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Hassan S, Mushtaq M, Ganiee SA, Zaman M, Yaseen A, Shah AJ, Ganai BA. Microbial oases in the ice: A state-of-the-art review on cryoconite holes as diversity hotspots and their scientific connotations. ENVIRONMENTAL RESEARCH 2024; 252:118963. [PMID: 38640991 DOI: 10.1016/j.envres.2024.118963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2023] [Revised: 04/13/2024] [Accepted: 04/16/2024] [Indexed: 04/21/2024]
Abstract
Cryoconite holes, small meltwater pools on the surface of glaciers and ice sheets, represent extremely cold ecosystems teeming with diverse microbial life. Cryoconite holes exhibit greater susceptibility to the impacts of climate change, underlining the imperative nature of investigating microbial communities as an essential module of polar and alpine ecosystem monitoring efforts. Microbes in cryoconite holes play a critical role in nutrient cycling and can produce bioactive compounds, holding promise for industrial and pharmaceutical innovation. Understanding microbial diversity in these delicate ecosystems is essential for effective conservation strategies. Therefore, this review discusses the microbial diversity in these extreme environments, aiming to unveil the complexity of their microbial communities. The current study envisages that cryoconite holes as distinctive ecosystems encompass a multitude of taxonomically diverse and functionally adaptable microorganisms that exhibit a rich microbial diversity and possess intricate ecological functions. By investigating microbial diversity and ecological functions of cryoconite holes, this study aims to contribute valuable insights into the broader field of environmental microbiology and enhance further understanding of these ecosystems. This review seeks to provide a holistic overview regarding the formation, evolution, characterization, and molecular adaptations of cryoconite holes. Furthermore, future research directions and challenges underlining the need for long-term monitoring, and ethical considerations in preserving these pristine environments are also provided. Addressing these challenges and resolutely pursuing future research directions promises to enrich our comprehension of microbial diversity within cryoconite holes, revealing the broader ecological and biogeochemical implications. The inferences derived from the present study will provide researchers, ecologists, and policymakers with a profound understanding of the significance and utility of cryoconite holes in unveiling the microbial diversity and its potential applications.
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Affiliation(s)
- Shahnawaz Hassan
- Department of Environmental Science, University of Kashmir, Srinagar, 190006, India.
| | - Misba Mushtaq
- Centre of Research for Development, University of Kashmir, Srinagar, 190006, India
| | - Shahid Ahmad Ganiee
- Department of Environmental Science, University of Kashmir, Srinagar, 190006, India
| | - Muzafar Zaman
- Department of Environmental Science, University of Kashmir, Srinagar, 190006, India
| | - Aarif Yaseen
- Department of Environmental Science, University of Kashmir, Srinagar, 190006, India
| | - Abdul Jalil Shah
- Department of Pharmaceutical Sciences, University of Kashmir, Srinagar, 190006, India
| | - Bashir Ahmad Ganai
- Centre of Research for Development, University of Kashmir, Srinagar, 190006, India.
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Männistö MK, Ahonen SHK, Ganzert L, Tiirola M, Stark S, Häggblom MM. Bacterial and fungal communities in sub-Arctic tundra heaths are shaped by contrasting snow accumulation and nutrient availability. FEMS Microbiol Ecol 2024; 100:fiae036. [PMID: 38549428 PMCID: PMC10996926 DOI: 10.1093/femsec/fiae036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 02/26/2024] [Accepted: 03/27/2024] [Indexed: 04/06/2024] Open
Abstract
Climate change is affecting winter snow conditions significantly in northern ecosystems but the effects of the changing conditions for soil microbial communities are not well-understood. We utilized naturally occurring differences in snow accumulation to understand how the wintertime subnivean conditions shape bacterial and fungal communities in dwarf shrub-dominated sub-Arctic Fennoscandian tundra sampled in mid-winter, early, and late growing season. Phospholipid fatty acid (PLFA) and quantitative PCR analyses indicated that fungal abundance was higher in windswept tundra heaths with low snow accumulation and lower nutrient availability. This was associated with clear differences in the microbial community structure throughout the season. Members of Clavaria spp. and Sebacinales were especially dominant in the windswept heaths. Bacterial biomass proxies were higher in the snow-accumulating tundra heaths in the late growing season but there were only minor differences in the biomass or community structure in winter. Bacterial communities were dominated by members of Alphaproteobacteria, Actinomycetota, and Acidobacteriota and were less affected by the snow conditions than the fungal communities. The results suggest that small-scale spatial patterns in snow accumulation leading to a mosaic of differing tundra heath vegetation shapes bacterial and fungal communities as well as soil carbon and nutrient availability.
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Affiliation(s)
- Minna K Männistö
- Natural Resources Institute Finland, Ounasjoentie 6, FI-96200 Rovaniemi, Finland
| | - Saija H K Ahonen
- Ecology and Genetics Research Unit, University of Oulu, Pentti Kaiteran katu 1, FI-90014 Oulu, Finland
| | - Lars Ganzert
- Natural Resources Institute Finland, Ounasjoentie 6, FI-96200 Rovaniemi, Finland
- Plankton and Microbial Ecology, Leibniz Institute of Freshwater Ecology and Inland Fisheries, Zur alten Fischerhütte 2, 16775 Stechlin, Germany
| | - Marja Tiirola
- Department of Biological and Environmental Science, University of Jyväskylä, Survontie 9, FI-40014 Jyväskylä, Finland
| | - Sari Stark
- Arctic Centre, University of Lapland, Pohjoisranta 4, Fl-96101 Rovaniemi, Finland
| | - Max M Häggblom
- Natural Resources Institute Finland, Ounasjoentie 6, FI-96200 Rovaniemi, Finland
- Department of Biochemistry and Microbiology, Rutgers University, 76 Lipman Drive, New Brunswick, NJ 08901, United States
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Distinct Growth Responses of Tundra Soil Bacteria to Short-Term and Long-Term Warming. Appl Environ Microbiol 2023; 89:e0154322. [PMID: 36847530 PMCID: PMC10056963 DOI: 10.1128/aem.01543-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2023] Open
Abstract
Increases in Arctic temperatures have thawed permafrost and accelerated tundra soil microbial activity, releasing greenhouse gases that amplify climate warming. Warming over time has also accelerated shrub encroachment in the tundra, altering plant input abundance and quality, and causing further changes to soil microbial processes. To better understand the effects of increased temperature and the accumulated effects of climate change on soil bacterial activity, we quantified the growth responses of individual bacterial taxa to short-term warming (3 months) and long-term warming (29 years) in moist acidic tussock tundra. Intact soil was assayed in the field for 30 days using 18O-labeled water, from which taxon-specific rates of 18O incorporation into DNA were estimated as a proxy for growth. Experimental treatments warmed the soil by approximately 1.5°C. Short-term warming increased average relative growth rates across the assemblage by 36%, and this increase was attributable to emergent growing taxa not detected in other treatments that doubled the diversity of growing bacteria. However, long-term warming increased average relative growth rates by 151%, and this was largely attributable to taxa that co-occurred in the ambient temperature controls. There was also coherence in relative growth rates within broad taxonomic levels with orders tending to have similar growth rates in all treatments. Growth responses tended to be neutral in short-term warming and positive in long-term warming for most taxa and phylogenetic groups co-occurring across treatments regardless of phylogeny. Taken together, growing bacteria responded distinctly to short-term and long-term warming, and taxa growing in each treatment exhibited deep phylogenetic organization. IMPORTANCE Soil carbon stocks in the tundra and underlying permafrost have become increasingly vulnerable to microbial decomposition due to climate change. The microbial responses to Arctic warming must be understood in order to predict the effects of future microbial activity on carbon balance in a warming Arctic. In response to our warming treatments, tundra soil bacteria grew faster, consistent with increased rates of decomposition and carbon flux to the atmosphere. Our findings suggest that bacterial growth rates may continue to increase in the coming decades as faster growth is driven by the accumulated effects of long-term warming. Observed phylogenetic organization of bacterial growth rates may also permit taxonomy-based predictions of bacterial responses to climate change and inclusion into ecosystem models.
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Lee RM, Griffin N, Jones E, Abbott BW, Frei RJ, Bratsman S, Proteau M, Errigo IM, Shogren A, Bowden WB, Zarnetske JP, Aanderud ZT. Bacterioplankton dispersal and biogeochemical function across Alaskan Arctic catchments. Environ Microbiol 2022; 24:5690-5706. [PMID: 36273269 DOI: 10.1111/1462-2920.16259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Accepted: 10/21/2022] [Indexed: 01/12/2023]
Abstract
In Arctic catchments, bacterioplankton are dispersed through soils and streams, both of which freeze and thaw/flow in phase, seasonally. To characterize this dispersal and its potential impact on biogeochemistry, we collected bacterioplankton and measured stream physicochemistry during snowmelt and after vegetation senescence across multiple stream orders in alpine, tundra, and tundra-dominated-by-lakes catchments. In all catchments, differences in community composition were associated with seasonal thaw, then attachment status (i.e. free floating or sediment associated), and then stream order. Bacterioplankton taxonomic diversity and richness were elevated in sediment-associated fractions and in higher-order reaches during snowmelt. Families Chthonomonadaceae, Pyrinomonadaceae, and Xiphinematobacteraceae were abundantly different across seasons, while Flavobacteriaceae and Microscillaceae were abundantly different between free-floating and sediment-associated fractions. Physicochemical data suggested there was high iron (Fe+ ) production (alpine catchment); Fe+ production and chloride (Cl- ) removal (tundra catchment); and phosphorus (SRP) removal and ammonium (NH4 + ) production (lake catchment). In tundra landscapes, these 'hot spots' of Fe+ production and Cl- removal accompanied shifts in species richness, while SRP promoted the antecedent community. Our findings suggest that freshet increases bacterial dispersal from headwater catchments to receiving catchments, where bacterioplankton-mineral relations stabilized communities in free-flowing reaches, but bacterioplankton-nutrient relations stabilized those punctuated by lakes.
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Affiliation(s)
- Raymond M Lee
- Department of Plant and Wildlife Sciences, Brigham Young University, Provo, Utah, USA
| | - Natasha Griffin
- College of Earth, Ocean, and Atmospheric Sciences, Oregon State University, Corvalis, Oregon, USA
| | - Erin Jones
- Department of Plant and Wildlife Sciences, Brigham Young University, Provo, Utah, USA
| | - Benjamin W Abbott
- Department of Plant and Wildlife Sciences, Brigham Young University, Provo, Utah, USA
| | - Rebecca J Frei
- Department of Renewable Resources, University of Alberta, Edmonton, Alberta, Canada
| | - Samuel Bratsman
- Department of Plant and Wildlife Sciences, Brigham Young University, Provo, Utah, USA
| | - Mary Proteau
- Department of Plant and Wildlife Sciences, Brigham Young University, Provo, Utah, USA
| | - Isabella M Errigo
- Department of Plant and Wildlife Sciences, Brigham Young University, Provo, Utah, USA
| | - Arial Shogren
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, Alabama, USA
| | - William B Bowden
- The Rubenstein School of Environment and Natural Resources, University of Vermont, Burlington, Vermont, USA
| | - Jay P Zarnetske
- Department of Earth and Environmental Sciences, Michigan State University, East Lansing, Michigan, USA
| | - Zachary T Aanderud
- Department of Plant and Wildlife Sciences, Brigham Young University, Provo, Utah, USA
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Altshuler I, Raymond-Bouchard I, Magnuson E, Tremblay J, Greer CW, Whyte LG. Unique high Arctic methane metabolizing community revealed through in situ 13CH 4-DNA-SIP enrichment in concert with genome binning. Sci Rep 2022; 12:1160. [PMID: 35064149 PMCID: PMC8782848 DOI: 10.1038/s41598-021-04486-z] [Citation(s) in RCA: 4] [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: 07/19/2021] [Accepted: 11/30/2021] [Indexed: 12/15/2022] Open
Abstract
Greenhouse gas (GHG) emissions from Arctic permafrost soils create a positive feedback loop of climate warming and further GHG emissions. Active methane uptake in these soils can reduce the impact of GHG on future Arctic warming potential. Aerobic methane oxidizers are thought to be responsible for this apparent methane sink, though Arctic representatives of these organisms have resisted culturing efforts. Here, we first used in situ gas flux measurements and qPCR to identify relative methane sink hotspots at a high Arctic cytosol site, we then labeled the active microbiome in situ using DNA Stable Isotope Probing (SIP) with heavy 13CH4 (at 100 ppm and 1000 ppm). This was followed by amplicon and metagenome sequencing to identify active organisms involved in CH4 metabolism in these high Arctic cryosols. Sequencing of 13C-labeled pmoA genes demonstrated that type II methanotrophs (Methylocapsa) were overall the dominant active methane oxidizers in these mineral cryosols, while type I methanotrophs (Methylomarinovum) were only detected in the 100 ppm SIP treatment. From the SIP-13C-labeled DNA, we retrieved nine high to intermediate quality metagenome-assembled genomes (MAGs) belonging to the Proteobacteria, Gemmatimonadetes, and Chloroflexi, with three of these MAGs containing genes associated with methanotrophy. A novel Chloroflexi MAG contained a mmoX gene along with other methane oxidation pathway genes, identifying it as a potential uncultured methane oxidizer. This MAG also contained genes for copper import, synthesis of biopolymers, mercury detoxification, and ammonia uptake, indicating that this bacterium is strongly adapted to conditions in active layer permafrost and providing new insights into methane biogeochemical cycling. In addition, Betaproteobacterial MAGs were also identified as potential cross-feeders with methanotrophs in these Arctic cryosols. Overall, in situ SIP labeling combined with metagenomics and genome binning demonstrated to be a useful tool for discovering and characterizing novel organisms related to specific microbial functions or biogeochemical cycles of interest. Our findings reveal a unique and active Arctic cryosol microbial community potentially involved in CH4 cycling.
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Affiliation(s)
- Ianina Altshuler
- Department of Natural Resource Sciences, McGill University, 21,111 Lakeshore Rd., Ste. Anne de Bellevue, QC, H9X 3V9, Canada.
- Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences NMBU, Universitetstunet 3, 1430, Ås, Norway.
| | - Isabelle Raymond-Bouchard
- Department of Natural Resource Sciences, McGill University, 21,111 Lakeshore Rd., Ste. Anne de Bellevue, QC, H9X 3V9, Canada
| | - Elisse Magnuson
- Department of Natural Resource Sciences, McGill University, 21,111 Lakeshore Rd., Ste. Anne de Bellevue, QC, H9X 3V9, Canada
| | - Julien Tremblay
- Energy, Mining and Environment Research Centre, National Research Council of Canada, 6100 Royalmount Ave., Montreal, QC, H4P 2R2, Canada
| | - Charles W Greer
- Department of Natural Resource Sciences, McGill University, 21,111 Lakeshore Rd., Ste. Anne de Bellevue, QC, H9X 3V9, Canada
- Energy, Mining and Environment Research Centre, National Research Council of Canada, 6100 Royalmount Ave., Montreal, QC, H4P 2R2, Canada
| | - Lyle G Whyte
- Department of Natural Resource Sciences, McGill University, 21,111 Lakeshore Rd., Ste. Anne de Bellevue, QC, H9X 3V9, Canada
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Varliero G, Rafiq M, Singh S, Summerfield A, Sgouridis F, Cowan DA, Barker G. Microbial characterisation and Cold-Adapted Predicted Protein (CAPP) database construction from the active layer of Greenland's permafrost. FEMS Microbiol Ecol 2021; 97:fiab127. [PMID: 34468725 PMCID: PMC8445667 DOI: 10.1093/femsec/fiab127] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 08/30/2021] [Indexed: 11/29/2022] Open
Abstract
Permafrost represents a reservoir for the biodiscovery of cold-adapted proteins which are advantageous in industrial and medical settings. Comparisons between different thermo-adapted proteins can give important information for cold-adaptation bioengineering. We collected permafrost active layer samples from 34 points along a proglacial transect in southwest Greenland. We obtained a deep read coverage assembly (>164x) from nanopore and Illumina sequences for the purposes of i) analysing metagenomic and metatranscriptomic trends of the microbial community of this area, and ii) creating the Cold-Adapted Predicted Protein (CAPP) database. The community showed a similar taxonomic composition in all samples along the transect, with a solid permafrost-shaped community, rather than microbial trends typical of proglacial systems. We retrieved 69 high- and medium-quality metagenome-assembled clusters, 213 complete biosynthetic gene clusters and more than three million predicted proteins. The latter constitute the CAPP database that can provide cold-adapted protein sequence information for protein- and taxon-focused amino acid sequence modifications for the future bioengineering of cold-adapted enzymes. As an example, we focused on the enzyme polyphenol oxidase, and demonstrated how sequence variation information could inform its protein engineering.
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Affiliation(s)
- Gilda Varliero
- School of Life Sciences, University of Bristol, 24 Tyndall Ave, Bristol BS8 1TQ, United Kingdom
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Natural Sciences 2 Building, Private Bag X20, Hatfield 0028, South Africa
| | - Muhammad Rafiq
- Department of Microbiology, Faculty of Life Sciences and Informatics, Balochistan University of Information Technology, Engineering and Management Sciences, Airport Road, Baleli, Quetta, Balochistan, Pakistan
- School of Geographical Sciences, University of Bristol, Wills Memorial Building, Bristol BS8 1RL, United Kingdom
| | - Swati Singh
- School of Life Sciences, University of Bristol, 24 Tyndall Ave, Bristol BS8 1TQ, United Kingdom
- School of Chemistry, University of Bristol, Cantock's Cl, Bristol BS8 1TS, United Kingdom
| | - Annabel Summerfield
- School of Life Sciences, University of Bristol, 24 Tyndall Ave, Bristol BS8 1TQ, United Kingdom
| | - Fotis Sgouridis
- School of Geographical Sciences, University of Bristol, Wills Memorial Building, Bristol BS8 1RL, United Kingdom
| | - Don A Cowan
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Natural Sciences 2 Building, Private Bag X20, Hatfield 0028, South Africa
| | - Gary Barker
- School of Life Sciences, University of Bristol, 24 Tyndall Ave, Bristol BS8 1TQ, United Kingdom
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Xue Y, Jonassen I, Øvreås L, Taş N. Metagenome-assembled genome distribution and key functionality highlight importance of aerobic metabolism in Svalbard permafrost. FEMS Microbiol Ecol 2020; 96:5821278. [PMID: 32301987 PMCID: PMC7174036 DOI: 10.1093/femsec/fiaa057] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 04/09/2020] [Indexed: 12/17/2022] Open
Abstract
Permafrost underlies a large portion of the land in the Northern Hemisphere. It is proposed to be an extreme habitat and home for cold-adaptive microbial communities. Upon thaw permafrost is predicted to exacerbate increasing global temperature trend, where awakening microbes decompose millennia old carbon stocks. Yet our knowledge on composition, functional potential and variance of permafrost microbiome remains limited. In this study, we conducted a deep comparative metagenomic analysis through a 2 m permafrost core from Svalbard, Norway to determine key permafrost microbiome in this climate sensitive island ecosystem. To do so, we developed comparative metagenomics methods on metagenomic-assembled genomes (MAG). We found that community composition in Svalbard soil horizons shifted markedly with depth: the dominant phylum switched from Acidobacteria and Proteobacteria in top soils (active layer) to Actinobacteria, Bacteroidetes, Chloroflexi and Proteobacteria in permafrost layers. Key metabolic potential propagated through permafrost depths revealed aerobic respiration and soil organic matter decomposition as key metabolic traits. We also found that Svalbard MAGs were enriched in genes involved in regulation of ammonium, sulfur and phosphate. Here, we provide a new perspective on how permafrost microbiome is shaped to acquire resources in competitive and limited resource conditions of deep Svalbard soils.
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Affiliation(s)
- Yaxin Xue
- Computational Biology Unit, Department of Informatics, University of Bergen,Thormøhlensgt 55 N-5008, Bergen, Norway
| | - Inge Jonassen
- Computational Biology Unit, Department of Informatics, University of Bergen,Thormøhlensgt 55 N-5008, Bergen, Norway
| | - Lise Øvreås
- Department of Biological Sciences, University of Bergen, Thormøhlensgt 53 N-5020, Bergen, Norway.,University Center in Svalbard, UNIS, N-9171, Longyearbyen, Norway
| | - Neslihan Taş
- Ecology Department, Earth and Environmental Sciences Area, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA.,Environmental Genomics and Systems Biology, Biosciences Area, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
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Cary C, Cowan DA, McMinn A, Häggblom MM. Editorial: Thematic issue on polar and alpine microbiology. FEMS Microbiol Ecol 2020; 96:5875089. [PMID: 32697840 DOI: 10.1093/femsec/fiaa136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 07/07/2020] [Indexed: 11/12/2022] Open
Affiliation(s)
- Craig Cary
- International Centre for Terrestrial Antarctic Research, University of Waikato - Te Whare Wānanga o Waikato, Hamilton 3240, New Zealand
| | - Don A Cowan
- Centre for Microbial Ecology and Genomics, University of Pretoria, Hatfield 0028, Pretoria, South Africa
| | - Andrew McMinn
- Institute for Marine and Antarctic Studies, College of Science and Engineering, University of Tasmania, Battery Point, Tasmania, Australia
| | - Max M Häggblom
- Department of Biochemistry and Microbiology, School of Environmental and Biological Sciences, Rutgers University, New Brunswick, NJ 08901, USA
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