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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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Darham S, Zakaria NN, Zulkharnain A, Sabri S, Khalil KA, Merican F, Gomez-Fuentes C, Lim S, Ahmad SA. Antarctic heavy metal pollution and remediation efforts: state of the art of research and scientific publications. Braz J Microbiol 2023; 54:2011-2026. [PMID: 36973583 PMCID: PMC10485231 DOI: 10.1007/s42770-023-00949-9] [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: 07/09/2022] [Accepted: 03/09/2023] [Indexed: 03/29/2023] Open
Abstract
In Antarctica, human activities have been reported to be the major cause of the accumulation of heavy metal contaminants. A comprehensive bibliometric analysis of publications on heavy metal contamination in Antarctica from year 2000 to 2020 was performed to obtain an overview of the current landscape in this line of research. A total of 106 documents were obtained from Scopus, the largest citation database. Extracted data were analysed, and VOSviewer software was used to visualise trends. The result showed an increase in publications and citations in the past 20 years indicating the rising interest on heavy metal contamination in the Antarctic region. Based on the analysis of keywords, the publications largely discuss various types of heavy metals found in the Antarctic water and sediment. The analysis on subject areas detects multiple disciplines involved, wherein the environmental science was well-represented. The top countries and authors producing the most publication in this field were from Australia, China, Brazil and Chile. Numerous efforts have been exercised to investigate heavy metal pollution and its mitigation approaches in the region in the past decades. This paper not only is relevant for scholars to understand the development status and trends in this field but also offers clear insights on the future direction of Antarctic heavy metal contamination and remediation research.
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Affiliation(s)
- Syazani Darham
- Faculty of Biotechnology and Biomolecular Sciences, Department of Biochemistry, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
| | - Nur Nadhirah Zakaria
- Faculty of Biotechnology and Biomolecular Sciences, Department of Biochemistry, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
| | - Azham Zulkharnain
- Department of Bioscience and Engineering, College of Systems Engineering and Science, Shibaura Institute of Technology, 307 Fukasaku, Minuma-Ku, Saitama, 337-8570, Japan
| | - Suriana Sabri
- Faculty of Biotechnology and Biomolecular Sciences, Department of Microbiology, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
| | - Khalilah Abdul Khalil
- Faculty of Applied Sciences, School of Biology, Universiti Teknologi MARA, 40450, Shah Alam, Selangor, Malaysia
| | - Faradina Merican
- School of Biological Sciences, Universiti Sains Malaysia, 11800, Minden, Pulai Pinang, Malaysia
| | - Claudio Gomez-Fuentes
- Department of Chemical Engineering, Universidad de Magallanes, Avda. Bulnes 01855, Punta Arenas, Chile
- Center for Research and Antarctic Environmental Monitoring (CIMAA), Universidad de Magallanes, Avda. Bulnes 01855, Punta Arenas, Chile
| | - Sooa Lim
- Department of Pharmaceutical Engineering, Hoseo University, Asan-Si 31499, Chungnam, Republic of Korea
| | - Siti Aqlima Ahmad
- Faculty of Biotechnology and Biomolecular Sciences, Department of Biochemistry, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia.
- Center for Research and Antarctic Environmental Monitoring (CIMAA), Universidad de Magallanes, Avda. Bulnes 01855, Punta Arenas, Chile.
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Effects of Diesel, Heavy Metals and Plastics Pollution on Penguins in Antarctica: A Review. Animals (Basel) 2021; 11:ani11092505. [PMID: 34573474 PMCID: PMC8465831 DOI: 10.3390/ani11092505] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 08/19/2021] [Accepted: 08/23/2021] [Indexed: 11/16/2022] Open
Abstract
Simple Summary Antarctica is contaminated by anthropogenic pollution. Due to the persistent low temperatures, the toxic impacts of pollution to the environment can be extensive. The severity of the effects varies according to the animal species, chemical type and level of exposure. Penguins are at major risk as they are the most prominent group of animals in Antarctica. This review highlights the background of penguins in Antarctica, the anthropogenic pollution and cases, as well as the toxic effects of diesel, heavy metals and microplastics toward penguins. A bibliometric analysis is also included. Abstract Antarctica is a relatively pristine continent that attracts scientists and tourists alike. However, the risk of environmental pollution in Antarctica is increasing with the increase in the number of visitors. Recently, there has been a surge in interest regarding diesel, heavy metals and microplastics pollution. Contamination from these pollutants poses risks to the environment and the health of organisms inhabiting the continent. Penguins are one of the most prominent and widely distributed animals in Antarctica and are at major risk due to pollution. Even on a small scale, the impacts of pollution toward penguin populations are extensive. This review discusses the background of penguins in Antarctica, the anthropogenic pollution and cases, as well as the impacts of diesel, heavy metals and microplastics toxicities on penguins. The trends of the literature for the emerging risks of these pollutants are also reviewed through a bibliometric approach and network mapping analysis. A sum of 27 articles are analyzed on the effects of varying pollutants on penguins in Antarctica from 2000 to 2020 using the VOSviewer bibliometric software, Microsoft Excel and Tableau Public. Research articles collected from the Scopus database are evaluated for the most applicable research themes according to the bibliometric indicators (articles, geography distribution, annual production, integrated subject areas, key source journals and keyword or term interactions). Although bibliometric studies on the present research theme are not frequent, our results are sub-optimal due to the small number of search query matches from the Scopus database. As a result, our findings offer only a fragmentary comprehension of the topics in question. Nevertheless, this review provides valuable inputs regarding prospective research avenues for researchers to pursue in the future.
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Evans C, Brandsma J, Meredith MP, Thomas DN, Venables HJ, Pond DW, Brussaard CPD. Shift from Carbon Flow through the Microbial Loop to the Viral Shunt in Coastal Antarctic Waters during Austral Summer. Microorganisms 2021; 9:460. [PMID: 33672195 PMCID: PMC7927135 DOI: 10.3390/microorganisms9020460] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 02/17/2021] [Accepted: 02/18/2021] [Indexed: 11/30/2022] Open
Abstract
The relative flow of carbon through the viral shunt and the microbial loop is a pivotal factor controlling the contribution of secondary production to the food web and to rates of nutrient remineralization and respiration. The current study examines the significance of these processes in the coastal waters of the Antarctic during the productive austral summer months. Throughout the study a general trend towards lower bacterioplankton and heterotrophic nanoflagellate (HNF) abundances was observed, whereas virioplankton concentration increased. A corresponding decline of HNF grazing rates and shift towards viral production, indicative of viral infection, was measured. Carbon flow mediated by HNF grazing decreased by more than half from 5.7 µg C L-1 day-1 on average in December and January to 2.4 µg C L-1 day-1 in February. Conversely, carbon flow through the viral shunt increased substantially over the study from on average 0.9 µg C L-1 day-1 in December to 7.6 µg C L-1 day-1 in February. This study shows that functioning of the coastal Antarctic microbial community varied considerably over the productive summer months. In early summer, the system favors transfer of matter and energy to higher trophic levels via the microbial loop, however towards the end of summer carbon flow is redirected towards the viral shunt, causing a switch towards more recycling and therefore increased respiration and regeneration.
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Affiliation(s)
- Claire Evans
- Royal Netherlands Institute for Sea Research, P.O. Box 59, Den Burg, 1790 AB Texel, The Netherlands; (J.B.); (C.P.D.B.)
- Ocean BioGeosciences, National Oceanography Centre, Southampton, European Way, Southampton SO14 3ZH, UK
| | - Joost Brandsma
- Royal Netherlands Institute for Sea Research, P.O. Box 59, Den Burg, 1790 AB Texel, The Netherlands; (J.B.); (C.P.D.B.)
- Austere Environments Consortium for Enhanced Sepsis Outcomes, Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20814, USA
| | - Michael P. Meredith
- British Antarctic Survey, Natural Environmental Research Council, High Cross, Madingley Road, Cambridge CB3 0ET, UK; (M.P.M.); (H.J.V.); (D.W.P.)
| | - David N. Thomas
- Ecosystems & Environment, Faculty of Biological and Environmental Sciences, University of Helsinki, 00014 Helsinki, Finland;
| | - Hugh J. Venables
- British Antarctic Survey, Natural Environmental Research Council, High Cross, Madingley Road, Cambridge CB3 0ET, UK; (M.P.M.); (H.J.V.); (D.W.P.)
| | - David W. Pond
- British Antarctic Survey, Natural Environmental Research Council, High Cross, Madingley Road, Cambridge CB3 0ET, UK; (M.P.M.); (H.J.V.); (D.W.P.)
- Faculty of Natural Sciences, University of Stirling, Stirling FK9 4LA, UK
| | - Corina P. D. Brussaard
- Royal Netherlands Institute for Sea Research, P.O. Box 59, Den Burg, 1790 AB Texel, The Netherlands; (J.B.); (C.P.D.B.)
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Significance of Viral Activity for Regulating Heterotrophic Prokaryote Community Dynamics along a Meridional Gradient of Stratification in the Northeast Atlantic Ocean. Viruses 2020; 12:v12111293. [PMID: 33198110 PMCID: PMC7696675 DOI: 10.3390/v12111293] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 11/05/2020] [Accepted: 11/09/2020] [Indexed: 11/17/2022] Open
Abstract
How microbial populations interact influences the availability and flux of organic carbon in the ocean. Understanding how these interactions vary over broad spatial scales is therefore a fundamental aim of microbial oceanography. In this study, we assessed variations in the abundances, production, virus and grazing induced mortality of heterotrophic prokaryotes during summer along a meridional gradient in stratification in the North Atlantic Ocean. Heterotrophic prokaryote abundance and activity varied with phytoplankton biomass, while the relative distribution of prokaryotic subpopulations (ratio of high nucleic acid fluorescent (HNA) and low nucleic acid fluorescent (LNA) cells) was significantly correlated to phytoplankton mortality mode (i.e., viral lysis to grazing rate ratio). Virus-mediate morality was the primary loss process regulating the heterotrophic prokaryotic communities (average 55% of the total mortality), which may be attributed to the strong top-down regulation of the bacterivorous protozoans. Host availability, encounter rate, and HNA:LNA were important factors regulating viral dynamics. Conversely, the abundance and activity of bacterivorous protozoans were largely regulated by temperature and turbulence. The ratio of total microbial mediated mortality to total available prokaryote carbon reveals that over the latitudinal gradient the heterotrophic prokaryote community gradually moved from a near steady state system regulated by high turnover in subtropical region to net heterotrophic production in the temperate region.
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Antarctic phytoplankton community composition and size structure: importance of ice type and temperature as regulatory factors. Polar Biol 2019. [DOI: 10.1007/s00300-019-02576-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Alcamán-Arias ME, Farías L, Verdugo J, Alarcón-Schumacher T, Díez B. Microbial activity during a coastal phytoplankton bloom on the Western Antarctic Peninsula in late summer. FEMS Microbiol Lett 2019; 365:4961137. [PMID: 29788084 DOI: 10.1093/femsle/fny090] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Accepted: 04/03/2018] [Indexed: 12/19/2022] Open
Abstract
Phytoplankton biomass during the austral summer is influenced by freezing and melting cycles as well as oceanographic processes that enable nutrient redistribution in the West Antarctic Peninsula (WAP). Microbial functional capabilities, metagenomic and metatranscriptomic activities as well as inorganic 13C- and 15N-assimilation rates were studied in the surface waters of Chile Bay during two contrasting summer periods in 2014. Concentrations of Chlorophyll a (Chla) varied from 0.3 mg m-3 in February to a maximum of 2.5 mg m-3 in March, together with a decrease in nutrients; however, nutrients were never depleted. The microbial community composition remained similar throughout both sampling periods; however, microbial abundance and activity changed with Chla levels. An increased biomass of Bacillariophyta, Haptophyceae and Cryptophyceae was observed along with night-grazing activity of Dinophyceae and ciliates (Alveolates). During high Chla conditions, HCO3- uptake rates during daytime incubations increased 5-fold (>2516 nmol C L-1 d-1), and increased photosynthetic transcript numbers that were mainly associated with cryptophytes; meanwhile night time NO3- (>706 nmol N L-1 d-1) and NH4+ (41.7 nmol N L-1 d-1) uptake rates were 2- and 3-fold higher, respectively, due to activity from Alpha-/Gammaproteobacteria and Bacteroidetes (Flavobacteriia). Due to a projected acceleration in climate change in the WAP, this information is valuable for predicting the composition and functional changes in Antarctic microbial communities.
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Affiliation(s)
- María E Alcamán-Arias
- Department of Oceanography, Universidad de Concepción, 4070386 Concepción, Chile.,Department of Molecular Genetics and Microbiology, Pontificia Universidad Católica de Chile, 6513677 Santiago, Chile.,Center for Climate and Resilience Research (CR) 2, Universidad de Chile, 8370448 Santiago, Chile
| | - Laura Farías
- Department of Oceanography, Universidad de Concepción, 4070386 Concepción, Chile.,Center for Climate and Resilience Research (CR) 2, Universidad de Chile, 8370448 Santiago, Chile
| | - Josefa Verdugo
- Alfred-Wegener-Institute Helmholtz-Centre for Polar and Marine Research, 27570 Bremerhaven, Germany
| | - Tomás Alarcón-Schumacher
- Department of Molecular Genetics and Microbiology, Pontificia Universidad Católica de Chile, 6513677 Santiago, Chile
| | - Beatriz Díez
- Department of Molecular Genetics and Microbiology, Pontificia Universidad Católica de Chile, 6513677 Santiago, Chile.,Center for Climate and Resilience Research (CR) 2, Universidad de Chile, 8370448 Santiago, Chile
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Alarcón-Schumacher T, Guajardo-Leiva S, Antón J, Díez B. Elucidating Viral Communities During a Phytoplankton Bloom on the West Antarctic Peninsula. Front Microbiol 2019; 10:1014. [PMID: 31139164 PMCID: PMC6527751 DOI: 10.3389/fmicb.2019.01014] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Accepted: 04/24/2019] [Indexed: 01/16/2023] Open
Abstract
In Antarctic coastal waters where nutrient limitations are low, viruses are expected to play a major role in the regulation of bloom events. Despite this, research in viral identification and dynamics is scarce, with limited information available for the Southern Ocean (SO). This study presents an integrative-omics approach, comparing variation in the viral and microbial active communities on two contrasting sample conditions from a diatom-dominated phytoplankton bloom occurring in Chile Bay in the West Antarctic Peninsula (WAP) in the summer of 2014. The known viral community, initially dominated by Myoviridae family (∼82% of the total assigned reads), changed to become dominated by Phycodnaviridae (∼90%), while viral activity was predominantly driven by dsDNA members of the Phycodnaviridae (∼50%) and diatom infecting ssRNA viruses (∼38%), becoming more significant as chlorophyll a increased. A genomic and phylogenetic characterization allowed the identification of a new viral lineage within the Myoviridae family. This new lineage of viruses infects Pseudoalteromonas and was dominant in the phage community. In addition, a new Phycodnavirus (PaV) was described, which is predicted to infect Phaeocystis antarctica, the main blooming haptophyte in the SO. This work was able to identify the changes in the main viral players during a bloom development and suggests that the changes observed in the virioplankton could be used as a model to understand the development and decay of blooms that occur throughout the WAP.
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Affiliation(s)
- Tomás Alarcón-Schumacher
- Department of Molecular Genetics and Microbiology, Pontificia Universidad Católica de Chile, Santiago, Chile.,Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Sergio Guajardo-Leiva
- Department of Molecular Genetics and Microbiology, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Josefa Antón
- Department of Physiology, Genetics, and Microbiology, University of Alicante, Alicante, Spain
| | - Beatriz Díez
- Department of Molecular Genetics and Microbiology, Pontificia Universidad Católica de Chile, Santiago, Chile.,Center for Climate and Resilience Research (CR2), University of Chile, Santiago, Chile
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