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Pearce DA, Magiopoulos I, Mowlem M, Tranter M, Holt G, Woodward J, Siegert MJ. Microbiology: lessons from a first attempt at Lake Ellsworth. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2016; 374:rsta.2014.0291. [PMID: 26667906 DOI: 10.1098/rsta.2014.0291] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 10/26/2015] [Indexed: 06/05/2023]
Abstract
During the attempt to directly access, measure and sample Subglacial Lake Ellsworth in 2012-2013, we conducted microbiological analyses of the drilling equipment, scientific instrumentation, field camp and natural surroundings. From these studies, a number of lessons can be learned about the cleanliness of deep Antarctic subglacial lake access leading to, in particular, knowledge of the limitations of some of the most basic relevant microbiological principles. Here, we focus on five of the core challenges faced and describe how cleanliness and sterilization were implemented in the field. In the light of our field experiences, we consider how effective these actions were, and what can be learnt for future subglacial exploration missions. The five areas covered are: (i) field camp environment and activities, (ii) the engineering processes surrounding the hot water drilling, (iii) sample handling, including recovery, stability and preservation, (iv) clean access methodologies and removal of sample material, and (v) the biodiversity and distribution of bacteria around the Antarctic. Comparisons are made between the microbiology of the Lake Ellsworth field site and other Antarctic systems, including the lakes on Signy Island, and on the Antarctic Peninsula at Lake Hodgson. Ongoing research to better define and characterize the behaviour of natural and introduced microbial populations in response to deep-ice drilling is also discussed. We recommend that future access programmes: (i) assess each specific local environment in enhanced detail due to the potential for local contamination, (ii) consider the sterility of the access in more detail, specifically focusing on single cell colonization and the introduction of new species through contamination of pre-existing microbial communities, (iii) consider experimental bias in methodological approaches, (iv) undertake in situ biodiversity detection to mitigate risk of non-sample return and post-sample contamination, and (v) address the critical question of how important these microbes are in the functioning of Antarctic ecosystems.
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Affiliation(s)
- D A Pearce
- Department of Applied Sciences, Faculty of Health and Life Sciences, University of Northumbria, Ellison Building, Newcastle upon Tyne NE1 8ST, UK British Antarctic Survey, High Cross, Madingley Road, Cambridge CB3 0ET, UK Department of Arctic Biology, University Centre in Svalbard, Longyearbyen 9171, Norway
| | - I Magiopoulos
- National Oceanography Centre, University of Southampton Waterfront Campus, European Way, Southampton SO14 3ZH, UK
| | - M Mowlem
- National Oceanography Centre, University of Southampton Waterfront Campus, European Way, Southampton SO14 3ZH, UK
| | - M Tranter
- Centre for Glaciology, University of Bristol, 12 Berkeley Square, University Road, Clifton, Bristol BS8 1SS, UK
| | - G Holt
- Department of Applied Sciences, Faculty of Health and Life Sciences, University of Northumbria, Ellison Building, Newcastle upon Tyne NE1 8ST, UK
| | - J Woodward
- Department of Applied Sciences, Faculty of Health and Life Sciences, University of Northumbria, Ellison Building, Newcastle upon Tyne NE1 8ST, UK
| | - M J Siegert
- Grantham Institute and Department of Earth Science and Engineering, Imperial College London, South Kensington, London SW7 2AZ, UK
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Matsui K, Yoshinami S, Narita M, Chien MF, Phung LT, Silver S, Endo G. Mercury resistance transposons in Bacilli strains from different geographical regions. FEMS Microbiol Lett 2016; 363:fnw013. [PMID: 26802071 DOI: 10.1093/femsle/fnw013] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/30/2015] [Indexed: 11/14/2022] Open
Abstract
A total of 65 spore-forming mercury-resistant bacteria were isolated from natural environments worldwide in order to understand the acquisition of additional genes by and dissemination of mercury resistance transposons across related Bacilli genera by horizontal gene movement. PCR amplification using a single primer complementary to the inverted repeat sequence of TnMERI1-like transposons showed that 12 of 65 isolates had a transposon-like structure. There were four types of amplified fragments: Tn5084, Tn5085, Tn(d)MER3 (a newly identified deleted transposon-like fragment) and Tn6294 (a newly identified transposon). Tn(d)MER3 is a 3.5-kb sequence that carries a merRETPA operon with no merB or transposase genes. It is related to the mer operon of Bacillus licheniformis strain FA6-12 from Russia. DNA homology analysis shows that Tn6294 is an 8.5-kb sequence that is possibly derived from Tn(d)MER3 by integration of a TnMERI1-type transposase and resolvase genes and in addition the merR2 and merB1 genes. Bacteria harboring Tn6294 exhibited broad-spectrum mercury resistance to organomercurial compounds, although Tn6294 had only merB1 and did not have the merB2 and merB3 sequences for organomercurial lyases found in Tn5084 of B. cereus strain RC607. Strains with Tn6294 encode mercuric reductase (MerA) of less than 600 amino acids in length with a single N-terminal mercury-binding domain, whereas MerA encoded by strains MB1 and RC607 has two tandem domains. Thus, Tn(d)MER3 and Tn6294 are shorter prototypes for TnMERI1-like transposons. Identification of Tn6294 in Bacillus sp. from Taiwan and in Paenibacillus sp. from Antarctica indicates the wide horizontal dissemination of TnMERI1-like transposons across bacterial species and geographical barriers.
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Affiliation(s)
- Kazuaki Matsui
- Department of Civil and Environmental Engineering, Kinki University, Higashiosaka, Osaka 577-8502, Japan
| | - Satoshi Yoshinami
- Department of Civil and Environmental Engineering, Kinki University, Higashiosaka, Osaka 577-8502, Japan
| | - Masaru Narita
- Tohoku Afforestation and Environmental Protection Co, Sendai, Miyagi 980-0014, Japan Laboratory of Environmental Biotechnology, Tohoku Gakuin University, Tagajo, Miyagi 985-8537, Japan
| | - Mei-Fang Chien
- Laboratory of Environmental Biotechnology, Tohoku Gakuin University, Tagajo, Miyagi 985-8537, Japan Graduate School of Environmental Studies, Tohoku University, Sendai, Miyagi 980-8579, Japan
| | - Le T Phung
- Department of Microbiology and Immunology, University of Illinois at Chicago, Chicago, IL 60612 USA
| | - Simon Silver
- Department of Microbiology and Immunology, University of Illinois at Chicago, Chicago, IL 60612 USA
| | - Ginro Endo
- Laboratory of Environmental Biotechnology, Tohoku Gakuin University, Tagajo, Miyagi 985-8537, Japan
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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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Snow surface microbiome on the High Antarctic Plateau (DOME C). PLoS One 2014; 9:e104505. [PMID: 25101779 PMCID: PMC4125213 DOI: 10.1371/journal.pone.0104505] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2014] [Accepted: 07/14/2014] [Indexed: 12/22/2022] Open
Abstract
The cryosphere is an integral part of the global climate system and one of the major habitable ecosystems of Earth's biosphere. These permanently frozen environments harbor diverse, viable and metabolically active microbial populations that represent almost all the major phylogenetic groups. In this study, we investigated the microbial diversity in the surface snow surrounding the Concordia Research Station on the High Antarctic Plateau through a polyphasic approach, including direct prokaryotic quantification by flow cytometry and catalyzed reporter deposition fluorescence in situ hybridization (CARD-FISH), and phylogenetic identification by 16S RNA gene clone library sequencing and 454 16S amplicon pyrosequencing. Although the microbial abundance was low (<103 cells/ml of snowmelt), concordant results were obtained with the different techniques. The microbial community was mainly composed of members of the Alpha-proteobacteria class (e.g. Kiloniellaceae and Rhodobacteraceae), which is one of the most well-represented bacterial groups in marine habitats, Bacteroidetes (e.g. Cryomorphaceae and Flavobacteriaceae) and Cyanobacteria. Based on our results, polar microorganisms could not only be considered as deposited airborne particles, but as an active component of the snowpack ecology of the High Antarctic Plateau.
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