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Liu Y, Jiao N, Xu Zhong K, Zang L, Zhang R, Xiao X, Shi Y, Zhang Z, Tao Y, Bai L, Gao B, Yang Y, Huang X, Ji M, Liu J, Liu P, Yao T. Diversity and function of mountain and polar supraglacial DNA viruses. Sci Bull (Beijing) 2023; 68:2418-2433. [PMID: 37739838 DOI: 10.1016/j.scib.2023.09.007] [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] [Received: 04/29/2023] [Revised: 05/29/2023] [Accepted: 06/30/2023] [Indexed: 09/24/2023]
Abstract
Mountain and polar glaciers cover 10% of the Earth's surface and are typically extreme environments that challenge life of all forms. Viruses are abundant and active in supraglacial ecosystems and play a crucial role in controlling the supraglacial microbial communities. However, our understanding of virus ecology on glacier surfaces and their potential impacts on downstream ecosystems remains limited. Here, we present the supraglacial virus genome (SgVG) catalog, a 15-fold expanded genomic inventory of 10,840 DNA-virus species from 38 mountain and polar glaciers, spanning habitats such as snow, ice, meltwater, and cryoconite. Supraglacial DNA-viruses were highly specific compared to viruses in other ecosystems yet exhibited low public health risks. Supraglacial viral communities were primarily constrained by habitat, with cryoconite displaying the highest viral activity levels. We observed a prevalence of lytic viruses in all habitats, especially in cryoconite, but a high level of lysogenic viruses in snow and ice. Additionally, we found that supraglacial viruses could be linked to ∼83% of obtained prokaryotic phyla/classes and possessed the genetic potential to promote metabolism and increase cold adaptation, cell mobility, and phenolic carbon use of hosts in hostile environmental conditions using diverse auxiliary metabolic genes. Our results provide the first systematic characterization of the diversity, function, and public health risks evaluation of mountain and polar supraglacial DNA viruses. This understanding of glacial viruses is crucial for function assessments and ecological modeling of glacier ecosystems, especially for the Tibetan Plateau's Mountain glaciers, which support ∼20% of the human populations on Earth.
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Affiliation(s)
- Yongqin Liu
- Center for Pan-third Pole Environment, Lanzhou University, Lanzhou 730000, China; 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 100101, China.
| | - Nianzhi Jiao
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361005, China
| | - Kevin Xu Zhong
- Department of Earth, Ocean, and Atmospheric Sciences, The University of British Columbia, Vancouver V6T 1Z4, Canada
| | - Lin Zang
- 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 100101, China
| | - Rui Zhang
- Institute for Advanced Study, Shenzhen University, Shenzhen 518000, China
| | - Xiang Xiao
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yi Shi
- University of Chinese Academy of Sciences, Beijing 100101, China; CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - 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 100101, China
| | - Ye Tao
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China
| | - Liping Bai
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu 610041, China
| | - Bianli Gao
- Center for Pan-third Pole Environment, Lanzhou University, Lanzhou 730000, China
| | - Yunlan Yang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361005, China
| | - Xingyu Huang
- State Key Laboratory of Tibetan Plateau Earth System, Resources and Environment (TPESRE), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, China
| | - Mukan Ji
- Center for Pan-third Pole Environment, Lanzhou University, Lanzhou 730000, China
| | - Junzhi Liu
- Center for Pan-third Pole Environment, Lanzhou University, Lanzhou 730000, China
| | - Pengfei Liu
- Center for Pan-third Pole Environment, Lanzhou University, Lanzhou 730000, China.
| | - Tandong Yao
- State Key Laboratory of Tibetan Plateau Earth System, Resources and Environment (TPESRE), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, China
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Ruiz-Blas F, Muñoz-Hisado V, Garcia-Lopez E, Moreno A, Bartolomé M, Leunda M, Martinez-Alonso E, Alcázar A, Cid C. The hidden microbial ecosystem in the perennial ice from a Pyrenean ice cave. Front Microbiol 2023; 14:1110091. [PMID: 36778858 PMCID: PMC9909108 DOI: 10.3389/fmicb.2023.1110091] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 01/03/2023] [Indexed: 01/27/2023] Open
Abstract
Over the last years, perennial ice deposits located within caves have awakened interest as places to study microbial communities since they represent unique cryospheric archives of climate change. Since the beginning of the twentieth century, the temperature has gradually increased, and it is estimated that by the end of this century the increase in average temperature could be around 4.0°C. In this context of global warming the ice deposits of the Pyrenean caves are undergoing a significant regression. Among this type of caves, that on the Cotiella Massif in the Southern Pyrenees is one of the southernmost studied in Europe. These types of caves house microbial communities which have so far been barely explored, and therefore their study is necessary. In this work, the microbial communities of the Pyrenean ice cave A294 were identified using metabarcoding techniques. In addition, research work was carried out to analyze how the age and composition of the ice affect the composition of the bacterial and microeukaryotic populations. Finally, the in vivo effect of climate change on the cellular machinery that allow microorganisms to live with increasing temperatures has been studied using proteomic techniques.
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Affiliation(s)
- Fátima Ruiz-Blas
- Centro de Astrobiología (CAB), CSIC-INTA, Madrid, Spain
- Section Geomicrobiology, GFZ German Research Centre for Geosciences, Potsdam, Germany
| | | | | | - Ana Moreno
- Departamento de Procesos Geoambientales y Cambio Global, Instituto Pirenaico de Ecología - CSIC, Zaragoza, Spain
| | - Miguel Bartolomé
- Departamento de Procesos Geoambientales y Cambio Global, Instituto Pirenaico de Ecología - CSIC, Zaragoza, Spain
- Institut für Geologie und Mineralogie, Universität zu Köln, Köln, Germany
| | - Maria Leunda
- Institute of Plant Sciences and Oeschger Centre for Climate Change Research, University of Bern, Bern, Switzerland
- Swiss Federal Research Institute for Forest, Snow and Landscape Research WSL, Zurich, Switzerland
- Department of Plant Biology and Ecology, University of the Basque Country, Leioa, Spain
| | - Emma Martinez-Alonso
- Department of Investigation, Instituto Ramón y Cajal de Investigación Sanitaria, Hospital Ramón y Cajal, Madrid, Spain
| | - Alberto Alcázar
- Department of Investigation, Instituto Ramón y Cajal de Investigación Sanitaria, Hospital Ramón y Cajal, Madrid, Spain
| | - Cristina Cid
- Centro de Astrobiología (CAB), CSIC-INTA, Madrid, Spain
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Garcia-Lopez E, Ruiz-Blas F, Sanchez-Casanova S, Peña Perez S, Martin-Cerezo ML, Cid C. Microbial Communities in Volcanic Glacier Ecosystems. Front Microbiol 2022; 13:825632. [PMID: 35547132 PMCID: PMC9084427 DOI: 10.3389/fmicb.2022.825632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 03/17/2022] [Indexed: 11/13/2022] Open
Abstract
Glaciers constitute a polyextremophilic environment characterized by low temperatures, high solar radiation, a lack of nutrients, and low water availability. However, glaciers located in volcanic regions have special characteristics, since the volcanic foci provide them with heat and nutrients that allow the growth of microbial communities highly adapted to this environment. Most of the studies on these glacial ecosystems have been carried out in volcanic environments in the northern hemisphere, including Iceland and the Pacific Northwest. To better know, the microbial diversity of the underexplored glacial ecosystems and to check what their specific characteristics were, we studied the structure of bacterial communities living in volcanic glaciers in Deception Island, Antarctica, and in the Kamchatka peninsula. In addition to geographic coordinates, many other glacier environmental factors (like volcanic activity, altitude, temperature, pH, or ice chemical composition) that can influence the diversity and distribution of microbial communities were considered in this study. Finally, using their taxonomic assignments, an attempt was made to compare how different or similar are the biogeochemical cycles in which these microbiomes are involved.
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Affiliation(s)
- Eva Garcia-Lopez
- Department of Molecular Evolution, Centro de Astrobiologia (CSIC-INTA), Torrejón de Ardoz, Spain
| | - Fatima Ruiz-Blas
- Department of Molecular Evolution, Centro de Astrobiologia (CSIC-INTA), Torrejón de Ardoz, Spain
| | | | - Sonia Peña Perez
- Department of Molecular Evolution, Centro de Astrobiologia (CSIC-INTA), Torrejón de Ardoz, Spain
| | | | - Cristina Cid
- Department of Molecular Evolution, Centro de Astrobiologia (CSIC-INTA), Torrejón de Ardoz, Spain
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Mondini A, Anwar MZ, Ellegaard-Jensen L, Lavin P, Jacobsen CS, Purcarea C. Heat Shock Response of the Active Microbiome From Perennial Cave Ice. Front Microbiol 2022; 12:809076. [PMID: 35360653 PMCID: PMC8960993 DOI: 10.3389/fmicb.2021.809076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Accepted: 12/28/2021] [Indexed: 11/13/2022] Open
Abstract
Ice caves constitute the newly investigated frozen and secluded model habitats for evaluating the resilience of ice-entrapped microbiomes in response to climate changes. This survey identified the total and active prokaryotic and eukaryotic communities from millennium-old ice accumulated in Scarisoara cave (Romania) using Illumina shotgun sequencing of the ribosomal RNA (rRNA) and messenger RNA (mRNA)-based functional analysis of the metatranscriptome. Also, the response of active microbiome to heat shock treatment mimicking the environmental shift during ice melting was evaluated at both the taxonomic and metabolic levels. The putatively active microbial community was dominated by bacterial taxa belonging to Proteobacteria and Bacteroidetes, which are highly resilient to thermal variations, while the scarcely present archaea belonging to Methanomicrobia was majorly affected by heat shock. Among eukaryotes, the fungal rRNA community was shared between the resilient Chytridiomycota and Blastocladiomycota, and the more sensitive Ascomycota and Basidiomycota taxa. A complex microeukaryotic community highly represented by Tardigrada and Rotifera (Metazoa), Ciliophora and Cercozoa (Protozoa), and Chlorophyta (Plantae) was evidenced for the first time in this habitat. This community showed a quick reaction to heat shock, followed by a partial recovery after prolonged incubation at 4°C due to possible predation processes on the prokaryotic cluster. Analysis of mRNA differential gene expression revealed the presence of an active microbiome in the perennial ice from the Scarisoara cave and associated molecular mechanisms for coping with temperature variations by the upregulation of genes involved in enzyme recovery, energy storage, carbon and nitrogen regulation, and cell motility. This first report on the active microbiome embedded in perennial ice from caves and its response to temperature stress provided a glimpse into the impact of glaciers melting and the resilience mechanisms in this habitat, contributing to the knowledge on the functional role of active microbes in frozen environments and their response to climatic changes.
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Affiliation(s)
- Antonio Mondini
- Department of Microbiology, Institute of Biology, Bucharest, Romania
| | - Muhammad Zohaib Anwar
- Department of Environmental Science, Aarhus University, RISØ Campus, Roskilde, Denmark
- Center for Infectious Disease Genomics and One Health, Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada
| | - Lea Ellegaard-Jensen
- Department of Environmental Science, Aarhus University, RISØ Campus, Roskilde, Denmark
| | - Paris Lavin
- Centre of Biotechnology and Bioengineering (CeBiB), Universidad de Antofagasta, Antofagasta, Chile
- Departamento de Biotecnología, Facultad de Ciencias del Mar y Recursos Biológicos, Universidad de Antofagasta, Antofagasta, Chile
| | - Carsten Suhr Jacobsen
- Department of Environmental Science, Aarhus University, RISØ Campus, Roskilde, Denmark
| | - Cristina Purcarea
- Department of Microbiology, Institute of Biology, Bucharest, Romania
- *Correspondence: Cristina Purcarea,
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