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Mikucki JA, Schuler CG, Digel I, Kowalski J, Tuttle MJ, Chua M, Davis R, Purcell AM, Ghosh D, Francke G, Feldmann M, Espe C, Heinen D, Dachwald B, Clemens J, Lyons WB, Tulaczyk S. Field-Based Planetary Protection Operations for Melt Probes: Validation of Clean Access into the Blood Falls, Antarctica, Englacial Ecosystem. ASTROBIOLOGY 2023; 23:1165-1178. [PMID: 37962840 DOI: 10.1089/ast.2021.0102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Subglacial environments on Earth offer important analogs to Ocean World targets in our solar system. These unique microbial ecosystems remain understudied due to the challenges of access through thick glacial ice (tens to hundreds of meters). Additionally, sub-ice collections must be conducted in a clean manner to ensure sample integrity for downstream microbiological and geochemical analyses. We describe the field-based cleaning of a melt probe that was used to collect brine samples from within a glacier conduit at Blood Falls, Antarctica, for geomicrobiological studies. We used a thermoelectric melting probe called the IceMole that was designed to be minimally invasive in that the logistical requirements in support of drilling operations were small and the probe could be cleaned, even in a remote field setting, so as to minimize potential contamination. In our study, the exterior bioburden on the IceMole was reduced to levels measured in most clean rooms, and below that of the ice surrounding our sampling target. Potential microbial contaminants were identified during the cleaning process; however, very few were detected in the final englacial sample collected with the IceMole and were present in extremely low abundances (∼0.063% of 16S rRNA gene amplicon sequences). This cleaning protocol can help minimize contamination when working in remote field locations, support microbiological sampling of terrestrial subglacial environments using melting probes, and help inform planetary protection challenges for Ocean World analog mission concepts.
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Affiliation(s)
- J A Mikucki
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, USA
| | - C G Schuler
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, USA
| | - I Digel
- FH Aachen - Campus Jülich, Institute of Bioengineering, Julich, Nordrhein-Westfalen, Germany
| | - J Kowalski
- RWTH Aachen University, Aachen, North Rhine-Westfalia, Germany
| | - M J Tuttle
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, USA
| | - M Chua
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, USA
| | - R Davis
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, USA
| | - A M Purcell
- Northern Arizona University, Flagstaff, Arizona, USA
| | - D Ghosh
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, USA
| | - G Francke
- RWTH Aachen University, Aachen, North Rhine-Westfalia, Germany
| | - M Feldmann
- RWTH Aachen University, Aachen, North Rhine-Westfalia, Germany
| | - C Espe
- RWTH Aachen University, Aachen, North Rhine-Westfalia, Germany
| | - D Heinen
- RWTH Aachen University, Aachen, North Rhine-Westfalia, Germany
| | - B Dachwald
- RWTH Aachen University, Aachen, North Rhine-Westfalia, Germany
| | - J Clemens
- University of Bremen, Bremen, Germany
| | - W B Lyons
- The Ohio State University, Byrd Polar Research Center, Columbus, Ohio, USA
| | - S Tulaczyk
- University of California Santa Cruz, Santa Cruz, California, USA
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2
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Schuler CG, Winebrenner DP, Elam WT, Burnett J, Boles BW, Mikucki JA. Microbial Transport by a Descending Ice Melting Probe: Implications for Subglacial and Ocean World Exploration. ASTROBIOLOGY 2023; 23:1153-1164. [PMID: 37279037 DOI: 10.1089/ast.2021.0106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Ocean Worlds beneath thick ice covers in our solar system, as well as subglacial lakes on Earth, may harbor biological systems. In both cases, thick ice covers (>100 s of meters) present significant barriers to access. Melt probes are emerging as tools for reaching and sampling these realms due to their small logistical footprint, ability to transport payloads, and ease of cleaning in the field. On Earth, glaciers are immured with various abundances of microorganisms and debris. The potential for bioloads to accumulate around and be dragged by a probe during descent has not previously been investigated. Due to the pristine nature of these environments, minimizing and understanding the risk of forward contamination and considering the potential of melt probes to act as instrument-induced special regions are essential. In this study, we examined the effect that two engineering descent strategies for melt probes have on the dragging of bioloads. We also tested the ability of a field cleaning protocol to rid a common contaminant, Bacillus. These tests were conducted in a synthetic ice block immured with bioloads using the Ice Diver melt probe. Our data suggest minimal dragging of bioloads by melt probes, but conclude that modifications for further minimization and use in special regions should be made.
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Affiliation(s)
- Caleb G Schuler
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, USA
| | - Dale P Winebrenner
- Applied Physics Laboratory, University of Washington, Seattle, Washington, USA
| | - W Timothy Elam
- Applied Physics Laboratory, University of Washington, Seattle, Washington, USA
| | - Justin Burnett
- Applied Physics Laboratory, University of Washington, Seattle, Washington, USA
| | - Bruce W Boles
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, USA
| | - Jill A Mikucki
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, USA
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3
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Nosalova L, Mekadim C, Mrazek J, Pristas P. Thiothrix and Sulfurovum genera dominate bacterial mats in Slovak cold sulfur springs. ENVIRONMENTAL MICROBIOME 2023; 18:72. [PMID: 37730677 PMCID: PMC10512639 DOI: 10.1186/s40793-023-00527-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 09/10/2023] [Indexed: 09/22/2023]
Abstract
Microbiota of sulfur-rich environments has been extensively studied due to the biotechnological potential of sulfur bacteria, or as a model of ancient life. Cold terrestrial sulfur springs are less studied compared to sulfur-oxidizing microbiota of hydrothermal vents, volcanic environments, or soda lakes. Despite that, several studies suggested that sulfur springs harbor diverse microbial communities because of the unique geochemical conditions of upwelling waters. In this study, the microbiota of five terrestrial sulfur springs was examined using a 16 S rRNA gene sequencing. The clear dominance of the Proteobacteria and Campylobacterota phyla of cold sulfur springs microbiota was observed. Contrary to that, the microbiota of the hot sulfur spring was dominated by the Aquificota and Firmicutes phylum respectively. Sulfur-oxidizing genera constituted a dominant part of the microbial populations with the Thiothrix and Sulfurovum genera identified as the core microbiota of cold sulfur terrestrial springs in Slovakia. Additionally, the study emphasizes that sulfur springs in Slovakia support unique, poorly characterized bacterial communities of sulfur-oxidizing bacteria.
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Affiliation(s)
- Lea Nosalova
- Department of Microbiology, Institute of Biology and Ecology, Faculty of Science, Pavol Jozef Safarik University in Kosice, Srobarova 2, Kosice, 041 54, Slovakia
| | - Chahrazed Mekadim
- Laboratory of Anaerobic Microbiology, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Videnska, Prague, 1083, 14220, Czech Republic
| | - Jakub Mrazek
- Laboratory of Anaerobic Microbiology, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Videnska, Prague, 1083, 14220, Czech Republic
| | - Peter Pristas
- Department of Microbiology, Institute of Biology and Ecology, Faculty of Science, Pavol Jozef Safarik University in Kosice, Srobarova 2, Kosice, 041 54, Slovakia.
- Institute of Animal Physiology, Centre of Biosciences, Slovak Academy of Sciences, Soltesovej 4-6, Kosice, 040 01, Slovakia.
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Trivedi CB, Keuschnig C, Larose C, Rissi DV, Mourot R, Bradley JA, Winkel M, Benning LG. DNA/RNA Preservation in Glacial Snow and Ice Samples. Front Microbiol 2022; 13:894893. [PMID: 35677909 PMCID: PMC9168539 DOI: 10.3389/fmicb.2022.894893] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Accepted: 04/29/2022] [Indexed: 11/13/2022] Open
Abstract
The preservation of nucleic acids for high-throughput sequencing is an ongoing challenge for field scientists. In particular, samples that are low biomass, or that have to be collected and preserved in logistically challenging environments (such as remote sites or during long sampling campaigns) can pose exceptional difficulties. With this work, we compare and assess the effectiveness of three preservation methods for DNA and RNA extracted from microbial communities of glacial snow and ice samples. Snow and ice samples were melted and filtered upon collection in Iceland, and filters were preserved using: (i) liquid nitrogen flash freezing, (ii) storage in RNAlater, or (iii) storage in Zymo DNA/RNA Shield. Comparative statistics covering nucleic acid recovery, sequencing library preparation, genome assembly, and taxonomic diversity were used to determine best practices for the preservation of DNA and RNA samples from these environments. Our results reveal that microbial community composition based on DNA was comparable at the class level across preservation types. Based on extracted RNA, the taxonomic composition of the active community was primarily driven by the filtered sample volume (i.e., biomass content). In low biomass samples (where <200 ml of sample volume was filtered) the taxonomic and functional signatures trend toward the composition of the control samples, while in samples where a larger volume (more biomass) was filtered our data showed comparable results independent of preservation type. Based on all comparisons our data suggests that flash freezing of filters containing low biomass is the preferred method for preserving DNA and RNA (notwithstanding the difficulties of accessing liquid nitrogen in remote glacial field sites). Generally, RNAlater and Zymo DNA/RNA Shield solutions work comparably well, especially for DNA from high biomass samples, but Zymo DNA/RNA Shield is favored due to its higher yield of preserved RNA. Biomass quantity from snow and ice samples appears to be the most important factor in regards to the collection and preservation of samples from glacial environments.
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Affiliation(s)
- Christopher B Trivedi
- Interface Geochemistry, GFZ German Research Centre for Geosciences, Potsdam, Germany
| | | | - Catherine Larose
- Environmental Microbial Genomics, Université de Lyon, Ecully Cedex, France
| | | | - Rey Mourot
- Interface Geochemistry, GFZ German Research Centre for Geosciences, Potsdam, Germany.,Department of Earth Sciences, Freie Universität Berlin, Berlin, Germany
| | - James A Bradley
- Interface Geochemistry, GFZ German Research Centre for Geosciences, Potsdam, Germany.,School of Geography, Queen Mary University of London, London, United Kingdom
| | - Matthias Winkel
- Interface Geochemistry, GFZ German Research Centre for Geosciences, Potsdam, Germany
| | - Liane G Benning
- Interface Geochemistry, GFZ German Research Centre for Geosciences, Potsdam, Germany.,Department of Earth Sciences, Freie Universität Berlin, Berlin, Germany
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Garber AI, Zehnpfennig JR, Sheik CS, Henson MW, Ramírez GA, Mahon AR, Halanych KM, Learman DR. Metagenomics of Antarctic Marine Sediment Reveals Potential for Diverse Chemolithoautotrophy. mSphere 2021; 6:e0077021. [PMID: 34817234 PMCID: PMC8612310 DOI: 10.1128/msphere.00770-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Accepted: 11/10/2021] [Indexed: 11/30/2022] Open
Abstract
The microbial biogeochemical processes occurring in marine sediment in Antarctica remain underexplored due to limited access. Further, these polar habitats are unique, as they are being exposed to significant changes in their climate. To explore how microbes drive biogeochemistry in these sediments, we performed a shotgun metagenomic survey of marine surficial sediment (0 to 3 cm of the seafloor) collected from 13 locations in western Antarctica and assembled 16 high-quality metagenome assembled genomes for focused interrogation of the lifestyles of some abundant lineages. We observe an abundance of genes from pathways for the utilization of reduced carbon, sulfur, and nitrogen sources. Although organotrophy is pervasive, nitrification and sulfide oxidation are the dominant lithotrophic pathways and likely fuel carbon fixation via the reverse tricarboxylic acid and Calvin cycles. Oxygen-dependent terminal oxidases are common, and genes for reduction of oxidized nitrogen are sporadically present in our samples. Our results suggest that the underlying benthic communities are well primed for the utilization of settling organic matter, which is consistent with findings from highly productive surface water. Despite the genetic potential for nitrate reduction, the net catabolic pathway in our samples remains aerobic respiration, likely coupled to the oxidation of sulfur and nitrogen imported from the highly productive Antarctic water column above. IMPORTANCE The impacts of climate change in polar regions, like Antarctica, have the potential to alter numerous ecosystems and biogeochemical cycles. Increasing temperature and freshwater runoff from melting ice can have profound impacts on the cycling of organic and inorganic nutrients between the pelagic and benthic ecosystems. Within the benthos, sediment microbial communities play a critical role in carbon mineralization and the cycles of essential nutrients like nitrogen and sulfur. Metagenomic data collected from sediment samples from the continental shelf of western Antarctica help to examine this unique system and document the metagenomic potential for lithotrophic metabolisms and the cycles of both nitrogen and sulfur, which support not only benthic microbes but also life in the pelagic zone.
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Affiliation(s)
- Arkadiy I. Garber
- Biodesign Center for Mechanisms for Evolution, Arizona State University, Tempe, Arizona, USA
| | | | - Cody S. Sheik
- Biology Department and Large Lakes Observatory, University of Minnesota Duluth, Duluth, Minnesota, USA
| | - Michael W. Henson
- Department of Biology, Central Michigan University, Mt. Pleasant, Michigan, USA
| | - Gustavo A. Ramírez
- College of Veterinary Medicine, Western University of Health Sciences, Pomona, California, USA
- Department of Marine Biology, Haifa University, Haifa, Israel
| | - Andrew R. Mahon
- Department of Biology, Central Michigan University, Mt. Pleasant, Michigan, USA
| | - Kenneth M. Halanych
- Center for Marine Science, University of North Carolina Wilmington, Wilmington, North Carolina, USA
| | - Deric R. Learman
- Department of Biology, Central Michigan University, Mt. Pleasant, Michigan, USA
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6
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Li S, Pang Y, Ji G. Increase of N 2O production during nitrate reduction after long-term sulfide addition in lake sediment microcosms. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 291:118231. [PMID: 34571071 DOI: 10.1016/j.envpol.2021.118231] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 09/19/2021] [Accepted: 09/23/2021] [Indexed: 06/13/2023]
Abstract
Microbial denitrification is a main source of nitrous oxide (N2O) emissions which have strong greenhouse effect and destroy stratospheric ozone. Though the importance of sulfide driven chemoautotrophic denitrification has been recognized, its contribution to N2O emissions in nature remains elusive. We built up long-term sulfide-added microcosms with sediments from two freshwater lakes. Chemistry analysis confirmed sulfide could drive nitrate respiration in long term. N2O accumulated to over 1.5% of nitrate load in both microcosms after long-term sulfide addition, which was up to 12.9 times higher than N2O accumulation without sulfide addition. Metagenomes were extracted and sequenced during microcosm incubations. 16 S rRNA genes of Thiobacillus and Defluviimonas were gradually enriched. The nitric oxide reductase with c-type cytochromes as electron donors (cNorB) increased in abundance, while the nitric oxide reductase receiving electrons from quinols (qNorB) decreased in abundance. cnorB genes similar to Thiobacillus were enriched in both microcosms. In parallel, enrichment was observed for enzymes involved in sulfur oxidation, which supplied electrons to nitrate respiration, and enzymes involved in Calvin Cycle, which sustained autotrophic cell growth, implying the coupling relationship between carbon, nitrogen and sulfur cycling processes. Our results suggested sulfur pollution considerably increased N2O emissions in natural environments.
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Affiliation(s)
- Shengjie Li
- Key Laboratory of Water and Sediment Sciences, Ministry of Education, Department of Environmental Engineering, Peking University, Beijing, 100871, China
| | - Yunmeng Pang
- Key Laboratory of Water and Sediment Sciences, Ministry of Education, Department of Environmental Engineering, Peking University, Beijing, 100871, China; Collaborative Innovation Center for Advanced Nuclear Energy Technology, INET, Tsinghua University, Beijing, 100084, China
| | - Guodong Ji
- Key Laboratory of Water and Sediment Sciences, Ministry of Education, Department of Environmental Engineering, Peking University, Beijing, 100871, China.
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7
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Aguinaga OE, White KN, Dean AP, Pittman JK. Addition of organic acids to acid mine drainage polluted wetland sediment leads to microbial community structure and functional changes and improved water quality. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 290:118064. [PMID: 34481302 DOI: 10.1016/j.envpol.2021.118064] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 08/24/2021] [Accepted: 08/26/2021] [Indexed: 06/13/2023]
Abstract
Acid mine drainage (AMD) is a serious environmental problem worldwide that requires efficient and sustainable remediation technologies including the use of biological mechanisms. A key challenge for AMD bioremediation is to provide optimal conditions for microbial-mediated immobilisation of trace metals. Although organic carbon and oxygen can enhance treatment efficiency, the effect on microbial communities is unclear. In this study, surface sediments from a natural wetland with proven efficiency for AMD bioremediation were artificially exposed to oxygen (by aeration) and/or organic carbon (in the form of mixed organic acids) and incubated under laboratory conditions. In addition to measuring changes in water chemistry, a metagenomics approach was used to determine changes in sediment bacterial, archaeal and fungal community structure, and functional gene abundance. The addition of organic carbon produced major changes in the abundance of microorganisms related to iron and sulfur metabolism (including Geobacter and Pelobacter) and increased levels of particulate metals via sulfate reduction. Aeration resulted in an increase in Sideroxydans abundance but no significant changes in metal chemistry were observed. The study concludes that the utilisation of organic carbon by microorganisms is more important for achieving efficient AMD treatment than the availability of oxygen, yet the combination of oxygen with organic carbon addition did not inhibit the improvements to water quality.
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Affiliation(s)
- Oscar E Aguinaga
- Department of Earth and Environmental Sciences, School of Natural Sciences, Faculty of Science and Engineering, The University of Manchester, Michael Smith Building, Oxford Road, Manchester, M13 9PT, UK; Departamento de Ingeniería, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Keith N White
- Department of Earth and Environmental Sciences, School of Natural Sciences, Faculty of Science and Engineering, The University of Manchester, Michael Smith Building, Oxford Road, Manchester, M13 9PT, UK
| | - Andrew P Dean
- Department of Natural Sciences, Faculty of Science and Engineering, Manchester Metropolitan University, Oxford Road, Manchester, M1 5GD, UK
| | - Jon K Pittman
- Department of Earth and Environmental Sciences, School of Natural Sciences, Faculty of Science and Engineering, The University of Manchester, Michael Smith Building, Oxford Road, Manchester, M13 9PT, UK.
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Wang B, Zheng X, Zhang H, Yu X, Lian Y, Yang X, Yu H, Hu R, He Z, Xiao F, Yan Q. Metagenomic insights into the effects of submerged plants on functional potential of microbial communities in wetland sediments. MARINE LIFE SCIENCE & TECHNOLOGY 2021; 3:405-415. [PMID: 37073260 PMCID: PMC10077182 DOI: 10.1007/s42995-021-00100-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/03/2021] [Accepted: 03/16/2021] [Indexed: 05/03/2023]
Abstract
Submerged plants in wetlands play important roles as ecosystem engineers to improve self-purification and promote elemental cycling. However, their effects on the functional capacity of microbial communities in wetland sediments remain poorly understood. Here, we provide detailed metagenomic insights into the biogeochemical potential of microbial communities in wetland sediments with and without submerged plants (i.e., Vallisneria natans). A large number of functional genes involved in carbon (C), nitrogen (N) and sulfur (S) cycling were detected in the wetland sediments. However, most functional genes showed higher abundance in sediments with submerged plants than in those without plants. Based on the comparison of annotated functional genes in the N and S cycling databases (i.e., NCycDB and SCycDB), we found that genes involved in nitrogen fixation (e.g., nifD/H/K/W), assimilatory nitrate reduction (e.g., nasA and nirA), denitrification (e.g., nirK/S and nosZ), assimilatory sulfate reduction (e.g., cysD/H/J/N/Q and sir), and sulfur oxidation (e.g., glpE, soeA, sqr and sseA) were significantly higher (corrected p < 0.05) in vegetated vs. unvegetated sediments. This could be mainly driven by environmental factors including total phosphorus, total nitrogen, and C:N ratio. The binning of metagenomes further revealed that some archaeal taxa could have the potential of methane metabolism including hydrogenotrophic, acetoclastic, and methylotrophic methanogenesis, which are crucial to the wetland methane budget and carbon cycling. This study opens a new avenue for linking submerged plants with microbial functions, and has further implications for understanding global carbon, nitrogen and sulfur cycling in wetland ecosystems. Supplementary Information The online version contains supplementary material available at 10.1007/s42995-021-00100-3.
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Affiliation(s)
- Binhao Wang
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, Guangzhou, 510006 China
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058 China
| | - Xiafei Zheng
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, Guangzhou, 510006 China
| | - Hangjun Zhang
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 310036 China
| | - Xiaoli Yu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, Guangzhou, 510006 China
| | - Yingli Lian
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, Guangzhou, 510006 China
| | - Xueqin Yang
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, Guangzhou, 510006 China
| | - Huang Yu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, Guangzhou, 510006 China
| | - Ruiwen Hu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, Guangzhou, 510006 China
| | - Zhili He
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, Guangzhou, 510006 China
- College of Agronomy, Hunan Agricultural University, Changsha, 410128 China
| | - Fanshu Xiao
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, Guangzhou, 510006 China
| | - Qingyun Yan
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, Guangzhou, 510006 China
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Castro-Severyn J, Pardo-Esté C, Mendez KN, Fortt J, Marquez S, Molina F, Castro-Nallar E, Remonsellez F, Saavedra CP. Living to the High Extreme: Unraveling the Composition, Structure, and Functional Insights of Bacterial Communities Thriving in the Arsenic-Rich Salar de Huasco Altiplanic Ecosystem. Microbiol Spectr 2021; 9:e0044421. [PMID: 34190603 PMCID: PMC8552739 DOI: 10.1128/spectrum.00444-21] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 06/07/2021] [Indexed: 01/03/2023] Open
Abstract
Microbial communities inhabiting extreme environments such as Salar de Huasco (SH) in northern Chile are adapted to thrive while exposed to several abiotic pressures and the presence of toxic elements such as arsenic (As). Hence, we aimed to uncover the role of As in shaping bacterial composition, structure, and functional potential in five different sites in this altiplanic wetland using a shotgun metagenomic approach. The sites exhibit wide gradients of As (9 to 321 mg/kg), and our results showed highly diverse communities and a clear dominance exerted by the Proteobacteria and Bacteroidetes phyla. Functional potential analyses show broadly convergent patterns, contrasting with their great taxonomic variability. As-related metabolism, as well as other functional categories such as those related to the CH4 and S cycles, differs among the five communities. Particularly, we found that the distribution and abundance of As-related genes increase as the As concentration rises. Approximately 75% of the detected genes for As metabolism belong to expulsion mechanisms; arsJ and arsP pumps are related to sites with higher As concentrations and are present almost exclusively in Proteobacteria. Furthermore, taxonomic diversity and functional potential are reflected in the 12 reconstructed high-quality metagenome assembled genomes (MAGs) belonging to the Bacteroidetes (5), Proteobacteria (5), Cyanobacteria (1), and Gemmatimonadetes (1) phyla. We conclude that SH microbial communities are diverse and possess a broad genetic repertoire to thrive under extreme conditions, including increasing concentrations of highly toxic As. Finally, this environment represents a reservoir of unknown and undescribed microorganisms, with great metabolic versatility, which needs further study. IMPORTANCE As microbial communities inhabiting extreme environments are fundamental for maintaining ecosystems, many studies concerning composition, functionality, and interactions have been carried out. However, much is still unknown. Here, we sampled microbial communities in the Salar de Huasco, an extreme environment subjected to several abiotic stresses (high UV radiation, salinity and arsenic; low pressure and temperatures). We found that although microbes are taxonomically diverse, functional potential seems to have an important degree of convergence, suggesting high levels of adaptation. Particularly, arsenic metabolism showed differences associated with increasing concentrations of the metalloid throughout the area, and it effectively exerts a significant pressure over these organisms. Thus, the significance of this research is that we describe highly specialized communities thriving in little-explored environments subjected to several pressures, considered analogous of early Earth and other planets, that have the potential for unraveling technologies to face the repercussions of climate change in many areas of interest.
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Affiliation(s)
- Juan Castro-Severyn
- Laboratorio de Microbiología Aplicada y Extremófilos, Facultad de Ingeniería y Ciencias Geológicas, Universidad Católica del Norte, Antofagasta, Chile
| | - Coral Pardo-Esté
- Laboratorio de Microbiología Aplicada y Extremófilos, Facultad de Ingeniería y Ciencias Geológicas, Universidad Católica del Norte, Antofagasta, Chile
- Laboratorio de Microbiología Molecular, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | - Katterinne N. Mendez
- Center for Bioinformatics and Integrative Biology, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | - Jonathan Fortt
- Laboratorio de Microbiología Aplicada y Extremófilos, Facultad de Ingeniería y Ciencias Geológicas, Universidad Católica del Norte, Antofagasta, Chile
| | - Sebastian Marquez
- Center for Bioinformatics and Integrative Biology, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | - Franck Molina
- Sys2Diag, UMR9005 CNRS ALCEDIAG, Montpellier, France
| | - Eduardo Castro-Nallar
- Center for Bioinformatics and Integrative Biology, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | - Francisco Remonsellez
- Laboratorio de Microbiología Aplicada y Extremófilos, Facultad de Ingeniería y Ciencias Geológicas, Universidad Católica del Norte, Antofagasta, Chile
- Centro de Investigación Tecnológica del Agua en el Desierto-CEITSAZA, Universidad Católica del Norte, Antofagasta, Chile
| | - Claudia P. Saavedra
- Laboratorio de Microbiología Molecular, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
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10
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Cultivation and characterization of snowbound microorganisms from the South Pole. Extremophiles 2021; 25:159-172. [PMID: 33590336 DOI: 10.1007/s00792-021-01218-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 01/28/2021] [Indexed: 02/03/2023]
Abstract
Little is known about microbial ecosystems of interior Antarctica, if indeed such ecosystems exist. Although considerable research has assessed microorganisms indigenous to coastal regions of Antarctica, particularly their lakes, ponds, and soils, to our knowledge only one characterized bacterium, a strain of Pseudomonas, has been isolated from South Pole ice or snow. Metagenomic community analyses described in this work and elsewhere reveal that a diversity of bacteria exists in inland polar snows, yet attempts to culture and characterize these microbes from this extreme environment have been few to date. In this molecular and culture-dependent investigation of the microbiology of inland Antarctica, we enriched and isolated two new strains of bacteria and one strain of yeast (Fungi) from South Pole snow samples. The bacteria were of the genera Methylobacterium and Sphingomonas, and the yeast grouped with species of Naganishia (class Tremellocytes). In addition to phylogenetic analyses, characterization of these isolates included determinations of cell morphology, growth as a function of temperature, salinity tolerance, and carbon and energy source versatility. All organisms were found to be cold-adapted, and the yeast strain additionally showed considerable halotolerance. These descriptions expand our understanding of the diversity and metabolic activities of snowbound microorganisms of interior Antarctica.
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11
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Gutt J, Isla E, Xavier JC, Adams BJ, Ahn IY, Cheng CHC, Colesie C, Cummings VJ, di Prisco G, Griffiths H, Hawes I, Hogg I, McIntyre T, Meiners KM, Pearce DA, Peck L, Piepenburg D, Reisinger RR, Saba GK, Schloss IR, Signori CN, Smith CR, Vacchi M, Verde C, Wall DH. Antarctic ecosystems in transition - life between stresses and opportunities. Biol Rev Camb Philos Soc 2020; 96:798-821. [PMID: 33354897 DOI: 10.1111/brv.12679] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 12/08/2020] [Accepted: 12/10/2020] [Indexed: 12/23/2022]
Abstract
Important findings from the second decade of the 21st century on the impact of environmental change on biological processes in the Antarctic were synthesised by 26 international experts. Ten key messages emerged that have stakeholder-relevance and/or a high impact for the scientific community. They address (i) altered biogeochemical cycles, (ii) ocean acidification, (iii) climate change hotspots, (iv) unexpected dynamism in seabed-dwelling populations, (v) spatial range shifts, (vi) adaptation and thermal resilience, (vii) sea ice related biological fluctuations, (viii) pollution, (ix) endangered terrestrial endemism and (x) the discovery of unknown habitats. Most Antarctic biotas are exposed to multiple stresses and considered vulnerable to environmental change due to narrow tolerance ranges, rapid change, projected circumpolar impacts, low potential for timely genetic adaptation, and migration barriers. Important ecosystem functions, such as primary production and energy transfer between trophic levels, have already changed, and biodiversity patterns have shifted. A confidence assessment of the degree of 'scientific understanding' revealed an intermediate level for most of the more detailed sub-messages, indicating that process-oriented research has been successful in the past decade. Additional efforts are necessary, however, to achieve the level of robustness in scientific knowledge that is required to inform protection measures of the unique Antarctic terrestrial and marine ecosystems, and their contributions to global biodiversity and ecosystem services.
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Affiliation(s)
- Julian Gutt
- Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Columbusstr., Bremerhaven, 27568, Germany
| | - Enrique Isla
- Institute of Marine Sciences-CSIC, Passeig Maritim de la Barceloneta 37-49, Barcelona, 08003, Spain
| | - José C Xavier
- University of Coimbra, MARE - Marine and Environmental Sciences Centre, Faculty of Sciences and Technology, Coimbra, Portugal.,British Antarctic Survey, Natural Environmental Research Council, High Cross, Madingley Road, Cambridge, CB3 OET, U.K
| | - Byron J Adams
- Department of Biology and Monte L. Bean Museum, Brigham Young University, Provo, UT, U.S.A
| | - In-Young Ahn
- Korea Polar Research Institute, 26 Songdomirae-ro, Yeonsu-gu, Incheon, 21990, South Korea
| | - C-H Christina Cheng
- Department of Evolution, Ecology and Behavior, University of Illinois, Urbana, IL, U.S.A
| | - Claudia Colesie
- School of GeoSciences, University of Edinburgh, Alexander Crum Brown Road, Edinburgh, EH9 3FF, U.K
| | - Vonda J Cummings
- National Institute of Water and Atmosphere Research Ltd (NIWA), 301 Evans Bay Parade, Greta Point, Wellington, New Zealand
| | - Guido di Prisco
- Institute of Biosciences and BioResources (IBBR), National Research Council (CNR), Via Pietro Castellino 111, Naples, I-80131, Italy
| | - Huw Griffiths
- British Antarctic Survey, Natural Environmental Research Council, High Cross, Madingley Road, Cambridge, CB3 OET, U.K
| | - Ian Hawes
- Coastal Marine Field Station, University of Waikato, 58 Cross Road, Tauranga, 3100, New Zealand
| | - Ian Hogg
- School of Science, University of Waikato, Private Bag 3105, Hamilton, 3240, New Zealand.,Canadian High Antarctic Research Station, Polar Knowledge Canada, PO Box 2150, Cambridge Bay, NU, X0B 0C0, Canada
| | - Trevor McIntyre
- Department of Life and Consumer Sciences, University of South Africa, Private Bag X6, Florida, 1710, South Africa
| | - Klaus M Meiners
- Australian Antarctic Division, Department of Agriculture, Water and the Environment, and Australian Antarctic Program Partnership, University of Tasmania, 20 Castray Esplanade, Battery Point, TAS, 7004, Australia
| | - David A Pearce
- British Antarctic Survey, Natural Environmental Research Council, High Cross, Madingley Road, Cambridge, CB3 OET, U.K.,Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University at Newcastle, Northumberland Road, Newcastle upon Tyne, NE1 8ST, U.K
| | - Lloyd Peck
- British Antarctic Survey, Natural Environmental Research Council, High Cross, Madingley Road, Cambridge, CB3 OET, U.K
| | - Dieter Piepenburg
- Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Columbusstr., Bremerhaven, 27568, Germany
| | - Ryan R Reisinger
- Centre d'Etudes Biologique de Chizé, UMR 7372 du Centre National de la Recherche Scientifique - La Rochelle Université, Villiers-en-Bois, 79360, France
| | - Grace K Saba
- Center for Ocean Observing Leadership, Department of Marine and Coastal Sciences, Rutgers University, 71 Dudley Rd., New Brunswick, NJ, 08901, U.S.A
| | - Irene R Schloss
- Instituto Antártico Argentino, Buenos Aires, Argentina.,Centro Austral de Investigaciones Científicas, Bernardo Houssay 200, Ushuaia, Tierra del Fuego, CP V9410CAB, Argentina.,Universidad Nacional de Tierra del Fuego, Ushuaia, Tierra del Fuego, CP V9410CAB, Argentina
| | - Camila N Signori
- Oceanographic Institute, University of São Paulo, Praça do Oceanográfico, 191, São Paulo, CEP: 05508-900, Brazil
| | - Craig R Smith
- Department of Oceanography, University of Hawaii at Manoa, 1000 Pope Road, Honolulu, HI, 96822, U.S.A
| | - Marino Vacchi
- Institute for the Study of the Anthropic Impacts and the Sustainability of the Marine Environment (IAS), National Research Council of Italy (CNR), Via de Marini 6, Genoa, 16149, Italy
| | - Cinzia Verde
- Institute of Biosciences and BioResources (IBBR), National Research Council (CNR), Via Pietro Castellino 111, Naples, I-80131, Italy
| | - Diana H Wall
- Department of Biology and School of Global Environmental Sustainability, Colorado State University, Fort Collins, CO, U.S.A
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Abstract
A unique environment at Borup Fiord Pass is characterized by a sulfur-enriched glacial ecosystem in the low-temperature Canadian High Arctic. BFP represents one of the best terrestrial analog sites for studying icy, sulfur-rich worlds outside our own, such as Europa and Mars. The site also allows investigation of sulfur-based microbial metabolisms in cold environments here on Earth. Here, we report whole-genome sequencing data that suggest that sulfur cycling metabolisms at BFP are more widely used across bacterial taxa than predicted. From our analyses, the metabolic capability of sulfur oxidation among multiple community members appears likely due to functional redundancy present in their genomes. Functional redundancy, with respect to sulfur-oxidation at the BFP sulfur-ice environment, may indicate that this dynamic ecosystem hosts microorganisms that are able to use multiple sulfur electron donors alongside other metabolic pathways, including those for carbon and nitrogen. Biological sulfur cycling in polar, low-temperature ecosystems is an understudied phenomenon in part due to difficulty of access and the dynamic nature of glacial environments. One such environment where sulfur cycling is known to play an important role in microbial metabolisms is located at Borup Fiord Pass (BFP) in the Canadian High Arctic. Here, transient springs emerge from ice near the terminus of a glacier, creating a large area of proglacial aufeis (spring-derived ice) that is often covered in bright yellow/white sulfur, sulfate, and carbonate mineral precipitates accompanied by a strong odor of hydrogen sulfide. Metagenomic sequencing of samples from multiple sites and of various sample types across the BFP glacial system produced 31 metagenome-assembled genomes (MAGs) that were queried for sulfur, nitrogen, and carbon cycling/metabolism genes. An abundance of sulfur cycling genes was widespread across the isolated MAGs and sample metagenomes taxonomically associated with the bacterial classes Alphaproteobacteria and Gammaproteobacteria and Campylobacteria (formerly the Epsilonproteobacteria). This corroborates previous research from BFP implicating Campylobacteria as the primary class responsible for sulfur oxidation; however, data reported here suggested putative sulfur oxidation by organisms in both the alphaproteobacterial and gammaproteobacterial classes that was not predicted by previous work. These findings indicate that in low-temperature, sulfur-based environments, functional redundancy may be a key mechanism that microorganisms use to enable coexistence whenever energy is limited and/or focused by redox chemistry. IMPORTANCE A unique environment at Borup Fiord Pass is characterized by a sulfur-enriched glacial ecosystem in the low-temperature Canadian High Arctic. BFP represents one of the best terrestrial analog sites for studying icy, sulfur-rich worlds outside our own, such as Europa and Mars. The site also allows investigation of sulfur-based microbial metabolisms in cold environments here on Earth. Here, we report whole-genome sequencing data that suggest that sulfur cycling metabolisms at BFP are more widely used across bacterial taxa than predicted. From our analyses, the metabolic capability of sulfur oxidation among multiple community members appears likely due to functional redundancy present in their genomes. Functional redundancy, with respect to sulfur-oxidation at the BFP sulfur-ice environment, may indicate that this dynamic ecosystem hosts microorganisms that are able to use multiple sulfur electron donors alongside other metabolic pathways, including those for carbon and nitrogen.
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13
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Margesin R, Collins T. Microbial ecology of the cryosphere (glacial and permafrost habitats): current knowledge. Appl Microbiol Biotechnol 2019; 103:2537-2549. [PMID: 30719551 PMCID: PMC6443599 DOI: 10.1007/s00253-019-09631-3] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Revised: 01/04/2019] [Accepted: 01/07/2019] [Indexed: 11/28/2022]
Abstract
Microorganisms in cold ecosystems play a key ecological role in their natural habitats. Since these ecosystems are especially sensitive to climate changes, as indicated by the worldwide retreat of glaciers and ice sheets as well as permafrost thawing, an understanding of the role and potential of microbial life in these habitats has become crucial. Emerging technologies have added significantly to our knowledge of abundance, functional activity, and lifestyles of microbial communities in cold environments. The current knowledge of microbial ecology in glacial habitats and permafrost, the most studied habitats of the cryosphere, is reported in this review.
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Affiliation(s)
- Rosa Margesin
- Institute of Microbiology, University of Innsbruck, 6020, Innsbruck, Austria.
| | - Tony Collins
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, 4710-057, Braga, Portugal
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14
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Zhang Y, Wang X, Zhen Y, Mi T, He H, Yu Z. Microbial Diversity and Community Structure of Sulfate-Reducing and Sulfur-Oxidizing Bacteria in Sediment Cores from the East China Sea. Front Microbiol 2017; 8:2133. [PMID: 29163420 PMCID: PMC5682103 DOI: 10.3389/fmicb.2017.02133] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2017] [Accepted: 10/18/2017] [Indexed: 02/03/2023] Open
Abstract
Sulfate-reducing bacteria (SRB) and sulfur-oxidizing bacteria (SOB) have been studied extensively in marine sediments because of their vital roles in both sulfur and carbon cycles, but the available information regarding the highly diverse SRB and SOB communities is not comprehensive. High-throughput sequencing of functional gene amplicons provides tremendous insight into the structure and functional potential of complex microbial communities. Here, we explored the community structure, diversity, and abundance of SRB and SOB simultaneously through 16S rRNA, dsrB and soxB gene high-throughput sequencing and quantitative PCR analyses of core samples from the East China Sea. Overall, high-throughput sequencing of the dsrB and soxB genes achieved almost complete coverage (>99%) and revealed the high diversity, richness, and operational taxonomic unit (OTU) numbers of the SRB and SOB communities, which suggest the existence of an active sulfur cycle in the study area. Further analysis demonstrated that rare species make vital contributions to the high richness, diversity, and OTU numbers obtained. Depth-based distributions of the dsrB, soxB, and 16S rRNA gene abundances indicated that the SRB abundance might be more sensitive to the sedimentary dynamic environment than those of total bacteria and SOB. In addition, the results of unweighted pair group method with arithmetic mean (UPGMA) clustering analysis and redundancy analysis revealed that environmental parameters, such as depth and dissolved inorganic nitrogen concentrations, and the sedimentary dynamic environment, which differed between the two sampling stations, can significantly influence the community structures of total bacteria, SRB, and SOB. This study provided further comprehensive information regarding the characteristics of SRB and SOB communities.
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Affiliation(s)
- Yu Zhang
- College of Environmental Science and Engineering, Ocean University of China, Qingdao, China.,Key Laboratory of Marine Environment and Ecology, Ministry of Education, Qingdao, China.,Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Xungong Wang
- College of Environmental Science and Engineering, Ocean University of China, Qingdao, China.,Key Laboratory of Marine Environment and Ecology, Ministry of Education, Qingdao, China.,Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Yu Zhen
- College of Environmental Science and Engineering, Ocean University of China, Qingdao, China.,Key Laboratory of Marine Environment and Ecology, Ministry of Education, Qingdao, China.,Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Tiezhu Mi
- College of Environmental Science and Engineering, Ocean University of China, Qingdao, China.,Key Laboratory of Marine Environment and Ecology, Ministry of Education, Qingdao, China.,Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Hui He
- Key Laboratory of Marine Environment and Ecology, Ministry of Education, Qingdao, China.,Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,College of Marine Life Science, Ocean University of China, Qingdao, China
| | - Zhigang Yu
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Key Laboratory of Marine Chemical Theory and Technology, Ministry of Education, Qingdao, China
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15
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Watanabe T, Kojima H, Fukui M. Identity of major sulfur-cycle prokaryotes in freshwater lake ecosystems revealed by a comprehensive phylogenetic study of the dissimilatory adenylylsulfate reductase. Sci Rep 2016; 6:36262. [PMID: 27824124 PMCID: PMC5099947 DOI: 10.1038/srep36262] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Accepted: 10/12/2016] [Indexed: 11/24/2022] Open
Abstract
Adenylylsulfate reductase is a heterodimeric complex of two subunits, AprB and AprA, and is a key enzyme in dissimilatory sulfate reduction and sulfur oxidation. Common use of aprA as a functional marker gene has revealed the diversity of sulfur-cycle prokaryotes in diverse environments. In this study, we established a comprehensive sequence set of apr genes and employed it to reanalyze apr phylogeny, evaluate the coverage of a widely used primer set (AprA-1-FW/AprA-5-RV), and categorize environmental aprA sequences. Phylogenetic tree construction revealed new members of Apr lineage II and several previously unrecognized lateral gene transfer events. Using the established phylogenetic tree, we classified all previously reported aprA sequences amplified from freshwater lakes with the primer pair AprA-1-FW/AprA-5-RV in addition to the aprA sequences newly retrieved from freshwater lakes; the obtained results were complemented by 16S rRNA clone library analysis. Apr-based classifications of some of operational taxonomic units were supported by 16S rRNA-based analysis. This study updates our knowledge on the phylogeny of aprBA and shows the identities of several sulfur-cycle bacteria, which could not be classified to a known taxa until now. The established apr sequence set is publicly available and can be applied to assign environmental sequences to known lineages.
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Affiliation(s)
- Tomohiro Watanabe
- The Institute of Low Temperature Science, Hokkaido University, Sapporo, Japan
| | - Hisaya Kojima
- The Institute of Low Temperature Science, Hokkaido University, Sapporo, Japan
| | - Manabu Fukui
- The Institute of Low Temperature Science, Hokkaido University, Sapporo, Japan
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16
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Vick-Majors TJ, Mitchell AC, Achberger AM, Christner BC, Dore JE, Michaud AB, Mikucki JA, Purcell AM, Skidmore ML, Priscu JC. Physiological Ecology of Microorganisms in Subglacial Lake Whillans. Front Microbiol 2016; 7:1705. [PMID: 27833599 PMCID: PMC5081474 DOI: 10.3389/fmicb.2016.01705] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Accepted: 10/12/2016] [Indexed: 11/13/2022] Open
Abstract
Subglacial microbial habitats are widespread in glaciated regions of our planet. Some of these environments have been isolated from the atmosphere and from sunlight for many thousands of years. Consequently, ecosystem processes must rely on energy gained from the oxidation of inorganic substrates or detrital organic matter. Subglacial Lake Whillans (SLW) is one of more than 400 subglacial lakes known to exist under the Antarctic ice sheet; however, little is known about microbial physiology and energetics in these systems. When it was sampled through its 800 m thick ice cover in 2013, the SLW water column was shallow (~2 m deep), oxygenated, and possessed sufficient concentrations of C, N, and P substrates to support microbial growth. Here, we use a combination of physiological assays and models to assess the energetics of microbial life in SLW. In general, SLW microorganisms grew slowly in this energy-limited environment. Heterotrophic cellular carbon turnover times, calculated from 3H-thymidine and 3H-leucine incorporation rates, were long (60 to 500 days) while cellular doubling times averaged 196 days. Inferred growth rates (average ~0.006 d-1) obtained from the same incubations were at least an order of magnitude lower than those measured in Antarctic surface lakes and oligotrophic areas of the ocean. Low growth efficiency (8%) indicated that heterotrophic populations in SLW partition a majority of their carbon demand to cellular maintenance rather than growth. Chemoautotrophic CO2-fixation exceeded heterotrophic organic C-demand by a factor of ~1.5. Aerobic respiratory activity associated with heterotrophic and chemoautotrophic metabolism surpassed the estimated supply of oxygen to SLW, implying that microbial activity could deplete the oxygenated waters, resulting in anoxia. We used thermodynamic calculations to examine the biogeochemical and energetic consequences of environmentally imposed switching between aerobic and anaerobic metabolisms in the SLW water column. Heterotrophic metabolisms utilizing acetate and formate as electron donors yielded less energy than chemolithotrophic metabolisms when calculated in terms of energy density, which supports experimental results that showed chemoautotrophic activity in excess of heterotrophic activity. The microbial communities of subglacial lake ecosystems provide important natural laboratories to study the physiological and biogeochemical behavior of microorganisms inhabiting cold, dark environments.
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Affiliation(s)
- Trista J Vick-Majors
- Department of Land Resources and Environmental Sciences, Montana State University Bozeman, MT, USA
| | - Andrew C Mitchell
- Department of Geography and Earth Sciences, Aberystwyth University Aberystwyth, UK
| | - Amanda M Achberger
- Department of Biological Sciences, Louisiana State University Baton Rouge, LA, USA
| | - Brent C Christner
- Department of Microbiology and Cell Science, University of FloridaGainesville, FL, USA; Biodiversity Institute, University of FloridaGainesville, FL, USA
| | - John E Dore
- Department of Land Resources and Environmental Sciences, Montana State University Bozeman, MT, USA
| | - Alexander B Michaud
- Department of Land Resources and Environmental Sciences, Montana State University Bozeman, MT, USA
| | - Jill A Mikucki
- Department of Microbiology, University of Tennessee Knoxville, TN, USA
| | - Alicia M Purcell
- Department of Microbiology, University of Tennessee Knoxville, TN, USA
| | - Mark L Skidmore
- Department of Earth Sciences, Montana State University Bozeman, MT, USA
| | - John C Priscu
- Department of Land Resources and Environmental Sciences, Montana State University Bozeman, MT, USA
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17
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Achberger AM, Christner BC, Michaud AB, Priscu JC, Skidmore ML, Vick-Majors TJ. Microbial Community Structure of Subglacial Lake Whillans, West Antarctica. Front Microbiol 2016; 7:1457. [PMID: 27713727 PMCID: PMC5032586 DOI: 10.3389/fmicb.2016.01457] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Accepted: 08/31/2016] [Indexed: 11/13/2022] Open
Abstract
Subglacial Lake Whillans (SLW) is located beneath ∼800 m of ice on the Whillans Ice Stream in West Antarctica and was sampled in January of 2013, providing the first opportunity to directly examine water and sediments from an Antarctic subglacial lake. To minimize the introduction of surface contaminants to SLW during its exploration, an access borehole was created using a microbiologically clean hot water drill designed to reduce the number and viability of microorganisms in the drilling water. Analysis of 16S rRNA genes (rDNA) amplified from samples of the drilling and borehole water allowed an evaluation of the efficacy of this approach and enabled a confident assessment of the SLW ecosystem inhabitants. Based on an analysis of 16S rDNA and rRNA (i.e., reverse-transcribed rRNA molecules) data, the SLW community was found to be bacterially dominated and compositionally distinct from the assemblages identified in the drill system. The abundance of bacteria (e.g., Candidatus Nitrotoga, Sideroxydans, Thiobacillus, and Albidiferax) and archaea (Candidatus Nitrosoarchaeum) related to chemolithoautotrophs was consistent with the oxidation of reduced iron, sulfur, and nitrogen compounds having important roles as pathways for primary production in this permanently dark ecosystem. Further, the prevalence of Methylobacter in surficial lake sediments combined with the detection of methanogenic taxa in the deepest sediment horizons analyzed (34–36 cm) supported the hypothesis that methane cycling occurs beneath the West Antarctic Ice Sheet. Large ratios of rRNA to rDNA were observed for several operational taxonomic units abundant in the water column and sediments (e.g., Albidiferax, Methylobacter, Candidatus Nitrotoga, Sideroxydans, and Smithella), suggesting a potentially active role for these taxa in the SLW ecosystem. Our findings are consistent with chemosynthetic microorganisms serving as the ecological foundation in this dark subsurface environment, providing new organic matter that sustains a microbial ecosystem beneath the West Antarctic Ice Sheet.
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Affiliation(s)
- Amanda M Achberger
- Department of Biological Sciences, Louisiana State University, Baton Rouge LA, USA
| | - Brent C Christner
- Department of Biological Sciences, Louisiana State University, Baton RougeLA, USA; Department of Microbiology and Cell Science, University of Florida, GainesvilleFL, USA; Biodiversity Institute, University of Florida, GainesvilleFL, USA
| | - Alexander B Michaud
- Department of Land Resources and Environmental Science, Montana State University, Bozeman MT, USA
| | - John C Priscu
- Department of Land Resources and Environmental Science, Montana State University, Bozeman MT, USA
| | - Mark L Skidmore
- Department of Earth Sciences, Montana State University, Bozeman MT, USA
| | - Trista J Vick-Majors
- Department of Land Resources and Environmental Science, Montana State University, Bozeman MT, USA
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18
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Metatranscriptomic evidence of pervasive and diverse chemolithoautotrophy relevant to C, S, N and Fe cycling in a shallow alluvial aquifer. ISME JOURNAL 2016; 10:2106-17. [PMID: 26943628 PMCID: PMC4989316 DOI: 10.1038/ismej.2016.25] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Revised: 01/06/2016] [Accepted: 01/10/2016] [Indexed: 11/29/2022]
Abstract
Groundwater ecosystems are conventionally thought to be fueled by surface-derived allochthonous organic matter and dominated by heterotrophic microbes living under often-oligotrophic conditions. However, in a 2-month study of nitrate amendment to a perennially suboxic aquifer in Rifle (CO), strain-resolved metatranscriptomic analysis revealed pervasive and diverse chemolithoautotrophic bacterial activity relevant to C, S, N and Fe cycling. Before nitrate injection, anaerobic ammonia-oxidizing (anammox) bacteria accounted for 16% of overall microbial community gene expression, whereas during the nitrate injection, two other groups of chemolithoautotrophic bacteria collectively accounted for 80% of the metatranscriptome: (1) members of the Fe(II)-oxidizing Gallionellaceae family and (2) strains of the S-oxidizing species, Sulfurimonas denitrificans. Notably, the proportion of the metatranscriptome accounted for by these three groups was considerably greater than the proportion of the metagenome coverage that they represented. Transcriptional analysis revealed some unexpected metabolic couplings, in particular, putative nitrate-dependent Fe(II) and S oxidation among nominally microaerophilic Gallionellaceae strains, including expression of periplasmic (NapAB) and membrane-bound (NarGHI) nitrate reductases. The three most active groups of chemolithoautotrophic bacteria in this study had overlapping metabolisms that allowed them to occupy different yet related metabolic niches throughout the study. Overall, these results highlight the important role that chemolithoautotrophy can have in aquifer biogeochemical cycling, a finding that has broad implications for understanding terrestrial carbon cycling and is supported by recent studies of geochemically diverse aquifers.
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19
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Mikucki JA, Lee PA, Ghosh D, Purcell AM, Mitchell AC, Mankoff KD, Fisher AT, Tulaczyk S, Carter S, Siegfried MR, Fricker HA, Hodson T, Coenen J, Powell R, Scherer R, Vick-Majors T, Achberger AA, Christner BC, Tranter M. Subglacial Lake Whillans microbial biogeochemistry: a synthesis of current knowledge. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2016; 374:rsta.2014.0290. [PMID: 26667908 DOI: 10.1098/rsta.2014.0290] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Liquid water occurs below glaciers and ice sheets globally, enabling the existence of an array of aquatic microbial ecosystems. In Antarctica, large subglacial lakes are present beneath hundreds to thousands of metres of ice, and scientific interest in exploring these environments has escalated over the past decade. After years of planning, the first team of scientists and engineers cleanly accessed and retrieved pristine samples from a West Antarctic subglacial lake ecosystem in January 2013. This paper reviews the findings to date on Subglacial Lake Whillans and presents new supporting data on the carbon and energy metabolism of resident microbes. The analysis of water and sediments from the lake revealed a diverse microbial community composed of bacteria and archaea that are close relatives of species known to use reduced N, S or Fe and CH4 as energy sources. The water chemistry of Subglacial Lake Whillans was dominated by weathering products from silicate minerals with a minor influence from seawater. Contributions to water chemistry from microbial sulfide oxidation and carbonation reactions were supported by genomic data. Collectively, these results provide unequivocal evidence that subglacial environments in this region of West Antarctica host active microbial ecosystems that participate in subglacial biogeochemical cycling.
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Affiliation(s)
- J A Mikucki
- Department of Microbiology, University of Tennessee, Knoxville, TN 37996, USA Department of Biology, Middlebury College, Middlebury, VT 05753, USA
| | - P A Lee
- Hollings Marine Lab, College of Charleston, Charleston, SC 29412, USA
| | - D Ghosh
- Department of Microbiology, University of Tennessee, Knoxville, TN 37996, USA
| | - A M Purcell
- Department of Microbiology, University of Tennessee, Knoxville, TN 37996, USA
| | - A C Mitchell
- Department of Geography and Earth Sciences, Aberystwyth University, Aberystwyth, UK
| | - K D Mankoff
- Department of Geosciences, The Pennsylvania State University, University Park, PA 16802, USA
| | - A T Fisher
- Earth and Planetary Sciences, University of California, Santa Cruz, CA, USA
| | - S Tulaczyk
- Earth and Planetary Sciences, University of California, Santa Cruz, CA, USA
| | - S Carter
- Institute for Geophysics and Planetary Physics, Scripps Institution of Oceanography, University of California, San Diego, CA 92093, USA
| | - M R Siegfried
- Institute for Geophysics and Planetary Physics, Scripps Institution of Oceanography, University of California, San Diego, CA 92093, USA
| | - H A Fricker
- Institute for Geophysics and Planetary Physics, Scripps Institution of Oceanography, University of California, San Diego, CA 92093, USA
| | - T Hodson
- Department of Geology and Environmental Geosciences Northern, Illinois University, DeKalb, IL 60115, USA
| | - J Coenen
- Department of Geology and Environmental Geosciences Northern, Illinois University, DeKalb, IL 60115, USA
| | - R Powell
- Department of Geology and Environmental Geosciences Northern, Illinois University, DeKalb, IL 60115, USA
| | - R Scherer
- Department of Geology and Environmental Geosciences Northern, Illinois University, DeKalb, IL 60115, USA
| | - T Vick-Majors
- Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, MT 59717, USA
| | - A A Achberger
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - B C Christner
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - M Tranter
- Bristol Glaciology Centre, Geographical Sciences, University of Bristol, Bristol BS8 1SS, UK
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20
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Hodgson DA, Bentley MJ, Smith JA, Klepacki J, Makinson K, Smith AM, Saw K, Scherer R, Powell R, Tulaczyk S, Rose M, Pearce D, Mowlem M, Keen P, Siegert MJ. Technologies for retrieving sediment cores in Antarctic subglacial settings. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2016; 374:rsta.2015.0056. [PMID: 26667918 DOI: 10.1098/rsta.2015.0056] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 06/17/2015] [Indexed: 06/05/2023]
Abstract
Accumulations of sediment beneath the Antarctic Ice Sheet contain a range of physical and chemical proxies with the potential to document changes in ice sheet history and to identify and characterize life in subglacial settings. Retrieving subglacial sediments and sediment cores presents several unique challenges to existing technologies. This paper briefly reviews the history of sediment sampling in subglacial environments. It then outlines some of the technological challenges and constraints in developing the corers being used in sub-ice shelf settings (e.g. George VI Ice Shelf and Larsen Ice Shelf), under ice streams (e.g. Rutford Ice Stream), at or close to the grounding line (e.g. Whillans Ice Stream) and in subglacial lakes deep under the ice sheet (e.g. Lake Ellsworth). The key features of the corers designed to operate in each of these subglacial settings are described and illustrated together with comments on their deployment procedures.
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Affiliation(s)
- Dominic A Hodgson
- British Antarctic Survey, High Cross, Madingley Road, Cambridge CB3 0ET, UK Department of Geography, Science Laboratories, Durham University, South Road, Durham DH1 3LE, UK
| | - Michael J Bentley
- Department of Geography, Science Laboratories, Durham University, South Road, Durham DH1 3LE, UK
| | - James A Smith
- British Antarctic Survey, High Cross, Madingley Road, Cambridge CB3 0ET, UK
| | - Julian Klepacki
- British Antarctic Survey, High Cross, Madingley Road, Cambridge CB3 0ET, UK
| | - Keith Makinson
- British Antarctic Survey, High Cross, Madingley Road, Cambridge CB3 0ET, UK
| | - Andrew M Smith
- British Antarctic Survey, High Cross, Madingley Road, Cambridge CB3 0ET, UK
| | - Kevin Saw
- National Oceanography Centre, European Way, Southampton SO14 3ZH, UK
| | - Reed Scherer
- Department of Geology and Environmental Geosciences, Northern Illinois University, 1425 West Lincoln Hwy, DeKalb, IL 60115-2828, USA
| | - Ross Powell
- Department of Geology and Environmental Geosciences, Northern Illinois University, 1425 West Lincoln Hwy, DeKalb, IL 60115-2828, USA
| | - Slawek Tulaczyk
- Earth and Planetary Sciences Department, University of California Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA
| | - Mike Rose
- British Antarctic Survey, High Cross, Madingley Road, Cambridge CB3 0ET, UK
| | - David Pearce
- British Antarctic Survey, High Cross, Madingley Road, Cambridge CB3 0ET, UK Department of Applied Sciences, Northumbria University, Ellison Place 2, Newcastle-upon-Tyne NE1 8ST, UK
| | - Matt Mowlem
- National Oceanography Centre, European Way, Southampton SO14 3ZH, UK
| | - Peter Keen
- Keen Marine Limited, 15 Minerva Road, East Cowes, Isle of Wight PO32 6HD, UK
| | - Martin J Siegert
- The Grantham Institute and Department of Earth Science and Engineering, Imperial College London, South Kensington, London SW7 2AZ, UK
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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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Fisher AT, Mankoff KD, Tulaczyk SM, Tyler SW, Foley N. High geothermal heat flux measured below the West Antarctic Ice Sheet. SCIENCE ADVANCES 2015; 1:e1500093. [PMID: 26601210 PMCID: PMC4646773 DOI: 10.1126/sciadv.1500093] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2015] [Accepted: 05/19/2015] [Indexed: 05/24/2023]
Abstract
The geothermal heat flux is a critical thermal boundary condition that influences the melting, flow, and mass balance of ice sheets, but measurements of this parameter are difficult to make in ice-covered regions. We report the first direct measurement of geothermal heat flux into the base of the West Antarctic Ice Sheet (WAIS), below Subglacial Lake Whillans, determined from the thermal gradient and the thermal conductivity of sediment under the lake. The heat flux at this site is 285 ± 80 mW/m(2), significantly higher than the continental and regional averages estimated for this site using regional geophysical and glaciological models. Independent temperature measurements in the ice indicate an upward heat flux through the WAIS of 105 ± 13 mW/m(2). The difference between these heat flux values could contribute to basal melting and/or be advected from Subglacial Lake Whillans by flowing water. The high geothermal heat flux may help to explain why ice streams and subglacial lakes are so abundant and dynamic in this region.
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Affiliation(s)
- Andrew T. Fisher
- Department of Earth and Planetary Sciences, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Kenneth D. Mankoff
- Department of Earth and Planetary Sciences, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
- Department of Physical Oceanography, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, USA
| | - Slawek M. Tulaczyk
- Department of Earth and Planetary Sciences, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Scott W. Tyler
- Department of Geological Sciences and Engineering, University of Nevada, Reno, NV 89557, USA
| | - Neil Foley
- Department of Earth and Planetary Sciences, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
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