1
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Paiva AR, Pilloni G. Inferring Microbial Biomass Yield and Cell Weight Using Probabilistic Macrochemical Modeling. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2023; 20:442-454. [PMID: 35038296 DOI: 10.1109/tcbb.2021.3139290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Growth rates and biomass yields are key descriptors used in microbiology studies to understand how microbial species respond to changes in the environment. Of these, biomass yield estimates are typically obtained using cell counts and measurements of the feed substrate. These quantities are perturbed with measurement noise however. Perhaps most crucially, estimating biomass from cell counts, as needed to assess yields, relies on an assumed cell weight. Noise and discrepancies on these assumptions can lead to significant changes in conclusions regarding the microbes' response. This article proposes a methodology to address these challenges using probabilistic macrochemical models of microbial growth. It is shown that a model can be developed to fully use the experimental data, relax assumptions and greatly improve robustness to a priori estimates of the cell weight, and provides uncertainty estimates of key parameters. This methodology is demonstrated in the context of a specific case study and the estimation characteristics are validated in several scenarios using synthetically generated microbial growth data.
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2
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Hunt KA, von Netzer F, Gorman-Lewis D, Stahl DA. Microbial maintenance energy quantified and modeled with microcalorimetry. Biotechnol Bioeng 2022; 119:2413-2422. [PMID: 35680566 DOI: 10.1002/bit.28155] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 06/06/2022] [Accepted: 06/08/2022] [Indexed: 11/08/2022]
Abstract
Refining the energetic costs of cellular maintenance is essential for predicting microbial growth and survival in the environment. Here, we evaluate a simple batch culture method to quantify energy partitioning between growth and maintenance using microcalorimetry and thermodynamic modeling. The constants derived from the batch culture system were comparable to those that have been reported from meta-analyses of data derived from chemostat studies. The model accurately predicted temperature-dependent biomass yield and the upper temperature limit of growth for Desulfovibrio alaskensis G20, suggesting the method may have broad application. An Arrhenius temperature dependence for the specific energy consumption rate, inferred from substrate consumption and heat evolution, was observed over the entire viable temperature range. By combining this relationship for specific energy consumption rates and observed specific growth rates, the model describes an increase in nongrowth associated maintenance at higher temperatures and the corresponding decrease in energy available for growth. This analytical and thermodynamic formulation suggests that simply monitoring heat evolution in batch culture could be a useful complement to the recognized limitations of estimating maintenance using extrapolation to zero growth in chemostats.
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Affiliation(s)
- Kristopher A Hunt
- Department of Civil and Environmental Engineering, University of Washington, Seattle, Washington, USA
| | - Frederick von Netzer
- Department of Civil and Environmental Engineering, University of Washington, Seattle, Washington, USA
| | - Drew Gorman-Lewis
- Department of Earth and Space Sciences, University of Washington, Seattle, Washington, USA
| | - David A Stahl
- Department of Civil and Environmental Engineering, University of Washington, Seattle, Washington, USA
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3
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Ceron-Chafla P, García-Timermans C, de Vrieze J, Ganigué R, Boon N, Rabaey K, van Lier JB, Lindeboom REF. Pre-incubation conditions determine the fermentation pattern and microbial community structure in fermenters at mild hydrostatic pressure. Biotechnol Bioeng 2022; 119:1792-1807. [PMID: 35312065 PMCID: PMC9325544 DOI: 10.1002/bit.28085] [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: 08/26/2021] [Revised: 02/08/2022] [Accepted: 03/05/2022] [Indexed: 11/11/2022]
Abstract
Fermentation at elevated hydrostatic pressure is a novel strategy targeting product selectivity. However, the role of inoculum history and cross-resistance, that is, acquired tolerance from incubation under distinctive environmental stress, remains unclear in high-pressure operation. In our here presented work, we studied fermentation and microbial community responses of halotolerant marine sediment inoculum (MSI) and anaerobic digester inoculum (ADI), pre-incubated in serum bottles at different temperatures and subsequently exposed to mild hydrostatic pressure (MHP; < 10 MPa) in stainless steel reactors. Results showed that MHP effects on microbial growth, activity, and community structure were strongly temperature-dependent. At moderate temperature (20°C), biomass yield and fermentation were not limited by MHP; suggesting a cross-resistance effect from incubation temperature and halotolerance. Low temperatures (10°C) and MHP imposed kinetic and bioenergetic limitations, constraining growth and product formation. Fermentation remained favorable in MSI at 28°C and ADI at 37°C, despite reduced biomass yield resulting from maintenance and decay proportionally increasing with temperature. Microbial community structure was modified by temperature during the enrichment, and slight differences observed after MHP-exposure did not compromise functionality. Results showed that the relation incubation temperature-halotolerance proved to be a modifier of microbial responses to MHP and could be potentially exploited in fermentations to modulate product/biomass ratio.
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Affiliation(s)
- Pamela Ceron-Chafla
- Sanitary Engineering Section, Department of Water Management, Delft University of Technology, Delft, the Netherlands
| | - Cristina García-Timermans
- Faculty of Bioscience Engineering, Center for Microbial Ecology and Technology, Ghent University, Ghent, Belgium
| | - Jo de Vrieze
- Faculty of Bioscience Engineering, Center for Microbial Ecology and Technology, Ghent University, Ghent, Belgium.,Division of Soil and Water Management, Department of Earth and Environmental Sciences, KU Leuven, Leuven, Belgium.,Bio- and Chemical Systems Technology, Reactor Engineering and Safety (CREaS), Department of Chemical Engineering, KU Leuven, Leuven, Belgium
| | - Ramon Ganigué
- Faculty of Bioscience Engineering, Center for Microbial Ecology and Technology, Ghent University, Ghent, Belgium
| | - Nico Boon
- Faculty of Bioscience Engineering, Center for Microbial Ecology and Technology, Ghent University, Ghent, Belgium
| | - Korneel Rabaey
- Faculty of Bioscience Engineering, Center for Microbial Ecology and Technology, Ghent University, Ghent, Belgium.,Center for Advanced Process Technology for Urban Resource Recovery, Ghent, Belgium
| | - Jules B van Lier
- Sanitary Engineering Section, Department of Water Management, Delft University of Technology, Delft, the Netherlands
| | - Ralph E F Lindeboom
- Sanitary Engineering Section, Department of Water Management, Delft University of Technology, Delft, the Netherlands
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4
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Beulig F, Schubert F, Adhikari RR, Glombitza C, Heuer VB, Hinrichs KU, Homola KL, Inagaki F, Jørgensen BB, Kallmeyer J, Krause SJE, Morono Y, Sauvage J, Spivack AJ, Treude T. Rapid metabolism fosters microbial survival in the deep, hot subseafloor biosphere. Nat Commun 2022; 13:312. [PMID: 35078973 PMCID: PMC8789916 DOI: 10.1038/s41467-021-27802-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 12/10/2021] [Indexed: 11/25/2022] Open
Abstract
A fourth of the global seabed sediment volume is buried at depths where temperatures exceed 80 °C, a previously proposed thermal barrier for life in the subsurface. Here, we demonstrate, utilizing an extensive suite of radiotracer experiments, the prevalence of active methanogenic and sulfate-reducing populations in deeply buried marine sediment from the Nankai Trough subduction zone, heated to extreme temperature (up to ~120 °C). The small microbial community subsisted with high potential cell-specific rates of energy metabolism, which approach the rates of active surface sediments and laboratory cultures. Our discovery is in stark contrast to the extremely low metabolic rates otherwise observed in the deep subseafloor. As cells appear to invest most of their energy to repair thermal cell damage in the hot sediment, they are forced to balance delicately between subsistence near the upper temperature limit for life and a rich supply of substrates and energy from thermally driven reactions of the sedimentary organic matter. In the deep sedimentary biosphere, 80 °C has been proposed as an upper thermal barrier for life. Using a suite of radiotracer experiments, this study reports active methanogenic and sulfate-reducing microbial populations with high cell-specific metabolic rates in deeply buried marine sediments from the Nankai Trough subduction zone, which reach temperatures up to 120 °C.
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5
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Smith TP, Clegg T, Bell T, Pawar S. Systematic variation in the temperature dependence of bacterial carbon use efficiency. Ecol Lett 2021; 24:2123-2133. [PMID: 34240797 DOI: 10.1111/ele.13840] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 04/25/2021] [Accepted: 06/08/2021] [Indexed: 11/27/2022]
Abstract
Carbon use efficiency (CUE) is a key characteristic of microbial physiology and underlies community-level responses to changing environments. Yet, we currently lack general empirical insights into variation in microbial CUE at the level of individual taxa. Here, through experiments with 29 strains of environmentally isolated bacteria, we find that bacterial CUE typically responds either positively to temperature, or has no discernible response, within biologically meaningful temperature ranges. Using a global data synthesis, we show that these results are generalisable across most culturable groups of bacteria. This variation in the thermal responses of bacterial CUE is taxonomically structured, and stems from the fact that relative to respiration rates, bacterial population growth rates typically respond more strongly to temperature, and are also subject to weaker evolutionary constraints. Our results provide new insights into microbial physiology, and a basis for more accurately modelling the effects of thermal fluctuations on complex microbial communities.
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Affiliation(s)
- Thomas P Smith
- Department of Life Sciences, Imperial College London, Ascot, Berkshire, UK
| | - Tom Clegg
- Department of Life Sciences, Imperial College London, Ascot, Berkshire, UK
| | - Thomas Bell
- Department of Life Sciences, Imperial College London, Ascot, Berkshire, UK
| | - Samrāt Pawar
- Department of Life Sciences, Imperial College London, Ascot, Berkshire, UK
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6
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Influence of Temperature and Sulfate Concentration on the Sulfate/Sulfite Reduction Prokaryotic Communities in the Tibetan Hot Springs. Microorganisms 2021; 9:microorganisms9030583. [PMID: 33809110 PMCID: PMC8002027 DOI: 10.3390/microorganisms9030583] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 03/05/2021] [Accepted: 03/09/2021] [Indexed: 11/18/2022] Open
Abstract
The distribution and diversity of sulfate/sulfite reduction prokaryotic (SRP) communities in hot springs from the Quzhuomu and Daggyai Geothermal Zone of Tibetan, China, was reported for the first time. In hot springs that are naturally hyperthermal and anoxic, the sulfur cycle is one of the most active cycles of the elements. The distribution of SRP in response to temperature is of great importance to the understanding of biogeochemical cycling of sulfur in geothermal features. Little is known about the SRP in geothermal zone. In this study, the diversity of SRP was investigated in the sediments from the Daggyai and Quzhuomu geothermal zone using PCR amplification, cloning and sequencing of the dissimilatory sulfite reductase beta subunit gene (dsrB). The abundance of dsrB and 16S rRNA genes, were determined by quantitative polymerase chain reactions. In addition, correlations of the SRP assemblages with environmental factors were analyzed by the aggregated boosted tree (ABT) statistical analysis. The results showed that SRP populations were diverse, but were mainly composed of Desulfobacterales, Desulfovibrionales, Syntrophobacterales, Clostridia and Nitrospirales, and large fraction (25%) of novel sequences have branched groups in the dsrB phylogenetic tree. In Quzhuomu geothermal zone, sulfate-rich hot springs are characterized by thick bacterial mats that are green or red and the SRP populations mainly appear at mid-temperature (50 °C to 70 °C). In low-sulfate hot springs in the Daggyai geothermal zone, although gray or pink streamers are widely formed at 60 °C to 80 °C, they prefer to inhabit in green mat at lower temperature (30 °C to 50 °C). With increasing temperature, the diversity of the dsrB gene at the OTU level (cutoff 97%) decreased, while its relative abundance increased. This result suggests that temperature played an important role in affecting dsrB gene distribution.
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7
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Transcriptome Analysis of the Acid Stress Response of Desulfovibrio vulgaris ATCC 7757. Curr Microbiol 2020; 77:2702-2712. [DOI: 10.1007/s00284-020-02051-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 05/23/2020] [Indexed: 01/23/2023]
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8
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Xu YN, Chen Y. Advances in heavy metal removal by sulfate-reducing bacteria. WATER SCIENCE AND TECHNOLOGY : A JOURNAL OF THE INTERNATIONAL ASSOCIATION ON WATER POLLUTION RESEARCH 2020; 81:1797-1827. [PMID: 32666937 DOI: 10.2166/wst.2020.227] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Industrial development has led to generation of large volumes of wastewater containing heavy metals, which need to be removed before the wastewater is released into the environment. Chemical and electrochemical methods are traditionally applied to treat this type of wastewater. These conventional methods have several shortcomings, such as secondary pollution and cost. Bioprocesses are gradually gaining popularity because of their high selectivities, low costs, and reduced environmental pollution. Removal of heavy metals by sulfate-reducing bacteria (SRB) is an economical and effective alternative to conventional methods. The limitations of and advances in SRB activity have not been comprehensively reviewed. In this paper, recent advances from laboratory studies in heavy metal removal by SRB were reported. Firstly, the mechanism of heavy metal removal by SRB is introduced. Then, the factors affecting microbial activity and metal removal efficiency are elucidated and discussed in detail. In addition, recent advances in selection of an electron donor, enhancement of SRB activity, and improvement of SRB tolerance to heavy metals are reviewed. Furthermore, key points for future studies of the SRB process are proposed.
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Affiliation(s)
- Ya-Nan Xu
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China E-mail:
| | - Yinguang Chen
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China E-mail: ; Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, China
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9
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Abstract
The question whether organic compounds occur on Mars remained unanswered for decades. However, the recent discovery of various classes of organic matter in martian sediments by the Curiosity rover seems to strongly suggest that indigenous organic compounds exist on Mars. One intriguing group of detected organic compounds were thiophenes, which typically occur on Earth in kerogen, coal, and crude oil as well as in stromatolites and microfossils. Here we provide a brief synopsis of conceivable pathways for the generation and degradation of thiophenes on Mars. We show that the origin of thiophene derivatives can either be biotic or abiotic, for example, through sulfur incorporation in organic matter during early diagenesis. The potential of thiophenes to represent martian biomarkers is discussed as well as a correlation between abundances of thiophenes and sulfate-bearing minerals. Finally, this study provides suggestions for future investigations on Mars and in Earth-based laboratories to answer the question whether the martian thiophenes are of biological origin.
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Affiliation(s)
- Jacob Heinz
- Center for Astronomy and Astrophysics (ZAA), Astrobiology Research Group, Technische Universität Berlin, Berlin, Germany
| | - Dirk Schulze-Makuch
- Center for Astronomy and Astrophysics (ZAA), Astrobiology Research Group, Technische Universität Berlin, Berlin, Germany
- German Research Centre for Geosciences (GFZ), Section Geomicrobiology, Potsdam, Germany
- Department of Experimental Limnology, Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Stechlin, Germany
- School of the Environment, Washington State University, Pullman, WA, USA
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10
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Heiderscheidt E, Khan UA, Kujala K, Ronkanen AK, Postila H. Design, construction and monitoring of pilot systems to evaluate the effect of freeze-thaw cycles on pollutant retention in wetlands. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 703:134713. [PMID: 31734501 DOI: 10.1016/j.scitotenv.2019.134713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 09/04/2019] [Accepted: 09/27/2019] [Indexed: 06/10/2023]
Abstract
Due to the complexity of soil freeze/thaw processes and a variety of factors affecting pollutant removal in treatment wetlands, laboratory pilot systems are powerful tools offering a rare opportunity to observe processes that have a significant impact on year-round purification. This paper describes the design, construction, monitoring and operation of two replicate pilot peat-based wetlands subjected to two simulated freeze-thaw cycles. Undisturbed peat soil and pre-treated gold mine process wastewater were collected from a full-scale treatment wetland operating at a mining site in Northern Finland. The wastewater (pH ~7.8, electric conductivity ~3.6 mS/cm) contained a mix of metals/metalloids (e.g. arsenic 12 µg/L, antimony 19 µg/L) and other contaminants e.g. sulphate (~2 g/L). Fluctuations in removal efficiency of target compounds due to freezing and thawing conditions were observed. Overall, removal of sulphate and arsenic decreased during frost periods, while removal of antimony increased. Monitoring data from the full-scale treatment wetland were used to assess the representativeness of the results obtained. Comparisons of seasonal variations in pollutant concentrations in outflow samples from the full-scale wetland and those measured in the pilot wetlands revealed similar fluctuations in removal efficiency during frost and frost-free periods, suggesting that the pilot wetlands simulated the real system rather well. Carefully designed pilot systems can thus be valuable tools for assessing the effect of harsh winter conditions on wetland processes and operation.
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Affiliation(s)
- Elisangela Heiderscheidt
- Water, Energy and Environmental Engineering, Faculty of Technology, University of Oulu, 90014, Finland.
| | - Uzair Akbar Khan
- Water, Energy and Environmental Engineering, Faculty of Technology, University of Oulu, 90014, Finland
| | - Katharina Kujala
- Water, Energy and Environmental Engineering, Faculty of Technology, University of Oulu, 90014, Finland
| | - Anna-Kaisa Ronkanen
- Water, Energy and Environmental Engineering, Faculty of Technology, University of Oulu, 90014, Finland
| | - Heini Postila
- Water, Energy and Environmental Engineering, Faculty of Technology, University of Oulu, 90014, Finland
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11
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Jørgensen BB, Andrén T, Marshall IPG. Sub-seafloor biogeochemical processes and microbial life in the Baltic Sea. Environ Microbiol 2020; 22:1688-1706. [PMID: 31970880 DOI: 10.1111/1462-2920.14920] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 01/18/2020] [Accepted: 01/21/2020] [Indexed: 01/15/2023]
Abstract
The post-glacial Baltic Sea has experienced extreme changes that are archived today in the deep sediments. IODP Expedition 347 retrieved cores down to 100 m depth and studied the climate history and the deep biosphere. We here review the biogeochemical and microbiological highlights and integrate these with other studies from the Baltic seabed. Cell numbers, endospore abundance and organic matter mineralization rates are extremely high. A 100-fold drop in cell numbers with depth results from a small difference between growth and mortality in the ageing sediment. Evidence for growth derives from a D:L amino acid racemization model, while evidence for mortality derives from the abundance and potential activity of lytic viruses. The deep communities assemble at the bottom of the bioturbated zone from the founding surface community by selection of organisms suited for life under deep sediment conditions. The mean catabolic per-cell rate of microorganisms drops steeply with depth to a life in slow-motion, typical for the deep biosphere. The subsurface life under extreme energy limitation is facilitated by exploitation of recalcitrant substrates, by biochemical protection of nucleic acids and proteins and by repair mechanisms for random mismatches in DNA or damaged amino acids in proteins.
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Affiliation(s)
- Bo Barker Jørgensen
- Center for Geomicrobiology, Department of Bioscience, Aarhus University, Aarhus, Denmark
| | - Thomas Andrén
- School of Natural Sciences, Technology and Environmental Studies, Södertörn University, Huddinge, Sweden
| | - Ian P G Marshall
- Center for Geomicrobiology, Department of Bioscience, Aarhus University, Aarhus, Denmark.,Center for Electromicrobiology, Department of Bioscience, Aarhus University, Aarhus, Denmark
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12
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Seto M, Noguchi K, Cappellen PV. Potential for Aerobic Methanotrophic Metabolism on Mars. ASTROBIOLOGY 2019; 19:1187-1195. [PMID: 31173512 PMCID: PMC6785171 DOI: 10.1089/ast.2018.1943] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Accepted: 05/07/2019] [Indexed: 06/09/2023]
Abstract
Observational evidence supports the presence of methane (CH4) in the martian atmosphere on the order of parts per billion by volume (ppbv). Here, we assess whether aerobic methanotrophy is a potentially viable metabolism in the martian upper regolith, by calculating metabolic energy gain rates under assumed conditions of martian surface temperature, pressure, and atmospheric composition. Using kinetic parameters for 19 terrestrial aerobic methanotrophic strains, we show that even under the imposed low temperature and pressure extremes (180-280 K and 6-11 hPa), methane oxidation by oxygen (O2) should in principle be able to generate the minimum energy production rate required to support endogenous metabolism (i.e., cellular maintenance). Our results further indicate that the corresponding metabolic activity would be extremely low, with cell doubling times in excess of 4000 Earth years at the present-day ppbv-level CH4 mixing ratios in the atmosphere of Mars. Thus, while aerobic methanotrophic microorganisms similar to those found on Earth could theoretically maintain their vital functions, they are unlikely to constitute prolific members of hypothetical martian soil communities.
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Affiliation(s)
- Mayumi Seto
- Department of Chemistry, Biology, and Environmental Sciences, Faculty of Science, Nara Women's University, Nara, Japan
| | - Katsuyuki Noguchi
- Department of Chemistry, Biology, and Environmental Sciences, Faculty of Science, Nara Women's University, Nara, Japan
| | - Philippe Van Cappellen
- Ecohydrology Research Group, Department of Earth and Environmental Sciences, Water Institute, University of Waterloo, Waterloo, Canada
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13
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O'Donnell DR, Du Z, Litchman E. Experimental evolution of phytoplankton fatty acid thermal reaction norms. Evol Appl 2019; 12:1201-1211. [PMID: 31768190 PMCID: PMC6866708 DOI: 10.1111/eva.12798] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 03/13/2019] [Accepted: 04/02/2019] [Indexed: 01/12/2023] Open
Abstract
Temperature effects on the fatty acid (FA) profiles of phytoplankton, major primary producers in the ocean, have been widely studied due to their importance as industrial feedstocks and to their indispensable role as global producers of long-chain, polyunsaturated FA (PUFA), including omega-3 (ω3) FA required by organisms at higher trophic levels. The latter is of global ecological concern for marine food webs, as some evidence suggests an ongoing decline in global marine-derived ω3 FA due to both a global decline in phytoplankton abundance and to a physiological reduction in ω3 production by phytoplankton as temperatures rise. Here, we examined both short-term (physiological) and long-term (evolutionary) responses of FA profiles to temperature by comparing FA thermal reaction norms of the marine diatom Thalassiosira pseudonana after ~500 generations (ca. 2.5 years) of experimental evolution at low (16°C) and high (31°C) temperatures. We showed that thermal reaction norms for some key FA classes evolved rapidly in response to temperature selection, often in ways contrary to our predictions based on prior research. Notably, 31°C-selected populations showed higher PUFA percentages (including ω3 FA) than 16°C-selected populations at the highest assay temperature (31°C, above T. pseudonana's optimum temperature for population growth), suggesting that high-temperature selection led to an evolved ability to sustain high PUFA production at high temperatures. Rapid evolution may therefore mitigate some of the decline in global phytoplankton-derived ω3 FA production predicted by recent studies. Beyond its implications for marine food webs, knowledge of the effects of temperature on fatty acid profiles is of fundamental importance to our understanding of the mechanistic causes and consequences of thermal adaptation.
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Affiliation(s)
- Daniel R. O'Donnell
- W. K. Kellogg Biological StationMichigan State UniversityHickory CornersMichigan
- Department of Integrative BiologyMichigan State UniversityEast LansingMichigan
- Program in Ecology, Evolutionary Biology and BehaviorMichigan State UniversityEast LansingMichigan
| | - Zhi‐yan Du
- Department of Biochemistry and Molecular BiologyMichigan State UniversityEast LansingMichigan
- MSU‐DOE Plant Research LaboratoryMichigan State UniversityEast LansingMichigan
| | - Elena Litchman
- W. K. Kellogg Biological StationMichigan State UniversityHickory CornersMichigan
- Department of Integrative BiologyMichigan State UniversityEast LansingMichigan
- Program in Ecology, Evolutionary Biology and BehaviorMichigan State UniversityEast LansingMichigan
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14
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Jørgensen BB, Findlay AJ, Pellerin A. The Biogeochemical Sulfur Cycle of Marine Sediments. Front Microbiol 2019. [DOI: 10.10.3389/fmicb.2019.00849] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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15
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Jørgensen BB, Findlay AJ, Pellerin A. The Biogeochemical Sulfur Cycle of Marine Sediments. Front Microbiol 2019; 10:849. [PMID: 31105660 PMCID: PMC6492693 DOI: 10.3389/fmicb.2019.00849] [Citation(s) in RCA: 195] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Accepted: 04/02/2019] [Indexed: 11/13/2022] Open
Abstract
Microbial dissimilatory sulfate reduction to sulfide is a predominant terminal pathway of organic matter mineralization in the anoxic seabed. Chemical or microbial oxidation of the produced sulfide establishes a complex network of pathways in the sulfur cycle, leading to intermediate sulfur species and partly back to sulfate. The intermediates include elemental sulfur, polysulfides, thiosulfate, and sulfite, which are all substrates for further microbial oxidation, reduction or disproportionation. New microbiological discoveries, such as long-distance electron transfer through sulfide oxidizing cable bacteria, add to the complexity. Isotope exchange reactions play an important role for the stable isotope geochemistry and for the experimental study of sulfur transformations using radiotracers. Microbially catalyzed processes are partly reversible whereby the back-reaction affects our interpretation of radiotracer experiments and provides a mechanism for isotope fractionation. We here review the progress and current status in our understanding of the sulfur cycle in the seabed with respect to its microbial ecology, biogeochemistry, and isotope geochemistry.
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Affiliation(s)
- Bo Barker Jørgensen
- Department of Bioscience, Center for Geomicrobiology, Aarhus University, Aarhus, Denmark
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16
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Marín-Guirao L, Bernardeau-Esteller J, García-Muñoz R, Ramos A, Ontoria Y, Romero J, Pérez M, Ruiz JM, Procaccini G. Carbon economy of Mediterranean seagrasses in response to thermal stress. MARINE POLLUTION BULLETIN 2018; 135:617-629. [PMID: 30301080 DOI: 10.1016/j.marpolbul.2018.07.050] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Revised: 07/16/2018] [Accepted: 07/19/2018] [Indexed: 05/27/2023]
Abstract
Increased plant mortality in temperate seagrass populations has been recently observed after summer heatwaves, although the underlying causes of plant death are yet unknown. The potential energetic constrains resulting from anomalous thermal events could be the reason that triggered seagrass mortality, as demonstrated for benthic invertebrates. To test this hypothesis, the carbon balance of Posidonia oceanica and Cymodocea nodosa plants from contrasting thermal environments was investigated during a simulated heatwave, by analyzing their photosynthetic performance, carbon balance (ratio photosynthesis:respiration), carbohydrates content, growth and mortality. Both species were able to overcome and recover from the thermal stress produced by the six-week exposure to temperatures 4 °C above mean summer levels, albeit plants from cold waters were more sensitive to warming than plants from warm waters as reflected by their inability to maintain their P:R ratio unaltered. The strategies through which plants tend to preserve their energetic status varied depending on the biology of the species and the thermal origin of plants. These included respiratory homeostasis (P. oceanica warm-plants), carbon diversion from growth to respiration (C. nodosa cold-plants) or storage (P. oceanica warm-plants) and changes in biomass allocation (C. nodosa warm-plants). Findings suggest an important geographic heterogeneity in the overall response of Mediterranean seagrasses to warming with potential negative impacts on the functions and services offered by seagrass meadows including among others their capacity for carbon sequestration and carbon export to adjacent ecosystems.
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Affiliation(s)
- L Marín-Guirao
- Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Napoli, Italy.
| | - J Bernardeau-Esteller
- Seagrass Ecology Group, Oceanographic Center of Murcia, Spanish Institute of Oceanography C/Varadero, 30740 San Pedro del Pinatar, Murcia, Spain
| | - R García-Muñoz
- Seagrass Ecology Group, Oceanographic Center of Murcia, Spanish Institute of Oceanography C/Varadero, 30740 San Pedro del Pinatar, Murcia, Spain
| | - A Ramos
- Seagrass Ecology Group, Oceanographic Center of Murcia, Spanish Institute of Oceanography C/Varadero, 30740 San Pedro del Pinatar, Murcia, Spain
| | - Y Ontoria
- Department of Evolutionary Biology, Ecology, and Environmental Sciences, Universitat de Barcelona, Av. Diagonal 643, 08028 Barcelona, Spain
| | - J Romero
- Department of Evolutionary Biology, Ecology, and Environmental Sciences, Universitat de Barcelona, Av. Diagonal 643, 08028 Barcelona, Spain
| | - M Pérez
- Department of Evolutionary Biology, Ecology, and Environmental Sciences, Universitat de Barcelona, Av. Diagonal 643, 08028 Barcelona, Spain
| | - J M Ruiz
- Seagrass Ecology Group, Oceanographic Center of Murcia, Spanish Institute of Oceanography C/Varadero, 30740 San Pedro del Pinatar, Murcia, Spain
| | - G Procaccini
- Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Napoli, Italy
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Rüffel V, Maar M, Dammbrück MN, Hauröder B, Neu TR, Meier J. Thermodesulfobium sp. strain 3baa, an acidophilic sulfate reducing bacterium forming biofilms triggered by mineral precipitation. Environ Microbiol 2018; 20:3717-3731. [PMID: 30105784 DOI: 10.1111/1462-2920.14374] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Revised: 08/01/2018] [Accepted: 08/05/2018] [Indexed: 01/22/2023]
Abstract
Sulfate reducing prokaryotes are promising candidates for the remediation of acidic metal-rich waste waters. However, only few acidophilic species have been described to date. Chemolithoautotrophic strain 3baa was isolated from sediments of an acidic mine pit lake. Based on its 16S-rRNA gene sequence it belongs to the genus Thermodesulfobium. It was identified as an acidophile growing in artificial pore water medium in the range of pH 2.6-6.6. Though the highest sulfate reduction rates were obtained at the lower end of this range, elongated cells and extended lag phases demonstrated acid stress. Sulfate reduction at low pH was accompanied by the formation of mineral precipitates strongly adhering to solid surfaces. A structural investigation by laser scanning microscopy, electron microscopy and X-ray microanalysis revealed the formation of Al hydroxides and Fe sulfides which were densely populated by cells. Al hydroxides precipitated first, enabling initial cell attachment. Colonization of solid surfaces coincided with increased sulfate reducing activity indicating more favourable growth conditions within biofilms compared with free-living cells. These findings point out the importance of cell-mineral interaction for biofilm formation and contribute to our understanding how sulfate reducing prokaryotes thrive in both natural and engineered systems at low pH.
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Affiliation(s)
- Viola Rüffel
- Institute for Integrated Natural Sciences, University Koblenz-Landau, 56070, Koblenz, Germany
| | - Mona Maar
- Institute for Integrated Natural Sciences, University Koblenz-Landau, 56070, Koblenz, Germany
| | - Markus N Dammbrück
- Institute for Integrated Natural Sciences, University Koblenz-Landau, 56070, Koblenz, Germany
| | - Bärbel Hauröder
- Department of Pathology, Electron Microscopy, Bundeswehr Central Hospital Coblenz, 56070, Koblenz, Germany
| | - Thomas R Neu
- Department of River Ecology, Helmholtz Centre of Environmental Research - UFZ, 39114, Magdeburg, Germany
| | - Jutta Meier
- Institute for Integrated Natural Sciences, University Koblenz-Landau, 56070, Koblenz, Germany
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18
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Müller AL, Pelikan C, de Rezende JR, Wasmund K, Putz M, Glombitza C, Kjeldsen KU, Jørgensen BB, Loy A. Bacterial interactions during sequential degradation of cyanobacterial necromass in a sulfidic arctic marine sediment. Environ Microbiol 2018; 20:2927-2940. [PMID: 30051650 PMCID: PMC6175234 DOI: 10.1111/1462-2920.14297] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Revised: 05/02/2018] [Accepted: 05/24/2018] [Indexed: 11/26/2022]
Abstract
Seafloor microorganisms impact global carbon cycling by mineralizing vast quantities of organic matter (OM) from pelagic primary production, which is predicted to increase in the Arctic because of diminishing sea ice cover. We studied microbial interspecies-carbon-flow during anaerobic OM degradation in arctic marine sediment using stable isotope probing. We supplemented sediment incubations with 13 C-labeled cyanobacterial necromass (spirulina), mimicking fresh OM input, or acetate, an important OM degradation intermediate and monitored sulfate reduction rates and concentrations of volatile fatty acids (VFAs) during substrate degradation. Sequential 16S rRNA gene and transcript amplicon sequencing and fluorescence in situ hybridization combined with Raman microspectroscopy revealed that only few bacterial species were the main degraders of 13 C-spirulina necromass. Psychrilyobacter, Psychromonas, Marinifilum, Colwellia, Marinilabiaceae and Clostridiales species were likely involved in the primary hydrolysis and fermentation of spirulina. VFAs, mainly acetate, produced from spirulina degradation were mineralized by sulfate-reducing bacteria and an Arcobacter species. Cellular activity of Desulfobacteraceae and Desulfobulbaceae species during acetoclastic sulfate reduction was largely decoupled from relative 16S rRNA gene abundance shifts. Our findings provide new insights into the identities and physiological constraints that determine the population dynamics of key microorganisms during complex OM degradation in arctic marine sediments.© 2018 Society for Applied Microbiology and John Wiley & Sons Ltd.
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Affiliation(s)
- Albert L. Müller
- Division of Microbial Ecology, Department of Microbiology and Ecosystem ScienceResearch Network Chemistry meets Microbiology, University of ViennaViennaAustria
| | - Claus Pelikan
- Division of Microbial Ecology, Department of Microbiology and Ecosystem ScienceResearch Network Chemistry meets Microbiology, University of ViennaViennaAustria
- Austrian Polar Research InstituteViennaAustria
| | - Julia R. de Rezende
- Center for Geomicrobiology, Department of BioscienceAarhus UniversityAarhusDenmark
| | - Kenneth Wasmund
- Division of Microbial Ecology, Department of Microbiology and Ecosystem ScienceResearch Network Chemistry meets Microbiology, University of ViennaViennaAustria
- Austrian Polar Research InstituteViennaAustria
| | - Martina Putz
- Division of Microbial Ecology, Department of Microbiology and Ecosystem ScienceResearch Network Chemistry meets Microbiology, University of ViennaViennaAustria
| | | | - Kasper U. Kjeldsen
- Center for Geomicrobiology, Department of BioscienceAarhus UniversityAarhusDenmark
| | - Bo Barker Jørgensen
- Center for Geomicrobiology, Department of BioscienceAarhus UniversityAarhusDenmark
| | - Alexander Loy
- Division of Microbial Ecology, Department of Microbiology and Ecosystem ScienceResearch Network Chemistry meets Microbiology, University of ViennaViennaAustria
- Austrian Polar Research InstituteViennaAustria
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19
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Microbial turnover times in the deep seabed studied by amino acid racemization modelling. Sci Rep 2017; 7:5680. [PMID: 28720809 PMCID: PMC5516024 DOI: 10.1038/s41598-017-05972-z] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Accepted: 06/06/2017] [Indexed: 01/20/2023] Open
Abstract
The study of active microbial populations in deep, energy-limited marine sediments has extended our knowledge of the limits of life on Earth. Typically, microbial activity in the deep biosphere is calculated by transport-reaction modelling of pore water solutes or from experimental measurements involving radiotracers. Here we modelled microbial activity from the degree of D:L-aspartic acid racemization in microbial necromass (remains of dead microbial biomass) in sediments up to ten million years old. This recently developed approach (D:L-amino acid modelling) does not require incubation experiments and is highly sensitive in stable, low-activity environments. We applied for the first time newly established constraints on several important input parameters of the D:L-amino acid model, such as a higher aspartic acid racemization rate constant and a lower cell-specific carbon content of sub-seafloor microorganisms. Our model results show that the pool of necromass amino acids is turned over by microbial activity every few thousand years, while the turnover times of vegetative cells are in the order of years to decades. Notably, microbial turnover times in million-year-old sediment from the Peru Margin are up to 100-fold shorter than previous estimates, highlighting the influence of microbial activities on element cycling over geologic time scales.
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20
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Seel W, Derichs J, Lipski A. Increased Biomass Production by Mesophilic Food-Associated Bacteria through Lowering the Growth Temperature from 30°C to 10°C. Appl Environ Microbiol 2016; 82:3754-3764. [PMID: 27084015 PMCID: PMC4907174 DOI: 10.1128/aem.00211-16] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Accepted: 04/11/2016] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED Five isolates from chilled food and refrigerator inner surfaces and closely related reference strains of the species Escherichia coli, Listeria monocytogenes, Staphylococcus xylosus, Bacillus cereus, Pedobacter nutrimenti, and Pedobacter panaciterrae were tested for the effect of growth temperature (30°C and 10°C) on biomass formation. Growth was monitored via optical density, and biomass formation was measured at the early stationary phase based on the following parameters in complex and defined media: viable cell count, total cell count, cell dry weight, whole-cell protein content, and cell morphology. According to the lack of growth at 1°C, all strains were assigned to the thermal class of mesophiles. Glucose and ammonium consumption related to cell yield were analyzed in defined media. Except for the protein content, temperature had a significant (t test, P < 0.05) effect on all biomass formation parameters for each strain. The results show a significant difference between the isolates and the related reference strains. Isolates achieved an increase in biomass production between 20% and 110% at the 10°C temperature, which is 15 to 25°C lower than their maximum growth rate temperatures. In contrast, reference strains showed a maximum increase of only about 25%, and some reference strains showed no increase or a decrease of approximately 25%. As expected, growth rates for all strains were higher at 30°C than at 10°C, while biomass production for isolates was higher at 10°C than at 30°C. In contrast, the reference strains showed similar growth yields at the two temperatures. This also demonstrates for mesophilic bacterial strains more efficient nutrient assimilation during growth at low temperatures. Until now, this characteristic was attributed only to psychrophilic microorganisms. IMPORTANCE For several psychrophilic species, increased biomass formation was described at temperatures lower than optimum growth temperatures, which are defined by the highest growth rate. This work shows increased biomass formation at low growth temperatures for mesophilic isolates. A comparison with closely related reference strains from culture collections showed a significantly smaller increase or no increase in biomass formation. This indicates a loss of specific adaptive mechanisms (e.g., cold adaptation) for mesophiles during long-term cultivation. The increased biomass production for mesophiles under low-temperature conditions opens new avenues for a more efficient biotechnological transformation of nutrients to microbial biomass. These findings may also be important for risk assessment of cooled foods since risk potential is often correlated with the cell numbers present in food samples.
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Affiliation(s)
- Waldemar Seel
- Rheinische Friedrich-Wilhelms-Universität Bonn, Institut für Ernährungs- und Lebensmittelwissenschaften, Abteilung Lebensmittelmikrobiologie und -hygiene, Bonn, Germany
| | - Julia Derichs
- Rheinische Friedrich-Wilhelms-Universität Bonn, Institut für Ernährungs- und Lebensmittelwissenschaften, Abteilung Lebensmittelmikrobiologie und -hygiene, Bonn, Germany
| | - André Lipski
- Rheinische Friedrich-Wilhelms-Universität Bonn, Institut für Ernährungs- und Lebensmittelwissenschaften, Abteilung Lebensmittelmikrobiologie und -hygiene, Bonn, Germany
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21
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Seasonal Microbial Population Shifts in a Bioremediation System Treating Metal and Sulfate-Rich Seepage. MINERALS 2016. [DOI: 10.3390/min6020036] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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22
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Sensitive change of iso-branched fatty acid (iso-15:0) in Bacillus pumilus PAMC 23174 in response to environmental changes. Bioprocess Biosyst Eng 2015; 39:159-67. [DOI: 10.1007/s00449-015-1500-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Accepted: 10/29/2015] [Indexed: 11/26/2022]
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23
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Robador A, Müller AL, Sawicka JE, Berry D, Hubert CRJ, Loy A, Jørgensen BB, Brüchert V. Activity and community structures of sulfate-reducing microorganisms in polar, temperate and tropical marine sediments. ISME JOURNAL 2015; 10:796-809. [PMID: 26359912 DOI: 10.1038/ismej.2015.157] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Revised: 04/18/2015] [Accepted: 07/25/2015] [Indexed: 11/09/2022]
Abstract
Temperature has a fundamental impact on the metabolic rates of microorganisms and strongly influences microbial ecology and biogeochemical cycling in the environment. In this study, we examined the catabolic temperature response of natural communities of sulfate-reducing microorganisms (SRM) in polar, temperate and tropical marine sediments. In short-term sediment incubation experiments with (35)S-sulfate, we demonstrated how the cardinal temperatures for sulfate reduction correlate with mean annual sediment temperatures, indicating specific thermal adaptations of the dominant SRM in each of the investigated ecosystems. The community structure of putative SRM in the sediments, as revealed by pyrosequencing of bacterial 16S rRNA gene amplicons and phylogenetic assignment to known SRM taxa, consistently correlated with in situ temperatures, but not with sediment organic carbon concentrations or C:N ratios of organic matter. Additionally, several species-level SRM phylotypes of the class Deltaproteobacteria tended to co-occur at sites with similar mean annual temperatures, regardless of geographic distance. The observed temperature adaptations of SRM imply that environmental temperature is a major controlling variable for physiological selection and ecological and evolutionary differentiation of microbial communities.
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Affiliation(s)
- Alberto Robador
- Department of Biogeochemistry, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Albert L Müller
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, University of Vienna, Wien, Austria
| | - Joanna E Sawicka
- Department of Geological Sciences, Bolin Centre for Climate Research, Stockholm University, Stockholm, Sweden
| | - David Berry
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, University of Vienna, Wien, Austria
| | - Casey R J Hubert
- School of Civil Engineering and Geosciences, Newcastle University, Newcastle upon Tyne, UK
| | - Alexander Loy
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, University of Vienna, Wien, Austria.,Austrian Polar Research Institute, Vienna, Austria
| | - Bo Barker Jørgensen
- Department of Bioscience, Center for Geomicrobiology, Aarhus University, Aarhus C, Denmark
| | - Volker Brüchert
- Department of Geological Sciences, Bolin Centre for Climate Research, Stockholm University, Stockholm, Sweden
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24
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Characterization of the Bacterial and Sulphate Reducing Community in the Alkaline and Constantly Cold Water of the Closed Kotalahti Mine. MINERALS 2015. [DOI: 10.3390/min5030452] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
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25
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Robador A, Jungbluth SP, LaRowe DE, Bowers RM, Rappé MS, Amend JP, Cowen JP. Activity and phylogenetic diversity of sulfate-reducing microorganisms in low-temperature subsurface fluids within the upper oceanic crust. Front Microbiol 2015; 5:748. [PMID: 25642212 PMCID: PMC4295021 DOI: 10.3389/fmicb.2014.00748] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Accepted: 12/09/2014] [Indexed: 11/13/2022] Open
Abstract
The basaltic ocean crust is the largest aquifer system on Earth, yet the rates of biological activity in this environment are unknown. Low-temperature (<100°C) fluid samples were investigated from two borehole observatories in the Juan de Fuca Ridge (JFR) flank, representing a range of upper oceanic basement thermal and geochemical properties. Microbial sulfate reduction rates (SRR) were measured in laboratory incubations with 35S-sulfate over a range of temperatures and the identity of the corresponding sulfate-reducing microorganisms (SRM) was studied by analyzing the sequence diversity of the functional marker dissimilatory (bi)sulfite reductase (dsrAB) gene. We found that microbial sulfate reduction was limited by the decreasing availability of organic electron donors in higher temperature, more altered fluids. Thermodynamic calculations indicate energetic constraints for metabolism, which together with relatively higher cell-specific SRR reveal increased maintenance requirements, consistent with novel species-level dsrAB phylotypes of thermophilic SRM. Our estimates suggest that microbially-mediated sulfate reduction may account for the removal of organic matter in fluids within the upper oceanic crust and underscore the potential quantitative impact of microbial processes in deep subsurface marine crustal fluids on marine and global biogeochemical carbon cycling.
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Affiliation(s)
- Alberto Robador
- NASA Astrobiology Institute, University of Hawaii Honolulu, HI, USA
| | - Sean P Jungbluth
- Hawaii Institute of Marine Biology, School of Ocean and Earth Science and Technology, University of Hawaii Kaneohe, HI, USA ; Department of Oceanography, School of Ocean and Earth Science and Technology, University of Hawaii Honolulu, HI, USA
| | - Douglas E LaRowe
- Department of Earth Sciences, University of Southern California Los Angeles, CA, USA
| | - Robert M Bowers
- NASA Astrobiology Institute, University of Hawaii Honolulu, HI, USA
| | - Michael S Rappé
- Hawaii Institute of Marine Biology, School of Ocean and Earth Science and Technology, University of Hawaii Kaneohe, HI, USA
| | - Jan P Amend
- Department of Earth Sciences, University of Southern California Los Angeles, CA, USA ; Department of Biological Sciences, University of Southern California Los Angeles, CA, USA
| | - James P Cowen
- Department of Oceanography, School of Ocean and Earth Science and Technology, University of Hawaii Honolulu, HI, USA
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26
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Canion A, Overholt WA, Kostka JE, Huettel M, Lavik G, Kuypers MMM. Temperature response of denitrification and anaerobic ammonium oxidation rates and microbial community structure in Arctic fjord sediments. Environ Microbiol 2014; 16:3331-44. [DOI: 10.1111/1462-2920.12593] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2014] [Accepted: 08/03/2014] [Indexed: 11/30/2022]
Affiliation(s)
- Andy Canion
- Earth, Ocean, and Atmospheric Science Department; Florida State University; Tallahassee FL USA
| | - Will A. Overholt
- Schools of Biology and Earth and Atmospheric Science; Georgia Institute of Technology; Atlanta GA USA
| | - Joel E. Kostka
- Schools of Biology and Earth and Atmospheric Science; Georgia Institute of Technology; Atlanta GA USA
| | - Markus Huettel
- Earth, Ocean, and Atmospheric Science Department; Florida State University; Tallahassee FL USA
| | - Gaute Lavik
- Max Planck Institute for Marine Microbiology; Bremen Germany
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27
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García R, Holmer M, Duarte CM, Marbà N. Global warming enhances sulphide stress in a key seagrass species (NW Mediterranean). GLOBAL CHANGE BIOLOGY 2013; 19:3629-3639. [PMID: 24123496 DOI: 10.1111/gcb.12377] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2012] [Accepted: 08/15/2013] [Indexed: 06/02/2023]
Abstract
The build-up of sulphide concentrations in sediments, resulting from high inputs of organic matter and the mineralization through sulphate reduction, can be lethal to the benthos. Sulphate reduction is temperature dependent, thus global warming may contribute to even higher sulphide concentrations and benthos mortality. The seagrass Posidonia oceanica is very sensitive to sulphide stress. Hence, if concentrations build up with global warming, this key Mediterranean species could be seriously endangered. An 8-year monitoring of daily seawater temperature, the sulphur isotopic signatures of water (δ(34)S(water)), sediment (δ(34)SCRS ) and P. oceanica leaf tissue (δ(34)S(leaves)), along with total sulphur in leaves (TS(leaves)) and annual net population growth along the coast of the Balearic archipelago (Western Mediterranean) allowed us to determine if warming triggers P. oceanica sulphide stress and constrains seagrass survival. From the isotopic S signatures, we estimated sulphide intrusion into the leaves (F(sulphide)) and sulphur incorporation into the leaves from sedimentary sulphides (SS(leaves)). We observed lower δ(34)S(leaves), higher F(sulphide) and SS(leaves) coinciding with a 6-year period when two heat waves were recorded. Warming triggered sulphide stress as evidenced by the negative temperature dependence of δ(34)S(leaves) and the positive one of F(sulphide), TS(leaves) and SS(leaves). Lower P. oceanica net population growth rates were directly related to higher contents of TS(leaves). At equivalent annual maximum sea surface water temperature (SST(max)), deep meadows were less affected by sulphide intrusion than shallow ones. Thus, water depth acts as a protecting mechanism against sulphide intrusion. However, water depth would be insufficient to buffer seagrass sulphide stress triggered by Mediterranean seawater summer temperatures projected for the end of the 21st century even under scenarios of moderate greenhouse gas emissions, A1B. Mediterranean warming, therefore, is expected to enhance P. oceanica sulphide stress, and thus compromise the survival of this key habitat along its entire depth distribution range.
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Affiliation(s)
- Rosa García
- Department of Global Change Research, IMEDEA (CSIC-UIB), Instituto Mediterráneo de Estudios Avanzados, Miquel Marquès 21, Esporles (Balearic Islands), 07190, Spain
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28
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Bayraktarov E, Price RE, Ferdelman TG, Finster K. The pH and pCO2 dependence of sulfate reduction in shallow-sea hydrothermal CO2 - venting sediments (Milos Island, Greece). Front Microbiol 2013; 4:111. [PMID: 23658555 PMCID: PMC3647119 DOI: 10.3389/fmicb.2013.00111] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2013] [Accepted: 04/17/2013] [Indexed: 11/13/2022] Open
Abstract
Microbial sulfate reduction (SR) is a dominant process of organic matter mineralization in sulfate-rich anoxic environments at neutral pH. Recent studies have demonstrated SR in low pH environments, but investigations on the microbial activity at variable pH and CO2 partial pressure are still lacking. In this study, the effect of pH and pCO2 on microbial activity was investigated by incubation experiments with radioactive (35)S targeting SR in sediments from the shallow-sea hydrothermal vent system of Milos, Greece, where pH is naturally decreased by CO2 release. Sediments differed in their physicochemical characteristics with distance from the main site of fluid discharge. Adjacent to the vent site (T ~40-75°C, pH ~5), maximal sulfate reduction rates (SRR) were observed between pH 5 and 6. SR in hydrothermally influenced sediments decreased at neutral pH. Sediments unaffected by hydrothermal venting (T ~26°C, pH ~8) expressed the highest SRR between pH 6 and 7. Further experiments investigating the effect of pCO2 on SR revealed a steep decrease in activity when the partial pressure increased from 2 to 3 bar. Findings suggest that sulfate reducing microbial communities associated with hydrothermal vent system are adapted to low pH and high CO2, while communities at control sites required a higher pH for optimal activity.
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Affiliation(s)
- Elisa Bayraktarov
- Department of Biogeochemistry, Max Planck Institute for Marine Microbiology Bremen, Germany
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29
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Microbial competition in polar soils: a review of an understudied but potentially important control on productivity. BIOLOGY 2013; 2:533-54. [PMID: 24832797 PMCID: PMC3960893 DOI: 10.3390/biology2020533] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/06/2013] [Revised: 03/11/2013] [Accepted: 03/12/2013] [Indexed: 01/29/2023]
Abstract
Intermicrobial competition is known to occur in many natural environments, and can result from direct conflict between organisms, or from differential rates of growth, colonization, and/or nutrient acquisition. It has been difficult to extensively examine intermicrobial competition in situ, but these interactions may play an important role in the regulation of the many biogeochemical processes that are tied to microbial communities in polar soils. A greater understanding of how competition influences productivity will improve projections of gas and nutrient flux as the poles warm, may provide biotechnological opportunities for increasing the degradation of contaminants in polar soil, and will help to predict changes in communities of higher organisms, such as plants.
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30
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Abstract
A great number of the bacteria and archaea on Earth are found in subsurface environments in a physiological state that is poorly represented or explained by laboratory cultures. Microbial cells in these very stable and oligotrophic settings catabolize 10⁴- to 10⁶-fold more slowly than model organisms in nutrient-rich cultures, turn over biomass on timescales of centuries to millennia rather than hours to days, and subsist with energy fluxes that are 1,000-fold lower than the typical culture-based estimates of maintenance requirements. To reconcile this disparate state of being with our knowledge of microbial physiology will require a revised understanding of microbial energy requirements, including identifying the factors that comprise true basal maintenance and the adaptations that might serve to minimize these factors.
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31
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Könneke M, Kuever J, Galushko A, Jørgensen BB. Desulfoconvexum algidum gen. nov., sp. nov., a psychrophilic sulfate-reducing bacterium isolated from a permanently cold marine sediment. Int J Syst Evol Microbiol 2012; 63:959-964. [PMID: 22659505 DOI: 10.1099/ijs.0.043703-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A sulfate-reducing bacterium, designated JHA1(T), was isolated from a permanently cold marine sediment sampled in an Artic fjord on the north-west coast of Svalbard. The isolate was originally enriched at 4 °C in a highly diluted liquid culture amended with hydrogen and sulfate. Strain JHA1(T) was a psychrophile, growing fastest between 14 and 16 °C and not growing above 20 °C. Fastest growth was found at neutral pH (pH 7.2-7.4) and at marine concentrations of NaCl (20-30 g l(-1)). Phylogenetic analysis of 16S rRNA gene sequences revealed that strain JHA1(T) was a member of the family Desulfobacteraceae in the Deltaproteobacteria. The isolate shared 99 % 16S rRNA gene sequence similarity with an environmental sequence obtained from permanently cold Antarctic sediment. The closest recognized relatives were Desulfobacula phenolica DSM 3384(T) and Desulfobacula toluolica DSM 7467(T) (both <95 % sequence similarity). In contrast to its closest phylogenetic relatives, strain JHA1(T) grew chemolithoautotrophically with hydrogen as an electron donor. CO dehydrogenase activity indicated the operation of the reductive acetyl-CoA pathway for inorganic carbon assimilation. Beside differences in physiology and morphology, strain JHA1(T) could be distinguished chemotaxonomically from the genus Desulfobacula by the absence of the cellular fatty acid C16 : 0 10-methyl. Phylogenetic differentiation from other genera was further supported by DsrAB and AprBA sequence analysis. Based on the described phylogenetic and phenotypic differences between strain JHA1(T) and its closest relatives, the establishment of a novel genus and a novel species, Desulfoconvexum algidum gen. nov., sp. nov. is proposed. The type strain is JHA1(T) ( = DSM 21856(T) = JCM 16085(T)).
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Affiliation(s)
- Martin Könneke
- Max-Planck Institute for Marine Microbiology, Bremen, Germany
| | - Jan Kuever
- Bremen Institute for Materials Testing, Bremen, Germany
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32
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Sanz-Lázaro C, Valdemarsen T, Marín A, Holmer M. Effect of temperature on biogeochemistry of marine organic-enriched systems: implications in a global warming scenario. ECOLOGICAL APPLICATIONS : A PUBLICATION OF THE ECOLOGICAL SOCIETY OF AMERICA 2011; 21:2664-2677. [PMID: 22073651 DOI: 10.1890/10-2219.1] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Coastal biogeochemical cycles are expected to be affected by global warming. By means of a mesocosm experiment, the effect of increased water temperature on the biogeochemical cycles of coastal sediments affected by organic-matter enrichment was tested, focusing on the carbon, sulfur, and iron cycles. Nereis diversicolor was used as a model species to simulate macrofaunal bioirrigation activity in natural sediments. Although bioirrigation rates of N. diversicolor were not temperature dependent, temperature did have a major effect on the sediment metabolism. Under organic-enrichment conditions, the increase in sediment metabolism was greater than expected and occurred through the enhancement of anaerobic metabolic pathway rates, mainly sulfate reduction. There was a twofold increase in sediment metabolism and the accumulation of reduced sulfur. The increase in the benthic metabolism was maintained by the supply of electron acceptors through bioirrigation and as a result of the availability of iron in the sediment. As long as the sediment buffering capacity toward sulfides is not surpassed, an increase in temperature might promote the recovery of organic-enriched sediments by decreasing the time for mineralization of excess organic matter.
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Affiliation(s)
- Carlos Sanz-Lázaro
- Departamento de Ecología e Hidrología, Facultad de Biología, Universidad de Murcia, Campus de Espinardo, 30100 Murcia, Spain.
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Drevnick PE, Muir DCG, Lamborg CH, Horgan MJ, Canfield DE, Boyle JF, Rose NL. Increased accumulation of sulfur in lake sediments of the high arctic. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2010; 44:8415-8421. [PMID: 20973547 DOI: 10.1021/es101991p] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
We report a synchronous increase in accumulation of reduced inorganic sulfur since c. 1980 in sediment cores from eight of nine lakes studied in the Canadian Arctic and Svalbard (Norway). Sediment incubations and detailed analyses of sediment profiles from two of the lakes indicate that increases in sulfur accumulation may be due ultimately to a changing climate. Warming-induced lengthening of the ice-free season is resulting in well-documented increases in algal production and sedimentation of the resulting detrital matter. Algal detritus is a rich source of labile carbon, which in these sediments stimulates dissimilatory sulfate reduction. The sulfide produced is stored in sediment (as acid volatile sulfide), converted to other forms of sulfur, or reoxidized to sulfate and lost to the water column. An acceleration of the sulfur cycle in Arctic lakes could have profound effects on important biogeochemical processes, such as carbon burial and mercury methylation.
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Affiliation(s)
- Paul E Drevnick
- INRS-ETE, Université du Québec, 490 de la Couronne, Québec, QC G1K 9A9, Canada.
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Jørgensen BB, Dunker R, Grünke S, Røy H. Filamentous sulfur bacteria, Beggiatoa spp., in arctic marine sediments (Svalbard, 79 degrees N). FEMS Microbiol Ecol 2010; 73:500-13. [PMID: 20608982 DOI: 10.1111/j.1574-6941.2010.00918.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Fjord sediments on the west coast of the arctic archipelago Svalbard were surveyed to understand whether large filamentous sulfur bacteria of the genus Beggiatoa thrive at seawater temperatures permanently near freezing. Two sediments had abundant populations of Beggiatoa, while at six sites, only sporadic occurrences were observed. We conclude that Beggiatoa, although previously unnoticed, are widespread in these arctic fjord sediments. Beggiatoa ranged in diameter from 2 to 52 microm and, by those tested, stored nitrate in vacuoles at up to 260 mM. The 16S rRNA gene sequence of a 20-microm-wide filament is closely associated with other large, marine, nitrate-storing Beggiatoa. The Beggiatoa mostly occurred in the upper 2-5 cm of oxidized surface sediment between oxygen and the deeper sulfidic zone. In spite of a very low or an undetectable sulfide concentration, sulfate reduction provided abundant H(2)S in this zone. The total living biomass of Beggiatoa filaments at one study site varied over 3 years between 1.13 and 3.36 g m(-2). Because of their large size, Beggiatoa accounted for up to 15% of the total prokaryotic biomass, even though the filament counts at this site were rather low, comprising <1/10,000 of the bacterial numbers on a cell basis.
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Dunker R, Røy H, Jørgensen BB. Temperature regulation of gliding motility in filamentous sulfur bacteria, Beggiatoa spp. FEMS Microbiol Ecol 2010; 73:234-42. [DOI: 10.1111/j.1574-6941.2010.00887.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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Hubert C, Arnosti C, Brüchert V, Loy A, Vandieken V, Jørgensen BB. Thermophilic anaerobes in Arctic marine sediments induced to mineralize complex organic matter at high temperature. Environ Microbiol 2010; 12:1089-104. [PMID: 20192966 DOI: 10.1111/j.1462-2920.2010.02161.x] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Marine sediments harbour diverse populations of dormant thermophilic bacterial spores that become active in sediment incubation experiments at much higher than in situ temperature. This response was investigated in the presence of natural complex organic matter in sediments of two Arctic fjords, as well as with the addition of freeze-dried Spirulina or individual high-molecular-weight polysaccharides. During 50 degrees C incubation experiments, Arctic thermophiles catalysed extensive mineralization of the organic matter via extracellular enzymatic hydrolysis, fermentation and sulfate reduction. This high temperature-induced food chain mirrors sediment microbial processes occurring at cold in situ temperatures (near 0 degrees C), yet it is catalysed by a completely different set of microorganisms. Using sulfate reduction rates (SRR) as a proxy for organic matter mineralization showed that differences in organic matter reactivity determined the extent of the thermophilic response. Fjord sediments with higher in situ SRR also supported higher SRR at 50 degrees C. Amendment with Spirulina significantly increased volatile fatty acids production and SRR relative to unamended sediment in 50 degrees C incubations. Spirulina amendment also revealed temporally distinct sulfate reduction phases, consistent with 16S rRNA clone library detection of multiple thermophilic Desulfotomaculum spp. enriched at 50 degrees C. Incubations with four different fluorescently labelled polysaccharides at 4 degrees C and 50 degrees C showed that the thermophilic population in Arctic sediments produce a different suite of polymer-hydrolysing enzymes than those used in situ by the cold-adapted microbial community. Over time, dormant marine microorganisms like these are buried in marine sediments and might eventually encounter warmer conditions that favour their activation. Distinct enzymatic capacities for organic polymer degradation could allow specific heterotrophic populations like these to play a role in sustaining microbial metabolism in the deep, warm, marine biosphere.
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Affiliation(s)
- Casey Hubert
- Department of Biogeochemistry, Max Planck Institute for Marine Microbiology, Bremen, Germany.
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Mitchell K, Heyer A, Canfield DE, Hoek J, Habicht KS. Temperature effect on the sulfur isotope fractionation during sulfate reduction by two strains of the hyperthermophilicArchaeoglobus fulgidus. Environ Microbiol 2009; 11:2998-3006. [DOI: 10.1111/j.1462-2920.2009.02002.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Hubert C, Loy A, Nickel M, Arnosti C, Baranyi C, Brüchert V, Ferdelman T, Finster K, Christensen FM, Rosa de Rezende J, Vandieken V, Jørgensen BB. A constant flux of diverse thermophilic bacteria into the cold Arctic seabed. Science 2009; 325:1541-4. [PMID: 19762643 DOI: 10.1126/science.1174012] [Citation(s) in RCA: 126] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Microorganisms have been repeatedly discovered in environments that do not support their metabolic activity. Identifying and quantifying these misplaced organisms can reveal dispersal mechanisms that shape natural microbial diversity. Using endospore germination experiments, we estimated a stable supply of thermophilic bacteria into permanently cold Arctic marine sediment at a rate exceeding 10(8) spores per square meter per year. These metabolically and phylogenetically diverse Firmicutes show no detectable activity at cold in situ temperatures but rapidly mineralize organic matter by hydrolysis, fermentation, and sulfate reduction upon induction at 50 degrees C. The closest relatives to these bacteria come from warm subsurface petroleum reservoir and ocean crust ecosystems, suggesting that seabed fluid flow from these environments is delivering thermophiles to the cold ocean. These transport pathways may broadly influence microbial community composition in the marine environment.
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Affiliation(s)
- Casey Hubert
- Biogeochemistry Group, Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, D-28359 Bremen, Germany.
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Robador A, Brüchert V, Jørgensen BB. The impact of temperature change on the activity and community composition of sulfate-reducing bacteria in arctic versus temperate marine sediments. Environ Microbiol 2009; 11:1692-703. [DOI: 10.1111/j.1462-2920.2009.01896.x] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Nevot M, Deroncelé V, Montes MJ, Mercade E. Effect of incubation temperature on growth parameters ofPseudoalteromonas antarcticaNF3and its production of extracellular polymeric substances. J Appl Microbiol 2008; 105:255-63. [DOI: 10.1111/j.1365-2672.2008.03769.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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41
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Response of fermentation and sulfate reduction to experimental temperature changes in temperate and Arctic marine sediments. ISME JOURNAL 2008; 2:815-29. [DOI: 10.1038/ismej.2008.20] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Finke N, Vandieken V, Jørgensen BB. Acetate, lactate, propionate, and isobutyrate as electron donors for iron and sulfate reduction in Arctic marine sediments, Svalbard. FEMS Microbiol Ecol 2006; 59:10-22. [PMID: 17069623 DOI: 10.1111/j.1574-6941.2006.00214.x] [Citation(s) in RCA: 115] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
The contribution of volatile fatty acids (VFA) as e(-)-donors for anaerobic terminal oxidation of organic carbon through iron and sulfate reduction was studied in Arctic fjord sediment. Dissolved inorganic carbon, Fe(2+), VFA concentrations, and sulfate reduction were monitored in slurries from the oxidized (0-2 cm) and the reduced (5-9 cm) zone. In the 0-2 cm layer, 2/3 of the mineralization could be attributed to sulfate reduction and 1/3 to iron reduction. In the 5-9 cm layer, sulfate reduction was the sole mineralization process. Acetate and lactate turnover rates were measured by radiotracer. Inhibition of sulfate reduction with selenate resulted in the accumulation of acetate, propionate, and isobutyrate. The acetate turnover rates determined by radiotracer and accumulation after inhibition were similar. VFA turnover accounted for 21% and 52% of the mineralization through sulfate reduction in the 0-2 and 5-9 cm layer, respectively. Acetate and lactate turnover in the inhibited 0-2 cm slurry was attributed to iron reduction and accounted for 10% and 2% of the iron reduction. Therefore, 88% and 79% of the iron and sulfate reduction in the 0-2 cm layer, respectively, must be fueled by alternative e(-)-donors. The accumulation of VFA in the selenate-inhibited 0-2 cm slurry did not enhance iron reduction, indicating that iron reducers were not limited by VFA availability.
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Affiliation(s)
- Niko Finke
- Department of Biogeochemistry, Max Planck Institute for Marine Microbiology, Bremen, Germany.
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Gocheva YG, Krumova ET, Slokoska LS, Miteva JG, Vassilev SV, Angelova MB. Cell response of Antarctic and temperate strains of Penicillium spp. to different growth temperature. ACTA ACUST UNITED AC 2006; 110:1347-54. [PMID: 17070679 DOI: 10.1016/j.mycres.2006.08.007] [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] [Received: 01/24/2006] [Revised: 05/25/2006] [Accepted: 08/12/2006] [Indexed: 10/24/2022]
Abstract
The effect of growth temperature (10, 15, 20, 25, and 30 degrees C) on the cell response was compared between two Antarctic Penicillium sp. strains (Penicillium sp. p14 and Penicillium sp. m12) and a European temperate strain, Penicillium sp. t35. According to the temperature profiles, Penicillium sp. p14 was identified as psychrophilic, while Penicillium sp. m12 and Penicillium sp. t35 as mesophilic fungi, respectively. The results demonstrated that the growth at low temperature does clearly induce oxidative stress events in all strains tested. Decreases in growth temperature below the optimal coincided with markedly enhanced protein carbonyl content, an indicator of oxidatively damaged proteins. Also, the cellular response to growth temperature in terms of reserve carbohydrate was determined. In the mesophilic strains there was essentially no enhancement of glycogen content. This was in contrast to the psychrophilic Penicillium sp. p14, which gradually accumulated glycogen in response to cold (10 degrees C) during the exponential phase. In addition, elevated endogenous levels of trehalose upon low-temperature stress were exhibited by all model microorganisms. Compared with temperate mesophilic Penicillium sp. t35, Antarctic strains (psychrophilic Penicillium sp. p14 and mesophilic Penicillium sp. m12) demonstrated a marked rise in activities of protective enzymes such as superoxide dismutase and catalase at decreasing temperatures. The results suggested that low-temperature resistance is partially associated with enhanced scavenging systems.
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Affiliation(s)
- Yana G Gocheva
- Institute of Microbiology, Bulgarian Academy of Sciences, Academician G. Bonchev 26, 1113 Sofia, Bulgaria
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Vandieken V, Mußmann M, Niemann H, Jørgensen BB. Desulfuromonas svalbardensis sp. nov. and Desulfuromusa ferrireducens sp. nov., psychrophilic, Fe(III)-reducing bacteria isolated from Arctic sediments, Svalbard. Int J Syst Evol Microbiol 2006; 56:1133-1139. [PMID: 16627667 DOI: 10.1099/ijs.0.63639-0] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two psychrophilic, Gram-negative, rod-shaped, motile bacteria (strains 112T and 102T) that conserved energy from dissimilatory Fe(III) reduction concomitant with acetate oxidation were isolated from permanently cold Arctic marine sediments. Both strains grew at temperatures down to −2 °C, with respective temperature optima of 14 °C and 14–17 °C for strains 112T and 102T. The isolated strains reduced Fe(III) using common fermentation products such as acetate, lactate, propionate, formate or hydrogen as electron donors, and they also grew with fumarate as the sole substrate. As alternatives to Fe(III), they reduced fumarate, S0 and Mn(IV). Based on 16S rRNA gene sequence similarity, strain 112T was most closely related to Desulfuromonas acetoxidans (97.0 %) and Desulfuromonas thiophila NZ27T (95.5 %), and strain 102T to Malonomonas rubra Gra Mal 1T (96.3 %) and Desulfuromusa succinoxidans GylacT (95.9 %) within the Deltaproteobacteria. Strains 112T and 102T therefore represent novel species, for which the names Desulfuromonas svalbardensis sp. nov. (type strain 112T=DSM 16958T=JCM 12927T) and Desulfuromusa ferrireducens sp. nov. (type strain 102T=DSM 16956T=JCM 12926T) are proposed.
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Affiliation(s)
- Verona Vandieken
- Max-Planck-Institute for Marine Microbiology, Celsiusstrasse 1, 28359 Bremen, Germany
| | - Marc Mußmann
- Max-Planck-Institute for Marine Microbiology, Celsiusstrasse 1, 28359 Bremen, Germany
| | - Helge Niemann
- Max-Planck-Institute for Marine Microbiology, Celsiusstrasse 1, 28359 Bremen, Germany
| | - Bo Barker Jørgensen
- Max-Planck-Institute for Marine Microbiology, Celsiusstrasse 1, 28359 Bremen, Germany
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Abstract
Many archaea are extremophiles. They thrive at high temperatures, at high pressure and in concentrated acidic environments. Nevertheless, the largest proportion and greatest diversity of archaea exist in cold environments. Most of the Earth's biosphere is cold, and archaea represent a significant fraction of the biomass. Although psychrophilic archaea have long been the neglected majority, the study of these microorganisms is beginning to come of age. This review casts a spotlight on the ecology, adaptation biology and unique science that is being realized from studies on cold-adapted archaea.
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Affiliation(s)
- Ricardo Cavicchioli
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney NSW 2052, Australia.
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Tarpgaard IH, Boetius A, Finster K. Desulfobacter psychrotolerans sp. nov., a new psychrotolerant sulfate-reducing bacterium and descriptions of its physiological response to temperature changes. Antonie van Leeuwenhoek 2005; 89:109-24. [PMID: 16328859 DOI: 10.1007/s10482-005-9014-1] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2005] [Accepted: 09/15/2005] [Indexed: 11/25/2022]
Abstract
A psychrotrolerant acetate-oxidizing sulfate-reducing bacterium (strain akvb(T)) was isolated from sediment from the northern part of The North Sea with annual temperature fluctuations between 8 and 14 degrees C. Of the various substrates tested, strain akvb(T) grew exclusively by the oxidation of acetate coupled to the reduction of sulfate. The cells were motile, thick rods with round ends and grew in dense aggregates. Strain akvb(T) grew at temperatures ranging from -3.6 to 26.3 degrees C. Optimal growth was observed at 20 degrees C. The highest cell specific sulfate reduction rate of 6.2 fmol cell(-1) d(-1) determined by the (35)SO(2-)(40) method was measured at 26 degrees C. The temperature range of short-term sulfate reduction rates exceeded the temperature range of growth by 5 degrees C. The Arrhenius relationship for the temperature dependence of growth and sulfate reduction was linear, with two distinct slopes below the optimum temperatures of both processes. The critical temperature was 6.4 degrees C. The highest growth yield (4.3-4.5 g dry weight mol(-1) acetate) was determined at temperatures between 5 and 15 degrees C. The cellular fatty acid composition was determined with cultures grown at 4 and 20 degrees C, respectively. The relative proportion of cellular unsaturated fatty acids (e.g. 16:1omega7c) was higher in cells grown at 4 degrees C than in cells grown at 20 degrees C. The physiological responses to temperature changes showed that strain akvb(T) was well adapted to the temperature regime of the environment from which it was isolated. Phylogenetic analysis showed that strain akvb(T) is closest related to Desulfobacter hydrogenophilus, with a 16S rRNA gene sequence similarity of 98.6%. DNA-DNA-hybridization showed a similarity of 32% between D. hydrogenophilus and strain akvb(T). Based on phenotypic and DNA-based characteristics we propose that strain akvb(T) is a member of a new species, Desulfobacter psychrotolerans sp. nov.
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Affiliation(s)
- Irene H Tarpgaard
- Department of Microbiology, Bldg. 540, Institute of Biological Sciences, University of Aarhus, 8000 Aarhus, Denmark
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Girguis PR, Cozen AE, DeLong EF. Growth and population dynamics of anaerobic methane-oxidizing archaea and sulfate-reducing bacteria in a continuous-flow bioreactor. Appl Environ Microbiol 2005; 71:3725-33. [PMID: 16000782 PMCID: PMC1169053 DOI: 10.1128/aem.71.7.3725-3733.2005] [Citation(s) in RCA: 97] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The consumption of methane in anoxic marine sediments is a biogeochemical phenomenon mediated by two archaeal groups (ANME-1 and ANME-2) that exist syntrophically with sulfate-reducing bacteria. These anaerobic methanotrophs have yet to be recovered in pure culture, and key aspects of their ecology and physiology remain poorly understood. To characterize the growth and physiology of these anaerobic methanotrophs and the syntrophic sulfate-reducing bacteria, we incubated marine sediments using an anoxic, continuous-flow bioreactor during two experiments at different advective porewater flow rates. We examined the growth kinetics of anaerobic methanotrophs and Desulfosarcina-like sulfate-reducing bacteria using quantitative PCR as a proxy for cell counts, and measured methane oxidation rates using membrane-inlet mass spectrometry. Our data show that the specific growth rates of ANME-1 and ANME-2 archaea differed in response to porewater flow rates. ANME-2 methanotrophs had the highest rates in lower-flow regimes (mu(ANME-2) = 0.167 . week(-1)), whereas ANME-1 methanotrophs had the highest rates in higher-flow regimes (mu(ANME-1) = 0.218 . week(-1)). In both incubations, Desulfosarcina-like sulfate-reducing bacterial growth rates were approximately 0.3 . week(-1), and their growth dynamics suggested that sulfate-reducing bacterial growth might be facilitated by, but not dependent upon, an established anaerobic methanotrophic population. ANME-1 growth rates corroborate field observations that ANME-1 archaea flourish in higher-flow regimes. Our growth and methane oxidation rates jointly demonstrate that anaerobic methanotrophs are capable of attaining substantial growth over a range of environmental conditions used in these experiments, including relatively low methane partial pressures.
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Affiliation(s)
- Peter R Girguis
- Monterey Bay Aquarium Research Institute, 7700 Sandholdt Road, Moss Landing, California 95039, USA
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Goodchild A, Raftery M, Saunders NFW, Guilhaus M, Cavicchioli R. Cold Adaptation of the Antarctic Archaeon, Methanococcoides burtonii Assessed by Proteomics Using ICAT. J Proteome Res 2005; 4:473-80. [PMID: 15822924 DOI: 10.1021/pr049760p] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Using isotope coded affinity tag (ICAT) chromatography and liquid chromatography-mass spectrometry, 163 proteins were identified from the cold-adapted archaeon, Methanococcoides burtonii. 14 proteins were differentially expressed during growth at 4 degrees C and 23 degrees C. Knowledge of protein abundance, protein identity and gene arrangement was used to determine mechanisms of cold adaptation. Growth temperature was found to affect proteins involved in energy generation and biosynthesis linked to methanogenesis, membrane transport, transcription and protein folding, as well as affecting the expression of two hypothetical proteins. Pooling the data from this ICAT study with data from a previous two-dimensional gel electrophoresis study highlighted consistencies and differences between the two methods, and led us to conclude that the two approaches were generally complementary. This is the first report of ICAT applied to Archaea, or for the study of cold adaptation in any organism.
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Affiliation(s)
- Amber Goodchild
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, 2052, NSW, Australia
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Groudieva T, Kambourova M, Yusef H, Royter M, Grote R, Trinks H, Antranikian G. Diversity and cold-active hydrolytic enzymes of culturable bacteria associated with Arctic sea ice, Spitzbergen. Extremophiles 2004; 8:475-88. [PMID: 15252724 DOI: 10.1007/s00792-004-0409-0] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2004] [Accepted: 06/08/2004] [Indexed: 10/26/2022]
Abstract
The diversity of culturable bacteria associated with sea ice from four permanently cold fjords of Spitzbergen, Arctic Ocean, was investigated. A total of 116 psychrophilic and psychrotolerant strains were isolated under aerobic conditions at 4 degrees C. The isolates were grouped using amplified rDNA restriction analysis fingerprinting and identified by partial sequencing of 16S rRNA gene. The bacterial isolates fell in five phylogenetic groups: subclasses alpha and gamma of Proteobacteria, the Bacillus-Clostridium group, the order Actinomycetales, and the Cytophaga-Flexibacter-Bacteroides (CFB) phylum. Over 70% of the isolates were affiliated with the Proteobacteria gamma subclass. Based on phylogenetic analysis (<98% sequence similarity), over 40% of Arctic isolates represent potentially novel species or genera. Most of the isolates were psychrotolerant and grew optimally between 20 and 25 degrees C. Only a few strains were psychrophilic, with an optimal growth at 10-15 degrees C. The majority of the bacterial strains were able to secrete a broad range of cold-active hydrolytic enzymes into the medium at a cultivation temperature of 4 degrees C. The isolates that are able to degrade proteins (skim milk, casein), lipids (olive oil), and polysaccharides (starch, pectin) account for, respectively, 56, 31, and 21% of sea-ice and seawater strains. The temperature dependences for enzyme production during growth and enzymatic activity were determined for two selected enzymes, alpha-amylase and beta-galactosidase. Interestingly, high levels of enzyme productions were measured at growth temperatures between 4 and 10 degrees C, and almost no production was detected at higher temperatures (20-30 degrees C). Catalytic activity was detected even below the freezing point of water (at -5 degrees C), demonstrating the unique properties of these enzymes.
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Affiliation(s)
- Tatiana Groudieva
- Institute of Technical Microbiology, Technical University Hamburg-Harburg, Kasernenstr 12, 21073 Hamburg, Germany
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Bakermans C, Nealson KH. Relationship of critical temperature to macromolecular synthesis and growth yield in Psychrobacter cryopegella. J Bacteriol 2004; 186:2340-5. [PMID: 15060036 PMCID: PMC412111 DOI: 10.1128/jb.186.8.2340-2345.2004] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2003] [Accepted: 01/08/2004] [Indexed: 11/20/2022] Open
Abstract
Most microorganisms isolated from low-temperature environments (below 4 degrees C) are eury-, not steno-, psychrophiles. While psychrophiles maximize or maintain growth yield at low temperatures to compensate for low growth rate, the mechanisms involved remain unknown, as does the strategy used by eurypsychrophiles to survive wide ranges of temperatures that include subzero temperatures. Our studies involve the eurypsychrophilic bacterium Psychrobacter cryopegella, which was isolated from a briny water lens within Siberian permafrost, where the temperature is -12 degrees C. P. cryopegella is capable of reproducing from -10 to 28 degrees C, with its maximum growth rate at 22 degrees C. We examined the temperature dependence of growth rate, growth yield, and macromolecular (DNA, RNA, and protein) synthesis rates for P. cryopegella. Below 22 degrees C, the growth of P. cryopegella was separated into two domains at the critical temperature (T(critical) = 4 degrees C). RNA, protein, and DNA synthesis rates decreased exponentially with decreasing temperatures. Only the temperature dependence of the DNA synthesis rate changed at T(critical). When normalized to growth rate, RNA and protein synthesis reached a minimum at T(critical), while DNA synthesis remained constant over the entire temperature range. Growth yield peaked at about T(critical) and declined rapidly as temperature decreased further. Similar to some stenopsychrophiles, P. cryopegella maximized growth yield at low temperatures and did so by streamlining growth processes at T(critical). Identifying the specific processes which result in T(critical) will be vital to understanding both low-temperature growth and growth over a wide range of temperatures.
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Affiliation(s)
- Corien Bakermans
- Center for Microbial Ecology, Michigan State University, East Lansing, Michigan 48824, USA.
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