1
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Dawson HM, Connors E, Erazo NG, Sacks JS, Mierzejewski V, Rundell SM, Carlson LT, Deming JW, Ingalls AE, Bowman JS, Young JN. Microbial metabolomic responses to changes in temperature and salinity along the western Antarctic Peninsula. THE ISME JOURNAL 2023; 17:2035-2046. [PMID: 37709939 PMCID: PMC10579395 DOI: 10.1038/s41396-023-01475-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 06/28/2023] [Accepted: 06/30/2023] [Indexed: 09/16/2023]
Abstract
Seasonal cycles within the marginal ice zones in polar regions include large shifts in temperature and salinity that strongly influence microbial abundance and physiology. However, the combined effects of concurrent temperature and salinity change on microbial community structure and biochemical composition during transitions between seawater and sea ice are not well understood. Coastal marine communities along the western Antarctic Peninsula were sampled and surface seawater was incubated at combinations of temperature and salinity mimicking the formation (cold, salty) and melting (warm, fresh) of sea ice to evaluate how these factors may shape community composition and particulate metabolite pools during seasonal transitions. Bacterial and algal community structures were tightly coupled to each other and distinct across sea-ice, seawater, and sea-ice-meltwater field samples, with unique metabolite profiles in each habitat. During short-term (approximately 10-day) incubations of seawater microbial communities under different temperature and salinity conditions, community compositions changed minimally while metabolite pools shifted greatly, strongly accumulating compatible solutes like proline and glycine betaine under cold and salty conditions. Lower salinities reduced total metabolite concentrations in particulate matter, which may indicate a release of metabolites into the labile dissolved organic matter pool. Low salinity also increased acylcarnitine concentrations in particulate matter, suggesting a potential for fatty acid degradation and reduced nutritional value at the base of the food web during freshening. Our findings have consequences for food web dynamics, microbial interactions, and carbon cycling as polar regions undergo rapid climate change.
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Affiliation(s)
- H M Dawson
- School of Oceanography, University of Washington, Seattle, WA, 98195, USA.
| | - E Connors
- Scripps Institution of Oceanography, UC San Diego, La Jolla, CA, 92037, USA
| | - N G Erazo
- Scripps Institution of Oceanography, UC San Diego, La Jolla, CA, 92037, USA
- Center for Marine Biodiversity and Conservation, UC San Diego, La Jolla, CA, 92037, USA
| | - J S Sacks
- School of Oceanography, University of Washington, Seattle, WA, 98195, USA
| | - V Mierzejewski
- School of Earth and Space Exploration, Arizona State University, Tempe, AZ, 85287, USA
| | - S M Rundell
- School of Oceanography, University of Washington, Seattle, WA, 98195, USA
| | - L T Carlson
- School of Oceanography, University of Washington, Seattle, WA, 98195, USA
| | - J W Deming
- School of Oceanography, University of Washington, Seattle, WA, 98195, USA
| | - A E Ingalls
- School of Oceanography, University of Washington, Seattle, WA, 98195, USA
| | - J S Bowman
- Scripps Institution of Oceanography, UC San Diego, La Jolla, CA, 92037, USA
- Center for Marine Biodiversity and Conservation, UC San Diego, La Jolla, CA, 92037, USA
- Center for Microbiome Innovation, UC San Diego, La Jolla, CA, 92037, USA
| | - J N Young
- School of Oceanography, University of Washington, Seattle, WA, 98195, USA.
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2
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Hwang J, Kim B, Lee MJ, Kim EJ, Cho SM, Lee SG, Han SJ, Kim K, Lee JH, Do H. Importance of rigidity of ice-binding protein (FfIBP) for hyperthermal hysteresis activity and microbial survival. Int J Biol Macromol 2022; 204:485-499. [PMID: 35149098 DOI: 10.1016/j.ijbiomac.2022.02.032] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 02/05/2022] [Accepted: 02/07/2022] [Indexed: 01/18/2023]
Abstract
Ice-binding proteins (IBPs) are well-characterized proteins responsible for the cold-adaptation mechanisms. Despite extensive structural and biological investigation of IBPs and antifreeze proteins, only a few studies have considered the relationship between protein stabilization and thermal hysteresis (TH) activity as well as the implication of hyperactivity. Here, we investigated the important role of the head capping region in stabilization and the hyper-TH activity of FfIBP using molecular dynamics simulation. Data comparison revealed that residues on the ice-binding site of the hyperactive FfIBP are immobilized, which could be correlated with TH activity. Further comparison analysis indicated the disulfide bond in the head region is mainly involved in protein stabilization and is crucial for hyper-TH activity. This finding could also be generalized to known hyperactive IBPs. Furthermore, in mimicking the physiological conditions, bacteria with membrane-anchored FfIBP formed brine pockets in a TH activity-dependent manner. Cells with a higher number of TH-active IBPs showed an increased number of brine pockets, which may be beneficial for short- and long-term survival in cold environments by reducing the salt concentration. The newly identified conditions for hyper-TH activity and their implications on bacterial survival provide insights into novel mechanistic aspects of cold adaptation in polar microorganisms.
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Affiliation(s)
- Jisub Hwang
- Research Unit of Cryogenic Novel Material, Korea Polar Research Institute, Incheon 21990, Republic of Korea; Department of Polar Sciences, University of Science and Technology, Incheon 21990, Republic of Korea
| | - Bomi Kim
- Research Unit of Cryogenic Novel Material, Korea Polar Research Institute, Incheon 21990, Republic of Korea; Department of Polar Sciences, University of Science and Technology, Incheon 21990, Republic of Korea
| | - Min Ju Lee
- Research Unit of Cryogenic Novel Material, Korea Polar Research Institute, Incheon 21990, Republic of Korea
| | - Eun Jae Kim
- Division of Life Sciences, Korea Polar Research Institute, Incheon 21990, Republic of Korea
| | - Sung Mi Cho
- Division of Life Sciences, Korea Polar Research Institute, Incheon 21990, Republic of Korea
| | - Sung Gu Lee
- Research Unit of Cryogenic Novel Material, Korea Polar Research Institute, Incheon 21990, Republic of Korea; Department of Polar Sciences, University of Science and Technology, Incheon 21990, Republic of Korea
| | - Se Jong Han
- Department of Polar Sciences, University of Science and Technology, Incheon 21990, Republic of Korea; Division of Life Sciences, Korea Polar Research Institute, Incheon 21990, Republic of Korea
| | - Kitae Kim
- Research Unit of Cryogenic Novel Material, Korea Polar Research Institute, Incheon 21990, Republic of Korea; Department of Polar Sciences, University of Science and Technology, Incheon 21990, Republic of Korea.
| | - Jun Hyuck Lee
- Research Unit of Cryogenic Novel Material, Korea Polar Research Institute, Incheon 21990, Republic of Korea; Department of Polar Sciences, University of Science and Technology, Incheon 21990, Republic of Korea.
| | - Hackwon Do
- Research Unit of Cryogenic Novel Material, Korea Polar Research Institute, Incheon 21990, Republic of Korea; Department of Polar Sciences, University of Science and Technology, Incheon 21990, Republic of Korea.
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3
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Rapp JZ, Sullivan MB, Deming JW. Divergent Genomic Adaptations in the Microbiomes of Arctic Subzero Sea-Ice and Cryopeg Brines. Front Microbiol 2021; 12:701186. [PMID: 34367102 PMCID: PMC8339730 DOI: 10.3389/fmicb.2021.701186] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 06/29/2021] [Indexed: 11/16/2022] Open
Abstract
Subzero hypersaline brines are liquid microbial habitats within otherwise frozen environments, where concentrated dissolved salts prevent freezing. Such extreme conditions presumably require unique microbial adaptations, and possibly altered ecologies, but specific strategies remain largely unknown. Here we examined prokaryotic taxonomic and functional diversity in two seawater-derived subzero hypersaline brines: first-year sea ice, subject to seasonally fluctuating conditions; and ancient cryopeg, under relatively stable conditions geophysically isolated in permafrost. Overall, both taxonomic composition and functional potential were starkly different. Taxonomically, sea-ice brine communities (∼105 cells mL–1) had greater richness, more diversity and were dominated by bacterial genera, including Polaribacter, Paraglaciecola, Colwellia, and Glaciecola, whereas the more densely inhabited cryopeg brines (∼108 cells mL–1) lacked these genera and instead were dominated by Marinobacter. Functionally, however, sea ice encoded fewer accessory traits and lower average genomic copy numbers for shared traits, though DNA replication and repair were elevated; in contrast, microbes in cryopeg brines had greater genetic versatility with elevated abundances of accessory traits involved in sensing, responding to environmental cues, transport, mobile elements (transposases and plasmids), toxin-antitoxin systems, and type VI secretion systems. Together these genomic features suggest adaptations and capabilities of sea-ice communities manifesting at the community level through seasonal ecological succession, whereas the denser cryopeg communities appear adapted to intense bacterial competition, leaving fewer genera to dominate with brine-specific adaptations and social interactions that sacrifice some members for the benefit of others. Such cryopeg genomic traits provide insight into how long-term environmental stability may enable life to survive extreme conditions.
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Affiliation(s)
- Josephine Z Rapp
- School of Oceanography, University of Washington, Seattle, WA, United States
| | - Matthew B Sullivan
- Byrd Polar and Climate Research Center, Ohio State University, Columbus, OH, United States.,Department of Microbiology, Ohio State University, Columbus, OH, United States.,Department of Civil, Environmental and Geodetic Engineering, Ohio State University, Columbus, OH, United States.,Center of Microbiome Science, Ohio State University, Columbus, OH, United States
| | - Jody W Deming
- School of Oceanography, University of Washington, Seattle, WA, United States
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4
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Cappello S, Caruso G, Bergami E, Macrì A, Venuti V, Majolino D, Corsi I. New insights into the structure and function of the prokaryotic communities colonizing plastic debris collected in King George Island (Antarctica): Preliminary observations from two plastic fragments. JOURNAL OF HAZARDOUS MATERIALS 2021; 414:125586. [PMID: 34030422 DOI: 10.1016/j.jhazmat.2021.125586] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 02/28/2021] [Accepted: 03/02/2021] [Indexed: 06/12/2023]
Abstract
In Antarctic regions, the composition and metabolic activity of microbial assemblages associated with plastic debris ("plastisphere") are almost unknown. A macroplastic item from land (MaL, 30 cm) and a mesoplastic from the sea (MeS, 4 mm) were collected in Maxwell Bay (King George Island, South Shetland) and analyzed by Fourier transform infrared spectroscopy in attenuated total reflectance geometry (FTIR-ATR), which confirmed a polystyrene foam and a composite high-density polyethylene composition for MaL and MeS, respectively. The structure and function of the two plastic-associated prokaryotic communities were studied by complementary 16S ribosomal RNA gene clone libraries, total bacterioplankton and culturable heterotrophic bacterial counts, enzymatic activities of the whole community and enzymatic profiles of bacterial isolates. Results showed that Gamma- and Betaproteobacteria (31% and 28%, respectively) dominated in MeS, while Beta- and Alphaproteobacteria (21% and 13%, respectively) in MaL. Sequences related to oil degrading bacteria (Alcanivorax,Marinobacter) confirmed the known anthropogenic pressure in King George Island. This investigation on plastic-associated prokaryotic structure and function represents the first attempt to characterize the ecological role of plastisphere in this Antarctic region and provides the necessary background for future research on the significance of polymer type, surface characteristics and environmental conditions in shaping the plastisphere.
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Affiliation(s)
- Simone Cappello
- Institute for Biological Resources and Marine Biotechnologies (IRBIM), National Research Council (CNR), Spianata San Raineri 86, Messina 98122, Italy
| | - Gabriella Caruso
- Institute of Polar Sciences (ISP), National Research Council (CNR), Spianata San Raineri 86, Messina 98122, Italy.
| | - Elisa Bergami
- Department of Physical, Earth and Environmental Sciences, University of Siena, Via Mattioli 4, Siena 53100, Italy
| | - Angela Macrì
- Institute for Biological Resources and Marine Biotechnologies (IRBIM), National Research Council (CNR), Spianata San Raineri 86, Messina 98122, Italy; Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale Ferdinando Stagno D'Alcontres 31, Messina 98166, Italy
| | - Valentina Venuti
- Department of Mathematical and Computer Sciences, Physical Sciences and Earth Sciences, University of Messina, Viale Ferdinando Stagno D'Alcontres 31, Messina 98166, Italy
| | - Domenico Majolino
- Department of Mathematical and Computer Sciences, Physical Sciences and Earth Sciences, University of Messina, Viale Ferdinando Stagno D'Alcontres 31, Messina 98166, Italy
| | - Ilaria Corsi
- Department of Physical, Earth and Environmental Sciences, University of Siena, Via Mattioli 4, Siena 53100, Italy
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5
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Mudge MC, Nunn BL, Firth E, Ewert M, Hales K, Fondrie WE, Noble WS, Toner J, Light B, Junge KA. Subzero, saline incubations of
Colwellia psychrerythraea
reveal strategies and biomarkers for sustained life in extreme icy environments. Environ Microbiol 2021; 23:3840-3866. [DOI: 10.1111/1462-2920.15485] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 03/22/2021] [Indexed: 11/26/2022]
Affiliation(s)
- Miranda C. Mudge
- Department of Genome Sciences University of Washington Seattle WA USA
- Department of Molecular and Cellular Biology University of Washington Seattle WA USA
| | - Brook L. Nunn
- Department of Genome Sciences University of Washington Seattle WA USA
- Astrobiology Program University of Washington Seattle WA USA
| | - Erin Firth
- Applied Physics Lab, Polar Science Center University of Washington Seattle WA USA
| | - Marcela Ewert
- Applied Physics Lab, Polar Science Center University of Washington Seattle WA USA
| | - Kianna Hales
- Department of Genome Sciences University of Washington Seattle WA USA
| | | | - William S. Noble
- Department of Genome Sciences University of Washington Seattle WA USA
- Paul G. Allen School of Computer Science and Engineering University of Washington Seattle WA USA
| | - Jonathan Toner
- Department of Earth and Space Sciences University of Washington Seattle WA USA
| | - Bonnie Light
- Applied Physics Lab, Polar Science Center University of Washington Seattle WA USA
| | - Karen A. Junge
- Applied Physics Lab, Polar Science Center University of Washington Seattle WA USA
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6
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Cooper ZS, Rapp JZ, Carpenter SD, Iwahana G, Eicken H, Deming JW. Distinctive microbial communities in subzero hypersaline brines from Arctic coastal sea ice and rarely sampled cryopegs. FEMS Microbiol Ecol 2020; 95:5593952. [PMID: 31626297 PMCID: PMC6859516 DOI: 10.1093/femsec/fiz166] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Accepted: 10/15/2019] [Indexed: 11/29/2022] Open
Abstract
Hypersaline aqueous environments at subzero temperatures are known to be inhabited by microorganisms, yet information on community structure in subzero brines is very limited. Near Utqiaġvik, Alaska, we sampled subzero brines (–6°C, 115–140 ppt) from cryopegs, i.e. unfrozen sediments within permafrost that contain relic (late Pleistocene) seawater brine, as well as nearby sea-ice brines to examine microbial community composition and diversity using 16S rRNA gene amplicon sequencing. We also quantified the communities microscopically and assessed environmental parameters as possible determinants of community structure. The cryopeg brines harbored surprisingly dense bacterial communities (up to 108 cells mL–1) and millimolar levels of dissolved and particulate organic matter, extracellular polysaccharides and ammonia. Community composition and diversity differed between the two brine environments by alpha- and beta-diversity indices, with cryopeg brine communities appearing less diverse and dominated by one strain of the genus Marinobacter, also detected in other cold, hypersaline environments, including sea ice. The higher density and trend toward lower diversity in the cryopeg communities suggest that long-term stability and other features of a subzero brine are more important selective forces than in situ temperature or salinity, even when the latter are extreme.
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Affiliation(s)
- Zachary S Cooper
- School of Oceanography, University of Washington, P.O. Box 357940 Seattle, WA 98195, USA
| | - Josephine Z Rapp
- School of Oceanography, University of Washington, P.O. Box 357940 Seattle, WA 98195, USA
| | - Shelly D Carpenter
- School of Oceanography, University of Washington, P.O. Box 357940 Seattle, WA 98195, USA
| | - Go Iwahana
- International Arctic Research Center, University of Alaska Fairbanks, Fairbanks, AK 99775, USA
| | - Hajo Eicken
- International Arctic Research Center, University of Alaska Fairbanks, Fairbanks, AK 99775, USA
| | - Jody W Deming
- School of Oceanography, University of Washington, P.O. Box 357940 Seattle, WA 98195, USA
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7
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Lofthus S, Bakke I, Tremblay J, Greer CW, Brakstad OG. Biodegradation of weathered crude oil in seawater with frazil ice. MARINE POLLUTION BULLETIN 2020; 154:111090. [PMID: 32319919 DOI: 10.1016/j.marpolbul.2020.111090] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 03/16/2020] [Accepted: 03/17/2020] [Indexed: 06/11/2023]
Abstract
As ice extent in the Arctic is declining, oil and gas activities will increase, with higher risk of oil spills to the marine environment. To determine biotransformation of dispersed weathered oil in newly formed ice, oil dispersions (2-3 ppm) were incubated in a mixture of natural seawater and frazil ice for 125 days at -2 °C. Dispersed oil in seawater without frazil ice were included in the experimental setup. Presence or absence of frazil ice was a strong driver for microbial community structures and affected the rate of oil degradation. n-alkanes were degraded faster in the presence of frazil ice, the opposite was the case for naphthalenes and 2-3 ring PAHs. No degradation of 4-6 ring PAHs was observed in any of the treatments. The total petroleum oil was not degraded to any significant degree, suggesting that oil will freeze into the ice matrix and persist throughout the icy season.
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Affiliation(s)
- Synnøve Lofthus
- Norwegian University of Science and Technology, Department of Biotechnology and Food Science, Trondheim, Norway; SINTEF Ocean AS, Environment and New Resources, Trondheim, Norway.
| | - Ingrid Bakke
- Norwegian University of Science and Technology, Department of Biotechnology and Food Science, Trondheim, Norway
| | - Julien Tremblay
- National Research Council Canada, Energy, Mining and Environment Research Centre, Montreal, Quebec, Canada
| | - Charles W Greer
- National Research Council Canada, Energy, Mining and Environment Research Centre, Montreal, Quebec, Canada
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8
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Petermann JS, Roberts AL, Hemmerling C, Bajerski F, Pascual J, Overmann J, Weisser WW, Ruess L, Gossner MM. Direct and indirect effects of forest management on tree-hole inhabiting aquatic organisms and their functional traits. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 704:135418. [PMID: 31896218 DOI: 10.1016/j.scitotenv.2019.135418] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 11/04/2019] [Accepted: 11/05/2019] [Indexed: 06/10/2023]
Abstract
Ecological communities in forests have been shown to be strongly affected by forest management but a detailed understanding of how different components of management affect insect communities directly and indirectly via environmental variables, how management influences functional trait diversity and composition, and whether these results can be transferred to other functional groups besides insects (e.g. bacteria or nematodes) is still missing. To address these questions we used water-filled tree holes, which provide habitats for insect larvae and other aquatic organisms in forests, as a model system. We mapped all water-filled tree holes in 75 forest plots (1 ha) under different management intensity in three regions of Germany. We measured structural and climatic conditions at different spatial scales, sampled insect communities in 123 tree holes and bacterial and nematode communities in a subset of these. We found that forest management in terms of harvesting intensity and the proportion of non-natural tree species (species not part of the natural vegetation at the sites) negatively affected tree-hole abundance. An increased proportion of non-natural tree species had a positive direct effect on insect richness and functional diversity in the tree holes. However, a structural equation model showed that increasing management intensity had negative indirect effects on insect abundance and richness, operating via environmental variables at stand and tree-hole scale. Functional diversity and trait composition of insect communities similarly responded to changes in management-related variables. In contrast to insects, bacterial and nematode richness were not directly impacted by forest management but by other environmental variables. Our results suggest that forest management may strongly alter insect communities of tree holes, while nematodes and bacteria seem less affected. Most effects in our study were indirect and negative, indicating that management has often complex consequences for forest communities that should be taken into account in forest management schemes.
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Affiliation(s)
- Jana S Petermann
- Department of Biosciences, University of Salzburg, Hellbrunnerstrasse 34, A-5020 Salzburg, Austria.
| | - Anastasia L Roberts
- Department of Biosciences, University of Salzburg, Hellbrunnerstrasse 34, A-5020 Salzburg, Austria
| | - Christin Hemmerling
- Humboldt-Universität zu Berlin, Institute of Biology, Ecology Group, Philippstraße 13, 10115 Berlin, Germany
| | - Felizitas Bajerski
- Leibniz-Institut Deutsche Sammlung von Mikroorganismen und Zellkulturen, Inhoffenstrasse 7B, D-38124 Braunschweig, Germany
| | - Javier Pascual
- Leibniz-Institut Deutsche Sammlung von Mikroorganismen und Zellkulturen, Inhoffenstrasse 7B, D-38124 Braunschweig, Germany
| | - Jörg Overmann
- Leibniz-Institut Deutsche Sammlung von Mikroorganismen und Zellkulturen, Inhoffenstrasse 7B, D-38124 Braunschweig, Germany; Microbiology, Braunschweig University of Technology, Braunschweig, Germany
| | - Wolfgang W Weisser
- Technical University of Munich, Hans-von-Carlowitz-Platz 2, D-85354 Freising, Germany
| | - Liliane Ruess
- Humboldt-Universität zu Berlin, Institute of Biology, Ecology Group, Philippstraße 13, 10115 Berlin, Germany
| | - Martin M Gossner
- Forest Entomology, Swiss Federal Research Institute WSL, Zürcherstrasse 111, CH-8903 Birmensdorf, Switzerland
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9
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Claessen D, Errington J. Cell Wall Deficiency as a Coping Strategy for Stress. Trends Microbiol 2019; 27:1025-1033. [PMID: 31420127 DOI: 10.1016/j.tim.2019.07.008] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Revised: 07/02/2019] [Accepted: 07/23/2019] [Indexed: 12/22/2022]
Abstract
The cell wall is a surface layer located outside the cell membrane of almost all bacteria; it protects cells from environmental stresses and gives them their typical shape. The cell wall is highly conserved in bacteria and is the target for some of our best antibiotics. Surprisingly, some bacteria are able to shed their wall under the influence of stress, yielding cells that are cell-wall-deficient. Notably, wall-deficient cells are flexible and are able to maneuver through narrow spaces, insensitive to wall-targeting antibiotics, and capable of taking up and exchanging DNA. Moreover, given that wall-associated epitopes are often recognized by host defense systems, wall deficiency provides a plausible explanation for how some bacteria may hide in their host. In this review we focus on this paradoxical stress response, which provides cells with unique opportunities that are unavailable to walled cells.
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Affiliation(s)
- Dennis Claessen
- Institute of Biology, Leiden University, Sylviusweg 72, 2333, BE, Leiden, The Netherlands.
| | - Jeff Errington
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle-upon-Tyne, NE2 4AX, UK.
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10
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Torstensson A, Young JN, Carlson LT, Ingalls AE, Deming JW. Use of exogenous glycine betaine and its precursor choline as osmoprotectants in Antarctic sea-ice diatoms 1. JOURNAL OF PHYCOLOGY 2019; 55:663-675. [PMID: 30685888 DOI: 10.1111/jpy.12839] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2018] [Accepted: 01/14/2019] [Indexed: 06/09/2023]
Abstract
Wide salinity ranges experienced during the seasonal freeze and melt of sea ice likely constrain many biological processes. Microorganisms generally protect against fluctuating salinities through the uptake, production, and release of compatible solutes. Little is known, however, about the use or fate of glycine betaine (GBT hereafter), one of the most common compatible solutes, in sea-ice diatoms confronted with shifts in salinity. We quantified intracellular concentrations and used [14 C]-labeled compounds to track the uptake and fate of the nitrogen-containing osmolyte GBT and its precursor choline in three Antarctic sea-ice diatoms Nitzschia lecointei, Navicula cf. perminuta, and Fragilariopsis cylindrus at -1°C. Experiments show that these diatoms have effective transporters for GBT, but take up lesser amounts of choline. Neither compound was respired. Uptake of GBT protected cells against hyperosmotic shock and corresponded with reduced production of extracellular polysaccharides in N. lecointei cells, which released 85% of the retained GBT following hypoosmotic shock. The ability of sea-ice diatoms to rapidly scavenge and release compatible solutes is likely an important strategy for survival during steep fluctuations in salinity. The release and recycling of compatible solutes may play an important role in algal-bacterial interactions and nitrogen cycling within the semi-enclosed brines of sea ice.
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Affiliation(s)
- Anders Torstensson
- School of Oceanography, University of Washington, Box 357940, Seattle, Washington, 98195-7940, USA
| | - Jodi N Young
- School of Oceanography, University of Washington, Box 357940, Seattle, Washington, 98195-7940, USA
| | - Laura T Carlson
- School of Oceanography, University of Washington, Box 357940, Seattle, Washington, 98195-7940, USA
| | - Anitra E Ingalls
- School of Oceanography, University of Washington, Box 357940, Seattle, Washington, 98195-7940, USA
| | - Jody W Deming
- School of Oceanography, University of Washington, Box 357940, Seattle, Washington, 98195-7940, USA
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11
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Ultee E, Ramijan K, Dame RT, Briegel A, Claessen D. Stress-induced adaptive morphogenesis in bacteria. Adv Microb Physiol 2019; 74:97-141. [PMID: 31126537 DOI: 10.1016/bs.ampbs.2019.02.001] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Bacteria thrive in virtually all environments. Like all other living organisms, bacteria may encounter various types of stresses, to which cells need to adapt. In this chapter, we describe how cells cope with stressful conditions and how this may lead to dramatic morphological changes. These changes may not only allow harmless cells to withstand environmental insults but can also benefit pathogenic bacteria by enabling them to escape from the immune system and the activity of antibiotics. A better understanding of stress-induced morphogenesis will help us to develop new approaches to combat such harmful pathogens.
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Affiliation(s)
- Eveline Ultee
- Molecular Biotechnology, Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE Leiden, the Netherlands; Centre for Microbial Cell Biology, Leiden University, Leiden, the Netherlands
| | - Karina Ramijan
- Molecular Biotechnology, Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE Leiden, the Netherlands; Centre for Microbial Cell Biology, Leiden University, Leiden, the Netherlands
| | - Remus T Dame
- Centre for Microbial Cell Biology, Leiden University, Leiden, the Netherlands; Macromolecular Biochemistry, Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CE Leiden, the Netherlands
| | - Ariane Briegel
- Molecular Biotechnology, Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE Leiden, the Netherlands; Centre for Microbial Cell Biology, Leiden University, Leiden, the Netherlands
| | - Dennis Claessen
- Molecular Biotechnology, Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE Leiden, the Netherlands; Centre for Microbial Cell Biology, Leiden University, Leiden, the Netherlands
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12
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The complete genome sequence of Colwellia sp. NB097-1 reveals evidence for the potential genetic basis for its adaptation to cold environment. Mar Genomics 2018; 37:54-57. [PMID: 33250129 DOI: 10.1016/j.margen.2017.11.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Revised: 11/24/2017] [Accepted: 11/25/2017] [Indexed: 11/20/2022]
Abstract
Colwellia sp. NB097-1, isolated from a marine sediment sample from the Bering Sea, is a psychrophilic bacterium whose optimal and maximal growth temperatures were 13 and 25°C, respectively. Here, we present the complete genome of Colwellia sp. NB097-1, which was 4,661,274bp in length with a GC content of 38.5%. The genome provided evidence for the potential genetic basis for its adaptation to a cold environment, such as producing compatible solutes and cold-shock proteins, increasing membrane fluidity and synthesizing glycogen. Some cold-adaptive proteases were also detected in the genome of Colwellia sp. NB097-1. Protease activity analysis further showed that extracellular proteases of Colwellia sp. NB097-1 remained active at low temperatures. The complete genome sequence may be helpful to reveal how this strain survives at low temperature and to find cold-adaptive proteases that may be useful to industry.
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13
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Showalter GM, Deming JW. Low-temperature chemotaxis, halotaxis and chemohalotaxis by the psychrophilic marine bacterium Colwellia psychrerythraea 34H. ENVIRONMENTAL MICROBIOLOGY REPORTS 2018; 10:92-101. [PMID: 29235725 DOI: 10.1111/1758-2229.12610] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Revised: 11/18/2017] [Accepted: 11/21/2017] [Indexed: 06/07/2023]
Abstract
A variety of ecologically important processes are driven by bacterial motility and taxis, yet these basic bacterial behaviours remain understudied in cold habitats. Here, we present a series of experiments designed to test the chemotactic ability of the model marine psychrophilic bacterium Colwellia psychrerythraea 34H, when grown at optimal temperature and salinity (8°C, 35 ppt) or its original isolation conditions (-1°C, 35 ppt), towards serine and mannose at temperatures from -8°C to 27°C (above its upper growth temperature of 18°C), and at salinities of 15, 35 and 55 ppt (at 8°C and -1°C). Results indicate that C. psychrerythraea 34H is capable of chemotaxis at all temperatures tested, with strongest chemotaxis at the temperature at which it was first grown, whether 8°C or -1°C. This model marine psychrophile also showed significant halotaxis towards 15 and 55 ppt solutions, as well as strong substrate-specific chemohalotaxis. We suggest that such patterns of taxis may enable bacteria to colonize sea ice, position themselves optimally within its extremely cold, hypersaline and temporally fluctuating microenvironments, and respond to various chemical signals therein.
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Affiliation(s)
- G M Showalter
- School of Oceanography, University of Washington, Seattle, WA, USA
| | - J W Deming
- School of Oceanography, University of Washington, Seattle, WA, USA
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14
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Zhang C, Guo W, Wang Y, Chen X. Draft Genome Sequences of Two Psychrotolerant Strains, Colwellia polaris MCCC 1C00015 T and Colwellia chukchiensis CGMCC 1.9127 T. GENOME ANNOUNCEMENTS 2018; 6:e01575-17. [PMID: 29371370 PMCID: PMC5786696 DOI: 10.1128/genomea.01575-17] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 12/17/2017] [Accepted: 12/19/2017] [Indexed: 11/20/2022]
Abstract
Colwellia polaris MCCC 1C00015T and Colwellia chukchiensis CGMCC 1.9127T are psychrotolerant bacteria isolated from the Canadian Basin and Chukchi Sea, respectively. Here, we report the draft genome sequences of C. polaris MCCC 1C00015T and C. chukchiensis CGMCC 1.9127T, which will help reveal how they adapt to cold environments.
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Affiliation(s)
- Cong Zhang
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, State Oceanic Administration, Xiamen, People's Republic of China
| | - Wenbin Guo
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, State Oceanic Administration, Xiamen, People's Republic of China
| | - Yuguang Wang
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, State Oceanic Administration, Xiamen, People's Republic of China
| | - Xinhua Chen
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, State Oceanic Administration, Xiamen, People's Republic of China
- College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou, People's Republic of China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, People's Republic of China
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15
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Decho AW, Gutierrez T. Microbial Extracellular Polymeric Substances (EPSs) in Ocean Systems. Front Microbiol 2017; 8:922. [PMID: 28603518 PMCID: PMC5445292 DOI: 10.3389/fmicb.2017.00922] [Citation(s) in RCA: 251] [Impact Index Per Article: 35.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Accepted: 05/08/2017] [Indexed: 12/13/2022] Open
Abstract
Microbial cells (i.e., bacteria, archaea, microeukaryotes) in oceans secrete a diverse array of large molecules, collectively called extracellular polymeric substances (EPSs) or simply exopolymers. These secretions facilitate attachment to surfaces that lead to the formation of structured 'biofilm' communities. In open-water environments, they also lead to formation of organic colloids, and larger aggregations of cells, called 'marine snow.' Secretion of EPS is now recognized as a fundamental microbial adaptation, occurring under many environmental conditions, and one that influences many ocean processes. This relatively recent realization has revolutionized our understanding of microbial impacts on ocean systems. EPS occur in a range of molecular sizes, conformations and physical/chemical properties, and polysaccharides, proteins, lipids, and even nucleic acids are actively secreted components. Interestingly, however, the physical ultrastructure of how individual EPS interact with each other is poorly understood. Together, the EPS matrix molecules form a three-dimensional architecture from which cells may localize extracellular activities and conduct cooperative/antagonistic interactions that cannot be accomplished efficiently by free-living cells. EPS alter optical signatures of sediments and seawater, and are involved in biogeomineral precipitation and the construction of microbial macrostructures, and horizontal-transfers of genetic information. In the water-column, they contribute to the formation of marine snow, transparent exopolymer particles (TEPs), sea-surface microlayer biofilm, and marine oil snow. Excessive production of EPS occurs during later-stages of phytoplankton blooms as an excess metabolic by product and releases a carbon pool that transitions among dissolved-, colloidal-, and gel-states. Some EPS are highly labile carbon forms, while other forms appear quite refractory to degradation. Emerging studies suggest that EPS contribute to efficient trophic-transfer of environmental contaminants, and may provide a protective refugia for pathogenic cells within marine systems; one that enhances their survival/persistence. Finally, these secretions are prominent in 'extreme' environments ranging from sea-ice communities to hypersaline systems to the high-temperatures/pressures of hydrothermal-vent systems. This overview summarizes some of the roles of exopolymer in oceans.
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Affiliation(s)
- Alan W. Decho
- Department of Environmental Health Sciences, Arnold School of Public Health, University of South Carolina, ColumbiaSC, United States
| | - Tony Gutierrez
- School of Engineering and Physical Sciences, Heriot-Watt UniversityEdinburgh, United Kingdom
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16
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Ma Y, Wang Q, Gao X, Zhang Y. Biosynthesis and uptake of glycine betaine as cold-stress response to low temperature in fish pathogen Vibrio anguillarum. J Microbiol 2016; 55:44-55. [PMID: 28035596 DOI: 10.1007/s12275-017-6370-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Revised: 10/06/2016] [Accepted: 10/07/2016] [Indexed: 12/28/2022]
Abstract
Fish pathogen Vibrio anguillarum, a mesophile bacterium, is usually found in estuarine and marine coastal ecosystems worldwide that pose a constant stress to local organism by its fluctuation in salinity as well as notable temperature change. Though V. anguillarum is able to proliferate while maintain its pathogenicity under low temperature (5-18°C), so far, coldadaption molecular mechanism of the bacteria is unknown. In this study, V. anguillarum was found possessing a putative glycine betaine synthesis system, which is encoded by betABI and synthesizes glycine betaine from its precursor choline. Furthermore, significant up-regulation of the bet gene at the transcriptional level was noted in log phase in response to cold-stress. Moreover, the accumulation of betaine glycine was only found appearing at low growth temperatures, suggesting that response regulation of both synthesis system and transporter system are cold-dependent. Furthermore, in-frame deletion mutation in the two putative ABC transporters and three putative BCCT family transporters associated with glycine betaine uptake could not block cellular accumulation of betaine glycine in V. anguillarum under coldstress, suggesting the redundant feature in V. anguillarum betaine transporter system. These findings confirmed that glycine betaine serves as an effective cold stress protectant and highlighted an underappreciated facet of the acclimatization of V. anguillarum to cold environments.
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Affiliation(s)
- Yue Ma
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, P. R. China
- Shanghai Engineering Research Center of Maricultured Animal Vaccines, Shanghai, 200237, P. R. China
| | - Qiyao Wang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, P. R. China
- Shanghai Engineering Research Center of Maricultured Animal Vaccines, Shanghai, 200237, P. R. China
- Shanghai Collaborative Innovation Center for Biomanufacturing, Shanghai, 200237, P. R. China
| | - Xiating Gao
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, P. R. China
| | - Yuanxing Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, P. R. China.
- Shanghai Engineering Research Center of Maricultured Animal Vaccines, Shanghai, 200237, P. R. China.
- Shanghai Collaborative Innovation Center for Biomanufacturing, Shanghai, 200237, P. R. China.
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17
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Koh HY, Park H, Lee JH, Han SJ, Sohn YC, Lee SG. Proteomic and transcriptomic investigations on cold-responsive properties of the psychrophilic Antarctic bacterium Psychrobacter sp. PAMC 21119 at subzero temperatures. Environ Microbiol 2016; 19:628-644. [PMID: 27750393 DOI: 10.1111/1462-2920.13578] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Accepted: 10/12/2016] [Indexed: 11/28/2022]
Abstract
Psychrobacter sp. PAMC 21119, isolated from Antarctic permafrost soil, grows and proliferates at subzero temperatures. However, its major mechanism of cold adaptation regulation remains poorly understood. We investigated the transcriptomic and proteomic responses of this species to cold temperatures by comparing profiles at -5°C and 20°C to understand how extreme microorganisms survive under subzero conditions. We found a total of 2,906 transcripts and 584 differentially expressed genes (≥ twofold, P <0.005) by RNA-seq. Genes for translation, ribosomal structure and biogenesis were upregulated, and lipid transport and metabolism was downregulated at low temperatures. A total of 60 protein spots (≥ 1.8 fold, P < 0.005) showed differential expression on two-dimensional gel electrophoresis and the proteins were identified by mass spectrometry. The most prominent upregulated proteins in response to cold were involved in metabolite transport, protein folding and membrane fluidity. Proteins involved in energy production and conversion, and heme protein synthesis were downregulated. Moreover, isoform exchange of cold-shock proteins was detected at both temperatures. Interestingly, pathways for acetyl-CoA metabolism, putrescine synthesis and amino acid metabolism were upregulated. This study highlights some of the strategies and different physiological states that Psychrobacter sp. PAMC 21119 has developed to adapt to the cold environment in Antarctica.
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Affiliation(s)
- Hye Yeon Koh
- Unit of Polar Genomics Korea Polar Research Institute, Incheon, South Korea.,Department of Marine Molecular Biotechnology, Gangneung-Wonju National University, Gangneung, South Korea
| | - Hyun Park
- Unit of Polar Genomics Korea Polar Research Institute, Incheon, South Korea.,Department of Polar Sciences, University of Science and Technology, Incheon, South Korea
| | - Jun Hyuck Lee
- Unit of Polar Genomics Korea Polar Research Institute, Incheon, South Korea.,Department of Polar Sciences, University of Science and Technology, Incheon, South Korea
| | - Se Jong Han
- Unit of Polar Genomics Korea Polar Research Institute, Incheon, South Korea.,Department of Polar Sciences, University of Science and Technology, Incheon, South Korea
| | - Young Chang Sohn
- Department of Marine Molecular Biotechnology, Gangneung-Wonju National University, Gangneung, South Korea
| | - Sung Gu Lee
- Unit of Polar Genomics Korea Polar Research Institute, Incheon, South Korea.,Department of Polar Sciences, University of Science and Technology, Incheon, South Korea
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18
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Fernández-Méndez M, Turk-Kubo KA, Buttigieg PL, Rapp JZ, Krumpen T, Zehr JP, Boetius A. Diazotroph Diversity in the Sea Ice, Melt Ponds, and Surface Waters of the Eurasian Basin of the Central Arctic Ocean. Front Microbiol 2016; 7:1884. [PMID: 27933047 PMCID: PMC5120112 DOI: 10.3389/fmicb.2016.01884] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Accepted: 11/09/2016] [Indexed: 11/13/2022] Open
Abstract
The Eurasian basin of the Central Arctic Ocean is nitrogen limited, but little is known about the presence and role of nitrogen-fixing bacteria. Recent studies have indicated the occurrence of diazotrophs in Arctic coastal waters potentially of riverine origin. Here, we investigated the presence of diazotrophs in ice and surface waters of the Central Arctic Ocean in the summer of 2012. We identified diverse communities of putative diazotrophs through targeted analysis of the nifH gene, which encodes the iron protein of the nitrogenase enzyme. We amplified 529 nifH sequences from 26 samples of Arctic melt ponds, sea ice and surface waters. These sequences resolved into 43 clusters at 92% amino acid sequence identity, most of which were non-cyanobacterial phylotypes from sea ice and water samples. One cyanobacterial phylotype related to Nodularia sp. was retrieved from sea ice, suggesting that this important functional group is rare in the Central Arctic Ocean. The diazotrophic community in sea-ice environments appear distinct from other cold-adapted diazotrophic communities, such as those present in the coastal Canadian Arctic, the Arctic tundra and glacial Antarctic lakes. Molecular fingerprinting of nifH and the intergenic spacer region of the rRNA operon revealed differences between the communities from river-influenced Laptev Sea waters and those from ice-related environments pointing toward a marine origin for sea-ice diazotrophs. Our results provide the first record of diazotrophs in the Central Arctic and suggest that microbial nitrogen fixation may occur north of 77°N. To assess the significance of nitrogen fixation for the nitrogen budget of the Arctic Ocean and to identify the active nitrogen fixers, further biogeochemical and molecular biological studies are needed.
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Affiliation(s)
- Mar Fernández-Méndez
- HGF-MPG Group for Deep Sea Ecology and Technology, Alfred Wegener Institute Helmholtz Centre for Polar and Marine ResearchBremerhaven, Germany; HGF-MPG Group for Deep Sea Ecology and Technology, Max Planck Institute for Marine MicrobiologyBremen, Germany
| | - Kendra A Turk-Kubo
- Department of Ocean Sciences, University of California at Santa Cruz, Santa Cruz CA, USA
| | - Pier L Buttigieg
- HGF-MPG Group for Deep Sea Ecology and Technology, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research Bremerhaven, Germany
| | - Josephine Z Rapp
- HGF-MPG Group for Deep Sea Ecology and Technology, Alfred Wegener Institute Helmholtz Centre for Polar and Marine ResearchBremerhaven, Germany; HGF-MPG Group for Deep Sea Ecology and Technology, Max Planck Institute for Marine MicrobiologyBremen, Germany
| | - Thomas Krumpen
- Sea Ice Physics Section, Climate Sciences Department, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research Bremerhaven, Germany
| | - Jonathan P Zehr
- Department of Ocean Sciences, University of California at Santa Cruz, Santa Cruz CA, USA
| | - Antje Boetius
- HGF-MPG Group for Deep Sea Ecology and Technology, Alfred Wegener Institute Helmholtz Centre for Polar and Marine ResearchBremerhaven, Germany; HGF-MPG Group for Deep Sea Ecology and Technology, Max Planck Institute for Marine MicrobiologyBremen, Germany
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19
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Maccario L, Sanguino L, Vogel TM, Larose C. Snow and ice ecosystems: not so extreme. Res Microbiol 2015; 166:782-95. [PMID: 26408452 DOI: 10.1016/j.resmic.2015.09.002] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2015] [Revised: 09/02/2015] [Accepted: 09/11/2015] [Indexed: 11/18/2022]
Abstract
Snow and ice environments cover up to 21% of the Earth's surface. They have been regarded as extreme environments because of their low temperatures, high UV irradiation, low nutrients and low water availability, and thus, their microbial activity has not been considered relevant from a global microbial ecology viewpoint. In this review, we focus on why snow and ice habitats might not be extreme from a microbiological perspective. Microorganisms interact closely with the abiotic conditions imposed by snow and ice habitats by having diverse adaptations, that include genetic resistance mechanisms, to different types of stresses in addition to inhabiting various niches where these potential stresses might be reduced. The microbial communities inhabiting snow and ice are not only abundant and taxonomically diverse, but complex in terms of their interactions. Altogether, snow and ice seem to be true ecosystems with a role in global biogeochemical cycles that has likely been underestimated. Future work should expand past resistance studies to understanding the function of these ecosystems.
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Affiliation(s)
- Lorrie Maccario
- Environmental Microbial Genomics, Laboratoire Ampère, CNRS UMR 5005, Université de Lyon, Ecole Centrale de Lyon, 36 Avenue Guy de Collongue, 69134 Ecully, France
| | - Laura Sanguino
- Environmental Microbial Genomics, Laboratoire Ampère, CNRS UMR 5005, Université de Lyon, Ecole Centrale de Lyon, 36 Avenue Guy de Collongue, 69134 Ecully, France
| | - Timothy M Vogel
- Environmental Microbial Genomics, Laboratoire Ampère, CNRS UMR 5005, Université de Lyon, Ecole Centrale de Lyon, 36 Avenue Guy de Collongue, 69134 Ecully, France
| | - Catherine Larose
- Environmental Microbial Genomics, Laboratoire Ampère, CNRS UMR 5005, Université de Lyon, Ecole Centrale de Lyon, 36 Avenue Guy de Collongue, 69134 Ecully, France.
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20
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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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21
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Boetius A, Anesio AM, Deming JW, Mikucki JA, Rapp JZ. Microbial ecology of the cryosphere: sea ice and glacial habitats. Nat Rev Microbiol 2015; 13:677-90. [PMID: 26344407 DOI: 10.1038/nrmicro3522] [Citation(s) in RCA: 206] [Impact Index Per Article: 22.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The Earth's cryosphere comprises those regions that are cold enough for water to turn into ice. Recent findings show that the icy realms of polar oceans, glaciers and ice sheets are inhabited by microorganisms of all three domains of life, and that temperatures below 0 °C are an integral force in the diversification of microbial life. Cold-adapted microorganisms maintain key ecological functions in icy habitats: where sunlight penetrates the ice, photoautotrophy is the basis for complex food webs, whereas in dark subglacial habitats, chemoautotrophy reigns. This Review summarizes current knowledge of the microbial ecology of frozen waters, including the diversity of niches, the composition of microbial communities at these sites and their biogeochemical activities.
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Affiliation(s)
- Antje Boetius
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Am Handelshafen 12, 27570 Bremerhaven, Germany.,Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359 Bremen, Germany
| | - Alexandre M Anesio
- Bristol Glaciology Center, School of Geographical Sciences, University of Bristol, BS8 1SS, UK
| | - Jody W Deming
- School of Oceanography, Box 357940, University of Washington, Seattle, Washington 98195, USA
| | - Jill A Mikucki
- Department of Biology, 276 Bicentennial Way, Middlebury College, Middlebury, Vermont 05753, USA
| | - Josephine Z Rapp
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Am Handelshafen 12, 27570 Bremerhaven, Germany.,Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359 Bremen, Germany
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22
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Torstensson A, Dinasquet J, Chierici M, Fransson A, Riemann L, Wulff A. Physicochemical control of bacterial and protist community composition and diversity in Antarctic sea ice. Environ Microbiol 2015; 17:3869-81. [DOI: 10.1111/1462-2920.12865] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Revised: 03/20/2015] [Accepted: 03/31/2015] [Indexed: 11/28/2022]
Affiliation(s)
- Anders Torstensson
- Department of Biological and Environmental Sciences; University of Gothenburg; Göteborg SE-40530 Sweden
| | - Julie Dinasquet
- Marine Biological Section; Department of Biology; University of Copenhagen; Helsingør DK-3000 Denmark
| | - Melissa Chierici
- Department of Chemistry and Molecular Biology; University of Gothenburg; Göteborg SE-40530 Sweden
- Institute of Marine Research; Tromsø NO-9294 Norway
| | - Agneta Fransson
- Norwegian Polar Institute; Fram Centre; Tromsø NO-9296 Norway
- Department of Earth Sciences; University of Gothenburg; Göteborg SE-40530 Sweden
| | - Lasse Riemann
- Marine Biological Section; Department of Biology; University of Copenhagen; Helsingør DK-3000 Denmark
| | - Angela Wulff
- Department of Biological and Environmental Sciences; University of Gothenburg; Göteborg SE-40530 Sweden
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23
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Schostag M, Stibal M, Jacobsen CS, Bælum J, Taş N, Elberling B, Jansson JK, Semenchuk P, Priemé A. Distinct summer and winter bacterial communities in the active layer of Svalbard permafrost revealed by DNA- and RNA-based analyses. Front Microbiol 2015; 6:399. [PMID: 25983731 PMCID: PMC4415418 DOI: 10.3389/fmicb.2015.00399] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Accepted: 04/17/2015] [Indexed: 01/17/2023] Open
Abstract
The active layer of soil overlaying permafrost in the Arctic is subjected to dramatic annual changes in temperature and soil chemistry, which likely affect bacterial activity and community structure. We studied seasonal variations in the bacterial community of active layer soil from Svalbard (78°N) by co-extracting DNA and RNA from 12 soil cores collected monthly over a year. PCR amplicons of 16S rRNA genes (DNA) and reverse transcribed transcripts (cDNA) were quantified and sequenced to test for the effect of low winter temperature and seasonal variation in concentration of easily degradable organic matter on the bacterial communities. The copy number of 16S rRNA genes and transcripts revealed no distinct seasonal changes indicating potential bacterial activity during winter despite soil temperatures well below −10°C. Multivariate statistical analysis of the bacterial diversity data (DNA and cDNA libraries) revealed a season-based clustering of the samples, and, e.g., the relative abundance of potentially active Cyanobacteria peaked in June and Alphaproteobacteria increased over the summer and then declined from October to November. The structure of the bulk (DNA-based) community was significantly correlated with pH and dissolved organic carbon, while the potentially active (RNA-based) community structure was not significantly correlated with any of the measured soil parameters. A large fraction of the 16S rRNA transcripts was assigned to nitrogen-fixing bacteria (up to 24% in June) and phototrophic organisms (up to 48% in June) illustrating the potential importance of nitrogen fixation in otherwise nitrogen poor Arctic ecosystems and of phototrophic bacterial activity on the soil surface.
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Affiliation(s)
- Morten Schostag
- Department of Geosciences and Natural Resource Management, Center for Permafrost, University of Copenhagen Copenhagen, Denmark ; Geological Survey of Denmark and Greenland (GEUS) Copenhagen, Denmark ; Department of Biology, University of Copenhagen Copenhagen, Denmark
| | - Marek Stibal
- Department of Geosciences and Natural Resource Management, Center for Permafrost, University of Copenhagen Copenhagen, Denmark ; Geological Survey of Denmark and Greenland (GEUS) Copenhagen, Denmark
| | - Carsten S Jacobsen
- Department of Geosciences and Natural Resource Management, Center for Permafrost, University of Copenhagen Copenhagen, Denmark ; Geological Survey of Denmark and Greenland (GEUS) Copenhagen, Denmark ; Department of Environmental Sciences, Aarhus University Denmark
| | - Jacob Bælum
- Department of Environmental Sciences, Aarhus University Denmark
| | - Neslihan Taş
- Ecology Department, Lawrence Berkeley National Laboratory Berkeley, CA, USA
| | - Bo Elberling
- Department of Geosciences and Natural Resource Management, Center for Permafrost, University of Copenhagen Copenhagen, Denmark
| | - Janet K Jansson
- Biological Sciences Division, Pacific Northwest National Laboratory Richland, WA, USA
| | - Philipp Semenchuk
- Department of Geosciences and Natural Resource Management, Center for Permafrost, University of Copenhagen Copenhagen, Denmark ; Department of Arctic and Marine Biology, University of Tromsø Tromsø, Norway
| | - Anders Priemé
- Department of Geosciences and Natural Resource Management, Center for Permafrost, University of Copenhagen Copenhagen, Denmark ; Department of Biology, University of Copenhagen Copenhagen, Denmark
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