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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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Priest T, von Appen WJ, Oldenburg E, Popa O, Torres-Valdés S, Bienhold C, Metfies K, Boulton W, Mock T, Fuchs BM, Amann R, Boetius A, Wietz M. Atlantic water influx and sea-ice cover drive taxonomic and functional shifts in Arctic marine bacterial communities. THE ISME JOURNAL 2023; 17:1612-1625. [PMID: 37422598 PMCID: PMC10504371 DOI: 10.1038/s41396-023-01461-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 06/06/2023] [Accepted: 06/15/2023] [Indexed: 07/10/2023]
Abstract
The Arctic Ocean is experiencing unprecedented changes because of climate warming, necessitating detailed analyses on the ecology and dynamics of biological communities to understand current and future ecosystem shifts. Here, we generated a four-year, high-resolution amplicon dataset along with one annual cycle of PacBio HiFi read metagenomes from the East Greenland Current (EGC), and combined this with datasets spanning different spatiotemporal scales (Tara Arctic and MOSAiC) to assess the impact of Atlantic water influx and sea-ice cover on bacterial communities in the Arctic Ocean. Densely ice-covered polar waters harboured a temporally stable, resident microbiome. Atlantic water influx and reduced sea-ice cover resulted in the dominance of seasonally fluctuating populations, resembling a process of "replacement" through advection, mixing and environmental sorting. We identified bacterial signature populations of distinct environmental regimes, including polar night and high-ice cover, and assessed their ecological roles. Dynamics of signature populations were consistent across the wider Arctic; e.g. those associated with dense ice cover and winter in the EGC were abundant in the central Arctic Ocean in winter. Population- and community-level analyses revealed metabolic distinctions between bacteria affiliated with Arctic and Atlantic conditions; the former with increased potential to use bacterial- and terrestrial-derived substrates or inorganic compounds. Our evidence on bacterial dynamics over spatiotemporal scales provides novel insights into Arctic ecology and indicates a progressing Biological Atlantification of the warming Arctic Ocean, with consequences for food webs and biogeochemical cycles.
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Affiliation(s)
- Taylor Priest
- Max Planck Institute for Marine Microbiology, Bremen, 28359, Germany.
| | - Wilken-Jon von Appen
- Physical Oceanography of the Polar Seas, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, 27570, Germany
| | - Ellen Oldenburg
- Institute for Quantitative and Theoretical Biology, Heinrich Heine University Düsseldorf, Düsseldorf, 40225, Germany
| | - Ovidiu Popa
- Institute for Quantitative and Theoretical Biology, Heinrich Heine University Düsseldorf, Düsseldorf, 40225, Germany
| | - Sinhué Torres-Valdés
- Physical Oceanography of the Polar Seas, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, 27570, Germany
| | - Christina Bienhold
- Max Planck Institute for Marine Microbiology, Bremen, 28359, Germany
- Deep-Sea Ecology and Technology, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, 27570, Germany
| | - Katja Metfies
- Polar Biological Oceanography, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, 27570, Germany
| | - William Boulton
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, United Kingdom
- School of Computing Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, United Kingdom
| | - Thomas Mock
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, United Kingdom
| | - Bernhard M Fuchs
- Max Planck Institute for Marine Microbiology, Bremen, 28359, Germany
| | - Rudolf Amann
- Max Planck Institute for Marine Microbiology, Bremen, 28359, Germany
| | - Antje Boetius
- Max Planck Institute for Marine Microbiology, Bremen, 28359, Germany
- Deep-Sea Ecology and Technology, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, 27570, Germany
- MARUM - Center for Marine Environmental Sciences, University of Bremen, Bremen, 28359, Germany
| | - Matthias Wietz
- Max Planck Institute for Marine Microbiology, Bremen, 28359, Germany.
- Deep-Sea Ecology and Technology, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, 27570, Germany.
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Otte A, Winder JC, Deng L, Schmutz J, Jenkins J, Grigoriev IV, Hopes A, Mock T. The diatom Fragilariopsis cylindrus: A model alga to understand cold-adapted life. JOURNAL OF PHYCOLOGY 2023; 59:301-306. [PMID: 36856453 DOI: 10.1111/jpy.13325] [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: 02/17/2023] [Revised: 02/24/2023] [Accepted: 02/24/2023] [Indexed: 05/28/2023]
Abstract
Diatoms are significant primary producers especially in cold, turbulent, and nutrient-rich surface oceans. Hence, they are abundant in polar oceans, but also underpin most of the polar food webs and related biogeochemical cycles. The cold-adapted pennate diatom Fragilariopsis cylindrus is considered a keystone species in polar oceans and sea ice because it can thrive under different environmental conditions if temperatures are low. In this perspective paper, we provide insights into the latest molecular work that has been done on F. cylindrus and discuss its role as a model alga to understand cold-adapted life.
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Affiliation(s)
- Antonia Otte
- School of Environmental Sciences, University of East Anglia, Norwich, UK
| | - Johanna C Winder
- School of Environmental Sciences, University of East Anglia, Norwich, UK
| | - Longji Deng
- School of Environmental Sciences, University of East Anglia, Norwich, UK
| | - Jeremy Schmutz
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, USA
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Jerry Jenkins
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, USA
| | - Igor V Grigoriev
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Amanda Hopes
- School of Environmental Sciences, University of East Anglia, Norwich, UK
| | - Thomas Mock
- School of Environmental Sciences, University of East Anglia, Norwich, UK
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Genetic and Structural Diversity of Prokaryotic Ice-Binding Proteins from the Central Arctic Ocean. Genes (Basel) 2023; 14:genes14020363. [PMID: 36833289 PMCID: PMC9957290 DOI: 10.3390/genes14020363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 01/24/2023] [Accepted: 01/25/2023] [Indexed: 02/01/2023] Open
Abstract
Ice-binding proteins (IBPs) are a group of ecologically and biotechnologically relevant enzymes produced by psychrophilic organisms. Although putative IBPs containing the domain of unknown function (DUF) 3494 have been identified in many taxa of polar microbes, our knowledge of their genetic and structural diversity in natural microbial communities is limited. Here, we used samples from sea ice and sea water collected in the central Arctic Ocean as part of the MOSAiC expedition for metagenome sequencing and the subsequent analyses of metagenome-assembled genomes (MAGs). By linking structurally diverse IBPs to particular environments and potential functions, we reveal that IBP sequences are enriched in interior ice, have diverse genomic contexts and cluster taxonomically. Their diverse protein structures may be a consequence of domain shuffling, leading to variable combinations of protein domains in IBPs and probably reflecting the functional versatility required to thrive in the extreme and variable environment of the central Arctic Ocean.
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The search for ocean solutions. PLoS Biol 2022; 20:e3001860. [PMID: 36251692 PMCID: PMC9576035 DOI: 10.1371/journal.pbio.3001860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
The search for ways to protect and restore ocean health is rapidly accelerating and expanding. A new collection of articles draws on biological and social sciences to suggest changes in how ocean science and conservation are conducted to achieve a sustainable, healthy and inclusive future.
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