Andrew L. Kledzik
- Department of Marine and Environmental Systems; Florida Institute of Technology; Melbourne FL USA
| | - Kevin L. Vergin
- Department of Microbiology; Oregon State University; Corvallis OR USA
| | - Sean P. McNally
- Bermuda Institute for Ocean Science (BIOS); St. George's GE 01 Bermuda
- College of the Environment and Life Sciences; The University of Rhode Island; Kingston RI USA
| | - Alexander H. Treusch
- Department of Microbiology; Oregon State University; Corvallis OR USA
- Department of Biology; Nordic Centre for Earth Evolution; University of Southern Denmark; Odense Denmark
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17
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Pagès A, Grice K, Vacher M, Welsh DT, Teasdale PR, Bennett WW, Greenwood P. Characterizing microbial communities and processes in a modern stromatolite (Shark Bay) using lipid biomarkers and two-dimensional distributions of porewater solutes. Environ Microbiol 2014; 16:2458-74. [PMID: 24428563 DOI: 10.1111/1462-2920.12378] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2013] [Accepted: 12/31/2013] [Indexed: 11/29/2022]
Abstract
Modern microbial mats are highly complex and dynamic ecosystems. Diffusive equilibration in thin films (DET) and diffusive gradients in thin films (DGT) samplers were deployed in a modern smooth microbial mat from Shark Bay in order to observe, for the first time, two-dimensional distributions of porewater solutes during day and night time. Two-dimensional sulfide and alkalinity distributions revealed a strong spatial heterogeneity and a minor contribution of sulfide to alkalinity. Phosphate distributions were also very heterogeneous, while iron(II) distributions were quite similar during day and night with a few hotspots of mobilization. Lipid biomarkers from the three successive layers of the mat were also analysed in order to characterize the microbial communities regulating analyte distributions. The major hydrocarbon products detected in all layers included n-alkanes and isoprenoids, whilst other important biomarkers included hopanoids. Phospholipid fatty acid profiles revealed a decrease in cyanobacterial markers with depth, whereas sulfate-reducing bacteria markers increased in abundance in accordance with rising sulfide concentrations with depth. Despite the general depth trends in community structure and physiochemical conditions within the mat, two-dimensional solute distributions showed considerable small-scale lateral variability, indicating that the distributions and activities of the microbial communities regulating these solute distributions were equally heterogeneous and complex.
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Affiliation(s)
- Anais Pagès
- WA Organic & Isotope Geochemistry Centre, Department of Chemistry, Curtin University, GPO Box U1987, Perth, WA, 6845, Australia
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18
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Members of the Order Thermotogales: From Microbiology to Hydrogen Production. MICROBIAL BIOENERGY: HYDROGEN PRODUCTION 2014. [DOI: 10.1007/978-94-017-8554-9_9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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19
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Zhang K, Cao X, Sheng Y, Cao H. Spatial distribution of bacterial community in EGSB reactor treating synthetic sulfate-containing wastewater at low organic loading rate. CHINESE SCIENCE BULLETIN-CHINESE 2013. [DOI: 10.1007/s11434-013-0043-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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20
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Ramel F, Amrani A, Pieulle L, Lamrabet O, Voordouw G, Seddiki N, Brèthes D, Company M, Dolla A, Brasseur G. Membrane-bound oxygen reductases of the anaerobic sulfate-reducing Desulfovibrio vulgaris Hildenborough: roles in oxygen defence and electron link with periplasmic hydrogen oxidation. MICROBIOLOGY-SGM 2013; 159:2663-2673. [PMID: 24085836 DOI: 10.1099/mic.0.071282-0] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Cytoplasmic membranes of the strictly anaerobic sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough contain two terminal oxygen reductases, a bd quinol oxidase and a cc(b/o)o3 cytochrome oxidase (Cox). Viability assays pointed out that single Δbd, Δcox and double ΔbdΔcox deletion mutant strains were more sensitive to oxygen exposure than the WT strain, showing the involvement of these oxygen reductases in the detoxification of oxygen. The Δcox strain was slightly more sensitive than the Δbd strain, pointing to the importance of the cc(b/o)o3 cytochrome oxidase in oxygen protection. Decreased O2 reduction rates were measured in mutant cells and membranes using lactate, NADH, ubiquinol and menadiol as substrates. The affinity for oxygen measured with the bd quinol oxidase (Km, 300 nM) was higher than that of the cc(b/o)o3 cytochrome oxidase (Km, 620 nM). The total membrane activity of the bd quinol oxidase was higher than that of the cytochrome oxidase activity in line with the higher expression of the bd oxidase genes. In addition, analysis of the ΔbdΔcox mutant strain indicated the presence of at least one O2-scavenging membrane-bound system able to reduce O2 with menaquinol as electron donor with an O2 affinity that was two orders of magnitude lower than that of the bd quinol oxidase. The lower O2 reductase activity in mutant cells with hydrogen as electron donor and the use of specific inhibitors indicated an electron transfer link between periplasmic H2 oxidation and membrane-bound oxygen reduction via the menaquinol pool. This linkage is crucial in defence of the strictly anaerobic bacterium Desulfovibrio against oxygen stress.
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Affiliation(s)
- F Ramel
- Laboratoire de Chimie Bactérienne, CNRS-UMR7283, 31 Chemin Joseph Aiguier, 13402 Marseille CEDEX 20, France
| | - A Amrani
- Laboratoire de Chimie Bactérienne, CNRS-UMR7283, 31 Chemin Joseph Aiguier, 13402 Marseille CEDEX 20, France
| | - L Pieulle
- Laboratoire de Chimie Bactérienne, CNRS-UMR7283, 31 Chemin Joseph Aiguier, 13402 Marseille CEDEX 20, France
| | - O Lamrabet
- Laboratoire de Chimie Bactérienne, CNRS-UMR7283, 31 Chemin Joseph Aiguier, 13402 Marseille CEDEX 20, France
| | - G Voordouw
- Petroleum Microbiology Research Group, Department of Biological Sciences, University of Calgary, 2500 University Dr. NW, Calgary T2N 1N4, AB, Canada
| | - N Seddiki
- Laboratoire de Métabolisme Énergétique Cellulaire, IBGC-CNRS, et Université Bordeaux Segalen, 1 Rue Camille Saint-Saëns, 33077 Bordeaux CEDEX, France
| | - D Brèthes
- Laboratoire de Métabolisme Énergétique Cellulaire, IBGC-CNRS, et Université Bordeaux Segalen, 1 Rue Camille Saint-Saëns, 33077 Bordeaux CEDEX, France
| | - M Company
- Laboratoire de Chimie Bactérienne, CNRS-UMR7283, 31 Chemin Joseph Aiguier, 13402 Marseille CEDEX 20, France
| | - A Dolla
- Laboratoire de Chimie Bactérienne, CNRS-UMR7283, 31 Chemin Joseph Aiguier, 13402 Marseille CEDEX 20, France
| | - G Brasseur
- Laboratoire de Chimie Bactérienne, CNRS-UMR7283, 31 Chemin Joseph Aiguier, 13402 Marseille CEDEX 20, France
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21
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Klein R, Tischler JS, Mühling M, Schlömann M. Bioremediation of mine water. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2013; 141:109-72. [PMID: 24357145 DOI: 10.1007/10_2013_265] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Caused by the oxidative dissolution of sulfide minerals, mine waters are often acidic and contaminated with high concentrations of sulfates, metals, and metalloids. Because the so-called acid mine drainage (AMD) affects the environment or poses severe problems for later use, treatment of these waters is required. Therefore, various remediation strategies have been developed to remove soluble metals and sulfates through immobilization using physical, chemical, and biological approaches. Conventionally, iron and sulfate-the main pollutants in mine waters-are removed by addition of neutralization reagents and subsequent chemical iron oxidation and sulfate mineral precipitation. Biological treatment strategies take advantage of the ability of microorganisms that occur in mine waters to metabolize iron and sulfate. As a rule, these can be grouped into oxidative and reductive processes, reflecting the redox state of mobilized iron (reduced form) and sulfur (oxidized form) in AMD. Changing the redox states of iron and sulfur results in iron and sulfur compounds with low solubility, thus leading to their precipitation and removal. Various techniques have been developed to enhance the efficacy of these microbial processes, as outlined in this review.
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Affiliation(s)
- Robert Klein
- Institute of Biosciences, TU Bergakademie Freiberg, Leipziger Str. 29, 09599, Freiberg, Germany
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22
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Adler M, Erickstad M, Gutierrez E, Groisman A. Studies of bacterial aerotaxis in a microfluidic device. LAB ON A CHIP 2012; 12:4835-47. [PMID: 23010909 PMCID: PMC3520485 DOI: 10.1039/c2lc21006a] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Aerotaxis, the directional motion of bacteria in gradients of oxygen, was discovered in the late 19th century and has since been reported in a variety of bacterial species. Nevertheless, quantitative studies of aerotaxis have been complicated by the lack of tools for generation of stable gradients of oxygen concentration, [O(2)]. Here we report a series of experiments on aerotaxis of Escherichia coli in a specially built experimental setup consisting of a computer-controlled gas mixer and a two-layer microfluidic device made of polydimethylsiloxane (PDMS). The setup enables generation of a variety of stable linear profiles of [O(2)] across a long gradient channel, with characteristic [O(2)] ranging from aerobic to microaerobic conditions. A suspension of E. coli cells is perfused through the gradient channel at a low speed, allowing cells enough time to explore the [O(2)] gradient, and the distribution of cells across the gradient channel is analyzed near the channel outlet at a throughput of >10(5) cells per hour. Aerotaxis experiments are performed in [O(2)] gradients with identical logarithmic slopes and varying mean concentrations, as well as in gradients with identical mean concentrations and varying slopes. Experiments in gradients with [O(2)] ranging from 0 to ~11.5% indicate that, in contrast to some previous reports, E. coli cells do not congregate at some intermediate level of [O(2)], but rather prefer the highest accessible [O(2)]. The presented technology can be applied to studies of aerotaxis of other aerobic and microaerobic bacteria.
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Affiliation(s)
- Micha Adler
- Department of Physics, University of California, San Diego, 9500 Gilman Drive, MC 0374, La Jolla, CA, 92093, USA
| | - Michael Erickstad
- Department of Physics, University of California, San Diego, 9500 Gilman Drive, MC 0374, La Jolla, CA, 92093, USA
| | - Edgar Gutierrez
- Department of Physics, University of California, San Diego, 9500 Gilman Drive, MC 0374, La Jolla, CA, 92093, USA
| | - Alex Groisman
- Department of Physics, University of California, San Diego, 9500 Gilman Drive, MC 0374, La Jolla, CA, 92093, USA
- Corresponding author,
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23
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Giloteaux L, Duran R, Casiot C, Bruneel O, Elbaz-Poulichet F, Goñi-Urriza M. Three-year survey of sulfate-reducing bacteria community structure in Carnoulès acid mine drainage (France), highly contaminated by arsenic. FEMS Microbiol Ecol 2012; 83:724-37. [PMID: 23057444 DOI: 10.1111/1574-6941.12028] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2012] [Revised: 09/27/2012] [Accepted: 10/03/2012] [Indexed: 11/29/2022] Open
Abstract
A 3-year survey on sulfate-reducing bacteria (SRB) was conducted in the waters of the arsenic-rich acid mine drainage (AMD) located at Carnoulès (France) to determine the influence of environmental parameters on their community structure. The source (S5 station) exhibited most extreme conditions with pH lowering to ~1.2; iron, sulfate, and arsenic concentrations reaching 6843, 29 593, and 638 mg L(-1), respectively. The conditions were less extreme at the downstream stations S1 (pH ~3.7; iron, sulfate, and arsenic concentrations of 1114, 4207, and 167 mg L(-1), respectively) and COWG (pH ~3.4; iron, sulfate, and arsenic concentrations of 854, 3134, and 110 mg L(-1), respectively). SRB community structures were characterized by terminal restriction fragment length polymorphism and library analyses based on dsrAB genes. The predominant dsrAB sequences detected were most similar to the family Desulfobulbaceae. Additionally, certain phylotypes could be related to spatio-temporal fluctuations of pH, iron, and arsenic species. For example, Desulfohalobiaceae-related sequences were detected at the most acidic sample (pH 1.4) with high iron and arsenic concentrations (6379 and 524 mg L(-1), respectively). New dsrAB sequences, with no isolated representatives, were found exclusively in COWG. This study gives new insights on SRB community dynamics in AMD systems.
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Affiliation(s)
- Ludovic Giloteaux
- Equipe Environnement et Microbiologie - UMR IPREM5254, Université de Pau et des Pays de l'Adour, Pau Cedex, France
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24
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Gallagher KL, Kading TJ, Braissant O, Dupraz C, Visscher PT. Inside the alkalinity engine: the role of electron donors in the organomineralization potential of sulfate-reducing bacteria. GEOBIOLOGY 2012; 10:518-530. [PMID: 22925453 DOI: 10.1111/j.1472-4669.2012.00342.x] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2012] [Accepted: 07/19/2012] [Indexed: 06/01/2023]
Abstract
Mineral precipitation in microbial mats may have been the key to their preservation as fossil stromatolites, potentially documenting evidence of the earliest life on Earth. Two factors that contribute to carbonate mineral precipitation are the saturation index (SI) and the presence of nucleation sites. Both of these can be influenced by micro-organisms, which can either alter SI through their metabolisms, or produce and consume organic substances such as extracellular polymeric substances (EPS) that can affect nucleation. It is the balance of individual metabolisms within the mat community that determines the pH and the dissolved inorganic carbon concentration, thereby potentially increasing the alkalinity and consequently the SI. Sulfate-reducing bacteria (SRB) are an important component of this 'alkalinity engine.' The activity of SRB often peaks in layers where CaCO(3) precipitates, and mineral precipitation has been demonstrated in SRB cultures; however, the effect of their metabolism on the alkalinity engine and actual contribution to mineral precipitation is the subject of controversy. Here, we show through culture experiments, theoretical calculations, and geochemical modeling studies that the pH, alkalinity, and organomineralization potential will vary depending on the type of electron donor. Specifically, hydrogen and formate can increase the pH, but electron donors like lactate and ethanol, and to a lesser extent glycolate, decrease the pH. The implication of this for the lithification of mats is that the combination of processes supplying electron donors and the utilization of these compounds by SRB may be critical to promoting mineral precipitation.
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Affiliation(s)
- K L Gallagher
- Department of Marine Sciences, University of Connecticut, Groton, CT, USA
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25
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Bolhuis H, Stal LJ. Analysis of bacterial and archaeal diversity in coastal microbial mats using massive parallel 16S rRNA gene tag sequencing. THE ISME JOURNAL 2011; 5:1701-12. [PMID: 21544102 PMCID: PMC3197164 DOI: 10.1038/ismej.2011.52] [Citation(s) in RCA: 97] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2010] [Revised: 03/14/2011] [Accepted: 03/24/2011] [Indexed: 11/08/2022]
Abstract
Coastal microbial mats are small-scale and largely closed ecosystems in which a plethora of different functional groups of microorganisms are responsible for the biogeochemical cycling of the elements. Coastal microbial mats play an important role in coastal protection and morphodynamics through stabilization of the sediments and by initiating the development of salt-marshes. Little is known about the bacterial and especially archaeal diversity and how it contributes to the ecological functioning of coastal microbial mats. Here, we analyzed three different types of coastal microbial mats that are located along a tidal gradient and can be characterized as marine (ST2), brackish (ST3) and freshwater (ST3) systems. The mats were sampled during three different seasons and subjected to massive parallel tag sequencing of the V6 region of the 16S rRNA genes of Bacteria and Archaea. Sequence analysis revealed that the mats are among the most diverse marine ecosystems studied so far and consist of several novel taxonomic levels ranging from classes to species. The diversity between the different mat types was far more pronounced than the changes between the different seasons at one location. The archaeal community for these mats have not been studied before and revealed a strong reaction on a short period of draught during summer resulting in a massive increase in halobacterial sequences, whereas the bacterial community was barely affected. We concluded that the community composition and the microbial diversity were intrinsic of the mat type and depend on the location along the tidal gradient indicating a relation with salinity.
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Affiliation(s)
- Henk Bolhuis
- Department of Marine Microbiology, Centre for Estuarine and Marine Ecology (NIOO-KNAW), Yerseke, The Netherlands.
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Sánchez-Andrea I, Rodríguez N, Amils R, Sanz JL. Microbial diversity in anaerobic sediments at Rio Tinto, a naturally acidic environment with a high heavy metal content. Appl Environ Microbiol 2011; 77:6085-93. [PMID: 21724883 PMCID: PMC3165421 DOI: 10.1128/aem.00654-11] [Citation(s) in RCA: 115] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2011] [Accepted: 06/24/2011] [Indexed: 11/20/2022] Open
Abstract
The Tinto River is an extreme environment located at the core of the Iberian Pyritic Belt (IPB). It is an unusual ecosystem due to its size (100 km long), constant acidic pH (mean pH, 2.3), and high concentration of heavy metals, iron, and sulfate in its waters, characteristics that make the Tinto River Basin comparable to acidic mine drainage (AMD) systems. In this paper we present an extensive survey of the Tinto River sediment microbiota using two culture-independent approaches: denaturing gradient gel electrophoresis and cloning of 16S rRNA genes. The taxonomic affiliation of the Bacteria showed a high degree of biodiversity, falling into 5 different phyla: Proteobacteria, Firmicutes, Bacteroidetes, Acidobacteria, and Actinobacteria; meanwhile, all the Archaea were affiliated with the order Thermoplasmatales. Microorganisms involved in the iron (Acidithiobacillus ferrooxidans, Sulfobacillus spp., Ferroplasma spp., etc.), sulfur (Desulfurella spp., Desulfosporosinus spp., Thermodesulfobium spp., etc.), and carbon (Acidiphilium spp., Bacillus spp., Clostridium spp., Acidobacterium spp., etc.) cycles were identified, and their distribution was correlated with physicochemical parameters of the sediments. Ferric iron was the main electron acceptor for the oxidation of organic matter in the most acid and oxidizing layers, so acidophilic facultative Fe(III)-reducing bacteria appeared widely in the clone libraries. With increasing pH, the solubility of iron decreases and sulfate-reducing bacteria become dominant, with the ecological role of methanogens being insignificant. Considering the identified microorganisms-which, according to the rarefaction curves and Good's coverage values, cover almost all of the diversity-and their corresponding metabolism, we suggest a model of the iron, sulfur, and organic matter cycles in AMD-related sediments.
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MESH Headings
- Archaea/classification
- Archaea/genetics
- Bacteria/classification
- Bacteria/genetics
- Biodiversity
- Cloning, Molecular
- Cluster Analysis
- DNA, Archaeal/chemistry
- DNA, Archaeal/genetics
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/genetics
- Denaturing Gradient Gel Electrophoresis
- Genes, rRNA
- Geologic Sediments/microbiology
- Molecular Sequence Data
- Phylogeny
- RNA, Archaeal/genetics
- RNA, Bacterial/genetics
- RNA, Ribosomal, 16S/genetics
- Rivers
- Sequence Analysis, DNA
- Sequence Homology, Nucleic Acid
- Spain
- Water Microbiology
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Affiliation(s)
- Irene Sánchez-Andrea
- Universidad Autónoma de Madrid, Departamento de Biología Molecular, 28049 Madrid, Spain
- Centro de Biología Molecular Severo Ochoa, UAM-CSIC, 28049 Madrid, Spain
| | - Nuria Rodríguez
- Centro de Astrobiología, INTA-CSIC, Ctra. Ajalvir-Torrejón de Ardoz, 28850 Madrid, Spain
| | - Ricardo Amils
- Universidad Autónoma de Madrid, Departamento de Biología Molecular, 28049 Madrid, Spain
- Centro de Biología Molecular Severo Ochoa, UAM-CSIC, 28049 Madrid, Spain
- Centro de Astrobiología, INTA-CSIC, Ctra. Ajalvir-Torrejón de Ardoz, 28850 Madrid, Spain
| | - José Luis Sanz
- Universidad Autónoma de Madrid, Departamento de Biología Molecular, 28049 Madrid, Spain
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Oxygen uptake rates in the hyperthermophilic anaerobe Thermotoga maritima grown in a bioreactor under controlled oxygen exposure: clues to its defence strategy against oxidative stress. Arch Microbiol 2011; 193:429-38. [PMID: 21400100 DOI: 10.1007/s00203-011-0687-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2010] [Revised: 01/12/2011] [Accepted: 02/17/2011] [Indexed: 10/18/2022]
Abstract
A 2.3-L bioreactor was specially adapted to grow hyperthermophilic microorganisms under controlled conditions of temperature, pH, redox potential and dissolved O(2). Using this bioreactor regulated at 80°C and pH 7.0, we demonstrated that Thermotoga maritima recovered its growth despite being exposed to oxygen for a short time (30 min with a maximum concentration of 23 μM of dissolved oxygen). Under these conditions, we demonstrated that O(2) uptake rate, estimated at 73.6 μmoles O(2) min(-1) g proteins(-1) for dissolved oxygen, was optimal and constant, when dissolved oxygen was present in a range of 22-5 μM. Transcription analyses revealed that during short oxygen exposure, T. maritima expressed genes coding for enzymes to deal with O(2) and reactive oxygen species (ROS) such as peroxides. Thus, genes encoding ROS-scavenging systems, alkyl hydroperoxide reductase (ahp), thioredoxin-dependent thiol peroxidase (bcp 2) and to a lesser extent neelaredoxin (nlr) and rubrerythrin (rbr), were found to be upregulated during oxygen exposure. The oxygen reductase FprA, homologous to the rubredoxin-oxygen oxidoreductase (ROO) found in Desulfovibrio species, is proposed as a primary consumer of O(2) in T. maritima. Moreover, the expression of frpA was shown to depend on the redox (Eh) level of the culture medium.
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The Role of Sulfate Reduction in Stromatolites and Microbial Mats: Ancient and Modern Perspectives. ACTA ACUST UNITED AC 2011. [DOI: 10.1007/978-94-007-0397-1_25] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/19/2023]
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Thomas SH, Sanford RA, Amos BK, Leigh MB, Cardenas E, Löffler FE. Unique ecophysiology among U(VI)-reducing bacteria as revealed by evaluation of oxygen metabolism in Anaeromyxobacter dehalogenans strain 2CP-C. Appl Environ Microbiol 2010; 76:176-83. [PMID: 19897758 PMCID: PMC2798628 DOI: 10.1128/aem.01854-09] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2009] [Accepted: 11/02/2009] [Indexed: 11/20/2022] Open
Abstract
Anaeromyxobacter spp. respire soluble hexavalent uranium, U(VI), leading to the formation of insoluble U(IV), and are present at the uranium-contaminated Oak Ridge Integrated Field Research Challenge (IFC) site. Pilot-scale in situ bioreduction of U(VI) has been accomplished in area 3 of the Oak Ridge IFC site following biostimulation, but the susceptibility of the reduced material to oxidants (i.e., oxygen) compromises long-term U immobilization. Following oxygen intrusion, attached Anaeromyxobacter dehalogenans cells increased approximately 5-fold from 2.2x10(7)+/-8.6x10(6) to 1.0x10(8)+/-2.2x10(7) cells per g of sediment collected from well FW101-2. In the same samples, the numbers of cells of Geobacter lovleyi, a population native to area 3 and also capable of U(VI) reduction, decreased or did not change. A. dehalogenans cells captured via groundwater sampling (i.e., not attached to sediment) were present in much lower numbers (<1.3x10(4)+/-1.1x10(4) cells per liter) than sediment-associated cells, suggesting that A. dehalogenans cells occur predominantly in association with soil particles. Laboratory studies confirmed aerobic growth of A. dehalogenans strain 2CP-C at initial oxygen partial pressures (pO2) at and below 0.18 atm. A negative linear correlation [micro=(-0.09xpO2)+0.051; R2=0.923] was observed between the instantaneous specific growth rate micro and pO2, indicating that this organism should be classified as a microaerophile. Quantification of cells during aerobic growth revealed that the fraction of electrons released in electron donor oxidation and used for biomass production (fs) decreased from 0.52 at a pO2 of 0.02 atm to 0.19 at a pO2 of 0.18 atm. Hence, the apparent fraction of electrons utilized for energy generation (i.e., oxygen reduction) (fe) increased from 0.48 to 0.81 with increasing pO2, suggesting that oxygen is consumed in a nonrespiratory process at a high pO2. The ability to tolerate high oxygen concentrations, perform microaerophilic oxygen respiration, and preferentially associate with soil particles represents an ecophysiology that distinguishes A. dehalogenans from other known U(VI)-reducing bacteria in area 3, and these features may play roles for stabilizing immobilized radionuclides in situ.
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Affiliation(s)
- Sara H. Thomas
- School of Civil and Environmental Engineering, School of Biology, Georgia Institute of Technology, Atlanta, Georgia 30332-0512, Department of Geology, University of Illinois, Urbana, Illinois 61801-2352, Department of Biology and Wildlife and Institute of Arctic Biology, University of Alaska, Fairbanks, Alaska 99775, Center for Microbial Ecology, Michigan State University, East Lansing, Michigan 48824
| | - Robert A. Sanford
- School of Civil and Environmental Engineering, School of Biology, Georgia Institute of Technology, Atlanta, Georgia 30332-0512, Department of Geology, University of Illinois, Urbana, Illinois 61801-2352, Department of Biology and Wildlife and Institute of Arctic Biology, University of Alaska, Fairbanks, Alaska 99775, Center for Microbial Ecology, Michigan State University, East Lansing, Michigan 48824
| | - Benjamin K. Amos
- School of Civil and Environmental Engineering, School of Biology, Georgia Institute of Technology, Atlanta, Georgia 30332-0512, Department of Geology, University of Illinois, Urbana, Illinois 61801-2352, Department of Biology and Wildlife and Institute of Arctic Biology, University of Alaska, Fairbanks, Alaska 99775, Center for Microbial Ecology, Michigan State University, East Lansing, Michigan 48824
| | - Mary Beth Leigh
- School of Civil and Environmental Engineering, School of Biology, Georgia Institute of Technology, Atlanta, Georgia 30332-0512, Department of Geology, University of Illinois, Urbana, Illinois 61801-2352, Department of Biology and Wildlife and Institute of Arctic Biology, University of Alaska, Fairbanks, Alaska 99775, Center for Microbial Ecology, Michigan State University, East Lansing, Michigan 48824
| | - Erick Cardenas
- School of Civil and Environmental Engineering, School of Biology, Georgia Institute of Technology, Atlanta, Georgia 30332-0512, Department of Geology, University of Illinois, Urbana, Illinois 61801-2352, Department of Biology and Wildlife and Institute of Arctic Biology, University of Alaska, Fairbanks, Alaska 99775, Center for Microbial Ecology, Michigan State University, East Lansing, Michigan 48824
| | - Frank E. Löffler
- School of Civil and Environmental Engineering, School of Biology, Georgia Institute of Technology, Atlanta, Georgia 30332-0512, Department of Geology, University of Illinois, Urbana, Illinois 61801-2352, Department of Biology and Wildlife and Institute of Arctic Biology, University of Alaska, Fairbanks, Alaska 99775, Center for Microbial Ecology, Michigan State University, East Lansing, Michigan 48824
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Kjellerup BV, Kjeldsen KU, Lopes F, Abildgaard L, Ingvorsen K, Frølund B, Sowers KR, Nielsen PH. Biocorrosion and biofilm formation in a nutrient limited heating system subjected to alternating microaerophilic conditions. BIOFOULING 2009; 25:727-737. [PMID: 20183131 DOI: 10.1080/08927010903114611] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Severe biofilm formation and biocorrosion have been observed in heating systems even when the water quality complied with existing standards. The coupling between water chemistry, biofilm formation, species composition, and biocorrosion in a heating system was investigated by adding low concentrations of nutrients and oxygen under continuous and alternating dosing regimes. Molecular analysis of 16S rRNA gene fragments demonstrated that the amendments did not cause changes in the overall bacterial community composition. The combined alternating dosing of nutrients and oxygen caused increased rates of pitting (bio-) corrosion. Detection of bacteria involved in sulfide production and oxidation by retrieval of the functional dsrAB and apsA genes revealed the presence of Gram-positive sulfate- and sulfite-reducers and an unknown sulfur-oxidizer. Therefore, to control biocorrosion, sources of oxygen and nutrients must be limited, since the effect of the alternating operational conditions apparently is more important than the presence of potentially corrosive biofilm bacteria.
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Affiliation(s)
- B V Kjellerup
- Department of Biotechnology, Chemistry and Environmental Engineering, Aalborg University, Denmark.
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31
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Bühring SI, Smittenberg RH, Sachse D, Lipp JS, Golubic S, Sachs JP, Hinrichs KU, Summons RE. A hypersaline microbial mat from the Pacific Atoll Kiritimati: insights into composition and carbon fixation using biomarker analyses and a 13C-labeling approach. GEOBIOLOGY 2009; 7:308-323. [PMID: 19476506 DOI: 10.1111/j.1472-4669.2009.00198.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Modern microbial mats are widely recognized as useful analogs for the study of biogeochemical processes relevant to paleoenvironmental reconstruction in the Precambrian. We combined microscopic observations and investigations of biomarker composition to investigate community structure and function in the upper layers of a thick phototrophic microbial mat system from a hypersaline lake on Kiritimati (Christmas Island) in the Northern Line Islands, Republic of Kiribati. In particular, an exploratory incubation experiment with (13)C-labeled bicarbonate was conducted to pinpoint biomarkers from organisms actively fixing carbon. A high relative abundance of the cyanobacterial taxa Aphanocapsa and Aphanothece was revealed by microscopic observation, and cyanobacterial fatty acids and hydrocarbons showed (13)C-uptake in the labeling experiment. Microscopic observations also revealed purple sulfur bacteria (PSB) in the deeper layers. A cyclic C(19:0) fatty acid and farnesol were attributed to this group that was also actively fixing carbon. Background isotopic values indicate Calvin-Benson cycle-based autotrophy for cycC(19:0) and farnesol-producing PSBs. Biomarkers from sulfate-reducing bacteria (SRB) in the top layer of the mat and their (13)C-uptake patterns indicated a close coupling between SRBs and cyanobacteria. Archaeol, possibly from methanogens, was detected in all layers and was especially abundant near the surface where it contained substantial amounts of (13)C-label. Intact glycosidic tetraether lipids detected in the deepest layer indicated other archaea. Large amounts of ornithine and betaine bearing intact polar lipids could be an indicator of a phosphate-limited ecosystem, where organisms that are able to substitute these for phospholipids may have a competitive advantage.
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Affiliation(s)
- S I Bühring
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA.
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32
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Mouser PJ, Holmes DE, Perpetua LA, DiDonato R, Postier B, Liu A, Lovley DR. Quantifying expression of Geobacter spp. oxidative stress genes in pure culture and during in situ uranium bioremediation. ISME JOURNAL 2009; 3:454-65. [PMID: 19129865 DOI: 10.1038/ismej.2008.126] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
As part of an effort to diagnose the physiological status of Geobacter species during in situ bioremediation of uranium-contaminated groundwater, transcript levels for two genes potentially associated with oxidative stress, cydA and sodA, were quantified throughout a bioremediation field study in Rifle, CO, USA. Despite the accumulation of Fe(II) in the groundwater, which is inconsistent with the presence of dissolved oxygen, both genes were highly expressed during the bioremediation process. Therefore, the response to oxidative stress was further evaluated with Geobacter uraniireducens, an isolate from the Rifle site. When G. uraniireducens cultured with fumarate as the electron acceptor was exposed to 5% oxygen for 8 h, there was a significant increase in cydA and sodA transcripts as well as other genes associated with oxygen respiration or oxidative stress. Oxygen-exposed cells had lower transcript abundance for genes associated with anaerobic respiration, metabolism and motility. Short-term oxygen exposure had little impact on cydA transcript levels, as more than 1 h was required for increases to levels comparable to the subsurface. Abundance of cydA and sodA transcripts for the isolate G. sulfurreducens were always higher in cells cultured with Fe(III) compared with fumarate as an electron acceptor, even when fumarate-grown cells were exposed to oxygen, and Fe(III)-grown cells were grown anaerobically. These results suggest that the apparently high Geobacter cydA and sodA expression during bioremediation cannot necessarily be attributed to oxidative stress and demonstrate that diagnosis of the metabolic status of subsurface microorganisms through transcript analysis should be coupled with appropriate geochemical analyses.
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Affiliation(s)
- Paula J Mouser
- Department of Microbiology, University of Massachusetts, Amherst, MA, USA.
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33
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Tiquia SM. Diversity of sulfate-reducing genes (dsrAB) in sediments from Puget Sound. ENVIRONMENTAL TECHNOLOGY 2008; 29:1095-1108. [PMID: 18942577 DOI: 10.1080/09593330802190608] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
The aims of this study were to characterize the population structure and diversity of sulfate-reducing bacteria (SRB) from three distinct sites at Puget Sound, and relate the biogeochemical properties of the sediments to the sulfate-reducer communities. The population composition and diversity of sulfate-reducing bacteria carrying dsrAB genes from surface Puget Sound sediments was investigated using a polymerase chain reaction-based cloning approach. Sediment cores were collected from three different locations: Carr Inlet (C1A), Shallow Bud Inlet (S1A), and Turning Basin (T1A). A total of 498 dsrAB clones were sequenced from the three sites. Ecological indices indicated that T1A had the highest diversity and evenness values and C1A had the lowest. Correlations were also found between diversity indices and geochemical parameters. The diversity of the SRB decreased with decreasing carbon concentrations and sulfate reduction rates, and increasing levels of oxygen. A phylogenetic comparison revealed that the majority of the dsrAB sequences were associated with the delta-proteobacterial phylotypes Desulfonema, Desulfococcus and Desulfosarcina, suggesting that complete oxidizers with high substrate versatility dominate in the sediments. The environmental conditions and energy sources available in the sediments may have dictated microbial community structure and diversity of SRBs. Distinctive community structures of SRBs in Puget Sound sediments were found to vary at different sites with different redox profiles. The dominance of the Desulfobacteraceae-like sequences may be due to the presence of a diverse spectrum of substrates in the sediments. This study represents one of the first efforts to characterize the population of sulfate-reducing microbes in the oxygenated regions of Puget Sound sediments. The phylogenetic identification of dsrAB genes in the sediment samples allows the composition of sulfate-reducing prokaryotic communities to be inferred, and working hypotheses about their likely carbon substrates to be formed.
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Affiliation(s)
- S M Tiquia
- Department of Natural Sciences, 115F Science Building, The University of Michigan, Dearborn, MI 48128, USA
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Fourçans A, Ranchou-Peyruse A, Caumette P, Duran R. Molecular analysis of the spatio-temporal distribution of sulfate-reducing bacteria (SRB) in Camargue (France) hypersaline microbial mat. MICROBIAL ECOLOGY 2008; 56:90-100. [PMID: 17952491 DOI: 10.1007/s00248-007-9327-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2007] [Revised: 08/24/2007] [Accepted: 09/25/2007] [Indexed: 05/25/2023]
Abstract
The spatio-temporal distribution of sulfate-reducing bacteria (SRB) in the microbial mat of Camargue (Salins-de-Giraud, France) was investigated by molecular approaches at both microscale spatial resolution and different taxonomic organization levels. The vertical distribution of the SRB populations was correlated with oxygen and sulfide microgradient fluctuations. Comparisons of Terminal restriction fragment length polymorphism (T-RFLP) fingerprints showed distinct locations of some operational taxonomic units at daytime and at night (4:00 or 15:00 hours) revealing important differences on the structures of the bacterial communities. When oxygen penetrates the mat, SRB migration was observed either downward to reach deeper anoxic zones to escape oxygen or upward to reach oxic surface zones. When no migration was observed, both metabolism switches and aggregate formations were suspected. These behaviors allowed the aerotolerant SRB to deal with oxygen. The analysis of the Desulfococcus-Desulfonema-Desulfosarcina T-RFLP profiles revealed up-migrating populations related to both Desulfonema sp. and Desulfosarcina variabilis. T-RFLP profiles combined with 16S ribosomal ribonucleic acid gene library analysis of the Desulfobacter group revealed two distinct populations: a population related to the recently described Desulfotignum genus migrating upward during the night and a population of a new species of the Desulfobacter uniformly located throughout the mat independent of the period. Thus, the identification of the new oxygen-tolerant SRB will provide the basis for understanding the physiological adaptations to oxygen.
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Affiliation(s)
- Aude Fourçans
- Laboratoire de Génomique des Archaea, Institut de Génétique et Microbiologie, UMR CNRS 8621, Université Paris Sud XI, Bât 400, 91405 Orsay Cedex, France
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Quantitative microbial community analysis of three different sulfidic mine tailing dumps generating acid mine drainage. Appl Environ Microbiol 2008; 74:5211-9. [PMID: 18586975 DOI: 10.1128/aem.00649-08] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The microbial communities of three different sulfidic and acidic mine waste tailing dumps located in Botswana, Germany, and Sweden were quantitatively analyzed using quantitative real-time PCR (Q-PCR), fluorescence in situ hybridization (FISH), catalyzed reporter deposition-FISH (CARD-FISH), Sybr green II direct counting, and the most probable number (MPN) cultivation technique. Depth profiles of cell numbers showed that the compositions of the microbial communities are greatly different at the three sites and also strongly varied between zones of oxidized and unoxidized tailings. Maximum cell numbers of up to 10(9) cells g(-1) dry weight were determined in the pyrite or pyrrhotite oxidation zones, whereas cell numbers in unoxidized tailings were significantly lower. Bacteria dominated over Archaea and Eukarya at all tailing sites. The acidophilic Fe(II)- and/or sulfur-oxidizing Acidithiobacillus spp. dominated over the acidophilic Fe(II)-oxidizing Leptospirillum spp. among the Bacteria at two sites. The two genera were equally abundant at the third site. The acidophilic Fe(II)- and sulfur-oxidizing Sulfobacillus spp. were generally less abundant. The acidophilic Fe(III)-reducing Acidiphilium spp. could be found at only one site. The neutrophilic Fe(III)-reducing Geobacteraceae as well as the dsrA gene of sulfate reducers were quantifiable at all three sites. FISH analysis provided reliable data only for tailing zones with high microbial activity, whereas CARD-FISH, Q-PCR, Sybr green II staining, and MPN were suitable methods for a quantitative microbial community analysis of tailings in general.
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Kremer B, Kazmierczak J, Stal LJ. Calcium carbonate precipitation in cyanobacterial mats from sandy tidal flats of the North Sea. GEOBIOLOGY 2008; 6:46-56. [PMID: 18380885 DOI: 10.1111/j.1472-4669.2007.00128.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Precipitated calcium carbonate was found in annual cyanobacterial mats developing on the beaches of the North Sea barrier island Schiermonnikoog (the Netherlands). A variety of different calcium carbonate morphs were found in the cyanobacterial mucous secretions and identified by light- and scanning electron microscopy and X-ray diffraction. Most of the calcium carbonate seemed to be associated with degrading extracellular polymer. It is conceived that supersaturation of calcium carbonate resulted from the periodic evaporation of the mats and from the release of calcium from the cyanobacterial mucous as a result of its degradation. The analysis of the carbon stable isotopic composition of the calcium carbonate showed only a slight depletion of (13)C, indicating that it did not in major part originated from the decomposition of organic matter. The delta(18)O values of the calcium carbonate confirmed the temperature differences between spring and summer but excluded the possibility that excessive evaporative events controlled precipitation. The precipitation of calcium carbonate could represent a potential factor enhancing the stabilization of intertidal siliciclastic sediments through cementing the sand. The discovery of massive calcium carbonate precipitation in these cyanobacterial mats was unexpected and hitherto unknown.
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Affiliation(s)
- B Kremer
- Institute of Palaeobiology, Polish Academy of Sciences, Twarda 51/55, Warszawa 00-818, Poland.
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37
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Pereira PM, He Q, Xavier AV, Zhou J, Pereira IAC, Louro RO. Transcriptional response of Desulfovibrio vulgaris Hildenborough to oxidative stress mimicking environmental conditions. Arch Microbiol 2007; 189:451-61. [PMID: 18060664 DOI: 10.1007/s00203-007-0335-5] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2007] [Revised: 11/16/2007] [Accepted: 11/20/2007] [Indexed: 12/31/2022]
Abstract
Sulfate-reducing bacteria (SRB) are anaerobes readily found in oxic-anoxic interfaces. Multiple defense pathways against oxidative conditions were identified in these organisms and proposed to be differentially expressed under different concentrations of oxygen, contributing to their ability to survive oxic conditions. In this study, Desulfovibrio vulgaris Hildenborough cells were exposed to the highest concentration of oxygen that SRB are likely to encounter in natural habitats, and the global transcriptomic response was determined. Three hundred and seven genes were responsive, with cellular roles in energy metabolism, protein fate, cell envelope and regulatory functions, including multiple genes encoding heat shock proteins, peptidases and proteins with heat shock promoters. Of the oxygen reducing mechanisms of D. vulgaris only the periplasmic hydrogen-dependent mechanism was up-regulated, involving the [NiFeSe] hydrogenase, formate dehydrogenase(s) and the Hmc membrane complex. The oxidative defense response concentrated on damage repair by metal-free enzymes. These data, together with the down-regulation of the ferric uptake regulator operon, which restricts the availability of iron, and the lack of response of the peroxide-sensing regulator operon, suggest that a major effect of this oxygen stress is the inactivation and/or degradation of multiple metalloproteins present in D. vulgaris as a consequence of oxidative damage to their metal clusters.
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Affiliation(s)
- Patrícia M Pereira
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Lisbon, Portugal
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Brioukhanov AL, Netrusov AI. Aerotolerance of strictly anaerobic microorganisms and factors of defense against oxidative stress: A review. APPL BIOCHEM MICRO+ 2007. [DOI: 10.1134/s0003683807060014] [Citation(s) in RCA: 75] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Schmalenberger A, Drake HL, Küsel K. High unique diversity of sulfate-reducing prokaryotes characterized in a depth gradient in an acidic fen. Environ Microbiol 2007; 9:1317-28. [PMID: 17472643 DOI: 10.1111/j.1462-2920.2007.01251.x] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The dissimilatory reduction of sulfate contributes to the retention of sulfur in acidic mineratrophic peatlands. Novel sulfate-reducing prokaryotes (SRPs) colonize these low-sulfate fens. This study assessed the community structures of SRPs in a depth gradient (0-50 cm) in a fen, located in the Fichtelgebirge (Spruce Mountains), Germany. Detection of SRPs with multiplex (terminal-) restriction fragment length polymorphism analysis of amplified dissimilatory (bi)sulfite reductase genes (dsrAB) separated three subgroups derived from (i) the upper 5 and 10 cm, (ii) 15-25 cm, and (iii) 30-50 cm depth. Biogeochemical parameters measured in the soil solution from July 2001 to July 2004 documented that the upper 5-10 cm were exposed to drying and oxygenation prior to sampling. Periodic oxygenation reached a maximum depth of 25 cm in the water-saturated fen and was concomitant with relative high concentrations of nitrate (120 microM) and sulfate (up to 310 microM). The fen soil was permanently anoxic below 30 cm depth with average concentrations of sulfate below 40 microM and maximum concentrations of methane. Cloning of dsrAB PCR products from 5, 20 and 40 cm depth yielded a total of 84 unique dsrAB restriction patterns. Partial sequencing of 61 distinct clones resulted in 59 unique partial protein sequences that mainly clustered with DsrA sequences of uncultivated sulfate reducers. Syntrophobacter fumaroxidans- and Syntrophobacter wolinii-related bacteria appeared to be present only in 40 cm depth. Differences in the SRP community structures suggested that SRPs present in the upper fen soil have to tolerate O(2) and even drying, whereas SRPs present in deep anoxic zones may act as syntrophic fermentors in cooperation with H(2)-utilizing methanogens.
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Affiliation(s)
- Achim Schmalenberger
- Department of Ecological Microbiology, University of Bayreuth, Bayreuth 95440, Germany
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Fourçans A, Solé A, Diestra E, Ranchou-Peyruse A, Esteve I, Caumette P, Duran R. Vertical migration of phototrophic bacterial populations in a hypersaline microbial mat from Salins-de-Giraud (Camargue, France). FEMS Microbiol Ecol 2006; 57:367-77. [PMID: 16907751 DOI: 10.1111/j.1574-6941.2006.00124.x] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
The spatio-temporal distribution of phototrophic communities of the hypersaline photosynthetic Camarguc microbial mat (Salins-de-Giraud, France) was investigated over a diel cycle by combining microscopic and molecular approaches. Microcoleus chthonoplastes and Halomicronema excentricum, the dominant cyanobacteria of this oxyphotrophic community, were observed with confocal laser scanning microscopy to determine their biomass profiles. Both bacteria have similar vertical distributions, varying from a homogenous distribution through the mat during the night, to a specific localization in the upper oxic zone of 1.5 mm during the day. Terminal restriction fragment length polymorphism of PCR-amplified pufM gene fragments revealed three groups of anoxyphototrophic populations, which varied according to the two opposite periods of the diel cycle under study. They were either specifically detected in only one period, or homogenously distributed through the mat in all periods, or located in specific zones of the mat depending on the period considered. Oxygen concentrations, pH and biomass of the major filamentous cyanobacteria were the determinative factors in the distribution of these anoxyphototrophs across the mat. Thus, vertical migration, cell-cell aggregate formation and metabolic switches were the most evident defence of the photosynthetic populations against the adverse effects of sulfide and oxygen fluxes during a diel cycle.
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Affiliation(s)
- Aude Fourçans
- Laboratoire d'Ecologie Moléculaire EA 3525, Université de Pau et des Pays de l'Adour, avenue de l'Université, BP 1155, Pau Cedex, France
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41
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Coelho-Souza SA, Guimarães JRD, Mauro JBN, Miranda MR, Azevedo SMFO. Mercury methylation and bacterial activity associated to tropical phytoplankton. THE SCIENCE OF THE TOTAL ENVIRONMENT 2006; 364:188-99. [PMID: 16169057 DOI: 10.1016/j.scitotenv.2005.07.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2004] [Revised: 07/06/2005] [Accepted: 07/08/2005] [Indexed: 05/04/2023]
Abstract
The methylated form of mercury (Hg), methylmercury (MeHg), is one of the most toxic pollutants. Biotic and/or abiotic methylation, often associated to sulfate-reducing bacteria metabolism, occurs in aquatic environments and in many tropical areas, mostly in the periphyton associated to floating macrophyte roots. Data about mercury methylation by phytoplankton are scarce and the aim of this study was to verify the biotic influence in the methylation process in Microcystis aeruginosa and Sineccocystis sp. laboratory strains and in natural populations of phytoplankton from two different aquatic systems, the mesotrophic Ribeirão das Lajes reservoir and hypereutrophic oligohaline Jacarepaguá lagoon, Rio de Janeiro state, Brazil. Adapted radiochemical techniques were used to measure sulfate-reduction, mercury methylation and bacterial activity in phytoplankton samples. Methyl-(203)Hg formation from added inorganic (203)Hg and (3)H-Leucine uptake were measured by liquid scintillation as well as sulfate-reduction, estimated as H(2)(35)S produced from added Na(2)(35)SO(4). There was no significant difference in low methylation potentials (0.37%) among the two cyanobacterium species studied in laboratory conditions. At Ribeirão das Lajes reservoir, there was no significant difference in methylation, bacterial activity and sulfate-reduction of surface sediment between the sampling points. Methylation in sediments (3-4%) was higher than in phytoplankton (1.5%), the opposite being true for bacterial activity (sediment mean 6.6 against 150.3 nmol gdw(-1) h(-1) for phytoplankton samples). At Jacarepaguá lagoon, an expressive bacterial activity (477.1 x 10(3) nmol gdw(-1) h(-1) at a concentration of 1000 nM leucine) and sulfate-reduction ( approximately 21% H(2)(35)S trapped) associated to phytoplankton (mostly cyanobacteria M. aeruginosa) was observed, but mercury methylation was not detected.
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Affiliation(s)
- Sérgio A Coelho-Souza
- Laboratório de Traçadores Wolfgang Pfeiffer, SL 62, Instituto de Biofísica Carlos Chagas Filho, Bloco G, Ilha do Fundão, Universidade Federal do Rio de Janeiro (IBCCF/UFRJ), RJ, CEP 21949-900, Brasil
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42
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Dolla A, Fournier M, Dermoun Z. Oxygen defense in sulfate-reducing bacteria. J Biotechnol 2006; 126:87-100. [PMID: 16713001 DOI: 10.1016/j.jbiotec.2006.03.041] [Citation(s) in RCA: 140] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2005] [Revised: 02/27/2006] [Accepted: 03/29/2006] [Indexed: 11/24/2022]
Abstract
Sulfate-reducing bacteria (SRB) are strict anaerobes that are often found in biotopes where oxic conditions can temporarily exist. The bacteria have developed several defense strategies in order to survive exposure to oxygen. These strategies includes peculiar behaviors in the presence of oxygen, like aggregation or aerotaxis, and enzymatic systems dedicated to the reduction and the elimination of oxygen and its reactive species. Sulfate-reducing bacteria, and specially Desulfovibrio species, possess a variety of enzymes acting together to achieve an efficient defense against oxidative stress. The function and occurrence of these enzymatic systems are described.
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Affiliation(s)
- Alain Dolla
- Laboratoire de Bioénergétique et Ingénierie des Protéines, CNRS - 31 chemin Joseph Aiguier, 13402 Marseille cedex 20, France.
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43
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Fournier M, Aubert C, Dermoun Z, Durand MC, Moinier D, Dolla A. Response of the anaerobe Desulfovibrio vulgaris Hildenborough to oxidative conditions: proteome and transcript analysis. Biochimie 2006; 88:85-94. [PMID: 16040186 DOI: 10.1016/j.biochi.2005.06.012] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2005] [Accepted: 06/20/2005] [Indexed: 10/25/2022]
Abstract
The method of two-dimensional protein gel electrophoresis was used to evaluate the changes at the proteins level following oxygen exposure of the anaerobic sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough. Fifty-seven proteins showed significant differential expression. The cellular concentration of 35 proteins decreased while that of nineteen increased as a specific consequence of oxidative conditions. The proteins that were less abundant belonged to various functional categories such as nucleic acid and protein biosynthesis, detoxification mechanisms, or cell division. Interestingly, quantitative real-time PCR revealed that the genes encoding detoxification enzymes (rubrerythrins, superoxide reductase) are down regulated. The loss of viability of D. vulgaris Hildenborough under these oxidative conditions (Fournier et al., J. Biol. Chem. 279 (2004) 1785) can be directly related to the decrease in the cellular concentrations of these proteins, thereby specifying the toxicity of oxygen for the cells. Among the proteins that were more abundant under oxygen exposure, several thiol-specific peroxidases (thiol-peroxidase, BCP-like protein, and putative glutaredoxin) were identified. Using RT-PCR, the up-regulation of the genes encoding the thiol-peroxidase and the BCP was demonstrated. That is the first time that these proteins have been shown to be involved in the defense of D. vulgaris toward an oxidative stress. Several hypothetical proteins were also shown to be differentially expressed. A function in the defense mechanism against an oxidative stress is proposed for these uncharacterized proteins.
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Affiliation(s)
- Marjorie Fournier
- Laboratoire de bioénergétique et ingénierie des protéines, IBSM-CNRS, BIP, 31, chemin Joseph-Aiguier, 13402 Marseille cedex 20, France
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Matsui GY, Ringelberg DB, Lovell CR. Sulfate-reducing bacteria in tubes constructed by the marine infaunal polychaete Diopatra cuprea. Appl Environ Microbiol 2005; 70:7053-65. [PMID: 15574900 PMCID: PMC535212 DOI: 10.1128/aem.70.12.7053-7065.2004] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Marine infaunal burrows and tubes greatly enhance solute transport between sediments and the overlying water column and are sites of elevated microbial activity. Biotic and abiotic controls of the compositions and activities of burrow and tube microbial communities are poorly understood. The microbial communities in tubes of the marine infaunal polychaete Diopatria cuprea collected from two different sediment habitats were examined. The bacterial communities in the tubes from a sandy sediment differed from those in the tubes from a muddy sediment. The difference in community structure also extended to the sulfate-reducing bacterial (SRB) assemblage, although it was not as pronounced for this functional group of species. PCR-amplified 16S rRNA gene sequences recovered from Diopatra tube SRB by clonal library construction and screening were all related to the family Desulfobacteriaceae. This finding was supported by phospholipid fatty acid analysis and by hybridization of 16S rRNA probes specific for members of the genera Desulfosarcina, Desulfobacter, Desulfobacterium, Desulfobotulus, Desulfococcus, and Desulfovibrio and some members of the genera Desulfomonas, Desulfuromonas, and Desulfomicrobium with 16S rRNA gene sequences resolved by denaturing gradient gel electrophoresis. Two of six SRB clones from the clone library were not detected in tubes from the sandy sediment. The habitat in which the D. cuprea tubes were constructed had a strong influence on the tube bacterial community as a whole, as well as on the SRB assemblage.
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Affiliation(s)
- George Y Matsui
- Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA
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45
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Jonkers HM, Koh IO, Behrend P, Muyzer G, de Beer D. Aerobic organic carbon mineralization by sulfate-reducing bacteria in the oxygen-saturated photic zone of a hypersaline microbial mat. MICROBIAL ECOLOGY 2005; 49:291-300. [PMID: 15965719 DOI: 10.1007/s00248-004-0260-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2003] [Accepted: 02/24/2004] [Indexed: 05/03/2023]
Abstract
The sulfate-reducing bacterium strain SRB D2 isolated from the photic zone of a hypersaline microbial mat, from Lake Chiprana, NE Spain, respired pyruvate, alanine, and alpha-ketoglutarate but not formate, lactate, malate, succinate, and serine at significant rates under fully oxic conditions. Dehydrogenase enzymes of only the former substrates are likely oxygen-tolerant as all substrates supported anaerobic sulfate reduction. No indications were found, however, that aerobic respiration supported growth. Although strain SRB D2 appeared phylogenetically closely related to the oxygen-tolerant sulfate-reducing bacterium Desulfovibrio oxyclinae, substrate spectra were markedly different. Most-probable-number (MPN) estimates of sulfate-reducing bacteria and aerobic heterotrophic bacteria indicated that the latter were numerically dominant in both the photic and aphotic zones of the mat. Moreover, substrate spectra of representative isolates showed that the aerobic heterotrophic bacteria are metabolically more diverse. These findings indicate that sulfate-reducing bacteria in the fully oxic photic zone of mats have to compete with aerobic heterotrophic bacteria for organic substrates. Porewater analysis revealed that total carbohydrates and low-molecular-weight carbon compounds (LMWC) made up substantial fractions of the total dissolved organic carbon (DOC) pool and that nighttime degradation of the former was concomitant with increased concentration of the latter. Our findings indicate that aerobic respiration by sulfate-reducing bacteria contributes to organic carbon mineralization in the oxic zone of microbial mats as daytime porewater LMWC concentrations are above typical half-saturation constants.
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Affiliation(s)
- H M Jonkers
- Max Planck Institute for Marine Microbiology, D-28359, Bremen, Germany.
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Wieland A, Zopfi J, Benthien M, Kühl M. Biogeochemistry of an iron-rich hypersaline microbial mat (Camargue, France). MICROBIAL ECOLOGY 2005; 49:34-49. [PMID: 15614465 DOI: 10.1007/s00248-003-2033-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2003] [Accepted: 10/30/2003] [Indexed: 05/24/2023]
Abstract
In situ microsensor measurements were combined with biogeochemical methods to determine oxygen, sulfur, and carbon cycling in microbial mats growing in a solar saltern (Salin-de-Giraud, France). Sulfate reduction rates closely followed the daily temperature changes and were highest during the day at 25 degrees C and lowest during the night at 11 degrees C, most probably fueled by direct substrate interactions between cyanobacteria and sulfate-reducing bacteria. Sulfate reduction was the major mineralization process during the night and the contribution of aerobic respiration to nighttime DIC production decreased. This decrease of aerobic respiration led to an increasing contribution of sulfide (and iron) oxidation to nighttime O2 consumption. A peak of elemental sulfur in a layer of high sulfate reduction at low sulfide concentration underneath the oxic zone indicated anoxygenic photosynthesis and/or sulfide oxidation by iron, which strongly contributed to sulfide consumption. We found a significant internal carbon cycling in the mat, and sulfate reduction directly supplied DIC for photosynthesis. The mats were characterized by a high iron content of 56 micromol Fe cm(-3), and iron cycling strongly controlled the sulfur cycle in the mat. This included sulfide precipitation resulting in high FeS contents with depth, and reactions of iron oxides with sulfide, especially after sunset, leading to a pronounced gap between oxygen and sulfide gradients and an unusual persistence of a pH peak in the uppermost mat layer until midnight.
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Affiliation(s)
- A Wieland
- Marine Biological Laboratory, University of Copenhagen, Strandpromenaden 5, DK-3000, Helsingør, Denmark.
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Alexandre G, Greer-Phillips S, Zhulin IB. Ecological role of energy taxis in microorganisms. FEMS Microbiol Rev 2004; 28:113-26. [PMID: 14975533 DOI: 10.1016/j.femsre.2003.10.003] [Citation(s) in RCA: 123] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2003] [Revised: 10/03/2003] [Accepted: 10/15/2003] [Indexed: 11/29/2022] Open
Abstract
Motile microorganisms rapidly respond to changes in various physico-chemical gradients by directing their motility to more favorable surroundings. Energy generation is one of the most important parameters for the survival of microorganisms in their environment. Therefore it is not surprising that microorganisms are able to monitor changes in the cellular energy generating processes. The signal for this behavioral response, which is called energy taxis, originates within the electron transport system. By coupling energy metabolism and behavior, energy taxis is fine-tuned to the environment a cell finds itself in and allows efficient adaptation to changing conditions that affect cellular energy levels. Thus, energy taxis provides cells with a versatile sensory system that enables them to navigate to niches where energy generation is optimized. This behavior is likely to govern vertical species stratification and the active migration of motile cells in response to shifting gradients of electron donors and/or acceptors which are observed within microbial mats, sediments and soil pores. Energy taxis has been characterized in several species and might be widespread in the microbial world. Genome sequencing revealed that many microorganisms from aquatic and soil environments possess large numbers of chemoreceptors and are likely to be capable of energy taxis. In contrast, species that have a fewer number of chemoreceptors are often found in specific, confined environments, where relatively constant environmental conditions are expected. Future studies focusing on characterizing behavioral responses in species that are adapted to diverse environmental conditions should unravel the molecular mechanisms underlying sensory behavior in general and energy taxis in particular. Such knowledge is critical to a better understanding of the ecological role of energy taxis.
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Affiliation(s)
- Gladys Alexandre
- Department of Biology, Georgia State University, Atlanta, GA 30303, USA.
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48
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Fournier M, Dermoun Z, Durand MC, Dolla A. A New Function of the Desulfovibrio vulgaris Hildenborough [Fe] Hydrogenase in the Protection against Oxidative Stress. J Biol Chem 2004; 279:1787-93. [PMID: 14594815 DOI: 10.1074/jbc.m307965200] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Sulfate-reducing bacteria, like Desulfovibrio vulgaris Hildenborough, have developed a set of reactions allowing them to survive in oxic environments and even to reduce molecular oxygen to water. D. vulgaris contains a cytoplasmic superoxide reductase (SOR) and a periplasmic superoxide dismutase (SOD) involved in the elimination of superoxide anions. To assign the function of SOD, the periplasmic [Fe] hydrogenase activity was followed in both wild-type and sod deletant strains. This activity was lower in the strain lacking the SOD than in the wild-type when the cells were exposed to oxygen for a short time. The periplasmic SOD is thus involved in the protection of sensitive iron-sulfur-containing enzyme against superoxide-induced damages. Surprisingly, production of the periplasmic [Fe] hydrogenase was higher in the cells exposed to oxygen than in those kept in anaerobic conditions. A similar increase in the amount of [Fe] hydrogenase was observed when an increase in the redox potential was induced by addition of chromate. Viability of the strain lacking the gene encoding [Fe] hydrogenase after exposure to oxygen for 1 h was lower than that of the wild-type. These data reveal for the first time that production of the periplasmic [Fe] hydrogenase is up-regulated in response to an oxidative stress. A new function of the periplasmic [Fe] hydrogenase in the protective mechanisms of D. vulgaris Hildenborough toward an oxidative stress is proposed.
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Affiliation(s)
- Marjorie Fournier
- Laboratoire de Bioénergétique et Ingénierie des Protéines, CNRS 31, Chemin Joseph Aiguier, 13402 Marseille cedex 20, France
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Ito T, Okabe S, Satoh H, Watanabe Y. Successional development of sulfate-reducing bacterial populations and their activities in a wastewater biofilm growing under microaerophilic conditions. Appl Environ Microbiol 2002; 68:1392-402. [PMID: 11872492 PMCID: PMC123773 DOI: 10.1128/aem.68.3.1392-1402.2002] [Citation(s) in RCA: 75] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2001] [Accepted: 11/28/2001] [Indexed: 11/20/2022] Open
Abstract
A combination of fluorescence in situ hybridization, microprofiles, denaturing gradient gel electrophoresis of PCR-amplified 16S ribosomal DNA fragments, and 16S rRNA gene cloning analysis was applied to investigate successional development of sulfate-reducing bacteria (SRB) community structure and in situ sulfide production activity within a biofilm growing under microaerophilic conditions (dissolved oxygen concentration in the bulk liquid was in the range of 0 to 100 microM) and in the presence of nitrate. Microelectrode measurements showed that oxygen penetrated 200 microm from the surface during all stages of biofilm development. The first sulfide production of 0.32 micromol of H(2)S m(-2) s(-1) was detected below ca. 500 microm in the 3rd week and then gradually increased to 0.70 micromol H(2)S m(-2) s(-1) in the 8th week. The most active sulfide production zone moved upward to the oxic-anoxic interface and intensified with time. This result coincided with an increase in SRB populations in the surface layer of the biofilm. The numbers of the probe SRB385- and 660-hybridized SRB populations significantly increased to 7.9 x 10(9) cells cm(-3) and 3.6 x 10(9) cells cm(-3), respectively, in the surface 400 microm during an 8-week cultivation, while those populations were relatively unchanged in the deeper part of the biofilm, probably due to substrate transport limitation. Based on 16S rRNA gene cloning analysis data, clone sequences that related to Desulfomicrobium hypogeium (99% sequence similarity) and Desulfobulbus elongatus (95% sequence similarity) were most frequently found. Different molecular analyses confirmed that Desulfobulbus, Desulfovibrio, and Desulfomicrobium were found to be the numerically important members of SRB in this wastewater biofilm.
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Affiliation(s)
- Tsukasa Ito
- Department of Urban and Environmental Engineering, Graduate School of Engineering, Hokkaido University, North 13 West 8, Kita-ku, Sapporo 060-8628, Japan
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Lemos RS, Gomes CM, Santana M, LeGall J, Xavier AV, Teixeira M. The 'strict' anaerobe Desulfovibrio gigas contains a membrane-bound oxygen-reducing respiratory chain. FEBS Lett 2001; 496:40-3. [PMID: 11343703 DOI: 10.1016/s0014-5793(01)02399-7] [Citation(s) in RCA: 74] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Sulfate-reducing bacteria are considered as strict anaerobic microorganisms, in spite of the fact that some strains have been shown to tolerate the transient presence of dioxygen. This report shows that membranes from Desulfovibrio gigas grown in fumarate/sulfate contain a respiratory chain fully competent to reduce dioxygen to water. In particular, a membrane-bound terminal oxygen reductase, of the cytochrome bd family, was isolated, characterized, and shown to completely reduce oxygen to water. This oxidase has two subunits with apparent molecular masses of 40 and 29 kDa. Using NADH or succinate as electron donors, the oxygen respiratory rates of D. gigas membranes are comparable to those of aerobic organisms (3.2 and 29 nmol O(2) min(-1) mg protein(-1), respectively). This 'strict anaerobic' bacterium contains all the necessary enzymatic complexes to live aerobically, showing that the relationships between oxygen and anaerobes are much more complex than originally thought.
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Affiliation(s)
- R S Lemos
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal
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