1
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Kang M, Liu L, Grossart HP. Spatio-temporal variations of methane fluxes in sediments of a deep stratified temperate lake. iScience 2024; 27:109520. [PMID: 38591008 PMCID: PMC11000008 DOI: 10.1016/j.isci.2024.109520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 12/09/2023] [Accepted: 03/14/2024] [Indexed: 04/10/2024] Open
Abstract
Spatio-temporal variability of sediment-mediated methane (CH4) production in freshwater lakes causes large uncertainties in predicting global lake CH4 emissions under different climate change and eutrophication scenarios. We conducted extensive sediment incubation experiments to investigate CH4 fluxes in Lake Stechlin, a deep, stratified temperate lake. Our results show contrasting spatial patterns in CH4 fluxes between littoral and profundal sites. The littoral sediments, ∼33% of the total sediment surface area, contributed ∼86.9% of the annual CH4 flux at the sediment-water interface. Together with sediment organic carbon quality, seasonal stratification is responsible for the striking spatial difference in sediment CH4 production between littoral and profundal zones owing to more sensitive CH4 production than oxidation to warming. While profundal sediments produce a relatively small amount of CH4, its production increases markedly as anoxia spreads in late summer. Our measurements indicate that future lake CH4 emissions will increase due to climate warming and concomitant hypoxia/anoxia.
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Affiliation(s)
- Manchun Kang
- Engineering Research Center of Eco-environment in Three Gorges Reservoir Region, Yichang 443002, China
- Hubei Field Observation and Scientific Research Stations for Water Ecosystem in Three Gorges Reservoir, Yichang 443002, China
| | - Liu Liu
- Yunnan Key Laboratory of Plateau Geographical Processes and Environmental Changes, Faculty of Geography, Yunnan Normal University, Kunming 650500, China
- Department of Plankton and Microbial Ecology, Leibniz Institute of Freshwater Ecology and Inland Fisheries, 16775 Stechlin, Germany
| | - Hans-Peter Grossart
- Department of Plankton and Microbial Ecology, Leibniz Institute of Freshwater Ecology and Inland Fisheries, 16775 Stechlin, Germany
- Institute of Biochemistry and Biology, Potsdam University, 14476 Potsdam, Germany
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2
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Xiong X, Li Y, Zhang C. Cable bacteria: Living electrical conduits for biogeochemical cycling and water environment restoration. WATER RESEARCH 2024; 253:121345. [PMID: 38394932 DOI: 10.1016/j.watres.2024.121345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 02/17/2024] [Accepted: 02/19/2024] [Indexed: 02/25/2024]
Abstract
Since the discovery of multicellular cable bacteria in marine sediments in 2012, they have attracted widespread attention and interest due to their unprecedented ability to generate and transport electrical currents over centimeter-scale long-range distances. The cosmopolitan distribution of cable bacteria in both marine and freshwater systems, along with their substantial impact on local biogeochemistry, has uncovered their important role in element cycling and ecosystem functioning of aquatic environments. Considerable research efforts have been devoted to the potential utilization of cable bacteria for various water management purposes during the past few years. However, there lacks a critical summary on the advances and contributions of cable bacteria to biogeochemical cycles and water environment restoration. This review aims to provide an up-to-date and comprehensive overview of the current research on cable bacteria, with a particular view on their participation in aquatic biogeochemical cycles and promising applications in water environment restoration. It systematically analyzes (i) the global distribution of cable bacteria in aquatic ecosystems and the major environmental factors affecting their survival, diversity, and composition, (ii) the interactive associations between cable bacteria and other microorganisms as well as aquatic plants and infauna, (iii) the underlying role of cable bacteria in sedimentary biogeochemical cycling of essential elements including but not limited to sulfur, iron, phosphorus, and nitrogen, (iv) the practical explorations of cable bacteria for water pollution control, greenhouse gas emission reduction, aquatic ecological environment restoration, as well as possible combinations with other water remediation technologies. It is believed to give a step-by-step introduction to progress on cable bacteria, highlight key findings, opportunities and challenges of using cable bacteria for water environment restoration, and propose directions for further exploration.
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Affiliation(s)
- Xinyan Xiong
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lake of Ministry of Education, College of Environment, Hohai University, Nanjing 210024, PR China
| | - Yi Li
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lake of Ministry of Education, College of Environment, Hohai University, Nanjing 210024, PR China.
| | - Chi Zhang
- College of Materials Science and Engineering, Hohai University, Changzhou 213200, PR China.
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3
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Von Eggers JM, Wisnoski NI, Calder JW, Capo E, Groff DV, Krist AC, Shuman B. Environmental filtering governs consistent vertical zonation in sedimentary microbial communities across disconnected mountain lakes. Environ Microbiol 2024; 26:e16607. [PMID: 38477387 DOI: 10.1111/1462-2920.16607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Accepted: 02/28/2024] [Indexed: 03/14/2024]
Abstract
Subsurface microorganisms make up the majority of Earth's microbial biomass, but ecological processes governing surface communities may not explain community patterns at depth because of burial. Depth constrains dispersal and energy availability, and when combined with geographic isolation across landscapes, may influence community assembly. We sequenced the 16S rRNA gene of bacteria and archaea from 48 sediment cores across 36 lakes in four disconnected mountain ranges in Wyoming, USA and used null models to infer assembly processes across depth, spatial isolation, and varying environments. Although we expected strong dispersal limitations across these isolated settings, community composition was primarily shaped by environmental selection. Communities consistently shifted from domination by organisms that degrade organic matter at the surface to methanogenic, low-energy adapted taxa in deeper zones. Stochastic processes-like dispersal limitation-contributed to differences among lakes, but because these effects weakened with depth, selection processes ultimately governed subsurface microbial biogeography.
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Affiliation(s)
- Jordan M Von Eggers
- Department of Geology and Geophysics, University of Wyoming, Laramie, Wyoming, USA
- Program in Ecology and Evolution, University of Wyoming, Laramie, Wyoming, USA
| | - Nathan I Wisnoski
- Wyoming Geographic Information Science Center, University of Wyoming, Laramie, Wyoming, USA
- Department of Biological Sciences, Mississippi State University, Mississippi State, Mississippi, USA
| | - John W Calder
- Department of Botany, University of Wyoming, Laramie, Wyoming, USA
| | - Eric Capo
- Department of Ecology and Environmental Science, Umeå University, Umeå, Sweden
| | - Dulcinea V Groff
- Department of Geology and Geophysics, University of Wyoming, Laramie, Wyoming, USA
| | - Amy C Krist
- Program in Ecology and Evolution, University of Wyoming, Laramie, Wyoming, USA
- Department of Zoology and Physiology, University of Wyoming, Laramie, Wyoming, USA
| | - Bryan Shuman
- Department of Geology and Geophysics, University of Wyoming, Laramie, Wyoming, USA
- Program in Ecology and Evolution, University of Wyoming, Laramie, Wyoming, USA
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4
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Zhuo T, He L, Chai B, Zhou S, Wan Q, Lei X, Zhou Z, Chen B. Micro-pressure promotes endogenous phosphorus release in a deep reservoir by favouring microbial phosphate mineralisation and solubilisation coupled with sulphate reduction. WATER RESEARCH 2023; 245:120647. [PMID: 37738938 DOI: 10.1016/j.watres.2023.120647] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 09/10/2023] [Accepted: 09/17/2023] [Indexed: 09/24/2023]
Abstract
Deep reservoirs vary in their hydrostatic pressure owing to artificial water level control. The potential migration of phosphorus (P) in reservoir sediments raises the risk of harmful algal blooms. To ascertain the mechanisms of endogenous P release in reservoirs, we characterised aquatic microbial communities associated with coupled iron (Fe), P and sulphur (S) cycling at the sediment-water interface. The responses of microbial communities to hydrostatic pressures of 0.2-0.7 mega pascals (MPa; that is, micro-pressures) were investigated through a 30-day simulation experiment. Our findings unravelled a potential mechanism that micro-pressure enhanced the solubilisation of Fe/aluminium (Al)-bound P caused by microbially-driven sulphate reduction, leading to endogenous P release in the deep reservoir. Although the vertical distribution of labile Fe was not affected by pressure changes, we did observe Fe resupply at sediment depths of 2-5 cm. Metagenomic analysis revealed increased abundances of functional genes for P mineralisation (phoD, phoA), P solubilisation (pqqC, ppx-gppA) and sulphate reduction (cysD, cysC) in sediments subjected to micro-pressure, which contrasted with the pattern of S oxidation gene (soxB). There was a tight connection between P and S cycling-related microbial communities, based on significant positive correlations between labile element (P and S) concentrations and functional gene (phoD, cysD) abundances. This provided strong support that Fe-P-S coupling processes were governed by micro-pressure through modulation of P and S cycling-related microbial functions. Key taxa involved in P and S cycling (for example, Bradyrhizobium, Methyloceanibacter) positively responded to micro-pressure and as such, indirectly drove P release from sediments by facilitating P mineralisation and solubilisation coupled with sulphate reduction.
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Affiliation(s)
- Tianyu Zhuo
- School of Environmental Science and Engineering, Tianjin University, Jinnan District, Tianjin 300350, China
| | - Lixin He
- Hebei Collaborative Innovation Center for the Regulation and Comprehensive Management of Water Resources and Water Environment, Hebei University of Engineering, Handan 056038, China; Hebei Key Laboratory of Intelligent Water Conservancy, School of Water Conservancy and Hydroelectric, Hebei University of Engineering, Handan 056038, China
| | - Beibei Chai
- Hebei Collaborative Innovation Center for the Regulation and Comprehensive Management of Water Resources and Water Environment, Hebei University of Engineering, Handan 056038, China; Hebei Key Laboratory of Intelligent Water Conservancy, School of Water Conservancy and Hydroelectric, Hebei University of Engineering, Handan 056038, China.
| | - Shilei Zhou
- Pollution Prevention Biotechnology Laboratory of Hebei Province, School of Environmental Science and Engineering, Hebei University of Science and Technology, Shijiazhuang 050018, China
| | - Qiong Wan
- School of Architecture and Civil Engineering, Xi'an University of Science and Technology, Xi'an 710054, China
| | - Xiaohui Lei
- State Key Laboratory of Simulation and Regulation of Water Cycle in River Basin, China Institute of Water Resources and Hydropower Research, Beijing 100038, China.
| | - Zhenming Zhou
- College of Civil Engineering, Huaqiao University, Xiamen 361021, China
| | - Bin Chen
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Beijing Normal University, Beijing 100875, China
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5
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Zhang P, Yang F, Dai W, Wei C. Variation of sulfate reducing bacteria communities in ionic rare earth tailings and the potential of a single cadmium resistant strain in bioremediation. CHEMOSPHERE 2023; 328:138615. [PMID: 37023895 DOI: 10.1016/j.chemosphere.2023.138615] [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: 10/25/2022] [Revised: 02/14/2023] [Accepted: 04/03/2023] [Indexed: 06/19/2023]
Abstract
Heap leaching ionic rare earth tailings might be prone to nourish sulfate reducing bacteria (SRB), but the SRB community in terrestrial ecosystems, such as tailings, has never been studied. This work was conducted to investigate the SRB communities in revegetated and bare tailings in Dingnan county, Jiangxi province, China, incorporating with indoor experiments to isolate SRB strain in bioremediation of Cd contamination. Significant increases in richness, accompanied by reductions in evenness and diversity, were found in the SRB community in revegetated tailings compared to bare tailings. At genus taxonomic level, two distinct dominant SRB were observed in samples from bare and revegetated tailings, with Desulfovibrio dominating in the former and Streptomyces dominating in the latter, respectively. A single SRB strain was screened out from the bare tailings (REO-01). The cell of REO-01 was rod-shaped and belonged to family Desulfuricans and genus Desulfovibrio. The Cd resistance of the strain was further examined, no changes in cell morphology were observed at 0.05 mM Cd, additionally, the atomic ratios of S, Cd, and Fe changed with the increase in Cd dosages, indicating FeS and CdS were produced simultaneously, XRD results further confirmed the production changed gradually from FeS to CdS with increasing Cd dosages from 0.05 to 0.2 mM. FT-IR analysis showed that functional groups containing amide, polysaccharide glycosidic linkage, hydroxyl, carboxy, methyl, phosphodiesters and sulfhydryl groups in extracellular polymeric substances (EPS) of REO-01 might have affinity with Cd. This study demonstrated the potential of a single SRB strain isolated from ionic rare earth tailings in bioremediation of Cd contamination.
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Affiliation(s)
- Ping Zhang
- Key Laboratory of Land Surface Pattern and Simulation, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing, 100101, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Fen Yang
- Key Laboratory of Land Surface Pattern and Simulation, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing, 100101, China
| | - Weijie Dai
- Key Laboratory of Land Surface Pattern and Simulation, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing, 100101, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chaoyang Wei
- Key Laboratory of Land Surface Pattern and Simulation, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing, 100101, China.
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6
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Barton LL, Duarte AG, Staicu LC. Genomic insight into iron acquisition by sulfate-reducing bacteria in microaerophilic environments. Biometals 2023; 36:339-350. [PMID: 35767096 DOI: 10.1007/s10534-022-00410-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 06/08/2022] [Indexed: 11/30/2022]
Abstract
Historically, sulfate-reducing bacteria (SRB) have been considered to be strict anaerobes, but reports in the past couple of decades indicate that SRB tolerate exposure to O2 and can even grow in aerophilic environments. With the transition from anaerobic to microaerophilic conditions, the uptake of Fe(III) from the environment by SRB would become important. In evaluating the metabolic capability for the uptake of iron, the genomes of 26 SRB, representing eight families, were examined. All SRB reviewed carry genes (feoA and feoB) for the ferrous uptake system to transport Fe(II) across the plasma membrane into the cytoplasm. In addition, all of the SRB genomes examined have putative genes for a canonical ABC transporter that may transport ferric siderophore or ferric chelated species from the environment. Gram-negative SRB have additional machinery to import ferric siderophores and ferric chelated species since they have the TonB system that can work alongside any of the outer membrane porins annotated in the genome. Included in this review is the discussion that SRB may use the putative siderophore uptake system to import metals other than iron.
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Affiliation(s)
- Larry L Barton
- Department of Biology, University of New Mexico, MSCO3 2020, Albuquerque, NM, 87131, USA
| | - Americo G Duarte
- Instituto de Tecnologia Química E Biológica António Xavier/Universidade NOVA de Lisboa, Av. República, Estação Agronómica Nacional, 2780-157, Oeiras, Portugal
| | - Lucian C Staicu
- Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096, Warsaw, Poland.
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7
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Rattray JE, Chakraborty A, Elizondo G, Ellefson E, Bernard B, Brooks J, Hubert CRJ. Endospores associated with deep seabed geofluid features in the eastern Gulf of Mexico. GEOBIOLOGY 2022; 20:823-836. [PMID: 35993193 PMCID: PMC9804197 DOI: 10.1111/gbi.12517] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 05/12/2022] [Accepted: 07/11/2022] [Indexed: 06/15/2023]
Abstract
Recent studies have reported up to 1.9 × 1029 bacterial endospores in the upper kilometre of deep subseafloor marine sediments, however, little is understood about their origin and dispersal. In cold ocean environments, the presence of thermospores (endospores produced by thermophilic bacteria) suggests that distribution is governed by passive migration from warm anoxic sources possibly facilitated by geofluid flow, such as advective hydrocarbon seepage sourced from petroleum deposits deeper in the subsurface. This study assesses this hypothesis by measuring endospore abundance and distribution across 60 sites in Eastern Gulf of Mexico (EGM) sediments using a combination of the endospore biomarker 2,6-pyridine dicarboxylic acid or 'dipicolinic acid' (DPA), sequencing 16S rRNA genes of thermospores germinated in 50°C sediment incubations, petroleum geochemistry in the sediments and acoustic seabed data from sub-bottom profiling. High endospore abundance is associated with geologically active conduit features (mud volcanoes, pockmarks, escarpments and fault systems), consistent with subsurface fluid flow dispersing endospores from deep warm sources up into the cold ocean. Thermospores identified at conduit sites were most closely related to bacteria associated with the deep biosphere habitats including hydrocarbon systems. The high endospore abundance at geological seep features demonstrated here suggests that recalcitrant endospores and their chemical components (such as DPA) can be used in concert with geochemical and geophysical analyses to locate discharging seafloor features. This multiproxy approach can be used to better understand patterns of advective fluid flow in regions with complex geology like the EGM basin.
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Affiliation(s)
- Jayne E. Rattray
- Department of Biological SciencesUniversity of CalgaryCalgaryAlbertaCanada
| | - Anirban Chakraborty
- Department of Biological SciencesUniversity of CalgaryCalgaryAlbertaCanada
- Department of Biological SciencesIdaho State UniversityPocatelloIdahoUSA
| | - Gretta Elizondo
- Department of Biological SciencesUniversity of CalgaryCalgaryAlbertaCanada
| | - Emily Ellefson
- Department of Biological SciencesUniversity of CalgaryCalgaryAlbertaCanada
- Geological SciencesStanford UniversityStanfordCaliforniaUSA
| | | | | | - Casey R. J. Hubert
- Department of Biological SciencesUniversity of CalgaryCalgaryAlbertaCanada
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8
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Suleiman M, Choffat Y, Daugaard U, Petchey OL. Large and interacting effects of temperature and nutrient addition on stratified microbial ecosystems in a small, replicated, and liquid-dominated Winogradsky column approach. Microbiologyopen 2021; 10:e1189. [PMID: 34180595 PMCID: PMC8123916 DOI: 10.1002/mbo3.1189] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 04/09/2021] [Accepted: 04/10/2021] [Indexed: 01/04/2023] Open
Abstract
Aquatic ecosystems are often stratified, with cyanobacteria in oxic layers and phototrophic sulfur bacteria in anoxic zones. Changes in stratification caused by the global environmental change are an ongoing concern. Increasing understanding of how such aerobic and anaerobic microbial communities, and associated abiotic conditions, respond to multifarious environmental changes is an important endeavor in microbial ecology. Insights can come from observational and experimental studies of naturally occurring stratified aquatic ecosystems, theoretical models of ecological processes, and experimental studies of replicated microbial communities in the laboratory. Here, we demonstrate a laboratory-based approach with small, replicated, and liquid-dominated Winogradsky columns, with distinct oxic/anoxic strata in a highly replicable manner. Our objective was to apply simultaneous global change scenarios (temperature, nutrient addition) on this micro-ecosystem to report how the microbial communities (full-length 16S rRNA gene seq.) and the abiotic conditions (O2 , H2 S, TOC) of the oxic/anoxic layer responded to these environmental changes. The composition of the strongly stratified microbial communities was greatly affected by temperature and by the interaction of temperature and nutrient addition, demonstrating the need of investigating global change treatments simultaneously. Especially phototrophic sulfur bacteria dominated the water column at higher temperatures and may indicate the presence of alternative stable states. We show that the establishment of such a micro-ecosystem has the potential to test global change scenarios in stratified eutrophic limnic systems.
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Affiliation(s)
- Marcel Suleiman
- Department of Evolutionary Biology and Environmental StudiesUniversity of ZurichZurichSwitzerland
| | - Yves Choffat
- Department of Evolutionary Biology and Environmental StudiesUniversity of ZurichZurichSwitzerland
| | - Uriah Daugaard
- Department of Evolutionary Biology and Environmental StudiesUniversity of ZurichZurichSwitzerland
| | - Owen L. Petchey
- Department of Evolutionary Biology and Environmental StudiesUniversity of ZurichZurichSwitzerland
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9
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Li L, Fuchs A, Ortega SH, Xue B, Casper P. Spatial methane pattern in a deep freshwater lake: Relation to water depth and topography. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 764:142829. [PMID: 33143919 DOI: 10.1016/j.scitotenv.2020.142829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Revised: 08/25/2020] [Accepted: 09/30/2020] [Indexed: 06/11/2023]
Abstract
Freshwater lakes are regarded as important methane (CH4) sources, accounting for ~20% of natural emission. To improve the assessment of the global greenhouse effect, it is necessary to consider spatial variability within lakes. Here, CH4 concentrations in the water column and sediment layers, as well as the sediment CH4 production potentials and diffusive fluxes, were studied in the littoral, intermediate, and profundal zones of the medium-sized (425 ha), deep (maximum depth 69.5 m) Lake Stechlin (Germany). Sediment CH4 concentrations, production potentials and sediment-water interface diffusive fluxes showed significant spatial heterogeneity and were highest in the profundal zone. CH4 concentrations in the surface water did not differ among the studied locations, indicating a decoupling from the production sites in the sediment. The high amount of CH4 in profundal sediments that might potentially be released to the atmosphere is either trapped or oxidized within the water column, while the surface water dissolved CH4 is more related to the dynamics in the epilimnion. The divergence in sediment physical (water content, grain size) and chemical (organic matter quantity or quality, sulfate) properties across the lake leads to variations in CH4 dynamics which are restricted to deeper habitats in this type of lake.
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Affiliation(s)
- Lingling Li
- College of Geography Science, Nanjing Normal University, Nanjing, China; State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China; Department of Experimental Limnology, Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Stechlin, Germany
| | - Andrea Fuchs
- Department of Experimental Limnology, Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Stechlin, Germany
| | - Sonia Herrero Ortega
- Department of Experimental Limnology, Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Stechlin, Germany
| | - Bin Xue
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China
| | - Peter Casper
- Department of Experimental Limnology, Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Stechlin, Germany.
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Li B, Feng M, Chen X, Wang Y, Shen Y, Wu QL. Abundant sediment organic matter potentially facilitates chemical iron reduction and surface water blackness in a Chinese deep lake. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 272:116002. [PMID: 33246758 DOI: 10.1016/j.envpol.2020.116002] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 10/21/2020] [Accepted: 11/03/2020] [Indexed: 06/12/2023]
Abstract
Black bloom has become an increasingly severe environmental and ecological problem in lots of lakes. Ferrous monosulfide (FeS), which is closely related to chemical iron reduction (CIR), is considered the major cause for black water in shallow lakes, but few studies focus on the effect of organic matters (OM) content on iron and sulfate reduction and its contribution to the black bloom in deep lakes. Here, in Lake Fuxian, a Chinese deep lake which has also suffered from black bloom, FeS was identified responsible for the surface water blackness by using multiple microscopy and element analyses. Dissolved oxygen (DO) penetrated 1.6-4.2 mm in all sediment sites, further indicating FeS formed in the sediments instead of the permanently oxic water column. Geochemical characteristics revealed by diffusive gradients in thin films (DGT) showed that DGT-Fe2+ concentration was 57.6-1919.4 times higher than the DGT-S2- concentration and both were positively correlated with DGT-PO43-. Combining DGT profiles and anaerobic OM remineralization rate according to bag incubation, iron reduction is more effective than sulfate reduction although the two processes coexisted. Moreover, correlation of DGT-Fe2+ and DGT-PO43- was better than that of DGT-PO43- and DGT-S2- at OM-depleted sites but opposite at OM-rich sites. In addition, total organic carbon (TOC) was significantly positively related to acid volatile sulfide (AVS). We therefore conclude that abundant OM potentially exacerbate chemical iron reduction and further lead to surface water blackness. Our study revealed the mechanisms behind the black bloom and gives credence to the management strategy of reducing OM loading to protect water quality in deep lakes.
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Affiliation(s)
- Biao Li
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China; University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Muhua Feng
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China.
| | - Xiangchao Chen
- Shanghai Tingying Environmental Technology Co., Ltd, Shanghai, 201707, China
| | - Yarui Wang
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China; University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Yue Shen
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China; University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Qinglong L Wu
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China; Sino-Danish Centre for Education and Research, University of Chinese Academy of Sciences, Beijing, 100039, China
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11
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Environmental filtering determines family-level structure of sulfate-reducing microbial communities in subsurface marine sediments. ISME JOURNAL 2019; 13:1920-1932. [PMID: 30894690 DOI: 10.1038/s41396-019-0387-y] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Revised: 01/22/2019] [Accepted: 02/28/2019] [Indexed: 01/09/2023]
Abstract
Recent work has shown that subsurface microbial communities assemble by selective survival of surface community members during sediment burial, but it remains unclear to what extent the compositions of the subsurface communities are a product of their founding population at the sediment surface or of the changing geochemical conditions during burial. Here we investigate this question for communities of sulfate-reducing microorganisms (SRMs). We collected marine sediment samples from the upper 3-5 m at four geochemically contrasting sites in the Skagerrak and Baltic Sea and measured SRM abundance (quantitative PCR of dsrB), metabolic activity (radiotracer rate measurements), and community composition (Illumina sequencing of dsrB amplicons). These data showed that SRM abundance, richness, and phylogenetic clustering as determined by the nearest taxon index peaked below the bioturbation zone and above the depth of sulfate depletion. Minimum cell-specific rates of sulfate reduction did not vary substantially between sites. SRM communities at different sites were best distinguished based on their composition of amplicon sequence variants (ASVs), while communities in different geochemical zones were best distinguished based on their composition of SRM families. This demonstrates environmental filtering of SRM communities in sediment while a site-specific fingerprint of the founding community is retained.
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12
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Mori F, Umezawa Y, Kondo R, Wada M. Dynamics of Sulfate-Reducing Bacteria Community Structure in Surface Sediment of a Seasonally Hypoxic Enclosed Bay. Microbes Environ 2018; 33:378-384. [PMID: 30449831 PMCID: PMC6308007 DOI: 10.1264/jsme2.me18092] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
We herein report on the dynamics of a sulfate-reducing bacteria (SRB) community structure in the surface sediment of a seasonally hypoxic enclosed bay for two consecutive years (2012 and 2013). The uppermost (0–5 mm) and subsurface (5–10 mm) layers of sediment were examined with a terminal-restriction fragment length polymorphism (T-RFLP) analysis based on the dissimilatory sulfite reductase (dsrA) gene. The SRB community significantly differed between the two sediment layers over the sampling period. This difference was mainly attributed to operational taxonomic units (OTUs) that were unique to either of the sediment layers. However, nearly 70% of total OTUs were shared between the two layers, with a few predominating. Therefore, no significant shift was observed in the SRB community structure under varying dissolved oxygen (DO) conditions in bottom water overlying the sediment surface. An additional analysis of 16S rRNA gene amplicon sequences, conducted for three uppermost sediment samples (July, August, and September in 2012), revealed that Desulfococcus, a member of SRB with high tolerance to oxygen, was the predominant Deltaproteobacteria across the uppermost sediment samples. Based on the predominance of shared OTUs across the SRB community in the sediment (0–10 mm) regardless of bottom-water DO, some SRB that are physiologically tolerant of a wide range of DO conditions may have dominated and masked changes in responsive SRB to DO concentrations. These results suggest that the SRB community structure in the enclosed bay became stable under repeated cycles of seasonal hypoxia, but may be compromised if the severity of hypoxia increases in the future.
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Affiliation(s)
- Fumiaki Mori
- Graduate School of Fisheries and Environmental Sciences, Nagasaki University
| | - Yu Umezawa
- Graduate School of Fisheries and Environmental Sciences, Nagasaki University
| | - Ryuji Kondo
- Department of Marine Science and Technology, Fukui Prefectural University
| | - Minoru Wada
- Graduate School of Fisheries and Environmental Sciences, Nagasaki University
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13
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Zhang B, Xu X, Zhu L. Structure and function of the microbial consortia of activated sludge in typical municipal wastewater treatment plants in winter. Sci Rep 2017; 7:17930. [PMID: 29263391 PMCID: PMC5738398 DOI: 10.1038/s41598-017-17743-x] [Citation(s) in RCA: 89] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Accepted: 11/29/2017] [Indexed: 12/01/2022] Open
Abstract
To better understand the relationship between the environmental variables and microbial communities of activated sludge, we took winter samples from different biological treatment units (anaerobic, oxic, etc) from the WWTP's of a number of Chinese cities. Differences in influent organic components and activated sludge microbial communities were identified by gas chromatography-mass spectrometry and high-throughput sequencing technology, respectively. Liquid nitrogen grinding pretreatment of samples was found to aid in the obtaining of a more bio-diversified sample. Influent type and dissolved oxygen concentration influenced the activated sludge microbial community structure. Nitrospira, Caldilineaceae and Anaerolineaceae were highly related to domestic wastewater treatment systems, whereas Thauera was the most abundant putative refractory aromatic hydrocarbon decomposer found in industrial wastewater treatment systems. Within the influent composition, we speculate that Thauera, Macellibacteroides and Desulfomicrobium are the key functional genera of the anaerobic environment of the textile dyeing industry wastewater treatment systems, whilst Thauera and Thiobacillus are key functional microbes in fine chemical wastewater treatment systems.
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Affiliation(s)
- Bo Zhang
- Department of Environmental Engineering, Zhejiang University, Hangzhou, 310058, P.R. China
| | - Xiangyang Xu
- Department of Environmental Engineering, Zhejiang University, Hangzhou, 310058, P.R. China
- Zhejiang Province Key Laboratory for Water Pollution Control and Environmental Safety, Hangzhou, 310058, P.R. China
| | - Liang Zhu
- Department of Environmental Engineering, Zhejiang University, Hangzhou, 310058, P.R. China.
- Zhejiang Province Key Laboratory for Water Pollution Control and Environmental Safety, Hangzhou, 310058, P.R. China.
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Wurzbacher C, Fuchs A, Attermeyer K, Frindte K, Grossart HP, Hupfer M, Casper P, Monaghan MT. Shifts among Eukaryota, Bacteria, and Archaea define the vertical organization of a lake sediment. MICROBIOME 2017; 5:41. [PMID: 28388930 PMCID: PMC5385010 DOI: 10.1186/s40168-017-0255-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Accepted: 03/15/2017] [Indexed: 05/10/2023]
Abstract
BACKGROUND Lake sediments harbor diverse microbial communities that cycle carbon and nutrients while being constantly colonized and potentially buried by organic matter sinking from the water column. The interaction of activity and burial remained largely unexplored in aquatic sediments. We aimed to relate taxonomic composition to sediment biogeochemical parameters, test whether community turnover with depth resulted from taxonomic replacement or from richness effects, and to provide a basic model for the vertical community structure in sediments. METHODS We analyzed four replicate sediment cores taken from 30-m depth in oligo-mesotrophic Lake Stechlin in northern Germany. Each 30-cm core spanned ca. 170 years of sediment accumulation according to 137Cs dating and was sectioned into layers 1-4 cm thick. We examined a full suite of biogeochemical parameters and used DNA metabarcoding to examine community composition of microbial Archaea, Bacteria, and Eukaryota. RESULTS Community β-diversity indicated nearly complete turnover within the uppermost 30 cm. We observed a pronounced shift from Eukaryota- and Bacteria-dominated upper layers (<5 cm) to Bacteria-dominated intermediate layers (5-14 cm) and to deep layers (>14 cm) dominated by enigmatic Archaea that typically occur in deep-sea sediments. Taxonomic replacement was the prevalent mechanism in structuring the community composition and was linked to parameters indicative of microbial activity (e.g., CO2 and CH4 concentration, bacterial protein production). Richness loss played a lesser role but was linked to conservative parameters (e.g., C, N, P) indicative of past conditions. CONCLUSIONS By including all three domains, we were able to directly link the exponential decay of eukaryotes with the active sediment microbial community. The dominance of Archaea in deeper layers confirms earlier findings from marine systems and establishes freshwater sediments as a potential low-energy environment, similar to deep sea sediments. We propose a general model of sediment structure and function based on microbial characteristics and burial processes. An upper "replacement horizon" is dominated by rapid taxonomic turnover with depth, high microbial activity, and biotic interactions. A lower "depauperate horizon" is characterized by low taxonomic richness, more stable "low-energy" conditions, and a dominance of enigmatic Archaea.
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Affiliation(s)
- Christian Wurzbacher
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Müggelseedamm 301, Berlin, 12587 Germany
- Berlin Center for Genomics in Biodiversity Research, Königin-Luise-Str. 6-8, Berlin, 14195 Germany
- Department of Biological and Environmental Sciences, University of Gothenburg, Box 100, Göteborg, Sweden
| | - Andrea Fuchs
- Carl-von-Ossietzky University Oldenburg, Ammerländer Heerstraße 114-118, Oldenburg, 26129 Germany
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Alte Fischerhütte 2, Stechlin, 16775 Germany
| | - Katrin Attermeyer
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Alte Fischerhütte 2, Stechlin, 16775 Germany
- Department of Ecology and Genetics, Uppsala University, Norbyvägen 18d, Uppsala, 75236 Sweden
| | - Katharina Frindte
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Alte Fischerhütte 2, Stechlin, 16775 Germany
- Institute of Crop Science and Resource Conservation – Molecular Biology of the Rhizosphere, Nussallee 13, Bonn, 53115 Germany
| | - Hans-Peter Grossart
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Alte Fischerhütte 2, Stechlin, 16775 Germany
- Institute for Biochemistry and Biology, Potsdam University, Maulbeerallee 2, Potsdam, 14469 Germany
| | - Michael Hupfer
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Müggelseedamm 301, Berlin, 12587 Germany
| | - Peter Casper
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Alte Fischerhütte 2, Stechlin, 16775 Germany
| | - Michael T. Monaghan
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Müggelseedamm 301, Berlin, 12587 Germany
- Berlin Center for Genomics in Biodiversity Research, Königin-Luise-Str. 6-8, Berlin, 14195 Germany
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15
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Ranchou‐Peyruse M, Gasc C, Guignard M, Aüllo T, Dequidt D, Peyret P, Ranchou‐Peyruse A. The sequence capture by hybridization: a new approach for revealing the potential of mono-aromatic hydrocarbons bioattenuation in a deep oligotrophic aquifer. Microb Biotechnol 2017; 10:469-479. [PMID: 27766749 PMCID: PMC5328808 DOI: 10.1111/1751-7915.12426] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Revised: 09/15/2016] [Accepted: 09/18/2016] [Indexed: 01/04/2023] Open
Abstract
The formation water of a deep aquifer (853 m of depth) used for geological storage of natural gas was sampled to assess the mono-aromatic hydrocarbons attenuation potential of the indigenous microbiota. The study of bacterial diversity suggests that Firmicutes and, in particular, sulphate-reducing bacteria (Peptococcaceae) predominate in this microbial community. The capacity of the microbial community to biodegrade toluene and m- and p-xylenes was demonstrated using a culture-based approach after several hundred days of incubation. In order to reveal the potential for biodegradation of these compounds within a shorter time frame, an innovative approach named the solution hybrid selection method, which combines sequence capture by hybridization and next-generation sequencing, was applied to the same original water sample. The bssA and bssA-like genes were investigated as they are considered good biomarkers for the potential of toluene and xylene biodegradation. Unlike a PCR approach which failed to detect these genes directly from formation water, this innovative strategy demonstrated the presence of the bssA and bssA-like genes in this oligotrophic ecosystem, probably harboured by Peptococcaceae. The sequence capture by hybridization shows significant potential to reveal the presence of genes of functional interest which have low-level representation in the biosphere.
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Affiliation(s)
- Magali Ranchou‐Peyruse
- Université de Pau et des Pays de l'AdourEquipe Environnement et Microbiologie, IPREM‐CNRS 5254F‐64013PauFrance
| | - Cyrielle Gasc
- Université d'AuvergneEA 4678 CIDAM63001Clermont‐FerrandFrance
| | - Marion Guignard
- Université de Pau et des Pays de l'AdourEquipe Environnement et Microbiologie, IPREM‐CNRS 5254F‐64013PauFrance
| | - Thomas Aüllo
- TIGF – Transport et Infrastructures Gaz France40 Avenue de l'Europe, CS2052264000PauFrance
| | - David Dequidt
- STORENGY – Geosciences DepartmentBois‐ColombesFrance
| | - Pierre Peyret
- Université d'AuvergneEA 4678 CIDAM63001Clermont‐FerrandFrance
| | - Anthony Ranchou‐Peyruse
- Université de Pau et des Pays de l'AdourEquipe Environnement et Microbiologie, IPREM‐CNRS 5254F‐64013PauFrance
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16
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Xia D, Ye H, Xie Y, Yang C, Chen M, Dang Z, Yi X, Lu G. Isotope geochemistry, hydrochemistry, and mineralogy of a river affected by acid mine drainage in a mining area, South China. RSC Adv 2017. [DOI: 10.1039/c7ra07809a] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
This work utilized stable isotopes to evaluate the processes that affect the sulfate content in the waters of an AMD-affected river.
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Affiliation(s)
- Di Xia
- School of Environment and Energy
- South China University of Technology
- Guangzhou 510006
- China
| | - Han Ye
- School of Environment and Energy
- South China University of Technology
- Guangzhou 510006
- China
| | - Yingying Xie
- School of Environment and Energy
- South China University of Technology
- Guangzhou 510006
- China
| | - Chengfang Yang
- School of Environment and Energy
- South China University of Technology
- Guangzhou 510006
- China
| | - Meiqin Chen
- School of Environmental and Biological Engineering
- Guangdong University of Petrochemical Technology
- Maoming 525000
- China
| | - Zhi Dang
- School of Environment and Energy
- South China University of Technology
- Guangzhou 510006
- China
- The Key Laboratory of Pollution Control and Ecosystem Restoration in Industry Clusters
| | - Xiaoyun Yi
- School of Environment and Energy
- South China University of Technology
- Guangzhou 510006
- China
- The Key Laboratory of Pollution Control and Ecosystem Restoration in Industry Clusters
| | - Guining Lu
- School of Environment and Energy
- South China University of Technology
- Guangzhou 510006
- China
- Guangdong Provincial Engineering and Technology Research Center for Environmental Risk Prevention and Emergency Disposal
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17
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Balk M, Keuskamp JA, Laanbroek HJ. Potential for Sulfate Reduction in Mangrove Forest Soils: Comparison between Two Dominant Species of the Americas. Front Microbiol 2016; 7:1855. [PMID: 27917167 PMCID: PMC5114281 DOI: 10.3389/fmicb.2016.01855] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Accepted: 11/03/2016] [Indexed: 12/05/2022] Open
Abstract
Avicennia and Rhizophora are globally occurring mangrove genera with different traits that place them in different parts of the intertidal zone. It is generally accepted that the oxidizing capacity of Avicennia roots is larger than that of Rhizophora roots, which initiates more reduced conditions in the soil below the latter genus. We hypothesize that the more reduced conditions beneath Rhizophora stands lead to more active sulfate-reducing microbial communities compared to Avicennia stands. To test this hypothesis, we measured sulfate reduction traits in soil samples collected from neighboring Avicennia germinans and Rhizophora mangle stands at three different locations in southern Florida. The traits measured were sulfate reduction rates (SRR) in flow-through reactors containing undisturbed soil layers in the absence and presence of easily degradable carbon compounds, copy numbers of the dsrB gene, which is specific for sulfate-reducing microorganisms, and numbers of sulfate-reducing cells that are able to grow in liquid medium on a mixture of acetate, propionate and lactate as electron donors. At the tidal locations Port of the Islands and South Hutchinson Islands, steady state SRR, dsrB gene copy numbers and numbers of culturable cells were higher at the A. germinans than at the R. mangle stands, although not significantly for the numbers at Port of the Islands. At the non-tidal location North Hutchinson Island, results are mixed with respect to these sulfate reduction traits. At all locations, the fraction of culturable cells were significantly higher at the R. mangle than at the A. germinans stands. The dynamics of the initial SRR implied a more in situ active sulfate-reducing community at the intertidal R. mangle stands. It was concluded that in agreement with our hypothesis R. mangle stands accommodate a more active sulfate-reducing community than A. germinans stands, but only at the tidal locations. The differences between R. mangle and A. germinans stands were absent at the non-tidal, impounded location.
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Affiliation(s)
- Melike Balk
- Department of Microbial Ecology, Netherlands Institute of Ecology-Royal Netherlands Academy of Arts and SciencesWageningen, Netherlands; Faculty of Geosciences, Utrecht UniversityUtrecht, Netherlands
| | - Joost A Keuskamp
- Department of Microbial Ecology, Netherlands Institute of Ecology-Royal Netherlands Academy of Arts and SciencesWageningen, Netherlands; Ecology and Biodiversity Group, Department of Biology, Utrecht UniversityUtrecht, Netherlands
| | - Hendrikus J Laanbroek
- Department of Microbial Ecology, Netherlands Institute of Ecology-Royal Netherlands Academy of Arts and SciencesWageningen, Netherlands; Ecology and Biodiversity Group, Department of Biology, Utrecht UniversityUtrecht, Netherlands
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18
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Lefèvre CT, Howse PA, Schmidt ML, Sabaty M, Menguy N, Luther GW, Bazylinski DA. Growth of magnetotactic sulfate-reducing bacteria in oxygen concentration gradient medium. ENVIRONMENTAL MICROBIOLOGY REPORTS 2016; 8:1003-1015. [PMID: 27701830 DOI: 10.1111/1758-2229.12479] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Although dissimilatory sulfate-reducing bacteria (SRB) are generally described as strictly anaerobic organisms with regard to growth, several reports have shown that some SRB, particularly Desulfovibrio species, are quite resistant to O2 . For example, SRB remain viable in many aerobic environments while some even reduce O2 to H2 O. However, reproducible aerobic growth of SRB has not been unequivocally documented. Desulfovibrio magneticus is a SRB that is also a magnetotactic bacterium (MTB). MTB biomineralize magnetosomes which are intracellular, membrane-bounded, magnetic iron mineral crystals. The ability of D. magneticus to grow aerobically in several different media under air where an O2 concentration gradient formed, or under O2 -free N2 gas was tested. Under air, cells grew as a microaerophilic band of cells at the oxic-anoxic interface in media lacking sulfate. These results show that D. magneticus is capable of aerobic growth with O2 as a terminal electron acceptor. This is the first report of consistent, reproducible aerobic growth of SRB. This finding is critical in determining important ecological roles SRB play in the environment. Interestingly, the crystal structure of the magnetite crystals of D. magneticus grown under microaerobic conditions showed significant differences compared with those produced anaerobically providing more evidence that environmental parameters influence magnetosome formation.
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Affiliation(s)
- Christopher T Lefèvre
- CNRS/CEA/Aix-Marseille Université UMR7265 Institut de biosciences et biotechnologies Laboratoire de Bioénergétique Cellulaire, Saint Paul lez Durance, 13108, France
| | - Paul A Howse
- School of Life Sciences, University of Nevada at Las Vegas, Las Vegas, NV, 89154-4004, USA
| | - Marian L Schmidt
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA
| | - Monique Sabaty
- CNRS/CEA/Aix-Marseille Université UMR7265 Institut de biosciences et biotechnologies Laboratoire de Bioénergétique Cellulaire, Saint Paul lez Durance, 13108, France
| | - Nicolas Menguy
- Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, Sorbonne Universités, Université Pierre et Marie Curie, UMR 7590 CNRS, Institut de Recherche pour le Développement UMR 206, Museum National d'Histoire Naturelle, Paris Cedex 05, 75252, France
| | - George W Luther
- School of Marine Science and Policy, University of Delaware, 700 Pilottown Rd. Lewes, DE, 19958, USA
| | - Dennis A Bazylinski
- School of Life Sciences, University of Nevada at Las Vegas, Las Vegas, NV, 89154-4004, USA
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19
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Marietou A. Nitrate reduction in sulfate-reducing bacteria. FEMS Microbiol Lett 2016; 363:fnw155. [DOI: 10.1093/femsle/fnw155] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/06/2016] [Indexed: 12/27/2022] Open
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20
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Liu H, Tan S, Yu T, Liu Y. Sulfate reducing bacterial community and in situ activity in mature fine tailings analyzed by real time qPCR and microsensor. J Environ Sci (China) 2016; 44:141-147. [PMID: 27266310 DOI: 10.1016/j.jes.2015.08.025] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2015] [Revised: 07/18/2015] [Accepted: 07/18/2015] [Indexed: 06/06/2023]
Abstract
Sulfate reducing bacteria (SRB) play significant roles in anaerobic environments in oil sands mature fine tailings (MFTs). Hydrogen sulfide (H2S) is produced during the biological sulfate reduction process. The production of toxic H2S is one of the concerns because it may hinder the landscape remediation efficiency of oil sands tailing ponds. In present study, the in situ activity and the community structure of SRB in MFT and gypsum amended MFT in two settling columns were investigated. Combined techniques of H2S microsensor and dissimilatory sulfite reductase β-subunit (dsrB) genes-based real time quantitative polymerase chain reaction (qPCR) were applied to detect the in situ H2S and the abundance of SRB. A higher diversity of SRB and more H2S were observed in gypsum amended MFT than that in MFT, indicating a higher sulfate reduction activity in gypsum amended MFT; in addition, the activity of SRB varied as depth in both MFT and gypsum amended MFT: the deeper the more H2S produced. Long-term plans for tailings management can be assessed more wisely with the information provided in this study.
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Affiliation(s)
- Hong Liu
- Department of Civil and Environmental Engineering, University of Alberta, Edmonton, Canada
| | - Shuying Tan
- Department of Civil and Environmental Engineering, University of Alberta, Edmonton, Canada
| | - Tong Yu
- Department of Civil and Environmental Engineering, University of Alberta, Edmonton, Canada.
| | - Yang Liu
- Department of Civil and Environmental Engineering, University of Alberta, Edmonton, Canada.
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21
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Frindte K, Allgaier M, Grossart HP, Eckert W. Microbial Response to Experimentally Controlled Redox Transitions at the Sediment Water Interface. PLoS One 2015; 10:e0143428. [PMID: 26599000 PMCID: PMC4657962 DOI: 10.1371/journal.pone.0143428] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Accepted: 11/04/2015] [Indexed: 11/29/2022] Open
Abstract
The sediment–water interface of freshwater lakes is characterized by sharp chemical gradients, shaped by the interplay between physical, chemical and microbial processes. As dissolved oxygen is depleted in the uppermost sediment, the availability of alternative electron acceptors, e.g. nitrate and sulfate, becomes the limiting factor. We performed a time series experiment in a mesocosm to simulate the transition from aerobic to anaerobic conditions at the sediment–water interface. Our goal was to identify changes in the microbial activity due to redox transitions induced by successive depletion of available electron acceptors. Monitoring critical hydrochemical parameters in the overlying water in conjunction with a new sampling strategy for sediment bacteria enabled us to correlate redox changes in the water to shifts in the active microbial community and the expression of functional genes representing specific redox-dependent microbial processes. Our results show that during several transitions from oxic-heterotrophic condition to sulfate-reducing condition, nitrate-availability and the on-set of sulfate reduction strongly affected the corresponding functional gene expression. There was evidence of anaerobic methane oxidation with NOx. DGGE analysis revealed redox-related changes in microbial activity and expression of functional genes involved in sulfate and nitrite reduction, whereas methanogenesis and methanotrophy showed only minor changes during redox transitions. The combination of high-frequency chemical measurements and molecular methods provide new insights into the temporal dynamics of the interplay between microbial activity and specific redox transitions at the sediment–water interface.
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Affiliation(s)
- Katharina Frindte
- Department of Soil Science, Institute for Crop Science and Resource Conservation (INRES), University of Bonn, Nußallee 13, Bonn, Germany
| | - Martin Allgaier
- Berlin Center for Genomics in Biodiversity Research (BeGenDiv), Königin-Luise-Straße 6-8, Berlin, Germany
| | - Hans-Peter Grossart
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Alte Fischerhütte 2, Stechlin, Germany
- Institute of Biochemistry and Biology, University of Potsdam, Am Neuen Palais 10, Potsdam, Germany
| | - Werner Eckert
- Israel Oceanographic and Limnological Research, The Yigal Allon Kinneret Limnological Laboratory, Migdal, Israel
- * E-mail:
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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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23
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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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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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25
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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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26
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Kang S, Van Nostrand JD, Gough HL, He Z, Hazen TC, Stahl DA, Zhou J. Functional gene array-based analysis of microbial communities in heavy metals-contaminated lake sediments. FEMS Microbiol Ecol 2013; 86:200-14. [DOI: 10.1111/1574-6941.12152] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2012] [Revised: 05/19/2013] [Accepted: 05/21/2013] [Indexed: 11/28/2022] Open
Affiliation(s)
- Sanghoon Kang
- Department of Microbiology and Plant Biology; Institute for Environmental Genomics; University of Oklahoma; Norman; OK; USA
| | - Joy D. Van Nostrand
- Department of Microbiology and Plant Biology; Institute for Environmental Genomics; University of Oklahoma; Norman; OK; USA
| | - Heidi L. Gough
- Department of Civil and Environmental Engineering; University of Washington; Seattle; WA; USA
| | - Zhili He
- Department of Microbiology and Plant Biology; Institute for Environmental Genomics; University of Oklahoma; Norman; OK; USA
| | - Terry C. Hazen
- Department of Earth and Planetary Sciences; University of Tennessee; Knoxville; TN; USA
| | - David A. Stahl
- Department of Civil and Environmental Engineering; University of Washington; Seattle; WA; USA
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27
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Sass AM, Eschemann A, Kühl M, Thar R, Sass H, Cypionka H. Growth and chemosensory behavior of sulfate-reducing bacteria in oxygen-sulfide gradients. FEMS Microbiol Ecol 2012; 40:47-54. [PMID: 19709210 DOI: 10.1111/j.1574-6941.2002.tb00935.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Growth and chemotactic behavior in oxic-anoxic gradients were studied with two freshwater and four marine strains of sulfate-reducing bacteria related to the genera Desulfovibrio, Desulfomicrobium or Desulfobulbus. Cells were grown in oxygen-sulfide counter-gradients within tubes filled with agar-solidified medium. The immobilized cells grew mainly in the anoxic zone, revealing a peak below the oxic-anoxic interface. All tested strains survived exposure to air for 8 h and all were capable of oxygen reduction with lactate. Most strains also oxidized sulfide with oxygen. Desulfovibrio desulfuricans responded chemotactically to lactate, nitrate, sulfate and thiosulfate, and even sulfide functioned as an attractant. In oxic-anoxic gradients the bacteria moved away from high oxygen concentrations and formed bands at the outer edge of the oxic zone at low oxygen concentration (<5% O2 saturation). They were able to actively change the extension and slope of the gradients by oxygen reduction with lactate or even sulfide as electron donor. Generally, the chemotactic behavior was in agreement with a defense strategy that re-establishes anoxic conditions, thus promoting anaerobic growth and, in a natural community, fermentative production of the preferred electron donors of the sulfate-reducing bacteria.
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Affiliation(s)
- Andrea M Sass
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, D-26111 Oldenburg, Germany
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He R, Xia FF, Bai Y, Wang J, Shen DS. Mechanism of H2S removal during landfill stabilization in waste biocover soil, an alterative landfill cover. JOURNAL OF HAZARDOUS MATERIALS 2012; 217-218:67-75. [PMID: 22459970 DOI: 10.1016/j.jhazmat.2012.02.061] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2011] [Revised: 02/07/2012] [Accepted: 02/27/2012] [Indexed: 05/31/2023]
Abstract
Hydrogen sulfide (H(2)S) is one of the primary contributors to odors at landfills. The mechanism of waste biocover soil (WBS) for H(2)S removal was investigated in simulated landfill systems with the contrast experiment of a landfill cover soil (LCS). The H(2)S removal efficiency was higher than 90% regardless of the WBS or LCS covers. The input of landfill gas (LFG) could stimulate the growth of aerobic heterotrophic bacteria, actinomycete, sulfate-reducing bacteria (SRB) and sulfur-oxidizing bacteria (SOB) in the WBS cover, while that caused a decrease of 1-2 orders of magnitude in the populations of actinomycete and fungi in the bottom layer of the LCS cover. As H(2)S inputted, the sulfide content in the WBS cover increased and reached the maximum on day 30. In the LCS cover, the highest soil sulfide content was exhibited in the bottom layer during the whole experiment. After exposure to LFG, the lower pH value and higher sulfate content were observed in the top layer of the WBS cover, while there was not a significant difference in different layers of the LCS cover. The results indicated a more rapid biotransformation between sulfide and sulfate occurred in the WBS cover compared to the LCS.
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Affiliation(s)
- Ruo He
- Department of Environmental Engineering, Zhejiang University, Hangzhou 310058, China.
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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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Dumont MG, Pommerenke B, Casper P, Conrad R. DNA-, rRNA- and mRNA-based stable isotope probing of aerobic methanotrophs in lake sediment. Environ Microbiol 2011; 13:1153-67. [PMID: 21261798 DOI: 10.1111/j.1462-2920.2010.02415.x] [Citation(s) in RCA: 106] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
A stable isotope probing (SIP) approach was used to study aerobic methane-oxidizing bacteria (methanotrophs) in lake sediment. Oligotrophic Lake Stechlin was chosen because it has a permanently oxic sediment surface. 16S rRNA and the pmoA gene, which encodes a subunit of the methane monooxygenase enzyme, were analysed following the incubation of sediment with (13) CH(4) and the separation of (13) C-labelled DNA and RNA from unlabelled nucleic acids. The incubation with (13) CH(4) was performed over a 4-day time-course and the pmoA genes and transcripts became progressively labelled such that approximately 70% of the pmoA genes and 80% of the transcripts were labelled at 96 h. The labelling of pmoA mRNA was quicker than pmoA genes, demonstrating that mRNA-SIP is more sensitive than DNA-SIP; however, the general rate of pmoA transcript labelling was comparable to that of the pmoA genes, indicating that the incorporation of (13) C into ribonucleic acids of methanotrophs was a gradual process. Labelling of Betaproteobacteria was clearly seen in analyses of 16S rRNA by DNA-SIP and not by RNA-SIP, suggesting that cross-feeding of the (13) C was primarily detected by DNA-SIP. In general, we show that the combination of SIP approaches provided valuable information about the activity and growth of the methanotrophic populations and the cross-feeding of methanotroph metabolites by other microorganisms.
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Affiliation(s)
- Marc G Dumont
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Strasse, Marburg, Germany.
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The haem–copper oxygen reductase of Desulfovibrio vulgaris contains a dihaem cytochrome c in subunit II. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2008; 1777:1528-34. [DOI: 10.1016/j.bbabio.2008.09.007] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2008] [Revised: 09/02/2008] [Accepted: 09/15/2008] [Indexed: 11/20/2022]
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Vladár P, Rusznyák A, Márialigeti K, Borsodi AK. Diversity of sulfate-reducing bacteria inhabiting the rhizosphere of Phragmites australis in Lake Velencei (Hungary) revealed by a combined cultivation-based and molecular approach. MICROBIAL ECOLOGY 2008; 56:64-75. [PMID: 18066486 DOI: 10.1007/s00248-007-9324-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2007] [Accepted: 09/14/2007] [Indexed: 05/25/2023]
Abstract
The community structure of sulfate-reducing bacteria (SRB) associated with reed (Phragmites australis) rhizosphere in Lake Velencei (Hungary) was investigated by using cultivation-based and molecular methods. The cultivation methods were restricted to recover lactate-utilizing species with the exclusion of Desulfobacter and some Desulfobacterium species presumably not being dominant members of the examined community. The most-probable-number (MPN) estimations of lactate-utilizing SRB showed that the cell counts in reed rhizosphere were at least one order of magnitude higher than that in the bulk sediment. The number of endospores was low compared to the total SRB counts. From the highest positive dilution of MPN series, 47 strains were isolated and grouped by restriction fragment length polymorphism (RFLP) analysis of the amplified 16S ribosomal RNA (rRNA) and dsrAB (dissimilatory sulfite reductase) genes. Contrary to the physiological diversity of the isolates, the combined results of RFLP analysis revealed higher diversity at species as well as at subspecies level. Based on the partial 16S rRNA sequences, the representative strains were closely affiliated with the genera Desulfovibrio and Desulfotomaculum. The partial dsrAB sequences of the clones, recovered after isolation and PCR amplification of the community DNA, were related to hitherto uncultured species of the genera Desulfovibrio and Desulfobulbus. Nevertheless, the representative of the second largest clone group was shown to be closely affiliated with the sequenced dsrAB gene of a strain isolated from the same environment and identified as Desulfovibrio alcoholivorans. Another clone sequence was closely related to a possible novel species also isolated within the scope of this work.
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Affiliation(s)
- Péter Vladár
- Department of Microbiology, Eötvös Loránd University, Pázmány P sétány 1/C, Budapest, Hungary
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33
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Presence and expression of terminal oxygen reductases in strictly anaerobic sulfate-reducing bacteria isolated from salt-marsh sediments. Anaerobe 2008; 14:145-56. [DOI: 10.1016/j.anaerobe.2008.03.001] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2007] [Revised: 03/08/2008] [Accepted: 03/14/2008] [Indexed: 11/23/2022]
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34
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Fichtel J, Köster J, Rullkötter J, Sass H. Spore dipicolinic acid contents used for estimating the number of endospores in sediments. FEMS Microbiol Ecol 2007; 61:522-32. [PMID: 17623026 DOI: 10.1111/j.1574-6941.2007.00354.x] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Endospores are heat-resistant bacterial resting stages that can remain viable for long periods of time and may thus accumulate in sediments as a function of sediment age. The number of spores in sediments has only rarely been quantified, because of methodological problems, and consequently little is known about the quantitative contribution of endospores to the total number of prokaryotic cells. We here report on a protocol to determine the number of endospores in sediments and cultures. The method is based on the fluorimetric determination of dipicolinic acid (DPA), a spore core-specific compound, after reaction with terbium chloride. The concentration of DPA in natural samples is converted into endospore numbers using endospore-forming pure cultures as standards. Quenching of the fluorescence by sediment constituents and background fluorescence due to humic substances hampered direct determination of DPA in sediments. To overcome those interferences, DPA was extracted using ethyl acetate prior to fluorimetric measurements of DPA concentrations. The first results indicated that endospore numbers obtained with this method are orders of magnitude higher than numbers obtained by cultivation after pasteurization. In one of the explored sediment cores, endospores accounted for 3% of all stainable prokaryotic cells.
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Affiliation(s)
- Jörg Fichtel
- Institut für Chemie und Biologie des Meeres (ICBM), Carl von Ossietzky Universität Oldenburg, Carl-von-Ossietzky-Strasse 9-11, Oldenburg, Germany
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35
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Fichtel J, Köster J, Scholz-Böttcher B, Sass H, Rullkötter J. A highly sensitive HPLC method for determination of nanomolar concentrations of dipicolinic acid, a characteristic constituent of bacterial endospores. J Microbiol Methods 2007; 70:319-27. [PMID: 17573136 DOI: 10.1016/j.mimet.2007.05.008] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2007] [Revised: 05/11/2007] [Accepted: 05/11/2007] [Indexed: 11/24/2022]
Abstract
A high-performance liquid chromatographic method with indirect fluorescence detection has been developed for quantification of dipicolinic acid, a major constituent of bacterial endospores. After separation on a reversed-phase column, a post-column reagent of sodium acetate at 1 mol l(-1) with 50 micromol l(-1) terbium chloride was added for complexation of dipicolinic acid. Terbium monodipicolinate complexes formed were quantified by measuring the fluorescence emission maximum at 548 nm after excitation with UV light at 270 nm wavelength. Parameters of post-column complexation were optimized to achieve a detection limit of 0.5 nmol DPA l(-1), corresponding to about 10(3) Desulfosporosinus orientis endospores per ml. The method was applied to the analysis of spore contamination in tuna and for estimating the endospore numbers in marine sediments.
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Affiliation(s)
- Jörg Fichtel
- Institut für Chemie und Biologie des Meeres, Carl von Ossietzky Universität Oldenburg, D-26129 Oldenburg, Germany.
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36
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Ramamoorthy S, Sass H, Langner H, Schumann P, Kroppenstedt RM, Spring S, Overmann J, Rosenzweig RF. Desulfosporosinus lacus sp. nov., a sulfate-reducing bacterium isolated from pristine freshwater lake sediments. Int J Syst Evol Microbiol 2006; 56:2729-2736. [PMID: 17158969 DOI: 10.1099/ijs.0.63610-0] [Citation(s) in RCA: 80] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel sulfate-reducing bacterium was isolated from pristine sediments of Lake Stechlin, Germany. This strain, STP12T, was found to contain predominantlyc-type cytochromes and to reduce sulfate, sulfite and thiosulfate using lactate as an electron donor. Although STP12Tcould not utilize elemental sulfur as an electron acceptor, it could support growth by dissimilatory Fe(III) reduction. In a comparison of 16S rRNA gene sequences, STP12Twas 96.7 % similar toDesulfosporosinus auripigmentiDSM 13351T, 96.5 % similar toDesulfosporosinus meridieiDSM 13257Tand 96.4 % similar toDesulfosporosinus orientisDSM 765T. DNA–DNA hybridization experiments revealed that strain STP12Tshows only 32 % reassociation with the type strain of the type species of the genus,D. orientisDSM 765T. These data, considered in conjunction with strain-specific differences in heavy metal tolerance, cell-wall chemotaxonomy and riboprint patterns, support recognition of strain STP12T(=DSM 15449T=JCM 12239T) as the type strain of a distinct and novel species within the genusDesulfosporosinus,Desulfosporosinus lacussp. nov.
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Affiliation(s)
- S Ramamoorthy
- Division of Biological Sciences, Program in Microbial Ecology, University of Montana, Missoula, MT 59812-4824, USA
| | - H Sass
- Institut für Chemie und Biologie des Meeres, Universität Oldenburg, D-26111 Oldenburg, Germany
| | - H Langner
- Department of Geology, University of Montana, Missoula, MT 59812, USA
| | - P Schumann
- DSMZ - Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Mascheroder Weg 1b, D-38124 Braunschweig, Germany
| | - R M Kroppenstedt
- DSMZ - Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Mascheroder Weg 1b, D-38124 Braunschweig, Germany
| | - S Spring
- DSMZ - Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Mascheroder Weg 1b, D-38124 Braunschweig, Germany
| | - J Overmann
- Section Microbiology, Department Biology I, Ludwig-Maximilians-Universität München, Maria-Ward-Str. 1a, D-80638 München, Germany
| | - R F Rosenzweig
- Division of Biological Sciences, Program in Microbial Ecology, University of Montana, Missoula, MT 59812-4824, USA
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37
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Leloup J, Quillet L, Berthe T, Petit F. Diversity of the dsrAB (dissimilatory sulfite reductase) gene sequences retrieved from two contrasting mudflats of the Seine estuary, France. FEMS Microbiol Ecol 2006; 55:230-8. [PMID: 16420631 DOI: 10.1111/j.1574-6941.2005.00021.x] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
The diversity of sulfate-reducing microorganisms was investigated in two contrasting mudflats of the Seine estuary, by PCR amplification, cloning and sequencing of the genes coding for parts of the alpha and beta subunits of dissimilatory sulfite reductase (dsrAB). One site is located in the mixing-zone and shows marine characteristics, with high salinity and sulfate concentration, whereas the other site shows freshwater characteristics, with low salinity and sulfate concentration. Diversity and abundance of dsrAB genes differed between the two sites. In the mixing-zone sediments, most of the dsrAB sequences were affiliated to those of marine Gram-negative bacteria belonging to the order of Desulfobacterales, whereas in the freshwater sediments, a majority of dsrAB sequences was related to those of the Gram-positive bacteria belonging to the genus Desulfotomaculum. It is speculated that this is related to the salinity and the sulfate concentration in the two mudflats.
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Affiliation(s)
- Julie Leloup
- Laboratoire de Microbiologie Du Froid, Groupe Biodiversité et Environnement, UPRES-2123, Université de Rouen, Mont Saint Aignan, France.
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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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Martens-Habbena W, Sass H. Sensitive Determination of Microbial Growth by Nucleic Acid Staining in Aqueous Suspension. Appl Environ Microbiol 2006; 72:87-95. [PMID: 16391029 PMCID: PMC1352258 DOI: 10.1128/aem.72.1.87-95.2006] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
ABSTRACT
The determination of cell numbers or biomass in laboratory cultures or environmental samples is usually based on turbidity measurements, viable counts, biochemical determinations (e.g., protein and lipid measurements), microscopic counting, or recently, flow cytometric analysis. In the present study, we developed a novel procedure for the sensitive quantification of microbial cells in cultures and most-probable-number series. The assay combines fluorescent nucleic acid staining and subsequent fluorescence measurement in suspension. Six different fluorescent dyes (acridine orange, DAPI [4′,6′-diamidino-2-phenylindole], ethidium bromide, PicoGreen, and SYBR green I and II) were evaluated. SYBR green I was found to be the most sensitive dye and allowed the quantification of 50,000 to up to 1.5 × 10
8
Escherichia coli
cells per ml sample. The rapid staining procedure was robust against interference from rRNA, sample fixation by the addition of glutaric dialdehyde, and reducing agents such as sodium dithionite, sodium sulfide, and ferrous sulfide. It worked well with phylogenetically distant bacterial and archaeal strains. Excellent agreement with optical density measurements of cell increases was achieved during growth experiments performed with aerobic and sulfate-reducing bacteria. The assay offers a time-saving, more sensitive alternative to epifluorescence microscopy analysis of most-probable-number dilution series. This method simplifies the quantification of microbial cells in pure cultures as well as enrichments and is particularly suited for low cell densities.
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Affiliation(s)
- Willm Martens-Habbena
- Paleomicrobiology Group, Institute for the Chemistry and Biology of the Marine Environment, University of Oldenburg, D-26111 Oldenburg, Germany
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40
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Lehours AC, Bardot C, Thenot A, Debroas D, Fonty G. Anaerobic microbial communities in Lake Pavin, a unique meromictic lake in France. Appl Environ Microbiol 2005; 71:7389-400. [PMID: 16269781 PMCID: PMC1287608 DOI: 10.1128/aem.71.11.7389-7400.2005] [Citation(s) in RCA: 98] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The Bacteria and Archaea from the meromictic Lake Pavin were analyzed in samples collected along a vertical profile in the anoxic monimolimnion and were compared to those in samples from the oxic mixolimnion. Nine targeted 16S rRNA oligonucleotide probes were used to assess the distribution of Bacteria and Archaea and to investigate the in situ occurrence of sulfate-reducing bacteria and methane-producing Archaea involved in the terminal steps of the anaerobic degradation of organic material. The diversity of the complex microbial communities was assessed from the 16S rRNA polymorphisms present in terminal restriction fragment (TRF) depth patterns. The densities of the microbial community increased in the anoxic layer, and Archaea detected with probe ARCH915 represented the largest microbial group in the water column, with a mean Archaea/Eubacteria ratio of 1.5. Terminal restriction fragment length polymorphism (TRFLP) analysis revealed an elevated archaeal and bacterial phylotype richness in anoxic bottom-water samples. The structure of the Archaea community remained rather homogeneous, while TRFLP patterns for the eubacterial community revealed a heterogeneous distribution of eubacterial TRFs.
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Affiliation(s)
- Anne-C Lehours
- Laboratoire de Biologie des Protistes, UMR CNRS 6023, 24 avenue des Landais, 63177 Aubière Cedex, France.
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Stevens H, Stübner M, Simon M, Brinkhoff T. Phylogeny of Proteobacteria and Bacteroidetes from oxic habitats of a tidal flat ecosystem. FEMS Microbiol Ecol 2005; 54:351-65. [PMID: 16332333 DOI: 10.1016/j.femsec.2005.04.008] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2004] [Revised: 01/13/2005] [Accepted: 04/26/2005] [Indexed: 11/22/2022] Open
Abstract
Bacteria of the phyla Proteobacteria and Bacteroidetes are known to be the most prominent heterotrophic organisms in marine surface waters. In order to investigate the occurrence of these phyla in a coastal environment, the tidal flat ecosystem German Wadden Sea, we analyzed a clone library of PCR-amplified and sequenced 16S rRNA gene fragments and isolated 46 new strains affiliated with these phyla from the water column with various polymers and complex media as substrates. The phylogenetic affiliation of these strains was analyzed on the basis of sequenced 16S rRNA gene fragments. Subsequently, a comprehensive phylogenetic analysis of Proteobacteria and Bacteroidetes including available sequences from oxic habitats of earlier studies of this ecosystem was performed. Sequences of the earlier studies were derived from isolation approaches and from denaturing gradient gel electrophoresis (DGGE) analyses of environmental samples and high dilution steps of MPN (most probable number) cultures. The majority of the 265 sequences included in this analysis affiliated with alpha-Proteobacteria (45.3%), gamma-Proteobacteria (31.7%), and Bacteroidetes (16.2%). Almost 7% belong to the delta-Proteobacteria and several of these clones affiliated with the Myxococcales, a group comprising obligate aerobic organisms. Within the alpha- and gamma-Proteobacteria specific clusters were identified including isolates from high dilution steps of dilution cultures and/or clones from the clone library or DGGE gels, implying a high abundance of some of these organisms. Within the gamma-Proteobacteria a new cluster is proposed, which consists of marine surface-attached organisms. This SAMMIC (Surface Attached Marine MICrobes) cluster comprises only uncultured phylotypes and exhibits a global distribution. Overall, the analysis indicates that Proteobacteria and Bacteroidetes of the Wadden Sea have a surprisingly high diversity, presumably a result of the signature of this ecosystem as a melting pot at the land-sea interface and comprising a great habitat variety.
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Affiliation(s)
- Heike Stevens
- Institute for Chemistry and Biology of the Marine Environment ICBM, University of Oldenburg, P.O. Box 2503, D-26111 Oldenburg, Germany
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Dandelot S, Matheron R, Le Petit J, Verlaque R, Cazaubon A. Variations temporelles des paramètres physicochimiques et microbiologiques de trois écosystèmes aquatiques (Sud-Est de la France) envahis par des Ludwigia. C R Biol 2005; 328:991-9. [PMID: 16286088 DOI: 10.1016/j.crvi.2005.09.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2005] [Revised: 09/23/2005] [Accepted: 09/27/2005] [Indexed: 10/25/2022]
Abstract
In France, two amphibious hydrophytes of alien Ludwigia (Onagraceae) have for about the past twenty years been causing serious ecological and economic problems: L. peploides (Kunth) Raven et L. grandiflora (Michaux) Greuter & Burdet. This bacteriological and physicochemical study, focused on three different Mediterranean aquatic ecosystems, reveals, for the first time, a direct negative impact of these American invaders. During summer, while plant growth is intensive, and the appearance in the water column of anoxic conditions and production of toxic compounds may be observed, notably in L. grandiflora stands. The toxicity is linked to a proliferation of sulphate-reducing bacteria producing sulphides that are very harmful for aquatic organisms.
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Affiliation(s)
- Sophie Dandelot
- Institut Méditerranéen d'Ecologie et de Paléoécologie, UMR 6116, Faculté des Sciences et Techniques de Saint-Jérôme, Université Paul-Cézanne, 13397 Marseille cedex 20, France.
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Dar SA, Kuenen JG, Muyzer G. Nested PCR-denaturing gradient gel electrophoresis approach to determine the diversity of sulfate-reducing bacteria in complex microbial communities. Appl Environ Microbiol 2005; 71:2325-30. [PMID: 15870318 PMCID: PMC1087575 DOI: 10.1128/aem.71.5.2325-2330.2005] [Citation(s) in RCA: 111] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Here, we describe a three-step nested-PCR-denaturing gradient gel electrophoresis (DGGE) strategy to detect sulfate-reducing bacteria (SRB) in complex microbial communities from industrial bioreactors. In the first step, the nearly complete 16S rRNA gene was amplified using bacterial primers. Subsequently, this product was used as a template in a second PCR with group-specific SRB primers. A third round of amplification was conducted to obtain fragments suitable for DGGE. The largest number of bands was observed in DGGE patterns of products obtained with primers specific for the Desulfovibrio-Desulfomicrobium group, indicating a large diversity of these SRBs. In addition, members of other phylogenetic SRB groups, i.e., Desulfotomaculum, Desulfobulbus, and Desulfococcus-Desulfonema-Desulfosarcina, were detected. Bands corresponding to Desulfobacterium and Desulfobacter were not detected in the bioreactor samples. Comparative sequence analysis of excised DGGE bands revealed the identity of the community members. The developed three-step PCR-DGGE strategy is a welcome tool for studying the diversity of sulfate-reducing bacteria.
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Affiliation(s)
- Shabir A Dar
- Dept. of Biotechnology, Delft University of Technology, Julianalaan 67, NL-2628 BC Delft, The Netherlands
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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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Dröge S, Limper U, Emtiazi F, Schönig I, Pavlus N, Drzyzga O, Fischer U, König H. In vitro and in vivo sulfate reduction in the gut contents of the termite Mastotermes darwiniensis and the rose-chafer Pachnoda marginata. J GEN APPL MICROBIOL 2005; 51:57-64. [PMID: 15942866 DOI: 10.2323/jgam.51.57] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Sulfate-reducing bacteria (SRB) from termites have been assigned to the genus Desulfovibrio. Desulfovibrio intestinalis lives in the gut of the Australian termite Mastotermes darwiniensis. For the first time we were able to enrich and identify a sulfate-reducing bacterium from the gut of the rose-chafer Pachnoda marginata, which showed the highest 16S rDNA sequence identity (93%) to Desulfovibrio intestinalis and Desulfovibrio strain STL1. Compared to Mastotermes darwiniensis (1x10(7) cells of SRB per ml gut contents), sulfate-reducing bacteria occurred in higher numbers in the gut contents of Pachnoda marginata reaching cell titers of up to 2x10(8) cells per ml gut contents. In vitro sulfate reduction rates were determined with SRB from the gut contents of the termite Mastotermes darwiniensis and the beetle Pachnoda marginata. Due to the higher cell titer, the sulfate reduction rate of Pachnoda marginata was 10(4) nmolxh-1xml-1 and therefore, 21 times higher than that of Mastotermes darwiniensis. In addition, we detected in vivo sulfate reduction in Mastotermes darwiniensis, which indicates that sulfate reducers play an active role in the sulfur metabolism in the termite gut.
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Affiliation(s)
- Stefan Dröge
- Institut für Mikrobiologie und Weinforschung, Johannes Gutenberg-Universität, Mainz, Germany
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Loy A, Küsel K, Lehner A, Drake HL, Wagner M. Microarray and functional gene analyses of sulfate-reducing prokaryotes in low-sulfate, acidic fens reveal cooccurrence of recognized genera and novel lineages. Appl Environ Microbiol 2004; 70:6998-7009. [PMID: 15574893 PMCID: PMC535148 DOI: 10.1128/aem.70.12.6998-7009.2004] [Citation(s) in RCA: 160] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2004] [Accepted: 07/27/2004] [Indexed: 11/20/2022] Open
Abstract
Low-sulfate, acidic (approximately pH 4) fens in the Lehstenbach catchment in the Fichtelgebirge mountains in Germany are unusual habitats for sulfate-reducing prokaryotes (SRPs) that have been postulated to facilitate the retention of sulfur and protons in these ecosystems. Despite the low in situ availability of sulfate (concentration in the soil solution, 20 to 200 microM) and the acidic conditions (soil and soil solution pHs, approximately 4 and 5, respectively), the upper peat layers of the soils from two fens (Schlöppnerbrunnen I and II) of this catchment displayed significant sulfate-reducing capacities. 16S rRNA gene-based oligonucleotide microarray analyses revealed stable diversity patterns for recognized SRPs in the upper 30 cm of both fens. Members of the family "Syntrophobacteraceae" were detected in both fens, while signals specific for the genus Desulfomonile were observed only in soils from Schlöppnerbrunnen I. These results were confirmed and extended by comparative analyses of environmentally retrieved 16S rRNA and dissimilatory (bi)sulfite reductase (dsrAB) gene sequences; dsrAB sequences from Desulfobacca-like SRPs, which were not identified by microarray analysis, were obtained from both fens. Hypotheses concerning the ecophysiological role of these three SRP groups in the fens were formulated based on the known physiological properties of their cultured relatives. In addition to these recognized SRP lineages, six novel dsrAB types that were phylogenetically unrelated to all known SRPs were detected in the fens. These dsrAB sequences had no features indicative of pseudogenes and likely represent novel, deeply branching, sulfate- or sulfite-reducing prokaryotes that are specialized colonists of low-sulfate habitats.
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Affiliation(s)
- Alexander Loy
- Department of Microbial Ecology, Institute of Ecology and Conservation Biology, University of Vienna, Vienna, Austria
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Hockin SL, Gadd GM. Linked redox precipitation of sulfur and selenium under anaerobic conditions by sulfate-reducing bacterial biofilms. Appl Environ Microbiol 2003; 69:7063-72. [PMID: 14660350 PMCID: PMC309891 DOI: 10.1128/aem.69.12.7063-7072.2003] [Citation(s) in RCA: 82] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2003] [Accepted: 08/27/2003] [Indexed: 11/20/2022] Open
Abstract
A biofilm-forming strain of sulfate-reducing bacteria (SRB), isolated from a naturally occurring mixed biofilm and identified by 16S rDNA analysis as a strain of Desulfomicrobium norvegicum, rapidly removed 200 micro M selenite from solution during growth on lactate and sulfate. Elemental selenium and elemental sulfur were precipitated outside SRB cells. Precipitation occurred by an abiotic reaction with bacterially generated sulfide. This appears to be a generalized ability among SRB, arising from dissimilatory sulfide biogenesis, and can take place under low redox conditions and in the dark. The reaction represents a new means for the deposition of elemental sulfur by SRB under such conditions. A combination of transmission electron microscopy, environmental scanning electron microscopy, and cryostage field emission scanning electron microscopy were used to reveal the hydrated nature of SRB biofilms and to investigate the location of deposited sulfur-selenium in relation to biofilm elements. When pregrown SRB biofilms were exposed to a selenite-containing medium, nanometer-sized selenium-sulfur granules were precipitated within the biofilm matrix. Selenite was therefore shown to pass through the biofilm matrix before reacting with bacterially generated sulfide. This constitutes an efficient method for the removal of toxic concentrations of selenite from solution. Implications for environmental cycling and the fate of sulfur and selenium are discussed, and a general model for the potential action of SRB in selenium transformations is presented.
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Affiliation(s)
- Simon L Hockin
- Division of Environmental and Applied Biology, Biological Sciences Institute, School of Life Sciences, University of Dundee, Dundee DD1 4HN, Scotland, United Kingdom
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Fareleira P, Santos BS, António C, Moradas-Ferreira P, LeGall J, Xavier AV, Santos H. Response of a strict anaerobe to oxygen: survival strategies in Desulfovibrio gigas. MICROBIOLOGY (READING, ENGLAND) 2003; 149:1513-1522. [PMID: 12777491 DOI: 10.1099/mic.0.26155-0] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The biochemical response to oxygen of the strictly anaerobic sulfate-reducing bacterium Desulfovibrio gigas was studied with the goal of elucidating survival strategies in oxic environments. Cultures of D. gigas on medium containing lactate and sulfate were exposed to oxygen (concentration 5-120 micro M). Growth was fully inhibited by oxygen, but the cultures resumed growth as soon as they were shifted back to anoxic conditions. Following 24 h exposure to oxygen the growth rate was as high as 70 % of the growth rates observed before oxygenation. Catalase levels and activity were enhanced by exposure to oxygen whereas superoxide-scavenging and glutathione reductase activities were not affected. The general pattern of cellular proteins as analysed by two-dimensional electrophoresis was altered in the presence of oxygen, the levels of approximately 12 % of the detected proteins being markedly increased. Among the induced proteins, a homologue of a 60 kDa eukaryotic heat-shock protein (Hsp60) was identified by immunoassay analysis. In the absence of external substrates, the steady-state levels of nucleoside triphosphates detected by in vivo (31)P-NMR under saturating concentrations of oxygen were 20 % higher than under anoxic conditions. The higher energy levels developed under oxygen correlated with a lower rate of substrate (glycogen) mobilization, but no experimental evidence for a contribution from oxidative phosphorylation was found. The hypothesis that oxygen interferes with ATP dissipation processes is discussed.
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Affiliation(s)
- Paula Fareleira
- Estação Agronómica Nacional, Instituto Nacional de Investigação Agrária, Quinta do Marquês, 2780-156 Oeiras, Portugal
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Rua da Quinta Grande, 6 Apartado 127, 2780-156 Oeiras, Portugal
| | - Bruno S Santos
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Rua da Quinta Grande, 6 Apartado 127, 2780-156 Oeiras, Portugal
| | - Célia António
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Rua da Quinta Grande, 6 Apartado 127, 2780-156 Oeiras, Portugal
| | | | - Jean LeGall
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Rua da Quinta Grande, 6 Apartado 127, 2780-156 Oeiras, Portugal
| | - António V Xavier
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Rua da Quinta Grande, 6 Apartado 127, 2780-156 Oeiras, Portugal
| | - Helena Santos
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Rua da Quinta Grande, 6 Apartado 127, 2780-156 Oeiras, Portugal
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Okabe S, Santegoeds CM, Watanabe Y, de Beer D. Successional development of sulfate-reducing bacterial populations and their activities in an activated sludge immobilized agar gel film. Biotechnol Bioeng 2002; 78:119-30. [PMID: 11870602 DOI: 10.1002/bit.10240] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
A combination of fluorescence in situ hybridization (FISH), microprofiles, and denaturing gradient gel electrophoresis (DGGE) analysis of PCR-amplified 16S rDNA fragments followed by hybridization analysis with specific probes was applied to investigate successional development of sulfate-reducing bacteria (SRB) community structure and in situ sulfide production activity within an activated sludge immobilized agar gel film. In this model biofilm system, since biases arising from biofilm heterogeneity can be ignored, the population dynamics of SRB in the agar gel is directly related to physiological capability and in situ activity of SRB. Microelectrode measurements showed that an anoxic zone was already developed at the beginning (0 day), a first sulfide production of 0.054 mumol H2S m(-2) x s(-1) was detected during the first week, and the rate increased gradually to 0.221 mumol H2S m(-2) x s(-1) in the fifth week. The most active sulfide production zone moved upward to the chemocline and intensified with time to form a narrow zone with high volumetric sulfide production rates. This result coincided with the shift of the spatial distributions of SRB populations determined by FISH. In situ hybridization with probe SRB385 for mainly general SRB of the delta Proteobacteria plus some gram-positive bacteria and probe 660 for Desulfobulbus indicated that the most abundant populations of SRB were primarily restricted to near the oxic/anoxic interface (chemocline). A close observation of the development of the vertical distributions of SRB populations revealed that the cell numbers of Desulfobulbus tripled (from 0.5 x 10(8) to 1.5 x 10(8) cells cm(-3)) near the oxic/anoxic interface. Similar growth (from 1.0 x10(8) to 4.5 x 10(8) cells cm(-3)) of Desulfovibrio-like SRB that hybridized with probe SRB385 was observed. PCR-DGGE followed by hybridization analysis revealed that one Desulfobulbus strain was detected from the beginning, and another strain appeared after 1 week, coinciding with the first detected sulfide production. In addition, three strains hybridizing with probe 687 (possibly Desulfovibrio) were also dominant SRB in the agar gel.
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Affiliation(s)
- Satoshi Okabe
- Department of Urban and Environmental Engineering, Graduate School of Engineering, Hokkaido University, Sapporo 060-8628, Japan.
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Kleikemper J, Schroth MH, Sigler WV, Schmucki M, Bernasconi SM, Zeyer J. Activity and diversity of sulfate-reducing bacteria in a petroleum hydrocarbon-contaminated aquifer. Appl Environ Microbiol 2002; 68:1516-23. [PMID: 11916663 PMCID: PMC123867 DOI: 10.1128/aem.68.4.1516-1523.2002] [Citation(s) in RCA: 134] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Microbial sulfate reduction is an important metabolic activity in petroleum hydrocarbon (PHC)-contaminated aquifers. We quantified carbon source-enhanced microbial SO(4)(2-) reduction in a PHC-contaminated aquifer by using single-well push-pull tests and related the consumption of sulfate and added carbon sources to the presence of certain genera of sulfate-reducing bacteria (SRB). We also used molecular methods to assess suspended SRB diversity. In four consecutive tests, we injected anoxic test solutions (1,000 liters) containing bromide as a conservative tracer, sulfate, and either propionate, butyrate, lactate, or acetate as reactants into an existing monitoring well. After an initial incubation period, 1,000 liters of test solution-groundwater mixture was extracted from the same well. Average total test duration was 71 h. We measured concentrations of bromide, sulfate, and carbon sources in native groundwater as well as in injection and extraction phase samples and characterized the SRB population by using fluorescence in situ hybridization (FISH) and denaturing gradient gel electrophoresis (DGGE). Enhanced sulfate reduction concomitant with carbon source degradation was observed in all tests. Computed first-order rate coefficients ranged from 0.19 to 0.32 day(-1) for sulfate reduction and from 0.13 to 0.60 day(-1) for carbon source degradation. Sulfur isotope fractionation in unconsumed sulfate indicated that sulfate reduction was microbially mediated. Enhancement of sulfate reduction due to carbon source additions in all tests and variability of rate coefficients suggested the presence of specific SRB genera and a high diversity of SRB. We confirmed this by using FISH and DGGE. A large fraction of suspended bacteria hybridized with SRB-targeting probes SRB385 plus SRB385-Db (11 to 24% of total cells). FISH results showed that the activity of these bacteria was enhanced by addition of sulfate and carbon sources during push-pull tests. However, DGGE profiles indicated that the bacterial community structure of the dominant species did not change during the tests. Thus, the combination of push-pull tests with molecular methods provided valuable insights into microbial processes, activities, and diversity in the sulfate-reducing zone of a PHC-contaminated aquifer.
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Affiliation(s)
- Jutta Kleikemper
- Institute of Terrestrial Ecol., Swiss Federal Institute of Technology Zürich, CH-8952 Schlieren, Switzerland.
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