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Heinrichs ME, Piedade GJ, Popa O, Sommers P, Trubl G, Weissenbach J, Rahlff J. Breaking the Ice: A Review of Phages in Polar Ecosystems. Methods Mol Biol 2024; 2738:31-71. [PMID: 37966591 DOI: 10.1007/978-1-0716-3549-0_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2023]
Abstract
Bacteriophages, or phages, are viruses that infect and replicate within bacterial hosts, playing a significant role in regulating microbial populations and ecosystem dynamics. However, phages from extreme environments such as polar regions remain relatively understudied due to challenges such as restricted ecosystem access and low biomass. Understanding the diversity, structure, and functions of polar phages is crucial for advancing our knowledge of the microbial ecology and biogeochemistry of these environments. In this review, we will explore the current state of knowledge on phages from the Arctic and Antarctic, focusing on insights gained from -omic studies, phage isolation, and virus-like particle abundance data. Metagenomic studies of polar environments have revealed a high diversity of phages with unique genetic characteristics, providing insights into their evolutionary and ecological roles. Phage isolation studies have identified novel phage-host interactions and contributed to the discovery of new phage species. Virus-like particle abundance and lysis rate data, on the other hand, have highlighted the importance of phages in regulating bacterial populations and nutrient cycling in polar environments. Overall, this review aims to provide a comprehensive overview of the current state of knowledge about polar phages, and by synthesizing these different sources of information, we can better understand the diversity, dynamics, and functions of polar phages in the context of ongoing climate change, which will help to predict how polar ecosystems and residing phages may respond to future environmental perturbations.
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Affiliation(s)
- Mara Elena Heinrichs
- Institute for Chemistry and Biology of the Marine Environment, Carl von Ossietzky University, Oldenburg, Germany
| | - Gonçalo J Piedade
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, 't Horntje, The Netherlands
- Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Amsterdam, The Netherlands
| | - Ovidiu Popa
- Institute of Quantitative and Theoretical Biology Heinrich-Heine University Duesseldorf, Duesseldorf, Germany
| | | | - Gareth Trubl
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Julia Weissenbach
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Department of Biology and Environmental Science, Linnaeus University, Kalmar, Sweden
| | - Janina Rahlff
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Department of Biology and Environmental Science, Linnaeus University, Kalmar, Sweden.
- Aero-Aquatic Virus Research Group, Friedrich Schiller University Jena, Jena, Germany.
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2
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Zhang Z, Liu Y, Zhao W, Ji M. Radiation impacts gene redundancy and biofilm regulation of cryoconite microbiomes in Northern Hemisphere glaciers. MICROBIOME 2023; 11:228. [PMID: 37848997 PMCID: PMC10583317 DOI: 10.1186/s40168-023-01621-y] [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: 04/06/2023] [Accepted: 07/14/2023] [Indexed: 10/19/2023]
Abstract
BACKGROUND Glaciers harbor diverse microorganisms adapted to extreme conditions with high radiation, fluctuating temperature, and low nutrient availability. In glacial ecosystems, cryoconite granules are hotspots of microbial metabolic activity and could influences the biogeochemical cycle on glacier surface. Climate change could influence glacier dynamics by changing regional meteorological factors (e.g., radiation, precipitation, temperature, wind, and evaporation). Moreover, meteorological factors not only influence glacier dynamics but also directly or indirectly influence cryoconite microbiomes. However, the relationship of the meteorological factors and cryoconite microbiome are poorly understood. RESULTS Here, we collected 88 metagenomes from 26 glaciers distributed in the Northern Hemisphere with corresponding public meteorological data to reveal the relationship between meteorological factors and variation of cryoconite microbiome. Our results showed significant differences in taxonomic and genomic characteristics between cryoconite generalists and specialists. Additionally, we found that the biogeography of both generalists and specialists was influenced by solar radiation. Specialists with smaller genome size and lower gene redundancy were more abundant under high radiation stress, implying that streamlined genomes are more adapted to high radiation conditions. Network analysis revealed that biofilm regulation is a ubiquitous function in response to radiation stress, and hub genes were associated with the formation and dispersion of biofilms. CONCLUSION These findings enhance our understanding of glacier cryoconite microbiome variation on a hemispheric scale and indicate the response mechanisms to radiation stress, which will support forecasts of the ecological consequences of future climate change. Video Abstract.
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Affiliation(s)
- Zhihao Zhang
- State Key Laboratory of Tibetan Plateau Earth System, Resources and Environment (TPESRE), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yongqin Liu
- State Key Laboratory of Tibetan Plateau Earth System, Resources and Environment (TPESRE), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- Center for Pan-Third Pole Environment, Lanzhou University, Lanzhou, 730000, China.
| | - Weishu Zhao
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
- SJTU Yazhou Bay Institute of Deepsea Sci-Tech, Yongyou Industrial Park, Sanya, 572024, China
- International Center for Deep Life Investigation (IC-DLI), Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Mukan Ji
- Center for Pan-Third Pole Environment, Lanzhou University, Lanzhou, 730000, China
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3
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Park H, Shah SSA, Korshin G, Angelidaki I, Choo KH. The impact of sunlight on fouling behaviors and microbial communities in membrane bioreactors. J Memb Sci 2023. [DOI: 10.1016/j.memsci.2023.121443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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4
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Buda J, Poniecka EA, Rozwalak P, Ambrosini R, Bagshaw EA, Franzetti A, Klimaszyk P, Nawrot A, Pietryka M, Richter D, Zawierucha K. Is Oxygenation Related to the Decomposition of Organic Matter in Cryoconite Holes? Ecosystems 2021. [DOI: 10.1007/s10021-021-00729-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
AbstractCryoconite is a sediment occurring on glacier surfaces worldwide which reduces ice albedo and concentrates glacier surface meltwater into small reservoirs called cryoconite holes. It consists of mineral and biogenic matter, including active microorganisms. This study presents an experimental insight into the influence of sediment oxygenation on the cryoconite ability to produce and decomposition of organic matter. Samples were collected from five glaciers in the Arctic and the European mainland. Cryoconite from three glaciers was incubated in stagnant and mechanically mixed conditions to imitate inter-hole water–sediment mixing by meltwater occurring on glaciers in Northern Hemisphere, and its effect on oxygen profiles and organic matter content. Moreover, we investigated short-term changes of oxygen conditions in cryoconite from four glaciers in illuminated and dark conditions. An anaerobic zone was present or approaching zero oxygen in all illuminated cryoconite samples, varying in depth depending on the origin of cryoconite: from 1500 µm from Steindalsbreen (Scandinavian Peninsula) and Forni Glacier (The Alps) to 3100 µm from Russell Glacier and Longyearbreen (Arctic) after incubation. Organic matter content varied between glaciers from 6.11% on Longyearbreen to 16.36% on Russell Glacier. The mixed sediment from the Forni Glacier had less organic matter than stagnant, the sediment from Longyearbreen followed this trend, but the difference was not statistically significant, while the sediment from Ebenferner did not differ between groups. Our results have implications for the understanding of biogeochemical processes on glacier surfaces, the adaptation of organisms to changing physical conditions due to abrupt sediment mixing, but also on the estimation of productivity of supraglacial systems.
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Millar JL, Bagshaw EA, Edwards A, Poniecka EA, Jungblut AD. Polar Cryoconite Associated Microbiota Is Dominated by Hemispheric Specialist Genera. Front Microbiol 2021; 12:738451. [PMID: 34899626 PMCID: PMC8660574 DOI: 10.3389/fmicb.2021.738451] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 10/11/2021] [Indexed: 01/04/2023] Open
Abstract
Cryoconite holes, supraglacial depressions containing water and microbe-mineral aggregates, are known to be hotspots of microbial diversity on glacial surfaces. Cryoconite holes form in a variety of locations and conditions, which impacts both their structure and the community that inhabits them. Using high-throughput 16S and 18S rRNA gene sequencing, we have investigated the communities of a wide range of cryoconite holes from 15 locations across the Arctic and Antarctic. Around 24 bacterial and 11 eukaryotic first-rank phyla were observed in total. The various biotic niches (grazer, predator, photoautotroph, and chemotroph), are filled in every location. Significantly, there is a clear divide between the bacterial and microalgal communities of the Arctic and that of the Antarctic. We were able to determine the groups contributing to this difference and the family and genus level. Both polar regions contain a "core group" of bacteria that are present in the majority of cryoconite holes and each contribute >1% of total amplicon sequence variant (ASV) abundance. Whilst both groups contain Microbacteriaceae, the remaining members are specific to the core group of each polar region. Additionally, the microalgal communities of Arctic cryoconite holes are dominated by Chlamydomonas whereas the Antarctic cryoconite holes are dominated by Pleurastrum. Therefore cryoconite holes may be a global feature of glacier landscapes, but they are inhabited by regionally distinct microbial communities. Our results are consistent with the notion that cryoconite microbiomes are adapted to differing conditions within the cryosphere.
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Affiliation(s)
- Jasmin L Millar
- School of Earth and Environmental Sciences, Cardiff University, Cardiff, United Kingdom.,Department of Life Sciences, The Natural History Museum, London, United Kingdom
| | - Elizabeth A Bagshaw
- School of Earth and Environmental Sciences, Cardiff University, Cardiff, United Kingdom
| | - Arwyn Edwards
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Ceredigion, United Kingdom
| | - Ewa A Poniecka
- School of Earth and Environmental Sciences, Cardiff University, Cardiff, United Kingdom
| | - Anne D Jungblut
- Department of Life Sciences, The Natural History Museum, London, United Kingdom
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6
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Park C, Takeuchi N. Unmasking photogranulation in decreasing glacial albedo and net autotrophic wastewater treatment. Environ Microbiol 2021; 23:6391-6404. [PMID: 34545673 PMCID: PMC9292683 DOI: 10.1111/1462-2920.15780] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 09/13/2021] [Accepted: 09/16/2021] [Indexed: 11/29/2022]
Abstract
In both natural and built environments, microbes on occasions manifest in spherical aggregates instead of substratum‐affixed biofilms. These microbial aggregates are conventionally referred to as granules. Cryoconites are mineral rich granules that appear on glacier surfaces and are linked with expanding surface darkening, thus decreasing albedo, and enhanced melt. The oxygenic photogranules (OPGs) are organic rich granules that grow in wastewater, which enables wastewater treatment with photosynthetically produced oxygen and which presents potential for net autotrophic wastewater treatment in a compact system. Despite obvious differences inherent in the two, cryoconite and OPG pose striking resemblance. In both, the order Oscillatoriales in Cyanobacteria envelope inner materials and develop dense spheroidal aggregates. We explore the mechanism of photogranulation on account of high similarity between cryoconites and OPGs. We contend that there is no universal external cause for photogranulation. However, cryoconites and OPGs, as well as their intravariations, which are all under different stress fields, are the outcome of universal physiological processes of the Oscillatoriales interfacing with goldilocks interactions of stresses. Finding the rules of photogranulation may enhance engineering of glacier and wastewater systems to manipulate their ecosystem impacts.
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Affiliation(s)
- Chul Park
- Department of Civil and Environmental Engineering, University of Massachusetts Amherst, Amherst, Massachusetts, 01003, USA
| | - Nozomu Takeuchi
- Department of Earth Sciences, Graduate School of Science, Chiba University, Chiba, 263-8522, Japan
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7
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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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8
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Sommers P, Porazinska DL, Darcy JL, Gendron EMS, Vimercati L, Solon AJ, Schmidt SK. Microbial Species-Area Relationships in Antarctic Cryoconite Holes Depend on Productivity. Microorganisms 2020; 8:E1747. [PMID: 33171740 PMCID: PMC7694949 DOI: 10.3390/microorganisms8111747] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 10/31/2020] [Accepted: 11/02/2020] [Indexed: 01/04/2023] Open
Abstract
The island species-area relationship (ISAR) is a positive association between the number of species and the area of an isolated, island-like habitat. ISARs are ubiquitous across domains of life, yet the processes generating ISARs remain poorly understood, particularly for microbes. Larger and more productive islands are hypothesized to have more species because they support larger populations of each species and thus reduce the probability of stochastic extinctions in small population sizes. Here, we disentangled the effects of "island" size and productivity on the ISAR of Antarctic cryoconite holes. We compared the species richness of bacteria and microbial eukaryotes on two glaciers that differ in their productivity across varying hole sizes. We found that cryoconite holes on the more productive Canada Glacier gained more species with increasing hole area than holes on the less productive Taylor Glacier. Within each glacier, neither productivity nor community evenness explained additional variation in the ISAR. Our results are, therefore, consistent with productivity shaping microbial ISARs at broad scales. More comparisons of microbial ISARs across environments with limited confounding factors, such as cryoconite holes, and experimental manipulations within these systems will further contribute to our understanding of the processes shaping microbial biogeography.
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Affiliation(s)
- Pacifica Sommers
- Department of Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, CO 80309, USA; (L.V.); (A.J.S.); (S.K.S.)
| | - Dorota L. Porazinska
- Department of Entomology and Nematology, University of Florida, Gainesville, FL 32611, USA; (D.L.P.); (E.M.S.G.)
| | - John L. Darcy
- Division of Biomedical Informatics and Personalized Medicine, University of Colorado School of Medicine, Aurora, CO 80045, USA;
| | - Eli M. S. Gendron
- Department of Entomology and Nematology, University of Florida, Gainesville, FL 32611, USA; (D.L.P.); (E.M.S.G.)
| | - Lara Vimercati
- Department of Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, CO 80309, USA; (L.V.); (A.J.S.); (S.K.S.)
| | - Adam J. Solon
- Department of Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, CO 80309, USA; (L.V.); (A.J.S.); (S.K.S.)
| | - Steven K. Schmidt
- Department of Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, CO 80309, USA; (L.V.); (A.J.S.); (S.K.S.)
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9
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Feng L, An Y, Xu J, Li X, Jiang B, Liao Y. Biochemical evolution of dissolved organic matter during snow metamorphism across the ablation season for a glacier on the central Tibetan Plateau. Sci Rep 2020; 10:6123. [PMID: 32273519 PMCID: PMC7145860 DOI: 10.1038/s41598-020-62851-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Accepted: 03/06/2020] [Indexed: 11/10/2022] Open
Abstract
The metamorphism of snow (snowmelt process) has a potential influence on chemical and physical process occurring within it. This study carried out a detailed study on the variation of dissolved organic matter (DOM) in different stages of snowmelt in a typical mountain glacier located at Tibetan Plateau through collecting four different surface snow/ice categories, i.e., fresh snow, fine firn, coarse firn, and granular ice during May to October in 2015. The dissolved organic carbon (DOC) was observed by lost 44% from fresh snow to fine firn and enriched 129% from fine firn to granular ice, reflecting the dynamic variability in DOC concentration during snow metamorphism. The absorbance properties of each snow category are positively correlated with DOC concentration. The result of excitation emission matrix fluorescence with parallel factor analysis (EEM-PARAFAC) and Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) highlighted the domination of lipid- and protein-like compounds in glacial-derived DOM. The molecular composition of the DOM also exhibited a new N-containing molecular formula (CHON classes) that was enriched during snow metamorphism. This study suggests that snow metamorphism could induce a loss of DOM as well as enrich and modify the DOM.
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Affiliation(s)
- Lin Feng
- State Key Laboratory of Cryospheric Science, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, China
- Aba Teachers University, Wenchuan, 623002, China
| | - Yanqing An
- State Key Laboratory of Cryospheric Science, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, China
| | - Jianzhong Xu
- State Key Laboratory of Cryospheric Science, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, China.
| | - Xiaofei Li
- State Key Laboratory of Cryospheric Science, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, China
| | - Bin Jiang
- State Key Laboratory of Organic Geochemistry, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou, 510640, China
| | - Yuhong Liao
- State Key Laboratory of Organic Geochemistry, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou, 510640, China
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10
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Sommers P, Fontenele RS, Kringen T, Kraberger S, Porazinska DL, Darcy JL, Schmidt SK, Varsani A. Single-Stranded DNA Viruses in Antarctic Cryoconite Holes. Viruses 2019; 11:E1022. [PMID: 31689942 PMCID: PMC6893807 DOI: 10.3390/v11111022] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2019] [Revised: 10/28/2019] [Accepted: 10/31/2019] [Indexed: 12/28/2022] Open
Abstract
Antarctic cryoconite holes, or small melt-holes in the surfaces of glaciers, create habitable oases for isolated microbial communities with tightly linked microbial population structures. Viruses may influence the dynamics of polar microbial communities, but the viromes of the Antarctic cryoconite holes have yet to be characterized. We characterize single-stranded DNA (ssDNA) viruses from three cryoconite holes in the Taylor Valley, Antarctica, using metagenomics. Half of the assembled metagenomes cluster with those in the viral family Microviridae (n = 7), and the rest with unclassified circular replication associated protein (Rep)-encoding single-stranded (CRESS) DNA viruses (n = 7). An additional 18 virus-like circular molecules encoding either a Rep, a capsid protein gene, or other unidentified but viral-like open reading frames were identified. The samples from which the genomes were identified show a strong gradient in microbial diversity and abundances, and the number of viral genomes detected in each sample mirror that gradient. Additionally, one of the CRESS genomes assembled here shares ~90% genome-wide pairwise identity with a virus identified from a freshwater pond on the McMurdo Ice Shelf (Antarctica). Otherwise, the similarity of these viruses to those previously identified is relatively low. Together, these patterns are consistent with the presence of a unique regional virome present in fresh water host populations of the McMurdo Dry Valley region.
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Affiliation(s)
- Pacifica Sommers
- Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, CO 80309, USA.
| | - Rafaela S Fontenele
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ 85287-5001, USA.
| | - Tayele Kringen
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ 85287-5001, USA.
| | - Simona Kraberger
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ 85287-5001, USA.
| | - Dorota L Porazinska
- Entomology and Nematology Department, University of Florida, Gainesville, FL 32611, USA.
| | - John L Darcy
- Division of Biomedical Informatics and Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA.
| | - Steven K Schmidt
- Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, CO 80309, USA.
| | - Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ 85287-5001, USA.
- Structural Biology Research Unit, Department of Integrative Biomedical Sciences, University of Cape Town, Observatory, Cape Town 7701, South Africa.
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11
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Sommers P, Porazinska DL, Darcy JL, Zamora F, Fountain AG, Schmidt SK. Experimental cryoconite holes as mesocosms for studying community ecology. Polar Biol 2019. [DOI: 10.1007/s00300-019-02572-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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12
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Chrismas NAM, Williamson CJ, Yallop ML, Anesio AM, Sánchez-Baracaldo P. Photoecology of the Antarctic cyanobacterium Leptolyngbya sp. BC1307 brought to light through community analysis, comparative genomics and in vitro photophysiology. Mol Ecol 2019; 27:5279-5293. [PMID: 30565777 DOI: 10.1111/mec.14953] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Accepted: 10/11/2018] [Indexed: 12/17/2022]
Abstract
Cyanobacteria are important photoautotrophs in extreme environments such as the McMurdo Dry Valleys, Antarctica. Terrestrial Antarctic cyanobacteria experience constant darkness during the winter and constant light during the summer which influences the ability of these organisms to fix carbon over the course of an annual cycle. Here, we present a unique approach combining community structure, genomic and photophysiological analyses to understand adaptation to Antarctic light regimes in the cyanobacterium Leptolyngbya sp. BC1307. We show that Leptolyngbya sp. BC1307 belongs to a clade of cyanobacteria that inhabits near-surface environments in the McMurdo Dry Valleys. Genomic analyses reveal that, unlike close relatives, Leptolyngbya sp. BC1307 lacks the genes necessary for production of the pigment phycoerythrin and is incapable of complimentary chromatic acclimation, while containing several genes responsible for known photoprotective pigments. Photophysiology experiments confirmed Leptolyngbya sp. BC1307 to be tolerant of short-term exposure to high levels of photosynthetically active radiation, while sustained exposure reduced its capacity for photoprotection. As such, Leptolyngbya sp. BC1307 likely exploits low-light microenvironments within cyanobacterial mats in the McMurdo Dry Valleys.
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Affiliation(s)
- Nathan A M Chrismas
- Marine Biological Association of the United Kingdom, The Laboratory, Citadel Hill, Plymouth, UK.,School of Geographical Sciences, University of Bristol, Bristol, UK
| | - Christopher J Williamson
- School of Geographical Sciences, University of Bristol, Bristol, UK.,School of Biological Sciences, Life Sciences Building, University of Bristol, Bristol, UK
| | - Marian L Yallop
- School of Biological Sciences, Life Sciences Building, University of Bristol, Bristol, UK
| | - Alexandre M Anesio
- School of Geographical Sciences, University of Bristol, Bristol, UK.,Department of Environmental Sciences, Aarhus University, Roskilde, Denmark
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13
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Lutz S, Ziolkowski LA, Benning LG. The Biodiversity and Geochemistry of Cryoconite Holes in Queen Maud Land, East Antarctica. Microorganisms 2019; 7:microorganisms7060160. [PMID: 31159414 PMCID: PMC6616603 DOI: 10.3390/microorganisms7060160] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Revised: 05/23/2019] [Accepted: 05/29/2019] [Indexed: 01/27/2023] Open
Abstract
Cryoconite holes are oases of microbial diversity on ice surfaces. In contrast to the Arctic, where during the summer most cryoconite holes are ‘open’, in Continental Antarctica they are most often ‘lidded’ or completely frozen year-round. Thus, they represent ideal systems for the study of microbial community assemblies as well as carbon accumulation, since individual cryoconite holes can be isolated from external inputs for years. Here, we use high-throughput sequencing of the 16S and 18S rRNA genes to describe the bacterial and eukaryotic community compositions in cryoconite holes and surrounding lake, snow, soil and rock samples in Queen Maud Land. We cross correlate our findings with a broad range of geochemical data including for the first time 13C and 14C analyses of Antarctic cryoconites. We show that the geographic location has a larger effect on the distribution of the bacterial community compared to the eukaryotic community. Cryoconite holes are distinct from the local soils in both 13C and 14C and their isotopic composition is different from similar samples from the Arctic. Carbon contents were generally low (≤0.2%) and older (6–10 ky) than the surrounding soils, suggesting that the cryoconite holes are much more isolated from the atmosphere than the soils.
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Affiliation(s)
- Stefanie Lutz
- GFZ German Research Centre for Geosciences, Telegrafenberg, 14473 Potsdam, Germany.
| | - Lori A Ziolkowski
- University of South Carolina, School of the Earth, Ocean and Environment, 701 Sumter St., EWS 617, Columbia, SC 29208, USA.
| | - Liane G Benning
- GFZ German Research Centre for Geosciences, Telegrafenberg, 14473 Potsdam, Germany.
- Department of Earth Sciences, Free University of Berlin, 12249 Berlin, Germany.
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14
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Sommers P, Darcy JL, Porazinska DL, Gendron EMS, Fountain AG, Zamora F, Vincent K, Cawley KM, Solon AJ, Vimercati L, Ryder J, Schmidt SK. Comparison of Microbial Communities in the Sediments and Water Columns of Frozen Cryoconite Holes in the McMurdo Dry Valleys, Antarctica. Front Microbiol 2019; 10:65. [PMID: 30778338 PMCID: PMC6369369 DOI: 10.3389/fmicb.2019.00065] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Accepted: 01/15/2019] [Indexed: 11/13/2022] Open
Abstract
Although cryoconite holes, sediment-filled melt holes on glacier surfaces, appear small and homogenous, their microbial inhabitants may be spatially partitioned. This partitioning could be particularly important for maintaining biodiversity in holes that remain isolated for many years, such as in Antarctica. We hypothesized that cryoconite holes with greater species richness and biomass should exhibit greater partitioning between the sediments and water, promoting greater biodiversity through spatial niche partitioning. We tested this hypothesis by sampling frozen cryoconite holes along a gradient of biomass and biodiversity in the Taylor Valley, Antarctica, where ice-lidded cryoconite holes are a ubiquitous feature of glaciers. We extracted DNA and chlorophyll a from the sediments and water of these samples to describe biodiversity and quantify proxies for biomass. Contrary to our expectation, we found that cryoconite holes with greater richness and biomass showed less partitioning of phylotypes by the sediments versus the water, perhaps indicating that the probability of sediment microbes being mixed into the water is higher from richer sediments. Another explanation may be that organisms from the water were compressed by freezing down to the sediment layer, leaving primarily relic DNA of dead cells to be detected higher in the frozen water. Further evidence of this explanation is that the dominant sequences unique to water closely matched organisms that do not live in cryoconite holes or the Dry Valleys (e.g., vertebrates); so this cryptic biodiversity could represent unknown microbial animals or DNA from atmospheric deposition of dead biomass in the otherwise low-biomass water. Although we cannot rule out spatial niche partitioning occurring at finer scales or in melted cryoconite holes, we found no evidence of partitioning between the sediments and water in frozen holes. Future work should include more sampling of cryoconite holes at a finer spatial scale, and characterizing the communities of the sediments and water when cryoconite holes are melted and active.
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Affiliation(s)
- Pacifica Sommers
- Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, CO, United States
| | - John L Darcy
- Department of Botany, University of Hawai'i Mānoa, Honolulu, HI, United States
| | - Dorota L Porazinska
- Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, CO, United States.,Department of Entomology and Nematology, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL, United States
| | - Eli M S Gendron
- Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, CO, United States
| | - Andrew G Fountain
- Geology Department, Portland State University, Portland, OR, United States
| | - Felix Zamora
- Geology Department, Portland State University, Portland, OR, United States
| | - Kim Vincent
- Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, CO, United States
| | - Kaelin M Cawley
- National Ecological Observatory Network Operated by Battelle, Boulder, CO, United States.,Institute of Arctic and Alpine Research, University of Colorado Boulder, Boulder, CO, United States
| | - Adam J Solon
- Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, CO, United States
| | - Lara Vimercati
- Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, CO, United States
| | - Jenna Ryder
- Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, CO, United States
| | - Steven K Schmidt
- Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, CO, United States
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15
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Darcy JL, King AJ, Gendron EMS, Schmidt SK. Spatial autocorrelation of microbial communities atop a debris-covered glacier is evidence of a supraglacial chronosequence. FEMS Microbiol Ecol 2017; 93:4002671. [PMID: 28830070 DOI: 10.1093/femsec/fix095] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Accepted: 07/14/2017] [Indexed: 12/17/2022] Open
Abstract
Although microbial communities from many glacial environments have been analyzed, microbes living in the debris atop debris-covered glaciers represent an understudied frontier in the cryosphere. The few previous molecular studies of microbes in supraglacial debris have either had limited phylogenetic resolution, limited spatial resolution (e.g. only one sample site on the glacier) or both. Here, we present the microbiome of a debris-covered glacier across all three domains of life, using a spatially-explicit sampling scheme to characterize the Middle Fork Toklat Glacier's microbiome from its terminus to sites high on the glacier. Our results show that microbial communities differ across the supraglacial transect, but surprisingly these communities are strongly spatially autocorrelated, suggesting the presence of a supraglacial chronosequence. This pattern is dominated by phototrophic microbes (both bacteria and eukaryotes) which are less abundant near the terminus and more abundant higher on the glacier. We use these data to refute the hypothesis that the inhabitants of the glacier are randomly deposited atmospheric microbes, and to provide evidence that succession from a predominantly photosynthetic to a more heterotrophic community is occurring on the glacier.
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Affiliation(s)
- John L Darcy
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO 80309, USA
| | - Andrew J King
- King Ecological Consulting, 2504 Scarlett Oak Ct, Knoxville, TN 37909, USA
| | - Eli M S Gendron
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO 80309, USA.,Molecular, Cellular, and Developmental Biology Department, University of Colorado, Boulder, CO 80309, USA
| | - Steven K Schmidt
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO 80309, USA
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16
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Anesio AM, Lutz S, Chrismas NAM, Benning LG. The microbiome of glaciers and ice sheets. NPJ Biofilms Microbiomes 2017; 3:10. [PMID: 28649411 PMCID: PMC5460203 DOI: 10.1038/s41522-017-0019-0] [Citation(s) in RCA: 120] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Revised: 03/17/2017] [Accepted: 03/23/2017] [Indexed: 01/09/2023] Open
Abstract
Glaciers and ice sheets, like other biomes, occupy a significant area of the planet and harbour biological communities with distinct interactions and feedbacks with their physical and chemical environment. In the case of the glacial biome, the biological processes are dominated almost exclusively by microbial communities. Habitats on glaciers and ice sheets with enough liquid water to sustain microbial activity include snow, surface ice, cryoconite holes, englacial systems and the interface between ice and overridden rock/soil. There is a remarkable similarity between the different specific glacial habitats across glaciers and ice sheets worldwide, particularly regarding their main primary producers and ecosystem engineers. At the surface, cyanobacteria dominate the carbon production in aquatic/sediment systems such as cryoconite holes, while eukaryotic Zygnematales and Chlamydomonadales dominate ice surfaces and snow dynamics, respectively. Microbially driven chemolithotrophic processes associated with sulphur and iron cycle and C transformations in subglacial ecosystems provide the basis for chemical transformations at the rock interface under the ice that underpin an important mechanism for the delivery of nutrients to downstream ecosystems. In this review, we focus on the main ecosystem engineers of glaciers and ice sheets and how they interact with their chemical and physical environment. We then discuss the implications of this microbial activity on the icy microbiome to the biogeochemistry of downstream ecosystems.
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Affiliation(s)
- Alexandre M. Anesio
- Bristol Glaciology Centre, School of Geographical Sciences, University of Bristol, Bristol, BS8 1SS UK
| | - Stefanie Lutz
- GFZ German Research Centre for Geosciences, Telegrafenberg, 14473 Potsdam, Germany
| | - Nathan A. M. Chrismas
- Bristol Glaciology Centre, School of Geographical Sciences, University of Bristol, Bristol, BS8 1SS UK
| | - Liane G. Benning
- GFZ German Research Centre for Geosciences, Telegrafenberg, 14473 Potsdam, Germany
- Department of Earth Sciences, Free University of Berlin, 12249 Berlin, Germany
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17
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Chen Y, Li XK, Si J, Wu GJ, Tian LD, Xiang SR. Changes of the Bacterial Abundance and Communities in Shallow Ice Cores from Dunde and Muztagata Glaciers, Western China. Front Microbiol 2016; 7:1716. [PMID: 27847503 PMCID: PMC5088206 DOI: 10.3389/fmicb.2016.01716] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Accepted: 10/13/2016] [Indexed: 02/02/2023] Open
Abstract
In this study, six bacterial community structures were analyzed from the Dunde ice core (9.5-m-long) using 16S rRNA gene cloning library technology. Compared to the Muztagata mountain ice core (37-m-long), the Dunde ice core has different dominant community structures, with five genus-related groups Blastococcus sp./Propionibacterium, Cryobacterium-related., Flavobacterium sp., Pedobacter sp., and Polaromas sp. that are frequently found in the six tested ice layers from 1990 to 2000. Live and total microbial density patterns were examined and related to the dynamics of physical-chemical parameters, mineral particle concentrations, and stable isotopic ratios in the precipitations collected from both Muztagata and Dunde ice cores. The Muztagata ice core revealed seasonal response patterns for both live and total cell density, with high cell density occurring in the warming spring and summer months indicated by the proxy value of the stable isotopic ratios. Seasonal analysis of live cell density for the Dunde ice core was not successful due to the limitations of sampling resolution. Both ice cores showed that the cell density peaks were frequently associated with high concentrations of particles. A comparison of microbial communities in the Dunde and Muztagata glaciers showed that similar taxonomic members exist in the related ice cores, but the composition of the prevalent genus-related groups is largely different between the two geographically different glaciers. This indicates that the micro-biogeography associated with geographic differences was mainly influenced by a few dominant taxonomic groups.
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Affiliation(s)
- Yong Chen
- School of Life Science, Lanzhou University, Lanzhou China
| | - Xiang-Kai Li
- School of Life Science, Lanzhou University, Lanzhou China
| | - Jing Si
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou China
| | - Guang-Jian Wu
- Key Laboratory of Tibetan Environment Changes and Land Surface Processes, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, BeijingChina; Laboratory of Ice Core and Cold Regions Environment, Cold and Arid Regions Environmental and Engineering Research Institute, Chinese Academy of Science, LanzhouChina
| | - Li-De Tian
- Key Laboratory of Tibetan Environment Changes and Land Surface Processes, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, BeijingChina; Laboratory of Ice Core and Cold Regions Environment, Cold and Arid Regions Environmental and Engineering Research Institute, Chinese Academy of Science, LanzhouChina
| | - Shu-Rong Xiang
- School of Life Science, Lanzhou University, LanzhouChina; Key Laboratory of Tibetan Environment Changes and Land Surface Processes, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, BeijingChina; Laboratory of Ice Core and Cold Regions Environment, Cold and Arid Regions Environmental and Engineering Research Institute, Chinese Academy of Science, LanzhouChina
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18
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Elster J, Margesin R, Wagner D, Häggblom M. Editorial: Polar and Alpine Microbiology—Earth's cryobiosphere. FEMS Microbiol Ecol 2016; 93:fiw221. [DOI: 10.1093/femsec/fiw221] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/18/2016] [Indexed: 11/12/2022] Open
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