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Dominguez-Mirazo M, Harris JD, Demory D, Weitz JS. Accounting for cellular-level variation in lysis: implications for virus-host dynamics. mBio 2024; 15:e0137624. [PMID: 39028198 PMCID: PMC11323501 DOI: 10.1128/mbio.01376-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2024] [Accepted: 05/24/2024] [Indexed: 07/20/2024] Open
Abstract
Viral impacts on microbial populations depend on interaction phenotypes-including viral traits spanning the adsorption rate, latent period, and burst size. The latent period is a key viral trait in lytic infections. Defined as the time from viral adsorption to viral progeny release, the latent period of bacteriophage is conventionally inferred via one-step growth curves in which the accumulation of free virus is measured over time in a population of infected cells. Developed more than 80 years ago, one-step growth curves do not account for cellular-level variability in the timing of lysis, potentially biasing inference of viral traits. Here, we use nonlinear dynamical models to understand how individual-level variation of the latent period impacts virus-host dynamics. Our modeling approach shows that inference of the latent period via one-step growth curves is systematically biased-generating estimates of shorter latent periods than the underlying population-level mean. The bias arises because variability in lysis timing at the cellular level leads to a fraction of early burst events, which are interpreted, artefactually, as an earlier mean time of viral release. We develop a computational framework to estimate latent period variability from joint measurements of host and free virus populations. Our computational framework recovers both the mean and variance of the latent period within simulated infections including realistic measurement noise. This work suggests that reframing the latent period as a distribution to account for variability in the population will improve the study of viral traits and their role in shaping microbial populations.IMPORTANCEQuantifying viral traits-including the adsorption rate, burst size, and latent period-is critical to characterize viral infection dynamics and develop predictive models of viral impacts across scales from cells to ecosystems. Here, we revisit the gold standard of viral trait estimation-the one-step growth curve-to assess the extent to which assumptions at the core of viral infection dynamics lead to ongoing and systematic biases in inferences of viral traits. We show that latent period estimates obtained via one-step growth curves systematically underestimate the mean latent period and, in turn, overestimate the rate of viral killing at population scales. By explicitly incorporating trait variability into a dynamical inference framework that leverages both virus and host time series, we provide a practical route to improve estimates of the mean and variance of viral traits across diverse virus-microbe systems.
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Affiliation(s)
- Marian Dominguez-Mirazo
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
- Interdisciplinary Graduate Program in Quantitative Biosciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Jeremy D. Harris
- Department of Mathematics, Rose-Hulman Institute of Technology, Terre Haute, Indiana, USA
| | - David Demory
- CNRS, Sorbonne Université, USR3579 Laboratoire de Biodiversité et Biotechnologies Microbiennes (LBBM), Observatoire Océanologique, Banyuls-sur-Mer, France
| | - Joshua S. Weitz
- Department of Biology, University of Maryland, College Park, Maryland, USA
- Department of Physics, University of Maryland, College Park, Maryland, USA
- Institut de Biologie, École Normale Supérieure, Paris, France
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2
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Denison ER, Zepernick BN, McKay RML, Wilhelm SW. Metatranscriptomic analysis reveals dissimilarity in viral community activity between an ice-free and ice-covered winter in Lake Erie. mSystems 2024; 9:e0075324. [PMID: 38940524 PMCID: PMC11264689 DOI: 10.1128/msystems.00753-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2024] [Accepted: 06/10/2024] [Indexed: 06/29/2024] Open
Abstract
Winter is a relatively under-studied season in freshwater ecology. The paucity of wintertime surveys has led to a lack of knowledge regarding microbial community activity during the winter in Lake Erie, a North American Great Lake. Viruses shape microbial communities and regulate biogeochemical cycles by acting as top-down controls, yet very few efforts have been made to examine active virus populations during the winter in Lake Erie. Furthermore, climate change-driven declines in seasonal ice cover have been shown to influence microbial community structure, but no studies have compared viral community activity between different ice cover conditions. We surveyed surface water metatranscriptomes for viral hallmark genes as a proxy for active virus populations and compared activity metrics between ice-covered and ice-free conditions from two sampled winters. Transcriptionally active viral communities were detected in both winters, spanning diverse phylogenetic clades of putative bacteriophage (Caudoviricetes), giant viruses (Nucleocytoviricota, or NCLDV), and RNA viruses (Orthornavirae). However, viral community activity metrics revealed pronounced differences between the ice-covered and ice-free winters. Viral community composition was distinct between winters and viral hallmark gene richness was reduced in the ice-covered relative to the ice-free conditions. In addition, the observed differences in viral communities correlated with microbial community activity metrics. Overall, these findings contribute to our understanding of the viral populations that are active during the winter in Lake Erie and suggest that viral community activity may be associated with ice cover extent.IMPORTANCEAs seasonal ice cover is projected to become increasingly rare on large temperate lakes, there is a need to understand how microbial communities might respond to changing ice conditions. Although it is widely recognized that viruses impact microbial community structure and function, there is little known regarding wintertime viral activity or the relationship between viral activity and ice cover extent. Our metatranscriptomic analyses indicated that viruses were transcriptionally active in the winter surface waters of Lake Erie. These findings also expanded the known diversity of viral lineages in the Great Lakes. Notably, viral community activity metrics were significantly different between the two sampled winters. The pronounced differences we observed in active viral communities between the ice-covered and ice-free samples merit further research regarding how viral communities will function in future, potentially ice-free, freshwater systems.
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Affiliation(s)
| | | | - R. Michael L. McKay
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, Ontario, Canada
| | - Steven W. Wilhelm
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, USA
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Grimwood RM, Waller SJ, Wierenga JR, Lim L, Dubrulle J, Holmes EC, Geoghegan JL. Viromes of Antarctic fish resemble the diversity found at lower latitudes. Virus Evol 2024; 10:veae050. [PMID: 39071139 PMCID: PMC11282168 DOI: 10.1093/ve/veae050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Revised: 06/09/2024] [Accepted: 07/10/2024] [Indexed: 07/30/2024] Open
Abstract
Antarctica harbours some of the most isolated and extreme environments on Earth, concealing a largely unexplored and unique component of the global animal virosphere. To understand the diversity and evolutionary histories of viruses in these polar species, we determined the viromes of gill metatranscriptomes from 11 Antarctic fish species with 248 samples collected from the Ross Sea region spanning the Perciformes, Gadiformes, and Scorpaeniformes orders. The continent's shift southward and cooling temperatures >20 million years ago led to a reduction in biodiversity and subsequent radiation of some marine fauna, such as the notothenioid fishes. Despite decreased host species richness in polar regions, we revealed a surprisingly complex virome diversity in Ross Sea fish, with the types and numbers of viruses per host species and individuals sampled comparable to that of fish in warmer marine environments with higher host community diversity. We also observed a higher number of closely related viruses likely representing instances of recent and historic host-switching events among the Perciformes (all notothenioids) than in the Gadiformes, suggesting that rapid speciation events within this order generated closely related host species with few genetic barriers to cross-species transmission. Additionally, we identified novel genomic variation in an arenavirus with a split nucleoprotein sequence containing a stable helical structure, indicating potential adaptation of viral proteins to extreme temperatures. These findings enhance our understanding of virus evolution and virus-host interactions in response to environmental shifts, especially in less diverse ecosystems that are more vulnerable to the impacts of anthropogenic and climate changes.
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Affiliation(s)
- Rebecca M Grimwood
- Department of Microbiology and Immunology, University of Otago, Dunedin 9016, New Zealand
| | - Stephanie J Waller
- Department of Microbiology and Immunology, University of Otago, Dunedin 9016, New Zealand
| | - Janelle R Wierenga
- Department of Microbiology and Immunology, University of Otago, Dunedin 9016, New Zealand
| | - Lauren Lim
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Camperdown, NSW 2006, Australia
| | - Jérémy Dubrulle
- Department of Microbiology and Immunology, University of Otago, Dunedin 9016, New Zealand
| | - Edward C Holmes
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Camperdown, NSW 2006, Australia
| | - Jemma L Geoghegan
- Department of Microbiology and Immunology, University of Otago, Dunedin 9016, New Zealand
- Institute of Environmental Science and Research, Wellington 5018, New Zealand
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4
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Hou S, Tang T, Cheng S, Liu Y, Xia T, Chen T, Fuhrman J, Sun F. DeepMicroClass sorts metagenomic contigs into prokaryotes, eukaryotes and viruses. NAR Genom Bioinform 2024; 6:lqae044. [PMID: 38711860 PMCID: PMC11071121 DOI: 10.1093/nargab/lqae044] [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: 09/07/2023] [Revised: 03/18/2024] [Accepted: 04/18/2024] [Indexed: 05/08/2024] Open
Abstract
Sequence classification facilitates a fundamental understanding of the structure of microbial communities. Binary metagenomic sequence classifiers are insufficient because environmental metagenomes are typically derived from multiple sequence sources. Here we introduce a deep-learning based sequence classifier, DeepMicroClass, that classifies metagenomic contigs into five sequence classes, i.e. viruses infecting prokaryotic or eukaryotic hosts, eukaryotic or prokaryotic chromosomes, and prokaryotic plasmids. DeepMicroClass achieved high performance for all sequence classes at various tested sequence lengths ranging from 500 bp to 100 kbps. By benchmarking on a synthetic dataset with variable sequence class composition, we showed that DeepMicroClass obtained better performance for eukaryotic, plasmid and viral contig classification than other state-of-the-art predictors. DeepMicroClass achieved comparable performance on viral sequence classification with geNomad and VirSorter2 when benchmarked on the CAMI II marine dataset. Using a coastal daily time-series metagenomic dataset as a case study, we showed that microbial eukaryotes and prokaryotic viruses are integral to microbial communities. By analyzing monthly metagenomes collected at HOT and BATS, we found relatively higher viral read proportions in the subsurface layer in late summer, consistent with the seasonal viral infection patterns prevalent in these areas. We expect DeepMicroClass will promote metagenomic studies of under-appreciated sequence types.
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Affiliation(s)
- Shengwei Hou
- Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen 518055, China
- Marine and Environmental Biology, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Tianqi Tang
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA
| | - Siliangyu Cheng
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA
| | - Yuanhao Liu
- Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen 518055, China
| | - Tian Xia
- Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen 518055, China
| | - Ting Chen
- Department of Computer Science and Technology, Institute of Artificial Intelligence & BNRist, Tsinghua University, Beijing 100084, China
| | - Jed A Fuhrman
- Marine and Environmental Biology, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Fengzhu Sun
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA
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Vega-Heredia S, Giffard-Mena I, Reverter M. Bacterial and viral co-infections in aquaculture under climate warming: co-evolutionary implications, diagnosis, and treatment. DISEASES OF AQUATIC ORGANISMS 2024; 158:1-20. [PMID: 38602294 DOI: 10.3354/dao03778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/12/2024]
Abstract
Climate change and the associated environmental temperature fluctuations are contributing to increases in the frequency and severity of disease outbreaks in both wild and farmed aquatic species. This has a significant impact on biodiversity and also puts global food production systems, such as aquaculture, at risk. Most infections are the result of complex interactions between multiple pathogens, and understanding these interactions and their co-evolutionary mechanisms is crucial for developing effective diagnosis and control strategies. In this review, we discuss current knowledge on bacteria-bacteria, virus-virus, and bacterial and viral co-infections in aquaculture as well as their co-evolution in the context of global warming. We also propose a framework and different novel methods (e.g. advanced molecular tools such as digital PCR and next-generation sequencing) to (1) precisely identify overlooked co-infections, (2) gain an understanding of the co-infection dynamics and mechanisms by knowing species interactions, and (3) facilitate the development multi-pathogen preventive measures such as polyvalent vaccines. As aquaculture disease outbreaks are forecasted to increase both due to the intensification of practices to meet the protein demand of the increasing global population and as a result of global warming, understanding and treating co-infections in aquatic species has important implications for global food security and the economy.
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Affiliation(s)
- Sarahí Vega-Heredia
- Universidad Autónoma de Baja California, Facultad de Ciencias Marinas, Ensenada, México, Egresada del Programa de Ecología Molecular y Biotecnología, carretera transpeninsular Ensenada-Tijuana No. 3917, C.P. 22860, México
| | - Ivone Giffard-Mena
- Universidad Autónoma de Baja California, Facultad de Ciencias Marinas, Ensenada, México
| | - Miriam Reverter
- School of Biological and Marine Sciences, Plymouth University, Drake Circus, Devon PL4 8AA, UK
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6
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He T, Jin M, Cui P, Sun X, He X, Huang Y, Xiao X, Zhang T, Zhang X. Environmental viromes reveal the global distribution signatures of deep-sea DNA viruses. J Adv Res 2024; 57:107-117. [PMID: 37075861 PMCID: PMC10918349 DOI: 10.1016/j.jare.2023.04.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 04/11/2023] [Accepted: 04/11/2023] [Indexed: 04/21/2023] Open
Abstract
INTRODUCTION Viruses are abundant and ecologically significant in marine ecosystems. However, the virome of deep-sea sediments is not extensively investigated. OBJECTIVES To explore the distribution pattern of deep-sea viruses on a global scale, the viromes of DNA viruses isolated from 138 sediments of 5 deep-sea ecosystems were characterized. METHODS The viral particles were purified from each sediment sample. Then the viral DNAs were extracted and subjected to viral metagenomic analysis. RESULTS Here, we constructed a global deep-sea environmental virome dataset by analyzing the viral DNA of 138 sediment samples. A total of 347,737 viral operational taxonomic units (vOTUs) were identified, of which 84.94% were hitherto unknown, indicating that deep sea was a reservoir of novel DNA viruses. Furthermore, circular viral genome analysis revealed 98,581 complete genomes. The classified vOTUs included eukaryotic (44.55%) and prokaryotic (25.75%) viruses, and were taxonomically assigned to 63 viral families. The composition and abundance of the deep-sea sediment viromes were dependent on the deep-sea ecosystem as opposed to geographical region. Further analysis revealed that the viral community differentiation in different deep-sea ecosystems was driven by the virus-mediated energy metabolism. CONCLUSION Our findings showed that deep-sea ecosystems are a reservoir of novel DNA viruses and the viral community is shaped by the environmental characteristics of deep-sea ecosystems, thus presenting critical information for determining the ecological significance of viruses in global deep-sea ecosystems.
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Affiliation(s)
- Tianliang He
- College of Life Sciences, Laboratory for Marine Biology and Biotechnology of Pilot National Laboratory for Marine Science and Technology (Qingdao) and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhejiang University, Hangzhou 310058, China; Key Laboratory of Marine Biotechnology of Fujian Province, Institute of Oceanology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Min Jin
- Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China
| | - Pei Cui
- College of Life Sciences, Laboratory for Marine Biology and Biotechnology of Pilot National Laboratory for Marine Science and Technology (Qingdao) and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhejiang University, Hangzhou 310058, China
| | - Xumei Sun
- College of Life Sciences, Laboratory for Marine Biology and Biotechnology of Pilot National Laboratory for Marine Science and Technology (Qingdao) and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhejiang University, Hangzhou 310058, China
| | - Xuebao He
- Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China
| | - Yaqin Huang
- Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China
| | - Xi Xiao
- Guangzhou Marine Geological Survey, China Geological Survey, Guangzhou 510760, China
| | - Tingting Zhang
- Guangzhou Marine Geological Survey, China Geological Survey, Guangzhou 510760, China
| | - Xiaobo Zhang
- College of Life Sciences, Laboratory for Marine Biology and Biotechnology of Pilot National Laboratory for Marine Science and Technology (Qingdao) and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhejiang University, Hangzhou 310058, China.
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7
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Kuhlisch C, Shemi A, Barak-Gavish N, Schatz D, Vardi A. Algal blooms in the ocean: hot spots for chemically mediated microbial interactions. Nat Rev Microbiol 2024; 22:138-154. [PMID: 37833328 DOI: 10.1038/s41579-023-00975-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/14/2023] [Indexed: 10/15/2023]
Abstract
The cycling of major nutrients in the ocean is affected by large-scale phytoplankton blooms, which are hot spots of microbial life. Diverse microbial interactions regulate bloom dynamics. At the single-cell level, interactions between microorganisms are mediated by small molecules in the chemical crosstalk that determines the type of interaction, ranging from mutualism to pathogenicity. Algae interact with viruses, bacteria, parasites, grazers and other algae to modulate algal cell fate, and these interactions are dependent on the environmental context. Recent advances in mass spectrometry and single-cell technologies have led to the discovery of a growing number of infochemicals - metabolites that convey information - revealing the ability of algal cells to govern biotic interactions in the ocean. The diversity of infochemicals seems to account for the specificity in cellular response during microbial communication. Given the immense impact of algal blooms on biogeochemical cycles and climate regulation, a major challenge is to elucidate how microscale interactions control the fate of carbon and the recycling of major elements in the ocean. In this Review, we discuss microbial interactions and the role of infochemicals in algal blooms. We further explore factors that can impact microbial interactions and the available tools to decipher them in the natural environment.
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Affiliation(s)
- Constanze Kuhlisch
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Adva Shemi
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Noa Barak-Gavish
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
- Institute of Microbiology, ETH Zurich, Zurich, Switzerland
| | - Daniella Schatz
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Assaf Vardi
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel.
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Cooney C, Sommer B, Marzinelli EM, Figueira WF. The role of microbial biofilms in range shifts of marine habitat-forming organisms. Trends Microbiol 2024; 32:190-199. [PMID: 37633773 DOI: 10.1016/j.tim.2023.07.015] [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: 03/14/2023] [Revised: 07/25/2023] [Accepted: 07/27/2023] [Indexed: 08/28/2023]
Abstract
Marine species, such as corals and kelp, are responding to climate change by altering their distributions. Microbial biofilms underpin key processes that affect the establishment, maintenance, and function of these dominant habitat-formers. Climate-mediated changes to microbial biofilms can therefore strongly influence species' range shifts. Here, we review emerging research on the interactions between benthic biofilms and habitat-formers and identify two key areas of interaction where climate change can impact this dynamic: (i) via direct effects on biofilm composition, and (ii) via impacts on the complex feedback loops which exist between the biofilm microbes and habitat-forming organisms. We propose that these key interactions will be fundamental in driving the speed and extent of tropicalisation of coastal ecosystems under climate change.
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Affiliation(s)
- Christopher Cooney
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2006, Australia.
| | - Brigitte Sommer
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2006, Australia; School of Life Sciences, University of Technology Sydney, Sydney, NSW 2007, Australia
| | - Ezequiel M Marzinelli
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2006, Australia; Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore
| | - Will F Figueira
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2006, Australia
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Wei W, Tian Y, Cai L, Xu Y, Xiao X, Wang Q, Wang H, Dong C, Shao Z, Jiao N, Zhang R. Survival of surface bacteriophages and their hosts in in situ deep-sea environments. Microbiol Spectr 2024; 12:e0453422. [PMID: 38051228 PMCID: PMC10783000 DOI: 10.1128/spectrum.04534-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 10/27/2023] [Indexed: 12/07/2023] Open
Abstract
IMPORTANCE The survival of the sinking prokaryotes and viruses in the deep-sea environment is crucial for deep-sea ecosystems and biogeochemical cycles. Through an in situ deep-sea long-term incubation device, our results showed that viral particles and infectivity had still not decayed completely after in situ incubation for 1 year. This suggests that, via infection and lysis, surface viruses with long-term infectious activity in situ deep-sea environments may influence deep-sea microbial populations in terms of activity, function, diversity, and community structure and ultimately affect deep-sea biogeochemical cycles, highlighting the need for additional research in this area.
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Affiliation(s)
- Wei Wei
- Research Center for Environmental Ecology and Engineering, School of Environmental Ecology and Biological Engineering, Wuhan Institute of Technology, Wuhan, China
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Yuan Tian
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Lanlan Cai
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Yongle Xu
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
| | - Xilin Xiao
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Qiong Wang
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Haowen Wang
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Chunming Dong
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
| | - Zongze Shao
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
| | - Nianzhi Jiao
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Rui Zhang
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
- Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, Guangdong, China
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10
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Ye Y, Zhang L, Hong X, Chen M, Liu X, Zhou S. Interspecies ecological competition rejuvenates decayed Geobacter electroactive biofilm. THE ISME JOURNAL 2024; 18:wrae118. [PMID: 38916438 PMCID: PMC11227281 DOI: 10.1093/ismejo/wrae118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Revised: 06/05/2024] [Accepted: 06/23/2024] [Indexed: 06/26/2024]
Abstract
Bioelectrochemical systems (BESs) exploit electroactive biofilms (EABs) for promising applications in biosensing, wastewater treatment, energy production, and chemical biosynthesis. However, during the operation of BESs, EABs inevitably decay. Seeking approaches to rejuvenate decayed EABs is critical for the sustainability and practical application of BESs. Prophage induction has been recognized as the primary reason for EAB decay. Herein, we report that introducing a competitive species of Geobacter uraniireducens suspended prophage induction in Geobacter sulfurreducens and thereby rejuvenated the decayed G. sulfurreducens EAB. The transcriptomic profile of G. sulfurreducens demonstrated that the addition of G. uraniireducens significantly affected the expression of metabolism- and stress response system-related genes and in particular suppressed the induction of phage-related genes. Mechanistic analyses revealed that interspecies ecological competition exerted by G. uraniireducens suppressed prophage induction. Our findings not only reveal a novel strategy to rejuvenate decayed EABs, which is significant for the sustainability of BESs, but also provide new knowledge for understanding phage-host interactions from an ecological perspective, with implications for developing therapies to defend against phage attack.
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Affiliation(s)
- Yin Ye
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Lu Zhang
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xiaohui Hong
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Man Chen
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xing Liu
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Shungui Zhou
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China
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11
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Balestreri C, Schroeder DC, Sampedro F, Marqués G, Palowski A, Urriola PE, van de Ligt JLG, Yancy HF, Shurson GC. Unexpected thermal stability of two enveloped megaviruses, Emiliania huxleyi virus and African swine fever virus, as measured by viability PCR. Virol J 2024; 21:1. [PMID: 38172919 PMCID: PMC10765680 DOI: 10.1186/s12985-023-02272-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 12/18/2023] [Indexed: 01/05/2024] Open
Abstract
BACKGROUND The particle structure of Emiliania huxleyi virus (EhV), an algal infecting member of nucleocytoplasmic large DNA viruses (NCLDVs), contains an outer lipid membrane envelope similar to that found in animal viruses such as African swine fever virus (ASFV). Despite both being enveloped NCLDVs, EhV and ASFV are known for their stability outside their host environment. METHOD Here we report for the first time, the application of a viability qPCR (V-qPCR) method to describe the unprecedented and similar virion thermal stability of both EhV and ASFV. This result contradicts the cell culture-based assay method that suggests that virus "infectivity" is lost in a matter of seconds (for EhV) and minutes (for ASFV) at temperature greater than 50 °C. Confocal microscopy and analytical flow cytometry methods was used to validate the V-qPCR data for EhV. RESULTS We observed that both EhV and ASFV particles has unprecedented thermal tolerances. These two NCLDVs are exceptions to the rule that having an enveloped virion anatomy is a predicted weakness, as is often observed in enveloped RNA viruses (i.e., the viruses causing Porcine Reproductive and Respiratory Syndrome (PRRS), COVID-19, Ebola, or seasonal influenza). Using the V-qPCR method, we confirm that no PRRSV particles were detectable after 20 min of exposure to temperatures up to 100 °C. We also show that the EhV particles that remain after 50 °C 20 min exposure was in fact still infectious only after the three blind passages in bioassay experiments. CONCLUSIONS This study raises the possibility that ASFV is not always eliminated or contained after applying time and temperature inactivation treatments in current decontamination or biosecurity protocols. This observation has practical implications for industries involved in animal health and food security. Finally, we propose that EhV could be used as a surrogate for ASFV under certain circumstances.
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Affiliation(s)
- Cecilia Balestreri
- Department of Veterinary Population Medicine, University of Minnesota, St. Paul, MN, 55108, USA
| | - Declan C Schroeder
- Department of Veterinary Population Medicine, University of Minnesota, St. Paul, MN, 55108, USA.
| | - Fernando Sampedro
- Environmental Health Sciences Division, University of Minnesota, St. Paul, MN, 55455, USA
| | - Guillermo Marqués
- Department of Neuroscience, University Imaging Centers, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Amanda Palowski
- Department of Veterinary Population Medicine, University of Minnesota, St. Paul, MN, 55108, USA
| | - Pedro E Urriola
- Department of Veterinary Population Medicine, University of Minnesota, St. Paul, MN, 55108, USA
- Department of Animal Science, University of Minnesota, St. Paul, MN, 55108, USA
| | | | - Haile F Yancy
- U.S. Food and Drug Administration, Center for Veterinary Medicine, Laurel, MD, 20708, USA
| | - Gerald C Shurson
- Department of Animal Science, University of Minnesota, St. Paul, MN, 55108, USA.
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12
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Ruiz Martínez E, Mckeown DA, Schroeder DC, Thuestad G, Sjøtun K, Sandaa RA, Larsen A, Hoell IA. Phaeoviruses Present in Cultured and Natural Kelp Species, Saccharina latissima and Laminaria hyperborea (Phaeophyceae, Laminariales) , in Norway. Viruses 2023; 15:2331. [PMID: 38140573 PMCID: PMC10747701 DOI: 10.3390/v15122331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 11/20/2023] [Accepted: 11/23/2023] [Indexed: 12/24/2023] Open
Abstract
Phaeoviruses (Phycodnaviridae) are large icosahedral viruses in the phylum Nucleocytoviricota with dsDNA genomes ranging from 160 to 560 kb, infecting multicellular brown algae (Phaeophyceae). The phaeoviral host range is broader than expected, not only infecting algae from the Ectocarpales but also from the Laminariales order. However, despite phaeoviral infections being reported globally, Norwegian kelp species have not been screened. A molecular analysis of cultured and wild samples of two economically important kelp species in Norway (Saccharina latissima and Laminaria hyperborea) revealed that phaeoviruses are recurrently present along the Norwegian coast. We found the viral prevalence in S. latissima to be significantly higher at the present time compared to four years ago. We also observed regional differences within older samples, in which infections were significantly lower in northern areas than in the south or the fjords. Moreover, up to three different viral sequences were found in the same algal individual, one of which does not belong to the Phaeovirus genus and has never been reported before. This master variant therefore represents a putative new member of an unclassified phycodnavirus genus.
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Affiliation(s)
- Eliana Ruiz Martínez
- Department of Safety, Chemistry and Biomedical Laboratory Sciences, Western Norway University of Applied Sciences, 5528 Haugesund, Norway; (G.T.); (I.A.H.)
| | - Dean A. Mckeown
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, Minneapolis, MN 55108, USA; (D.A.M.); (D.C.S.)
| | - Declan C. Schroeder
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, Minneapolis, MN 55108, USA; (D.A.M.); (D.C.S.)
| | - Gunnar Thuestad
- Department of Safety, Chemistry and Biomedical Laboratory Sciences, Western Norway University of Applied Sciences, 5528 Haugesund, Norway; (G.T.); (I.A.H.)
| | - Kjersti Sjøtun
- Department of Biological Sciences, University of Bergen, 5006 Bergen, Norway; (K.S.); (R.-A.S.)
| | - Ruth-Anne Sandaa
- Department of Biological Sciences, University of Bergen, 5006 Bergen, Norway; (K.S.); (R.-A.S.)
| | - Aud Larsen
- NORCE Norwegian Research Centre, 5008 Bergen, Norway;
| | - Ingunn Alne Hoell
- Department of Safety, Chemistry and Biomedical Laboratory Sciences, Western Norway University of Applied Sciences, 5528 Haugesund, Norway; (G.T.); (I.A.H.)
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13
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Santos-Medellín C, Blazewicz SJ, Pett-Ridge J, Firestone MK, Emerson JB. Viral but not bacterial community successional patterns reflect extreme turnover shortly after rewetting dry soils. Nat Ecol Evol 2023; 7:1809-1822. [PMID: 37770548 DOI: 10.1038/s41559-023-02207-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Accepted: 08/25/2023] [Indexed: 09/30/2023]
Abstract
As central members of soil trophic networks, viruses have the potential to drive substantial microbial mortality and nutrient turnover. Pinpointing viral contributions to terrestrial ecosystem processes remains a challenge, as temporal dynamics are difficult to unravel in the spatially and physicochemically heterogeneous soil environment. In Mediterranean grasslands, the first rainfall after seasonal drought provides an ecosystem reset, triggering microbial activity during a tractable window for capturing short-term dynamics. Here, we simulated precipitation in microcosms from four distinct dry grassland soils and generated 144 viromes, 84 metagenomes and 84 16S ribosomal RNA gene amplicon datasets to characterize viral, prokaryotic and relic DNA dynamics over 10 days. Vastly different viral communities in each soil followed remarkably similar successional trajectories. Wet-up triggered a significant increase in viral richness, followed by extensive compositional turnover. Temporal succession in prokaryotic communities was much less pronounced, perhaps suggesting differences in the scales of activity captured by viromes (representing recently produced, ephemeral viral particles) and total DNA. Still, differences in the relative abundances of Actinobacteria (enriched in dry soils) and Proteobacteria (enriched in wetted soils) matched those of their predicted phages, indicating viral predation of dominant bacterial taxa. Rewetting also rapidly depleted relic DNA, which subsequently reaccumulated, indicating substantial new microbial mortality in the days after wet-up, particularly of the taxa putatively under phage predation. Production of abundant, diverse viral particles via microbial host cell lysis appears to be a conserved feature of the early response to soil rewetting, and results suggest the potential for 'Cull-the-Winner' dynamics, whereby viruses infect and cull but do not decimate dominant host populations.
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Affiliation(s)
| | - Steven J Blazewicz
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Jennifer Pett-Ridge
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
- Life & Environmental Sciences Department, University of California, Merced, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
| | - Mary K Firestone
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA, USA
| | - Joanne B Emerson
- Department of Plant Pathology, University of California, Davis, CA, USA.
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14
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Kang N, Kim EA, Heo SY, Heo SJ. Structure-Based In Silico Screening of Marine Phlorotannins for Potential Walrus Calicivirus Inhibitor. Int J Mol Sci 2023; 24:15774. [PMID: 37958757 PMCID: PMC10647355 DOI: 10.3390/ijms242115774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 10/26/2023] [Accepted: 10/27/2023] [Indexed: 11/15/2023] Open
Abstract
A new calicivirus isolated from a walrus was reported in 2004. Since unknown marine mammalian zoonotic viruses could pose great risks to human health, this study aimed to develop therapeutic countermeasures to quell any potential outbreak of a pandemic caused by this virus. We first generated a 3D model of the walrus calicivirus capsid protein and identified compounds from marine natural products, especially phlorotannins, as potential walrus calicivirus inhibitors. A 3D model of the target protein was generated using homology modeling based on two publicly available template sequences. The sequence of the capsid protein exhibited 31.3% identity and 42.7% similarity with the reference templates. The accuracy and reliability of the predicted residues were validated via Ramachandran plotting. Molecular docking simulations were performed between the capsid protein 3D model and 17 phlorotannins. Among them, five phlorotannins demonstrated markedly stable docking profiles; in particular, 2,7-phloroglucinol-6,6-bieckol showed favorable structural integrity and stability during molecular dynamics simulations. The results indicate that the phlorotannins are promising walrus calicivirus inhibitors. Overall, the study findings showcase the rapid turnaround of in silico-based drug discovery approaches, providing useful insights for developing potential therapies against novel pathogenic viruses, especially when the 3D structures of the viruses remain experimentally unknown.
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Affiliation(s)
| | | | | | - Soo-Jin Heo
- Jeju Bio Research Center, Korea Institute of Ocean Science and Technology (KIOST), Jeju 63349, Republic of Korea; (N.K.); (E.-A.K.); (S.-Y.H.)
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15
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Hwang CY, Cho BC, Kang JK, Park J, Hardies SC. Genomic Analysis of Two Cold-Active Pseudoalteromonas Phages Isolated from the Continental Shelf in the Arctic Ocean. Viruses 2023; 15:2061. [PMID: 37896838 PMCID: PMC10612066 DOI: 10.3390/v15102061] [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: 09/01/2023] [Revised: 10/04/2023] [Accepted: 10/04/2023] [Indexed: 10/29/2023] Open
Abstract
Cold-active bacteriophages are bacterial viruses that infect and replicate at low temperatures (≤4 °C). Understanding remains limited of how cold-active phage-host systems sustain high viral abundance despite the persistently low temperatures in pelagic sediments in polar seas. In this study, two Pseudoalteromonas phages, ACA1 and ACA2, were isolated from sediment core samples of the continental shelf in the western Arctic Ocean. These phages exhibited successful propagation at a low temperature of 1 °C and displayed typical myovirus morphology with isometric icosahedral heads and contractile tails. The complete genome sequences of phages ACA1 and ACA2 were 36,825 bp and 36,826 bp in size, respectively, sharing almost the same gene content. These are temperate phages encoding lysogeny-related proteins such as anti-repressor, immunity repressor and integrase. The absence of cross-infection between the host strains, which were genomically distinct Pseudoalteromonas species, can likely be attributed to heavy divergence in the anti-receptor apparently mediated by an associated diversity-generating retroelement. HHpred searching identified genes for all of the structural components of a P2-like phage (family Peduoviridae), although the whole of the Peduoviridae family appeared to be divided between two anciently diverged tail modules. In contrast, Blast matching and whole genome tree analysis are dominated by a nonstructural gene module sharing high similarity with Pseudoalteromonas phage C5a (founder of genus Catalunyavirus). This study expands the knowledge of diversity of P2-like phages known to inhabit Peudoalteromonas and demonstrates their presence in the Arctic niche.
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Affiliation(s)
- Chung Yeon Hwang
- Microbial Oceanography Laboratory, School of Earth and Environmental Sciences and Research Institute of Oceanography, Seoul National University, Seoul 08826, Republic of Korea; (C.Y.H.); (B.C.C.); (J.K.K.); (J.P.)
| | - Byung Cheol Cho
- Microbial Oceanography Laboratory, School of Earth and Environmental Sciences and Research Institute of Oceanography, Seoul National University, Seoul 08826, Republic of Korea; (C.Y.H.); (B.C.C.); (J.K.K.); (J.P.)
- Saemangeum Environmental Research Center, Kunsan National University, Kunsan 54150, Republic of Korea
| | - Jin Kyeong Kang
- Microbial Oceanography Laboratory, School of Earth and Environmental Sciences and Research Institute of Oceanography, Seoul National University, Seoul 08826, Republic of Korea; (C.Y.H.); (B.C.C.); (J.K.K.); (J.P.)
| | - Jihye Park
- Microbial Oceanography Laboratory, School of Earth and Environmental Sciences and Research Institute of Oceanography, Seoul National University, Seoul 08826, Republic of Korea; (C.Y.H.); (B.C.C.); (J.K.K.); (J.P.)
| | - Stephen C. Hardies
- Department of Biochemistry and Structural Biology, UT Health, San Antonio, TX 78229, USA
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16
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Sabbagh EI, Calleja ML, Daffonchio D, Morán XAG. Seasonality of top-down control of bacterioplankton at two central Red Sea sites with different trophic status. Environ Microbiol 2023; 25:2002-2019. [PMID: 37286523 DOI: 10.1111/1462-2920.16439] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Accepted: 05/22/2023] [Indexed: 06/09/2023]
Abstract
The role of bottom-up (nutrient availability) and top-down (grazers and viruses mortality) controls on tropical bacterioplankton have been rarely investigated simultaneously from a seasonal perspective. We have assessed them through monthly samplings over 2 years in inshore and offshore waters of the central Red Sea differing in trophic status. Flow cytometric analysis allowed us to distinguish five groups of heterotrophic bacteria based on physiological properties (nucleic acid content, membrane integrity and active respiration), three groups of cyanobacteria (two populations of Synechococcus and Prochlorococcus), heterotrophic nanoflagellates (HNFs) and three groups of viruses based on nucleic acid content. The dynamics of bacterioplankton and their top-down controls varied with season and location, being more pronounced in inshore waters. HNFs abundances showed a strong preference for larger prey inshore (r = -0.62 to -0.59, p = 0.001-0.002). Positive relationships between viruses and heterotrophic bacterioplankton abundances were more marked inshore (r = 0.67, p < 0.001) than offshore (r = 0.44, p = 0.03). The negative correlation between HNFs and viruses abundances (r = -0.47, p = 0.02) in shallow waters indicates a persistent seasonal switch between protistan grazing and viral lysis that maintains the low bacterioplankton stocks in the central Red Sea area.
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Affiliation(s)
- Eman I Sabbagh
- Red Sea Research Center (RSRC), Division of Biological and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Maria Ll Calleja
- Red Sea Research Center (RSRC), Division of Biological and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Department of Climate Geochemistry, Max Plank Institute for Chemistry (MPIC), Mainz, Germany
| | - Daniele Daffonchio
- Red Sea Research Center (RSRC), Division of Biological and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Xosé Anxelu G Morán
- Red Sea Research Center (RSRC), Division of Biological and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
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17
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Jokinen M, Sallinen S, Jones MM, Sirén J, Guilbault E, Susi H, Laine AL. The first arriving virus shapes within-host viral diversity during natural epidemics. Proc Biol Sci 2023; 290:20231486. [PMID: 37700649 PMCID: PMC10498040 DOI: 10.1098/rspb.2023.1486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 08/17/2023] [Indexed: 09/14/2023] Open
Abstract
Viral diversity has been discovered across scales from host individuals to populations. However, the drivers of viral community assembly are still largely unknown. Within-host viral communities are formed through co-infections, where the interval between the arrival times of viruses may vary. Priority effects describe the timing and order in which species arrive in an environment, and how early colonizers impact subsequent community assembly. To study the effect of the first-arriving virus on subsequent infection patterns of five focal viruses, we set up a field experiment using naïve Plantago lanceolata plants as sentinels during a seasonal virus epidemic. Using joint species distribution modelling, we find both positive and negative effects of early season viral infection on late season viral colonization patterns. The direction of the effect depends on both the host genotype and which virus colonized the host early in the season. It is well established that co-occurring viruses may change the virulence and transmission of viral infections. However, our results show that priority effects may also play an important, previously unquantified role in viral community assembly. The assessment of these temporal dynamics within a community ecological framework will improve our ability to understand and predict viral diversity in natural systems.
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Affiliation(s)
- Maija Jokinen
- Department of Evolutionary Biology and Environmental Studies, University of Zürich, 8057 Zürich, Switzerland
| | - Suvi Sallinen
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, PO Box 65, 00014, Finland
| | - Mirkka M. Jones
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, PO Box 65, 00014, Finland
- Institute of Biotechnology, HiLIFE-Helsinki Institute of Life Science, University of Helsinki, PO Box 65, 00014, Finland
| | - Jukka Sirén
- Institute of Biotechnology, HiLIFE-Helsinki Institute of Life Science, University of Helsinki, PO Box 65, 00014, Finland
| | - Emy Guilbault
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, PO Box 65, 00014, Finland
| | - Hanna Susi
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, PO Box 65, 00014, Finland
| | - Anna-Liisa Laine
- Department of Evolutionary Biology and Environmental Studies, University of Zürich, 8057 Zürich, Switzerland
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, PO Box 65, 00014, Finland
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18
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Gvaladze T, Lehnherr H, Große-Kleimann J, Hertwig S. A Bacteriophage Cocktail Reduces Five Relevant Salmonella Serotypes at Low Multiplicities of Infection and Low Temperatures. Microorganisms 2023; 11:2298. [PMID: 37764141 PMCID: PMC10535997 DOI: 10.3390/microorganisms11092298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 08/31/2023] [Accepted: 09/08/2023] [Indexed: 09/29/2023] Open
Abstract
Salmonella are important pathogenic bacteria and, following Campylobacter, they are the second most common cause of bacterial foodborne infections worldwide. To reduce the presence of bacteria along the food chain, the application of bacteriophages (phages) may be a promising tool. In this study, the lytic properties of six phages against five relevant Salmonella serotypes (S. Enteritidis, S. Typhimurium, S. Infantis, S. Paratyphi B and S. Indiana) were analyzed. Three phages were able to lyse all five serotypes. We determined the lytic potential of each phage on indicator strains in vitro at room temperature (RT) and at 37 °C using low multiplicities of infection (MOIs). Most phages reduced their host more efficiently at RT than at 37 °C, even at the lowest MOI of 0.001. Following this, the lytic activity of a cocktail comprising five phages (MOI = 0.1) was examined with each of the five serotypes and a mix of them at RT, 15, 12, 10, 8 and 6 °C. All cultures of single serotypes as well as the mixture of strains were significantly reduced at temperatures as low as 8 °C. For single serotypes, reductions of up to 5 log10 units and up to 2.3 log10 units were determined after 6 h (RT) and 40 h (8 °C), respectively. The mixture of strains was reduced by 1.7 log10 units at 8 °C. The data clearly suggest that these phages are suitable candidates for biocontrol of various Salmonella serotypes under food manufacturing conditions.
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Affiliation(s)
- Tamar Gvaladze
- Department Biological Safety, German Federal Institute for Risk Assessment, 10589 Berlin, Germany;
| | | | - Julia Große-Kleimann
- Department for Biometry, Epidemiology and Information Processing, University of Veterinary Medicine Hannover, Foundation, 30559 Hannover, Germany;
| | - Stefan Hertwig
- Department Biological Safety, German Federal Institute for Risk Assessment, 10589 Berlin, Germany;
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19
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Prosdocimi F, Cortines JR, José MV, Farias ST. Decoding viruses: An alternative perspective on their history, origins and role in nature. Biosystems 2023; 231:104960. [PMID: 37437771 DOI: 10.1016/j.biosystems.2023.104960] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 06/16/2023] [Accepted: 06/17/2023] [Indexed: 07/14/2023]
Abstract
This article provides an alternative perspective on viruses, exploring their origins, ecology, and evolution. Viruses are recognized as the most prevalent biological entities on Earth, permeating nearly all environments and forming the virosphere-a significant biological layer. They play a crucial role in regulating bacterial populations within ecosystems and holobionts, influencing microbial communities and nutrient recycling. Viruses are also key drivers of molecular evolution, actively participating in the maintenance and regulation of ecosystems and cellular organisms. Many eukaryotic genomes contain genomic elements with viral origins, which contribute to organismal equilibrium and fitness. Viruses are involved in the generation of species-specific orphan genes, facilitating adaptation and the development of unique traits in biological lineages. They have been implicated in the formation of vital structures like the eukaryotic nucleus and the mammalian placenta. The presence of virus-specific genes absent in cellular organisms suggests that viruses may pre-date cellular life. Like progenotes, viruses are ribonucleoprotein entities with simpler capsid architectures compared to proteolipidic membranes. This article presents a comprehensive scenario describing major transitions in prebiotic evolution and proposes that viruses emerged prior to the Last Universal Common Ancestor (LUCA) during the progenote era. However, it is important to note that viruses do not form a monophyletic clade, and many viral taxonomic groups originated more recently as reductions of cellular structures. Thus, viral architecture should be seen as an ancient and evolutionarily stable strategy adopted by biological systems. The goal of this article is to reshape perceptions of viruses, highlighting their multifaceted significance in the complex tapestry of life and fostering a deeper understanding of their origins, ecological impact, and evolutionary dynamics.
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Affiliation(s)
- Francisco Prosdocimi
- Laboratório de Biologia Teórica e de Sistemas, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.
| | - Juliana Reis Cortines
- Departamento de Virologia, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Brazil
| | - Marco V José
- Theoretical Biology Group, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, 04510, CDMX, Mexico
| | - Sávio Torres Farias
- Laboratório de Genética Evolutiva Paulo Leminsk, Departamento de Biologia Molecular, Universidade Federal da Paraíba, João Pessoa, Paraíba, Brazil; Network of Researchers on the Chemical Evolution of Life (NoRCEL), Leeds, LS7 3RB, UK
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20
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Lian X, Huang J, Li H, He Y, Ouyang Z, Fu S, Zhao Y, Wang D, Wang R, Guan X. Heat waves accelerate the spread of infectious diseases. ENVIRONMENTAL RESEARCH 2023; 231:116090. [PMID: 37207737 PMCID: PMC10191724 DOI: 10.1016/j.envres.2023.116090] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Revised: 04/04/2023] [Accepted: 05/09/2023] [Indexed: 05/21/2023]
Abstract
COVID-19 pandemic appeared summer surge in 2022 worldwide and this contradicts its seasonal fluctuations. Even as high temperature and intense ultraviolet radiation can inhibit viral activity, the number of new cases worldwide has increased to >78% in only 1 month since the summer of 2022 under unchanged virus mutation influence and control policies. Using the attribution analysis based on the theoretical infectious diseases model simulation, we found the mechanism of the severe COVID-19 outbreak in the summer of 2022 and identified the amplification effect of heat wave events on its magnitude. The results suggest that approximately 69.3% of COVID-19 cases this summer could have been avoided if there is no heat waves. The collision between the pandemic and the heatwave is not an accident. Climate change is leading to more frequent extreme climate events and an increasing number of infectious diseases, posing an urgent threat to human health and life. Therefore, public health authorities must quickly develop coordinated management plans to deal with the simultaneous occurrence of extreme climate events and infectious diseases.
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Affiliation(s)
- Xinbo Lian
- Collaborative Innovation Center for Western Ecological Safety, College of Atmospheric Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Jianping Huang
- Collaborative Innovation Center for Western Ecological Safety, College of Atmospheric Sciences, Lanzhou University, Lanzhou, 730000, China.
| | - Han Li
- Collaborative Innovation Center for Western Ecological Safety, College of Atmospheric Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Yongli He
- Collaborative Innovation Center for Western Ecological Safety, College of Atmospheric Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Zhi Ouyang
- Collaborative Innovation Center for Western Ecological Safety, College of Atmospheric Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Songbo Fu
- Department of Endocrinology, The First Hospital of Lanzhou University, Lanzhou, 730000, China
| | - Yingjie Zhao
- Collaborative Innovation Center for Western Ecological Safety, College of Atmospheric Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Danfeng Wang
- Collaborative Innovation Center for Western Ecological Safety, College of Atmospheric Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Rui Wang
- Collaborative Innovation Center for Western Ecological Safety, College of Atmospheric Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Xiaodan Guan
- Collaborative Innovation Center for Western Ecological Safety, College of Atmospheric Sciences, Lanzhou University, Lanzhou, 730000, China
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21
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Khan MMT, Sklar L. Editorial: Environmental contaminants in aquatic systems and chemical safety for environmental and human health, volume II. Front Public Health 2023; 11:1157834. [PMID: 37383263 PMCID: PMC10299172 DOI: 10.3389/fpubh.2023.1157834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 05/08/2023] [Indexed: 06/30/2023] Open
Affiliation(s)
- Mohiuddin Md. Taimur Khan
- Department of Civil and Environmental Engineering, Washington State University Tri-Cities, Richland, WA, United States
| | - Larry Sklar
- Center for Molecular Discovery and Cancer Center, University of New Mexico, Albuquerque, NM, United States
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22
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Microbial and Viral Genome and Proteome Nitrogen Demand Varies across Multiple Spatial Scales within a Marine Oxygen Minimum Zone. mSystems 2023; 8:e0109522. [PMID: 36920198 PMCID: PMC10134851 DOI: 10.1128/msystems.01095-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2023] Open
Abstract
Nutrient availability can significantly influence microbial genomic and proteomic streamlining, for example, by selecting for lower nitrogen to carbon ratios. Oligotrophic open ocean microbes have streamlined genomic nitrogen requirements relative to those of their counterparts in nutrient-rich coastal waters. However, steep gradients in nutrient availability occur at meter-level, and even micron-level, spatial scales. It is unclear whether such gradients also structure genomic and proteomic stoichiometry. Focusing on the eastern tropical North Pacific oxygen minimum zone (OMZ), we use comparative metagenomics to examine how nitrogen availability shapes microbial and viral genome properties along the vertical gradient across the OMZ and between two size fractions, distinguishing free-living microbes versus particle-associated microbes. We find a substantial increase in the nitrogen content of encoded proteins in particle-associated over free-living bacteria and archaea across nitrogen availability regimes over depth. Within each size fraction, we find that bacterial and viral genomic nitrogen tends to increase with increasing nitrate concentrations with depth. In contrast to cellular genes, the nitrogen content of virus proteins does not differ between size fractions. We identified arginine as a key amino acid in the modulation of the C:N ratios of core genes for bacteria, archaea, and viruses. Functional analysis reveals that particle-associated bacterial metagenomes are enriched for genes that are involved in arginine metabolism and organic nitrogen compound catabolism. Our results are consistent with nitrogen streamlining in both cellular and viral genomes on spatial scales of meters to microns. These effects are similar in magnitude to those previously reported across scales of thousands of kilometers. IMPORTANCE The genomes of marine microbes can be shaped by nutrient cycles, with ocean-scale gradients in nitrogen availability being known to influence microbial amino acid usage. It is unclear, however, how genomic properties are shaped by nutrient changes over much smaller spatial scales, for example, along the vertical transition into oxygen minimum zones (OMZs) or from the exterior to the interior of detrital particles. Here, we measure protein nitrogen usage by marine bacteria, archaea, and viruses by using metagenomes from the nitracline of the eastern tropical North Pacific OMZ, including both particle-associated and nonassociated biomass. Our results show higher genomic and proteomic nitrogen content in particle-associated microbes and at depths with higher nitrogen availability for cellular and viral genomes. This discovery suggests that stoichiometry influences microbial and viral evolution across multiple scales, including the micrometer to millimeter scale associated with particle-associated versus free-living lifestyles.
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23
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Cai L, Xu B, Li H, Xu Y, Wei W, Zhang R. Spatiotemporal Shift of T4-Like Phage Community Structure in the Three Largest Estuaries of China. Microbiol Spectr 2023; 11:e0520322. [PMID: 36877016 PMCID: PMC10101079 DOI: 10.1128/spectrum.05203-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Accepted: 02/08/2023] [Indexed: 03/07/2023] Open
Abstract
Estuaries are one of the most highly productive and economically important ecosystems at the continent-ocean interface. Estuary productivity is largely determined by the microbial community structure and activity. Viruses are major agents of microbial mortality and are key drivers of global geochemical cycles. However, the taxonomic diversity of viral communities and their spatial-temporal distribution in estuarine ecosystems have been poorly studied. In this study, we investigated the T4-like viral community composition at three major Chinese estuaries in winter and in summer. Diverse T4-like viruses, which were divided into three main clusters (Clusters I to III), were revealed. The Marine Group of Cluster III, with seven identified subgroups, was the most dominant (averaging 76.5% of the total sequences) in the Chinese estuarine ecosystems. Significant variations of T4-like viral community composition were observed among estuaries and seasons, with higher diversity occurring in winter. Among various environmental variables, temperature was a main driver of the viral communities. This study demonstrates viral assemblage diversification and seasonality in Chinese estuarine ecosystems. IMPORTANCE Viruses are ubiquitous but largely uncharacterized members of aquatic environments that cause significant mortality in microbial communities. Recent large-scale oceanic projects have greatly advanced our understanding of viral ecology in marine environments, but those studies mostly focused on oceanic regions. There have yet to be spatiotemporal studies of viral communities in estuarine ecosystems, which are unique habitats that play a significant role in global ecology and biogeochemistry. This work is the first comprehensive study that provides a detailed picture of the spatial and seasonal variation of viral communities (specifically, T4-like viral communities) in three major estuarine ecosystems in China. These findings provide much-needed knowledge regarding estuarine viral ecosystems, which currently lags in oceanic ecosystem research.
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Affiliation(s)
- Lanlan Cai
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Bu Xu
- School of Environment, Harbin Institute of Technology, Harbin, China
- Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Huifang Li
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
- Key Laboratory of Coastal Salt Marsh Ecosystems and Resources, Ministry of Natural Resources, Jiangsu Ocean University, Lianyungang, China
| | - Yongle Xu
- Institute of Marine Science and Technology, Shandong University, Shandong, China
| | - Wei Wei
- School of Environmental Ecology and Biological Engineering, Wuhan Institute of Technology, Wuhan, China
| | - Rui Zhang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
- Institute for Advanced Study, Shenzhen University, Shenzhen, China
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24
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Langlois V, Girard C, Vincent WF, Culley AI. A Tale of Two Seasons: Distinct Seasonal Viral Communities in a Thermokarst Lake. Microorganisms 2023; 11:microorganisms11020428. [PMID: 36838393 PMCID: PMC9964402 DOI: 10.3390/microorganisms11020428] [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: 12/30/2022] [Revised: 02/03/2023] [Accepted: 02/03/2023] [Indexed: 02/11/2023] Open
Abstract
Thermokarst lakes are important features of subarctic landscapes and are a substantial source of greenhouse gases, although the extent of gas produced varies seasonally. Microbial communities are responsible for the production of methane and CO2 but the "top down" forces that influence microbial dynamics (i.e., grazers and viruses) and how they vary temporally within these lakes are still poorly understood. The aim of this study was to examine viral diversity over time to elucidate the seasonal structure of the viral communities in thermokarst lakes. We produced virus-enriched metagenomes from a subarctic peatland thermokarst lake in the summer and winter over three years. The vast majority of vOTUs assigned to viral families belonged to Caudovirales (Caudoviricetes), notably the morphological groups myovirus, siphovirus and podovirus. We identified two distinct communities: a dynamic, seasonal community in the oxygenated surface layer during the summer and a stable community found in the anoxic water layer at the bottom of the lake in summer and throughout much of the water column in winter. Comparison with other permafrost and northern lake metagenomes highlighted the distinct composition of viral communities in this permafrost thaw lake ecosystem.
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Affiliation(s)
- Valérie Langlois
- Département de Biochimie, de Microbiologie et de Bio-Informatique, Université Laval, Québec, QC G1V 0A6, Canada
- Centre D’études Nordiques (CEN), Université Laval, Québec, QC G1V 0A6, Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC G1V 0A6, Canada
- Takuvik International Research Laboratory, Université Laval, Québec, QC G1V 0A6, Canada
| | - Catherine Girard
- Centre D’études Nordiques (CEN), Université Laval, Québec, QC G1V 0A6, Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC G1V 0A6, Canada
- Département des Sciences Fondamentales, Université du Québec à Chicoutimi, Chicoutimi, QC G7H 2B1, Canada
| | - Warwick F. Vincent
- Centre D’études Nordiques (CEN), Université Laval, Québec, QC G1V 0A6, Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC G1V 0A6, Canada
- Takuvik International Research Laboratory, Université Laval, Québec, QC G1V 0A6, Canada
- Département de Biologie, Université Laval, Québec, QC G1V 0A6, Canada
| | - Alexander I. Culley
- Département de Biochimie, de Microbiologie et de Bio-Informatique, Université Laval, Québec, QC G1V 0A6, Canada
- Centre D’études Nordiques (CEN), Université Laval, Québec, QC G1V 0A6, Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC G1V 0A6, Canada
- Takuvik International Research Laboratory, Université Laval, Québec, QC G1V 0A6, Canada
- Correspondence:
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25
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Tithi SS, Aylward FO, Jensen RV, Zhang L. FastViromeExplorer-Novel: Recovering Draft Genomes of Novel Viruses and Phages in Metagenomic Data. JOURNAL OF COMPUTATIONAL BIOLOGY : A JOURNAL OF COMPUTATIONAL MOLECULAR CELL BIOLOGY 2023; 30:391-408. [PMID: 36607772 DOI: 10.1089/cmb.2022.0397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Despite the recent surge of viral metagenomic studies, recovering complete virus/phage genomes from metagenomic data is still extremely difficult and most viral contigs generated from de novo assembly programs are highly fragmented, posing serious challenges to downstream analysis and inference. In this study, we develop FastViromeExplorer (FVE)-novel, a computational pipeline for reconstructing complete or near-complete viral draft genomes from metagenomic data. The FVE-novel deploys FVE to efficiently map metagenomic reads to viral reference genomes, performs de novo assembly of the mapped reads to generate contigs, and extends the contigs through iterative assembly to produce final viral scaffolds. We applied FVE-novel to an ocean metagenomic sample and obtained 268 viral scaffolds that potentially come from novel viruses. Through manual examination and validation of the 10 longest scaffolds, we successfully recovered 4 complete viral genomes, 2 are novel as they cannot be found in the existing databases and the other 2 are related to known phages. This hybrid reference-based and de novo assembly approach used by FVE-novel represents a powerful new approach for uncovering near-complete viral genomes in metagenomic data.
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Affiliation(s)
| | - Frank O Aylward
- Department of Biological Sciences, Virginia Tech, Blacksburg, Virginia, USA
| | - Roderick V Jensen
- Department of Biological Sciences, Virginia Tech, Blacksburg, Virginia, USA
| | - Liqing Zhang
- Department of Computer Science, Virginia Tech, Blacksburg, Virginia, USA
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26
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Bachy C, Baudoux AC. [Diversity and ecological importance of viruses in the marine environment]. Med Sci (Paris) 2022; 38:1008-1015. [PMID: 36692280 DOI: 10.1051/medsci/2022165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The ocean is the largest reservoir of viruses on the planet with estimates of up to several billions per liter. These viruses represent a major driving force not only for the evolution and for structuring the microbial world, but also for the functioning and the balance of marine ecosystems. With the advances in high throughput sequencing techniques, we are beginning to uncover the diversity and the complexity of this marine virosphere. This review synthesizes milestones in the field of marine viral ecology, including the diversity of these fascinating microorganisms, their impact on microbial mortality and cycling of nutrients and energy in the ocean.
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Affiliation(s)
- Charles Bachy
- Sorbonne Université, CNRS, FR2424, Station biologique de Roscoff, Roscoff, 29680, France
| | - Anne-Claire Baudoux
- Sorbonne université, CNRS, Station biologique de Roscoff, Laboratoire adaptation et diversité en milieu marin, UMR7144, Roscoff, 29680, France
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27
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Castillo DJ, Dithugoe CD, Bezuidt OK, Makhalanyane TP. Microbial ecology of the Southern Ocean. FEMS Microbiol Ecol 2022; 98:6762916. [PMID: 36255374 DOI: 10.1093/femsec/fiac123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 09/23/2022] [Accepted: 10/14/2022] [Indexed: 01/21/2023] Open
Abstract
The Southern Ocean (SO) distributes climate signals and nutrients worldwide, playing a pivotal role in global carbon sequestration. Microbial communities are essential mediators of primary productivity and carbon sequestration, yet we lack a comprehensive understanding of microbial diversity and functionality in the SO. Here, we examine contemporary studies in this unique polar system, focusing on prokaryotic communities and their relationships with other trophic levels (i.e. phytoplankton and viruses). Strong seasonal variations and the characteristic features of this ocean are directly linked to community composition and ecosystem functions. Specifically, we discuss characteristics of SO microbial communities and emphasise differences from the Arctic Ocean microbiome. We highlight the importance of abundant bacteria in recycling photosynthetically derived organic matter. These heterotrophs appear to control carbon flux to higher trophic levels when light and iron availability favour primary production in spring and summer. Conversely, during winter, evidence suggests that chemolithoautotrophs contribute to prokaryotic production in Antarctic waters. We conclude by reviewing the effects of climate change on marine microbiota in the SO.
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Affiliation(s)
- Diego J Castillo
- Department of Biochemistry, Genetics and Microbiology, Microbiome Research Group, University of Pretoria, Pretoria 0028, South Africa.,Department of Science and Innovation/South African Research Chair in Marine Microbiomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria 0028, South Africa
| | - Choaro D Dithugoe
- Department of Biochemistry, Genetics and Microbiology, Microbiome Research Group, University of Pretoria, Pretoria 0028, South Africa.,Department of Science and Innovation/South African Research Chair in Marine Microbiomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria 0028, South Africa
| | - Oliver K Bezuidt
- Department of Biochemistry, Genetics and Microbiology, Microbiome Research Group, University of Pretoria, Pretoria 0028, South Africa.,Department of Science and Innovation/South African Research Chair in Marine Microbiomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria 0028, South Africa
| | - Thulani P Makhalanyane
- Department of Biochemistry, Genetics and Microbiology, Microbiome Research Group, University of Pretoria, Pretoria 0028, South Africa.,Department of Science and Innovation/South African Research Chair in Marine Microbiomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria 0028, South Africa
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28
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Shiah FK, Lai CC, Chen TY, Ko CY, Tai JH, Chang CW. Viral shunt in tropical oligotrophic ocean. SCIENCE ADVANCES 2022; 8:eabo2829. [PMID: 36223456 PMCID: PMC9555789 DOI: 10.1126/sciadv.abo2829] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 08/25/2022] [Indexed: 06/16/2023]
Abstract
Viruses cause massive bacterial mortality and thus modulate bacteria-governed carbon transfer and nutrient recycling at global scale. The viral shunt hypothesis states the crucial role of viral lysis in retaining microbial carbon into food web processes, while its applicability to nature has not been well identified for over two decades. Here, we conducted nine diel surveys in the tropical South China Sea and suggested that the time scale adopted in sampling and system trophic status determine the "visibility" of the viral shunt in the field. Specifically, viral abundance (VA), bacterial biomass (BB), and bacterial specific growth rate (SGR) varied synchronously and presented the significant VA-BB and VA-SGR linkages at an hourly scale, which reveals direct interactions between viruses and their hosts. The differential responses of the viral shunt to temperature, i.e., looser VA-SGR coupling in warm and tighter VA-SGR coupling in cold environments, imply an altered carbon cycling in tropical oceans under climatic warming.
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Affiliation(s)
- Fuh-Kwo Shiah
- Research Center for Environmental Changes, Academia Sinica, Taipei 11529, Taiwan
- Institute of Oceanography, National Taiwan University, Taipei 10617, Taiwan
- Institute of Marine Environment and Ecology, National Taiwan Ocean University, Keelung, Taiwan
| | - Chao-Chen Lai
- Research Center for Environmental Changes, Academia Sinica, Taipei 11529, Taiwan
| | - Tzong-Yueh Chen
- Institute of Marine Environment and Ecology, National Taiwan Ocean University, Keelung, Taiwan
| | - Chia-Ying Ko
- Institute of Fisheries Science, National Taiwan University, Taipei 10617, Taiwan
- Institute of Ecology and Evolutionary Biology and Master’s Program in Biodiversity, National Taiwan University, Taipei 10617, Taiwan
| | - Jen-Hua Tai
- Research Center for Environmental Changes, Academia Sinica, Taipei 11529, Taiwan
| | - Chun-Wei Chang
- Institute of Fisheries Science, National Taiwan University, Taipei 10617, Taiwan
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29
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Braga LPP, Orland C, Emilson EJS, Fitch AA, Osterholz H, Dittmar T, Basiliko N, Mykytczuk NCS, Tanentzap AJ. Viruses direct carbon cycling in lake sediments under global change. Proc Natl Acad Sci U S A 2022; 119:e2202261119. [PMID: 36206369 PMCID: PMC9564219 DOI: 10.1073/pnas.2202261119] [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: 02/08/2022] [Accepted: 08/18/2022] [Indexed: 11/18/2022] Open
Abstract
Global change is altering the vast amount of carbon cycled by microbes between land and freshwater, but how viruses mediate this process is poorly understood. Here, we show that viruses direct carbon cycling in lake sediments, and these impacts intensify with future changes in water clarity and terrestrial organic matter (tOM) inputs. Using experimental tOM gradients within sediments of a clear and a dark boreal lake, we identified 156 viral operational taxonomic units (vOTUs), of which 21% strongly increased with abundances of key bacteria and archaea, identified via metagenome-assembled genomes (MAGs). MAGs included the most abundant prokaryotes, which were themselves associated with dissolved organic matter (DOM) composition and greenhouse gas (GHG) concentrations. Increased abundances of virus-like particles were separately associated with reduced bacterial metabolism and with shifts in DOM toward amino sugars, likely released by cell lysis rather than higher molecular mass compounds accumulating from reduced tOM degradation. An additional 9.6% of vOTUs harbored auxiliary metabolic genes associated with DOM and GHGs. Taken together, these different effects on host dynamics and metabolism can explain why abundances of vOTUs rather than MAGs were better overall predictors of carbon cycling. Future increases in tOM quantity, but not quality, will change viral composition and function with consequences for DOM pools. Given their importance, viruses must now be explicitly considered in efforts to understand and predict the freshwater carbon cycle and its future under global environmental change.
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Affiliation(s)
- Lucas P. P. Braga
- Ecosystems and Global Change Group, Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom
- Institute of Chemistry, University of Sao Paulo, Sao Paulo 05508-900, Brazil
| | - Chloé Orland
- Ecosystems and Global Change Group, Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom
| | - Erik J. S. Emilson
- Ecosystems and Global Change Group, Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom
| | - Amelia A. Fitch
- Ecosystems and Global Change Group, Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom
| | - Helena Osterholz
- Institute for Chemistry and Biology of the Marine Environment and Helmholtz Institute for Functional Marine Biodiversity, University of Oldenburg, 26129 Oldenburg, Germany
| | - Thorsten Dittmar
- Institute for Chemistry and Biology of the Marine Environment and Helmholtz Institute for Functional Marine Biodiversity, University of Oldenburg, 26129 Oldenburg, Germany
| | - Nathan Basiliko
- Vale Living with Lakes Centre, Laurentian University, Sudbury, ON P3E2C6, Canada
| | | | - Andrew J. Tanentzap
- Ecosystems and Global Change Group, Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom
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30
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Bruneaux M, Ashrafi R, Kronholm I, Laanto E, Örmälä‐Tiznado A, Galarza JA, Zihan C, Kubendran Sumathi M, Ketola T. The effect of a temperature-sensitive prophage on the evolution of virulence in an opportunistic bacterial pathogen. Mol Ecol 2022; 31:5402-5418. [PMID: 35917247 PMCID: PMC9826266 DOI: 10.1111/mec.16638] [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: 03/01/2022] [Revised: 07/14/2022] [Accepted: 07/21/2022] [Indexed: 01/11/2023]
Abstract
Viruses are key actors of ecosystems and have major impacts on global biogeochemical cycles. Prophages deserve particular attention as they are ubiquitous in bacterial genomes and can enter a lytic cycle when triggered by environmental conditions. We explored how temperature affects the interactions between prophages and other biological levels using an opportunistic pathogen, the bacterium Serratia marcescens, which harbours several prophages and that had undergone an evolution experiment under several temperature regimes. We found that the release of one of the prophages was temperature-sensitive and malleable to evolutionary changes. We further discovered that the virulence of the bacterium in an insect model also evolved and was positively correlated with phage release rates. We determined through analysis of genetic and epigenetic data that changes in the bacterial outer cell wall structure possibly explain this phenomenon. We hypothezise that the temperature-dependent phage release rate acted as a selection pressure on S. marcescens and that it resulted in modified bacterial virulence in the insect host. Our study system illustrates how viruses can mediate the influence of abiotic environmental changes to other biological levels and thus be involved in ecosystem feedback loops.
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Affiliation(s)
- Matthieu Bruneaux
- Department of Biological and Environmental ScienceUniversity of JyväskyläJyväskyläFinland
| | - Roghaieh Ashrafi
- Department of Biological and Environmental ScienceUniversity of JyväskyläJyväskyläFinland
| | - Ilkka Kronholm
- Department of Biological and Environmental ScienceUniversity of JyväskyläJyväskyläFinland
| | - Elina Laanto
- Department of Biological and Environmental ScienceUniversity of JyväskyläJyväskyläFinland,Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental SciencesUniversity of HelsinkiHelsinkiFinland
| | | | - Juan A. Galarza
- Department of Biological and Environmental ScienceUniversity of JyväskyläJyväskyläFinland
| | - Chen Zihan
- Department of Biological and Environmental ScienceUniversity of JyväskyläJyväskyläFinland,Shenzhen Research InstituteThe Chinese University of Hong KongShenzhenChina
| | - Mruthyunjay Kubendran Sumathi
- Department of Biological and Environmental ScienceUniversity of JyväskyläJyväskyläFinland,Department of Ecology and Evolutionary BiologyUniversity of ArizonaTucsonArizonaUSA
| | - Tarmo Ketola
- Department of Biological and Environmental ScienceUniversity of JyväskyläJyväskyläFinland
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31
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Feng Y, Hou S, Roleda MY, Fu FX. Editorial: Responses of marine microbes to multiple environmental drivers of global change: The interplay of abiotic and biotic factors. Front Microbiol 2022; 13:975841. [PMID: 36147843 PMCID: PMC9488806 DOI: 10.3389/fmicb.2022.975841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 08/23/2022] [Indexed: 12/01/2022] Open
Affiliation(s)
- Yuanyuan Feng
- School of Oceanography, Shanghai Jiao Tong University, Shanghai, China
- Shanghai Frontiers Science Center of Polar Science (SCOPS), Shanghai, China
- *Correspondence: Yuanyuan Feng
| | - Shengwei Hou
- Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, China
- State Key Laboratory for Marine Environmental Science, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, China
- Shengwei Hou
| | - Michael Y. Roleda
- Division of Biotechnology and Plant Health, Norwegian Institute of Bioeconomy Research (NIBIO), Ås, Norway
- Biomarine Resource Valorisation, Division of Food Production and Society, Norwegian Institute of Bioeconomy Research (NIBIO), Bodø, Norway
- The Marine Science Institute, College of Science, University of the Philippines, Quezon City, Philippines
| | - Fei-Xue Fu
- Department of Biological Sciences – Marine and Environmental Biology, University of Southern California, Los Angeles, CA, United States
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32
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Han M, Luo G, He J, Liang Y, Chen X, Liu G, Su Y, Ge F, Yu H, Zhao J, Hao Q, Shao H, Sung YY, Mok WJ, Wong LL, McMinn A, Wang M. Distributions and relationships of virio- and picoplankton in the epi-, meso- and bathypelagic zones of the Amundsen Sea, West Antarctica during the austral summer. Front Microbiol 2022; 13:941323. [PMID: 35966700 PMCID: PMC9363919 DOI: 10.3389/fmicb.2022.941323] [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: 05/11/2022] [Accepted: 07/08/2022] [Indexed: 11/13/2022] Open
Abstract
Virioplankton and picoplankton are the most abundant marine biological entities on earth and mediate biogeochemical cycles in the Southern Ocean. However, understanding of their distribution and relationships with environmental factors is lacking. Here, we report on their distribution and relationships with environmental factors at 48 stations from 112.5° to 150°W and 67° to 75.5°S in the Amundsen Sea of West Antarctica. The epipelagic stations were grouped into four clusters based on the virio- and picoplankton composition and abundance. Clusters three and four, which were associated with the ice-edge blooms in the coastal and Amundsen Sea Polynya (ASP) areas, had high abundances of autotrophic picoeukaryotes; this resulted in subsequent high abundances of heterotrophic prokaryotes and viruses. Cluster two stations were in open oceanic areas, where the abundances of autotrophic and heterotrophic picoplankton were low. Cluster one stations were located between the areas of blooms and the oceanic areas, which had a low abundance of heterotrophic prokaryotes and picoeukaryotes and a high abundance of virioplankton. The abundance of viruses was significantly correlated with the abundances of autotrophic picoeukaryotes and Chl-a concentration in oceanic areas, although this reflected a time-lag with autotrophic picoeukaryote and heterotrophic prokaryotes abundances in ice-edge bloom areas. The upwelling of Circumpolar Deep Water (CDW) might have induced the high abundance of autotrophic picoeukaryotes in the epipelagic zone, and the sinking particulate organic carbon (POC) might have induced the high abundance of heterotrophic prokaryotes and virioplankton in the meso- and bathypelagic zones. This study shows that the summer distribution of virio- and picoplankton in the Amundsen Sea of West Antarctica was mainly controlled by upwelling of the CDW and the timing of ice-edge blooms.
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Affiliation(s)
- Meiaoxue Han
- College of Marine Life Sciences, Key Lab of Polar Oceanography and Global Ocean Change, Institute of Evolution and Marine Biodiversity, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
| | - Guangfu Luo
- Antarctic Great Wall Ecology National Observation and Research Station, Polar Research Institute of China, Shanghai, China
- MNR Key Laboratory for Polar Science, Polar Research Institute of China, Shanghai, China
- College of Environmental Science and Engineering, Tongji University, Shanghai, China
| | - Jianfeng He
- Antarctic Great Wall Ecology National Observation and Research Station, Polar Research Institute of China, Shanghai, China
- MNR Key Laboratory for Polar Science, Polar Research Institute of China, Shanghai, China
- College of Environmental Science and Engineering, Tongji University, Shanghai, China
- *Correspondence: Jianfeng He,
| | - Yantao Liang
- College of Marine Life Sciences, Key Lab of Polar Oceanography and Global Ocean Change, Institute of Evolution and Marine Biodiversity, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
- UMT-OUC Joint Centre for Marine Studies, Qingdao, China
- Yantao Liang,
| | - Xuechao Chen
- College of Marine Life Sciences, Key Lab of Polar Oceanography and Global Ocean Change, Institute of Evolution and Marine Biodiversity, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
| | - Gang Liu
- College of Marine Life Sciences, Key Lab of Polar Oceanography and Global Ocean Change, Institute of Evolution and Marine Biodiversity, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
| | - Yue Su
- College of Marine Life Sciences, Key Lab of Polar Oceanography and Global Ocean Change, Institute of Evolution and Marine Biodiversity, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
| | - Fuyue Ge
- College of Marine Life Sciences, Key Lab of Polar Oceanography and Global Ocean Change, Institute of Evolution and Marine Biodiversity, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
| | - Hao Yu
- College of Marine Life Sciences, Key Lab of Polar Oceanography and Global Ocean Change, Institute of Evolution and Marine Biodiversity, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
| | - Jun Zhao
- Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, China
| | - Qiang Hao
- Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, China
| | - Hongbing Shao
- College of Marine Life Sciences, Key Lab of Polar Oceanography and Global Ocean Change, Institute of Evolution and Marine Biodiversity, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
- UMT-OUC Joint Centre for Marine Studies, Qingdao, China
| | - Yeong Yik Sung
- UMT-OUC Joint Centre for Marine Studies, Qingdao, China
- Institute of Marine Biotechnology, University of Malaysia Terengganu (UMT), Kuala Terengganu, Malaysia
| | - Wen Jye Mok
- UMT-OUC Joint Centre for Marine Studies, Qingdao, China
- Institute of Marine Biotechnology, University of Malaysia Terengganu (UMT), Kuala Terengganu, Malaysia
| | - Li Lian Wong
- UMT-OUC Joint Centre for Marine Studies, Qingdao, China
- Institute of Marine Biotechnology, University of Malaysia Terengganu (UMT), Kuala Terengganu, Malaysia
| | - Andrew McMinn
- College of Marine Life Sciences, Key Lab of Polar Oceanography and Global Ocean Change, Institute of Evolution and Marine Biodiversity, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, TAS, Australia
| | - Min Wang
- College of Marine Life Sciences, Key Lab of Polar Oceanography and Global Ocean Change, Institute of Evolution and Marine Biodiversity, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
- UMT-OUC Joint Centre for Marine Studies, Qingdao, China
- Department of Critical Care Medicine, The Affiliated Hospital of Qingdao University, Qingdao, China
- Min Wang,
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33
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Rezakhani Moghaddam H, Ranjbaran S, Babazadeh T. The role of e-health literacy and some cognitive factors in adopting protective behaviors of COVID-19 in Khalkhal residents. Front Public Health 2022; 10:916362. [PMID: 35942262 PMCID: PMC9356231 DOI: 10.3389/fpubh.2022.916362] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Accepted: 06/24/2022] [Indexed: 11/28/2022] Open
Abstract
Background Several vaccines have recently been generated and are being utilized to prevent COVID-19 mortality. Although the disease is causing many fatalities worldwide, preventative practices should be prioritized, even if vaccines are available. Therefore, this study aimed to identify the role of e-health literacy and some cognitive factors in adopting protective behaviors against COVID-19 in Khalkhal residents. Methods In the present cross-sectional study we recruited 380 people aged 18–65 according to cluster sampling from September 2021 to December 2021 in Khalkhal County, Iran. Reliable and validated tools were applied to data collection, including the eHealth Literacy Scale (eHEALS) in Persian and the Cognitive factors assessment questionnaire based on the Health Belief Model (HBM). Data were analyzed using Chi-square, one-way ANOVA, independent samples t-test, and bivariate correlation. The predictors were also determined using hierarchical linear regression analysis. Results The average age of the participants was 35.26 ± 11.51 years. The regression analysis implied that gender (p-value = 0.032), education level (p-value = 0.001), occupational status (p-value = 0.002), income (p-value = 0.001), and marriage (p-value = 0.001) had statistically significant associations with e-HL. Additionally, education level (p-value = 0.001), occupational status (p-value = 0.001), income (p-value = 0.001), and marriage (p-value = 0.002) revealed statistically significant associations with COVID-19 preventive behaviors. Approximately 16.5% of the variation in the COVID-19 protective behaviors is explained by the cognitive factors and the demographic variables. Overall, demographic, cognitive, and e-HL variables were able to explain roughly 35.5% of the variation in COVID-19 protective behaviors. Furthermore, self-efficacy was the strongest predictor of protective behaviors (β = 0.214). Conclusions HBM constructs successfully predicted the role of e-health literacy and some cognitive factors in adopting COVID-19 protective behaviors. People with high socioeconomic levels were better at e-health literacy and COVID-19 protective behaviors during the pandemic. Moreover, applying approaches to adopting COVID-19 protective behaviors is essential, especially in low socioeconomic status (SES) groups.
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Affiliation(s)
| | - Soheila Ranjbaran
- Department of Public Health, Sarab Faculty of Medical Sciences, Sarab, Iran
| | - Towhid Babazadeh
- Department of Public Health, Sarab Faculty of Medical Sciences, Sarab, Iran
- *Correspondence: Towhid Babazadeh
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34
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Desvignes T, Lauridsen H, Valdivieso A, Fontenele RS, Kraberger S, Murray KN, Le François NR, Detrich HW, Kent ML, Varsani A, Postlethwait JH. A parasite outbreak in notothenioid fish in an Antarctic fjord. iScience 2022; 25:104588. [PMID: 35800770 PMCID: PMC9253362 DOI: 10.1016/j.isci.2022.104588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 05/25/2022] [Accepted: 06/07/2022] [Indexed: 11/18/2022] Open
Abstract
Climate changes can promote disease outbreaks, but their nature and potential impacts in remote areas have received little attention. In a hot spot of biodiversity on the West Antarctic Peninsula, which faces among the fastest changing climates on Earth, we captured specimens of two notothenioid fish species affected by large skin tumors at an incidence never before observed in the Southern Ocean. Molecular and histopathological analyses revealed that X-cell parasitic alveolates, members of a genus we call Notoxcellia, are the etiological agent of these tumors. Parasite-specific molecular probes showed that xenomas remained within the skin but largely outgrew host cells in the dermis. We further observed that tumors induced neovascularization in underlying tissue and detrimentally affected host growth and condition. Although many knowledge gaps persist about X-cell disease, including its mode of transmission and life cycle, these findings reveal potentially active biotic threats to vulnerable Antarctic ecosystems.
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Affiliation(s)
- Thomas Desvignes
- Institute of Neuroscience, University of Oregon, Eugene, OR 97403, USA
| | - Henrik Lauridsen
- Department of Clinical Medicine, Aarhus University; Palle Juul-Jensens Boulevard 99, 8200 Aarhus N, Denmark
| | - Alejandro Valdivieso
- Institut de Ciències del Mar, Consejo Superior de Investigaciones Científicas (CSIC), Barcelona Spain
| | - Rafaela S Fontenele
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine and School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Simona Kraberger
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine and School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Katrina N Murray
- Institute of Neuroscience, University of Oregon, Eugene, OR 97403, USA
| | - Nathalie R Le François
- Laboratoire Physiologie, Aquaculture et Conservation, Biodôme de Montréal/Espace pour la vie, 4777 Avenue Pierre-De Coubertin, Montreal, QC H1V 1B3, Canada
| | - H William Detrich
- Department of Marine and Environmental Sciences, Northeastern University Marine Science Center, 430 Nahant Rd, Nahant, MA 01908, USA
| | - Michael L Kent
- Department of Microbiology, Oregon State University, Corvallis, OR 97331, USA
| | - Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine and School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
- Structural Biology Research Unit, Department of Integrative Biomedical Sciences, University of Cape Town, 7925 Cape Town, South Africa
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35
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Xie L, Zhang R, Luo YW. Assessment of Explicit Representation of Dynamic Viral Processes in Regional Marine Ecological Models. Viruses 2022; 14:v14071448. [PMID: 35891428 PMCID: PMC9324674 DOI: 10.3390/v14071448] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Revised: 06/25/2022] [Accepted: 06/26/2022] [Indexed: 01/27/2023] Open
Abstract
Viruses, the most abundant microorganisms in the ocean, play important roles in marine ecosystems, mainly by killing their hosts and contributing to nutrient recycling. However, in models simulating ecosystems in real marine environments, the virus-mediated mortality (VMM) rates of their hosts are implicitly represented by constant parameters, thus ignoring the dynamics caused by interactions between viruses and hosts. Here, we construct a model explicitly representing marine viruses and the VMM rates of major hosts, heterotrophic bacteria, and apply it to two sites in the oligotrophic North Pacific and the more productive Arabian Sea. The impacts of the viral processes were assessed by comparing model results with the viral processes enabled and disabled. For reliable assessments, a data assimilation method was used to objectively optimize the model parameters in each run. The model generated spatiotemporally variable VMM rates, generally decreasing in the subsurface but increasing at the surface. Although the dynamics introduced by viruses could be partly stabilized by the ecosystems, they still caused substantial changes to the bacterial abundance, primary production and carbon export, with the changes greater at the more productive site. Our modeling experiments reveal the importance of explicitly simulating dynamic viral processes in marine ecological models.
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36
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Stepanova OA, Gaisky PV, Sholar SA. Influence of a Constant Magnetic Field on the Infectious Titer of Black Sea Algal Viruses. Biophysics (Nagoya-shi) 2022; 67:183-187. [PMID: 35789556 PMCID: PMC9244016 DOI: 10.1134/s000635092202021x] [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: 07/11/2021] [Revised: 12/18/2021] [Accepted: 12/21/2021] [Indexed: 11/23/2022] Open
Abstract
The change in the infectious titer of strains of the Black Sea algal viruses of three species of microalgae (Tetraselmis viridis-strain TvV-S21-1, Dunaliella viridis-strain DvV-S20-1 and Phaeodactylum tricornutum-strain PtV-S20-1) after incubation in a constant unidirectional magnetic field with a magnetic induction of 60 mT was studied experimentally. The studies were carried out using a laboratory installation with a duration of experiments ranging from 24-72 h to 6-8 days. A decrease in the infectious titer of algal viruses by 1-2 orders (10-100 times) was recorded after a magnetic load.
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Affiliation(s)
- O. A. Stepanova
- Institute of Natural and Technical Systems of Russian Academy of Sciences, 299011 Sevastopol, Russia
| | - P. V. Gaisky
- Federal Research Center “Marine Hydrophysical Institute of Russian Academy of Sciences”, 299011 Sevastopol, Russia
| | - S. A. Sholar
- Federal Research Center “Marine Hydrophysical Institute of Russian Academy of Sciences”, 299011 Sevastopol, Russia
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37
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Cohen-Rengifo M, Danion M, Gonzalez AA, Bégout ML, Cormier A, Noël C, Cabon J, Vitré T, Mark FC, Mazurais D. The extensive transgenerational transcriptomic effects of ocean acidification on the olfactory epithelium of a marine fish are associated with a better viral resistance. BMC Genomics 2022; 23:448. [PMID: 35710351 PMCID: PMC9204966 DOI: 10.1186/s12864-022-08647-w] [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: 12/22/2021] [Accepted: 05/05/2022] [Indexed: 11/19/2022] Open
Abstract
Background Progressive CO2-induced ocean acidification (OA) impacts marine life in ways that are difficult to predict but are likely to become exacerbated over generations. Although marine fishes can balance acid–base homeostasis efficiently, indirect ionic regulation that alter neurosensory systems can result in behavioural abnormalities. In marine invertebrates, OA can also affect immune system function, but whether this is the case in marine fishes is not fully understood. Farmed fish are highly susceptible to disease outbreak, yet strategies for overcoming such threats in the wake of OA are wanting. Here, we exposed two generations of the European sea bass (Dicentrarchus labrax) to end-of-century predicted pH levels (IPCC RCP8.5), with parents (F1) being exposed for four years and their offspring (F2) for 18 months. Our design included a transcriptomic analysis of the olfactory rosette (collected from the F2) and a viral challenge (exposing F2 to betanodavirus) where we assessed survival rates. Results We discovered transcriptomic trade-offs in both sensory and immune systems after long-term transgenerational exposure to OA. Specifically, RNA-Seq analysis of the olfactory rosette, the peripheral olfactory organ, from 18-months-old F2 revealed extensive regulation in genes involved in ion transport and neuronal signalling, including GABAergic signalling. We also detected OA-induced up-regulation of genes associated with odour transduction, synaptic plasticity, neuron excitability and wiring and down-regulation of genes involved in energy metabolism. Furthermore, OA-exposure induced up-regulation of genes involved in innate antiviral immunity (pathogen recognition receptors and interferon-stimulated genes) in combination with down-regulation of the protein biosynthetic machinery. Consistently, OA-exposed F2 challenged with betanodavirus, which causes damage to the nervous system of marine fish, had acquired improved resistance. Conclusion F2 exposed to long-term transgenerational OA acclimation showed superior viral resistance, though as their metabolic and odour transduction programs were altered, odour-mediated behaviours might be consequently impacted. Although it is difficult to unveil how long-term OA impacts propagated between generations, our results reveal that, across generations, trade-offs in plastic responses is a core feature of the olfactory epithelium transcriptome in OA-exposed F2 offspring, and will have important consequences for how cultured and wild fish interacts with its environment. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08647-w.
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Affiliation(s)
| | - Morgane Danion
- Ploufragan-Plouzané Laboratory, Fish Viral Pathology Unit, French Agency for Food, Environmental and Occupational Health and Safety (ANSES), Technopôle Brest-Iroise, 29280, Plouzané, France
| | - Anne-Alicia Gonzalez
- MGX, CNRS, INSERM, University of Montpellier, Biocampus Montpellier, Montpellier, France
| | - Marie-Laure Bégout
- MARBEC, University of Montpellier, CNRS, IFREMER, 34250, Palavas-les-Flots, IRD, France
| | | | - Cyril Noël
- IFREMER, SEBIMER, 29280, Plouzané, France
| | - Joëlle Cabon
- Ploufragan-Plouzané Laboratory, Fish Viral Pathology Unit, French Agency for Food, Environmental and Occupational Health and Safety (ANSES), Technopôle Brest-Iroise, 29280, Plouzané, France
| | | | - Felix C Mark
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research (AWI), Department of Integrative Ecophysiology, 27570, Bremerhaven, Germany
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Flynn KJ, Mitra A, Wilson WH, Kimmance SA, Clark DR, Pelusi A, Polimene L. 'Boom-and-busted' dynamics of phytoplankton-virus interactions explain the paradox of the plankton. THE NEW PHYTOLOGIST 2022; 234:990-1002. [PMID: 35179778 PMCID: PMC9313554 DOI: 10.1111/nph.18042] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 02/04/2022] [Indexed: 05/13/2023]
Abstract
Rapid virus proliferation can exert a powerful control on phytoplankton host populations, playing a significant role in marine biogeochemistry and ecology. We explore how marine lytic viruses impact phytoplankton succession, affecting host and nonhost populations. Using an in silico food web we conducted simulation experiments under a range of different abiotic and biotic conditions, exploring virus-host-grazer interactions and manipulating competition, allometry, motility and cyst cycles. Virus-host and predator-prey interactions, and interactions with competitors, generate bloom dynamics with a pronounced 'boom-and-busted' dynamic (BBeD) which leads to the suppression of otherwise potentially successful phytoplankton species. The BBeD is less pronounced at low nutrient loading through distancing of phytoplankton hosts, while high sediment loading and high nonhost biomass decrease the abundance of viruses through adsorption. Larger hosts are inherently more distanced, but motility increases virus attack, while cyst cycles promote spatial and temporal distancing. Virus control of phytoplankton bloom development appears more important than virus-induced termination of those blooms. This affects plankton succession - not only the growth of species infected by the virus, but also those that compete for the same resources and are collectively subjected to common grazer control. The role of viruses in structuring plankton communities via BBeDs can thus provide an explanation for the paradox of the plankton.
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Affiliation(s)
- Kevin J. Flynn
- Plymouth Marine LaboratoryProspect Place, West HoePlymouthPL1 3DHUK
| | - Aditee Mitra
- School of Earth and Environmental SciencesCardiff UniversityCardiffCF10 3ATUK
| | - William H. Wilson
- Marine Biological Association of the UK, The LaboratoryCitadel HillPlymouthPL1 2PBUK
- School of Biological and Marine SciencesUniversity of PlymouthPL4 8AAUK
| | | | - Darren R. Clark
- Plymouth Marine LaboratoryProspect Place, West HoePlymouthPL1 3DHUK
| | - Angela Pelusi
- School of Earth and Environmental SciencesCardiff UniversityCardiffCF10 3ATUK
| | - Luca Polimene
- Plymouth Marine LaboratoryProspect Place, West HoePlymouthPL1 3DHUK
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Hosseini H, Al-Jabri HM, Moheimani NR, Siddiqui SA, Saadaoui I. Marine microbial bioprospecting: Exploitation of marine biodiversity towards biotechnological applications-a review. J Basic Microbiol 2022; 62:1030-1043. [PMID: 35467037 DOI: 10.1002/jobm.202100504] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 03/14/2022] [Accepted: 04/07/2022] [Indexed: 11/09/2022]
Abstract
The increase in the human population causes an increase in the demand for nutritional supplies and energy resources. Thus, the novel, natural, and renewable resources became of great interest. Here comes the optimistic role of bioprospecting as a promising tool to isolate novel and interesting molecules and microorganisms from the marine environment as alternatives to the existing resources. Bioprospecting of marine metabolites and microorganisms with high biotechnological potentials has gained wide interest due to the variability and richness of the marine environment. Indeed, the existence of extreme conditions that increases the adaptability of marine organisms, especially planktons, allow the presence of interesting biological species that are able to produce novel compounds with multiple health benefits and high economical value. This review aims to provide a comprehensive overview of marine microbial bioprospecting as a growing field of interest. It emphasizes functional bioprospecting that facilitates the discovery of interesting metabolites. Marine bioprospecting was also discussed from a legal aspect for the first time, focusing on the shortcomings of international law. We also summarized the challenges facing bioprospecting in the marine environment including economic feasibility issues.
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Affiliation(s)
- Hoda Hosseini
- Algal Technologies Program, Centre for Sustainable Development, College of Arts and Sciences, Qatar University, Doha, Qatar
| | - Hareb M Al-Jabri
- Algal Technologies Program, Centre for Sustainable Development, College of Arts and Sciences, Qatar University, Doha, Qatar.,Department of Biological and Environmental Sciences, College of Arts and Sciences, Qatar University, Doha, Qatar
| | - Navid R Moheimani
- Algae R&D Centre, Harry Buttler Institute, Murdoch University, Murdoch, Western Australia, Australia
| | - Simil A Siddiqui
- Algal Technologies Program, Centre for Sustainable Development, College of Arts and Sciences, Qatar University, Doha, Qatar
| | - Imen Saadaoui
- Algal Technologies Program, Centre for Sustainable Development, College of Arts and Sciences, Qatar University, Doha, Qatar.,Department of Biological and Environmental Sciences, College of Arts and Sciences, Qatar University, Doha, Qatar
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40
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Gao Y, Lu Y, Dungait JAJ, Liu J, Lin S, Jia J, Yu G. The "Regulator" Function of Viruses on Ecosystem Carbon Cycling in the Anthropocene. Front Public Health 2022; 10:858615. [PMID: 35425734 PMCID: PMC9001988 DOI: 10.3389/fpubh.2022.858615] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 03/07/2022] [Indexed: 01/18/2023] Open
Abstract
Viruses act as "regulators" of the global carbon cycle because they impact the material cycles and energy flows of food webs and the microbial loop. The average contribution of viruses to the Earth ecosystem carbon cycle is 8.6‰, of which its contribution to marine ecosystems (1.4‰) is less than its contribution to terrestrial (6.7‰) and freshwater (17.8‰) ecosystems. Over the past 2,000 years, anthropogenic activities and climate change have gradually altered the regulatory role of viruses in ecosystem carbon cycling processes. This has been particularly conspicuous over the past 200 years due to rapid industrialization and attendant population growth. The progressive acceleration of the spread and reproduction of viruses may subsequently accelerate the global C cycle.
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Affiliation(s)
- Yang Gao
- Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing, China.,College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Yao Lu
- Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing, China.,College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Jennifer A J Dungait
- Geography, College of Life and Environmental Science, University of Exeter, Exeter, United Kingdom.,Carbon Management Centre, SRUC-Scotland's Rural College, Edinburgh, United Kingdom
| | - Jianbao Liu
- Key Laboratory of Alpine Ecology, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, China.,Chinese Academy of Sciences (CAS) Center for Excellence in Tibetan Plateau Earth Sciences, Chinese Academy of Sciences, Beijing, China
| | - Shunhe Lin
- Department of Obstetrics and Gynecology, Fujian Maternity and Child Health Hospital, Fuzhou, China
| | - Junjie Jia
- Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing, China.,College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Guirui Yu
- Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing, China.,College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
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41
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Cherabier P, Ferrière R. Eco-evolutionary responses of the microbial loop to surface ocean warming and consequences for primary production. THE ISME JOURNAL 2022; 16:1130-1139. [PMID: 34864820 PMCID: PMC8940968 DOI: 10.1038/s41396-021-01166-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 11/19/2021] [Accepted: 11/26/2021] [Indexed: 11/09/2022]
Abstract
Predicting the response of ocean primary production to climate warming is a major challenge. One key control of primary production is the microbial loop driven by heterotrophic bacteria, yet how warming alters the microbial loop and its function is poorly understood. Here we develop an eco-evolutionary model to predict the physiological response and adaptation through selection of bacterial populations in the microbial loop and how this will impact ecosystem function such as primary production. We find that the ecophysiological response of primary production to warming is driven by a decrease in regenerated production which depends on nutrient availability. In nutrient-poor environments, the loss of regenerated production to warming is due to decreasing microbial loop activity. However, this ecophysiological response can be opposed or even reversed by bacterial adaptation through selection, especially in cold environments: heterotrophic bacteria with lower bacterial growth efficiency are selected, which strengthens the "link" behavior of the microbial loop, increasing both new and regenerated production. In cold and rich environments such as the Arctic Ocean, the effect of bacterial adaptation on primary production exceeds the ecophysiological response. Accounting for bacterial adaptation through selection is thus critically needed to improve models and projections of the ocean primary production in a warming world.
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Affiliation(s)
- Philippe Cherabier
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Université Paris Sciences et Lettres, CNRS, INSERM, Paris, 75005, France.
| | - Régis Ferrière
- grid.462036.5Institut de Biologie de l’Ecole Normale Supérieure (IBENS), Université Paris Sciences et Lettres, CNRS, INSERM, Paris, 75005 France ,grid.134563.60000 0001 2168 186XDepartment of Ecology & Evolutionary Biology, University of Arizona, Tucson, AZ 85721 USA ,grid.134563.60000 0001 2168 186XInternational Research Laboratory for Interdisciplinary Global Environmental Studies (iGLOBES), CNRS, ENS-PSL University, University of Arizona, Tucson, AZ 85721 USA
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42
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Kolundžija S, Cheng DQ, Lauro FM. RNA Viruses in Aquatic Ecosystems through the Lens of Ecological Genomics and Transcriptomics. Viruses 2022; 14:702. [PMID: 35458432 PMCID: PMC9029791 DOI: 10.3390/v14040702] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 03/19/2022] [Accepted: 03/23/2022] [Indexed: 02/04/2023] Open
Abstract
Massive amounts of data from nucleic acid sequencing have changed our perspective about diversity and dynamics of marine viral communities. Here, we summarize recent metatranscriptomic and metaviromic studies targeting predominantly RNA viral communities. The analysis of RNA viromes reaffirms the abundance of lytic (+) ssRNA viruses of the order Picornavirales, but also reveals other (+) ssRNA viruses, including RNA bacteriophages, as important constituents of extracellular RNA viral communities. Sequencing of dsRNA suggests unknown diversity of dsRNA viruses. Environmental metatranscriptomes capture the dynamics of ssDNA, dsDNA, ssRNA, and dsRNA viruses simultaneously, unravelling the full complexity of viral dynamics in the marine environment. RNA viruses are prevalent in large size fractions of environmental metatranscriptomes, actively infect marine unicellular eukaryotes larger than 3 µm, and can outnumber bacteriophages during phytoplankton blooms. DNA and RNA viruses change abundance on hourly timescales, implying viral control on a daily temporal basis. Metatranscriptomes of cultured protists host a diverse community of ssRNA and dsRNA viruses, often with multipartite genomes and possibly persistent intracellular lifestyles. We posit that RNA viral communities might be more diverse and complex than formerly anticipated and that the influence they exert on community composition and global carbon flows in aquatic ecosystems may be underestimated.
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Affiliation(s)
- Sandra Kolundžija
- Asian School of the Environment, Nanyang Technological University, 50 Nanyang Avenue, Singapore 639798, Singapore;
| | - Dong-Qiang Cheng
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore;
| | - Federico M. Lauro
- Asian School of the Environment, Nanyang Technological University, 50 Nanyang Avenue, Singapore 639798, Singapore;
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore;
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43
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Albright MBN, Gallegos-Graves LV, Feeser KL, Montoya K, Emerson JB, Shakya M, Dunbar J. Experimental evidence for the impact of soil viruses on carbon cycling during surface plant litter decomposition. ISME COMMUNICATIONS 2022; 2:24. [PMID: 37938672 PMCID: PMC9723558 DOI: 10.1038/s43705-022-00109-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 02/13/2022] [Accepted: 02/16/2022] [Indexed: 06/01/2023]
Abstract
To date, the potential impact of viral communities on biogeochemical cycles in soil has largely been inferred from correlational evidence, such as virus-driven changes in microbial abundances, viral auxiliary metabolic genes, and links with soil physiochemical properties. To more directly test the impact of soil viruses on carbon cycling during plant litter decomposition, we added concentrated viral community suspensions to complex litter decomposer communities in 40-day microcosm experiments. Microbial communities from two New Mexico alpine soils, Pajarito (PJ) and Santa Fe (SF), were inoculated onto grass litter on sand, and three treatments were applied in triplicate to each set of microcosms: addition of buffer (no added virus), live virus (+virus), or killed-virus (+killed-virus) fractions extracted from the same soil. Significant differences in respiration were observed between the +virus and +killed-virus treatments in the PJ, but not the SF microcosms. Bacterial and fungal community composition differed significantly by treatment in both PJ and SF microcosms. Combining data across both soils, viral addition altered links between bacterial and fungal diversity, dissolved organic carbon and total nitrogen. Overall, we demonstrate that increasing viral pressure in complex microbial communities can impact terrestrial biogeochemical cycling but is context-dependent.
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Affiliation(s)
- Michaeline B N Albright
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, US.
- Allonnia LLC, Boston, MA, US.
| | | | - Kelli L Feeser
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, US
| | - Kyana Montoya
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, US
| | - Joanne B Emerson
- Department of Plant Pathology, University of California, Davis, Davis, CA, US
| | - Migun Shakya
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, US
| | - John Dunbar
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, US
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44
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Nair S, Li C, Mou S, Zhang Z, Zhang Y. A Novel Phage Indirectly Regulates Diatom Growth by Infecting a Diatom-Associated Biofilm-Forming Bacterium. Appl Environ Microbiol 2022; 88:e0213821. [PMID: 35020448 PMCID: PMC8904054 DOI: 10.1128/aem.02138-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 01/05/2022] [Indexed: 11/20/2022] Open
Abstract
Algae and heterotrophic bacteria have close and intricate interactions, which are regulated by multiple factors in the natural environment. Phages are the major factor determining bacterial mortality rates. However, their impacts on the alga-associated bacteria and thus on the alga-bacterium interactions are poorly understood. Here, we obtained a diatom-associated bacterium, Stappia indica SNL01, that could form a biofilm and had an inhibitory effect on the growth of the diatom Thalassiosira pseudonana. Meanwhile, phage SI01, with a double-stranded circular DNA genome (44,247 bp), infecting S. indica SNL01 was isolated. Phylogenetic analysis revealed that phage SI01 represents a novel member of the Podoviridae family. The phage contained multiple lysis genes encoding cell wall-lysing muramidase and spore cortex-lysing SleB, as well as depolymerase-like tail spike protein. By lysing the host bacterium and inhibiting the formation of biofilm, this phage could indirectly promote the growth of the diatom. Our results provide new insights into how phages indirectly regulate algal growth by infecting bacteria that are closely associated with algae or in the phycosphere. IMPORTANCE The impact of phage infection on the alga-bacterium relationship in the ocean is poorly understood. Here, a novel phage infecting the diatom-associated bacterium Stappia indica SNL01 was isolated. This bacterium could form a biofilm and had a negative effect on diatom growth. We revealed that this phage contained multiple lysis genes and could inhibit the formation of the bacterial biofilm, thus indirectly promoting diatom growth. This study suggests that phages not only are important regulators of bacteria but also have substantial indirect effects on algae and the alga-bacterium relationship.
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Affiliation(s)
- Shailesh Nair
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Chengcheng Li
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Shanli Mou
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zenghu Zhang
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
| | - Yongyu Zhang
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
- University of Chinese Academy of Sciences, Beijing, China
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45
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Maire J, Buerger P, Chan WY, Deore P, Dungan AM, Nitschke MR, van Oppen MJH. Effects of Ocean Warming on the Underexplored Members of the Coral Microbiome. Integr Comp Biol 2022; 62:1700-1709. [PMID: 35259253 PMCID: PMC9801979 DOI: 10.1093/icb/icac005] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2022] [Revised: 03/01/2022] [Accepted: 03/05/2022] [Indexed: 01/05/2023] Open
Abstract
The climate crisis is one of the most significant threats to marine ecosystems. It is leading to severe increases in sea surface temperatures and in the frequency and magnitude of marine heatwaves. These changing conditions are directly impacting coral reef ecosystems, which are among the most biodiverse ecosystems on Earth. Coral-associated symbionts are particularly affected because summer heatwaves cause coral bleaching-the loss of endosymbiotic microalgae (Symbiodiniaceae) from coral tissues, leading to coral starvation and death. Coral-associated Symbiodiniaceae and bacteria have been extensively studied in the context of climate change, especially in terms of community diversity and dynamics. However, data on other microorganisms and their response to climate change are scarce. Here, we review current knowledge on how increasing temperatures affect understudied coral-associated microorganisms such as archaea, fungi, viruses, and protists other than Symbiodiniaceae, as well as microbe-microbe interactions. We show that the coral-microbe symbiosis equilibrium is at risk under current and predicted future climate change and argue that coral reef conservation initiatives should include microbe-focused approaches.
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Affiliation(s)
| | - Patrick Buerger
- School of BioSciences, University of Melbourne, Parkville, VIC 3010, Australia,Applied BioSciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Wing Yan Chan
- School of BioSciences, University of Melbourne, Parkville, VIC 3010, Australia
| | - Pranali Deore
- School of BioSciences, University of Melbourne, Parkville, VIC 3010, Australia
| | - Ashley M Dungan
- School of BioSciences, University of Melbourne, Parkville, VIC 3010, Australia
| | | | - Madeleine J H van Oppen
- School of BioSciences, University of Melbourne, Parkville, VIC 3010, Australia,Australian Institute of Marine Science, Townsville, QLD 4810, Australia
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46
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Potapov SA, Tikhonova IV, Krasnopeev AY, Suslova MY, Zhuchenko NA, Drucker VV, Belykh OI. Communities of T4-like bacteriophages associated with bacteria in Lake Baikal: diversity and biogeography. PeerJ 2022. [DOI: 10.7717/peerj.12748] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Lake Baikal phage communities are important for lake ecosystem functioning. Here we describe the diversity of T4-bacteriophage associated with the bacterial fraction of filtered water samples collected from the pelagic zone, coastal zone and shallow bays. Although the study of the diversity of phages for the g23 gene has been carried out at Lake Baikal for more than ten years, shallow bays that comprise a significant part of the lake’s area have been neglected, and this gene has not previously been studied in the bacterial fraction. Phage communities were probed using amplicon sequencing methods targeting the gene of major capsid protein (g23) and compared phylogenetically across sample locations and with sequences previously retrieved from non-bacterial fractions (<0.2 um) and biofilms (non-fractionated). In this study, we examined six water samples, in which 24 to 74 viral OTUs were obtained. The sequences from shallow bays largely differed from those in the pelagic and coastal samples and formed individual subcluster in the UPGMA tree that was obtained from the comparison of phylogenetic distances of g23 sequence sets from various ecosystems, reflecting differences in viral communities depending on the productivity of various sites of Lake Baikal. According to the RefSeq database, from 58.3 to 73% of sequences of each sample had cultivated closest relatives belonging to cyanophages. In this study, for phylogenetic analysis, we chose the closest relatives not only from the RefSeq and GenBank NR databases but also from two marine and one freshwater viromes: eutrophic Osaka Bay (Japan), oligotrophic area of the Pacific Ocean (Station ALOHA) and mesotrophic and ancient Lake Biwa (Japan), which allowed us to more fully compare the diversity of marine and freshwater phages. The identity with marine sequences at the amino acid level ranged from 35 to 80%, and with the sequences from the viral fraction and bacterial one from Lake Biwa—from 35.3 to 98% and from 33.9 to 89.1%, respectively. Therefore, the sequences from marine viromes had a greater difference than those from freshwater viromes, which may indicate a close relationship between freshwater viruses and differences from marine viruses.
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Affiliation(s)
| | | | | | - Maria Yurjevna Suslova
- Limnological Institute Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia
| | | | | | - Olga Ivanovna Belykh
- Limnological Institute Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia
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47
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Chen X, Wei W, Xiao X, Wallace D, Hu C, Zhang L, Batt J, Liu J, Gonsior M, Zhang Y, LaRoche J, Hill P, Xu D, Wang J, Jiao N, Zhang R. Heterogeneous viral contribution to dissolved organic matter processing in a long-term macrocosm experiment. ENVIRONMENT INTERNATIONAL 2022; 158:106950. [PMID: 34715430 DOI: 10.1016/j.envint.2021.106950] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 09/21/2021] [Accepted: 10/20/2021] [Indexed: 06/13/2023]
Abstract
Viruses saturate environments throughout the world and play key roles in microbial food webs, yet how viral activities affect dissolved organic matter (DOM) processing in natural environments remains elusive. We established a large-scale long-term macrocosm experiment to explore viral dynamics and their potential impacts on microbial mortality and DOM quantity and quality in starved and stratified ecosystems. High viral infection dynamics and the virus-induced cell lysis (6.23-64.68% d-1) was found in the starved seawater macrocosm, which contributed to a significant transformation of microbial biomass into DOM (0.72-5.32 μg L-1 d-1). In the stratified macrocosm, a substantial amount of viral lysate DOM (2.43-17.87 μg L-1 d-1) was released into the upper riverine water, and viral lysis and DOM release (0.35-5.75 μg L-1 d-1) were reduced in the mixed water layer between riverine water and seawater. Viral lysis was stimulated at the bottom of stratified macrocosm, potentially fueled by the sinking of particulate organic carbon. Significant positive and negative associations between lytic viral production and different fluorescent DOM components were found in the starved and stratified macrocosm, indicating the potentially complex viral impacts on the production and utilization of DOM. Results also revealed the significant viral contribution to pools of both relatively higher molecular weight labile DOM and lower molecular weight recalcitrant DOM. Our study suggests that viruses have heterogeneous impact on the cycling and fate of DOM in aquatic environments.
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Affiliation(s)
- Xiaowei Chen
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, 361102 Xiamen, PR China; Joint Lab for Ocean Research and Education (LORE) of Dalhousie University, Canada, and Shandong University and Xiamen University, PR China
| | - Wei Wei
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, 361102 Xiamen, PR China; Joint Lab for Ocean Research and Education (LORE) of Dalhousie University, Canada, and Shandong University and Xiamen University, PR China; College of the Environment and Ecology, Xiamen University, Xiamen 361102, PR China
| | - Xilin Xiao
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, 361102 Xiamen, PR China; Joint Lab for Ocean Research and Education (LORE) of Dalhousie University, Canada, and Shandong University and Xiamen University, PR China
| | - Douglas Wallace
- Joint Lab for Ocean Research and Education (LORE) of Dalhousie University, Canada, and Shandong University and Xiamen University, PR China; Department of Oceanography, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
| | - Chen Hu
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, 361102 Xiamen, PR China; Joint Lab for Ocean Research and Education (LORE) of Dalhousie University, Canada, and Shandong University and Xiamen University, PR China
| | - Lianbao Zhang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, 361102 Xiamen, PR China; Joint Lab for Ocean Research and Education (LORE) of Dalhousie University, Canada, and Shandong University and Xiamen University, PR China
| | - John Batt
- Joint Lab for Ocean Research and Education (LORE) of Dalhousie University, Canada, and Shandong University and Xiamen University, PR China; Department of Oceanography, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
| | - Jihua Liu
- Joint Lab for Ocean Research and Education (LORE) of Dalhousie University, Canada, and Shandong University and Xiamen University, PR China; Institute of Marine Science and Technology, Shandong University, Qingdao 266237, PR China
| | - Michael Gonsior
- Chesapeake Biological Laboratory, University of Maryland Center for Environmental Science, Solomons, MD 20688, United States
| | - Yao Zhang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, 361102 Xiamen, PR China; Joint Lab for Ocean Research and Education (LORE) of Dalhousie University, Canada, and Shandong University and Xiamen University, PR China
| | - Julie LaRoche
- Joint Lab for Ocean Research and Education (LORE) of Dalhousie University, Canada, and Shandong University and Xiamen University, PR China; Department of Biology, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
| | - Paul Hill
- Department of Oceanography, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
| | - Dapeng Xu
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, 361102 Xiamen, PR China; Joint Lab for Ocean Research and Education (LORE) of Dalhousie University, Canada, and Shandong University and Xiamen University, PR China
| | - Jianning Wang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, 361102 Xiamen, PR China; Joint Lab for Ocean Research and Education (LORE) of Dalhousie University, Canada, and Shandong University and Xiamen University, PR China
| | - Nianzhi Jiao
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, 361102 Xiamen, PR China; Joint Lab for Ocean Research and Education (LORE) of Dalhousie University, Canada, and Shandong University and Xiamen University, PR China.
| | - Rui Zhang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, 361102 Xiamen, PR China; Joint Lab for Ocean Research and Education (LORE) of Dalhousie University, Canada, and Shandong University and Xiamen University, PR China.
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48
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Hatoum-Aslan A. The phages of staphylococci: critical catalysts in health and disease. Trends Microbiol 2021; 29:1117-1129. [PMID: 34030968 PMCID: PMC8578144 DOI: 10.1016/j.tim.2021.04.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 04/26/2021] [Accepted: 04/28/2021] [Indexed: 01/21/2023]
Abstract
The phages that infect Staphylococcus species are dominant residents of the skin microbiome that play critical roles in health and disease. While temperate phages, which can integrate into the host genome, have the potential to promote staphylococcal pathogenesis, the strictly lytic variety are powerful antimicrobials that are being exploited for therapeutic applications. This article reviews recent insights into the diversity of staphylococcal phages and newly described mechanisms by which they influence host pathogenicity. The latest efforts to harness these viruses to eradicate staphylococcal infections are also highlighted. Decades of research has focused on the temperate phages of Staphylococcus aureus as model systems, thus underscoring the need to broaden basic research efforts to include diverse phages that infect other clinically relevant Staphylococcus species.
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Affiliation(s)
- Asma Hatoum-Aslan
- University of Illinois at Urbana-Champaign, Department of Microbiology, Urbana, IL, 61801, USA.
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49
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Jian H, Xu G, Yi Y, Hao Y, Wang Y, Xiong L, Wang S, Liu S, Meng C, Wang J, Zhang Y, Chen C, Feng X, Luo H, Zhang H, Zhang X, Wang L, Wang Z, Deng Z, Xiao X. The origin and impeded dissemination of the DNA phosphorothioation system in prokaryotes. Nat Commun 2021; 12:6382. [PMID: 34737280 PMCID: PMC8569181 DOI: 10.1038/s41467-021-26636-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2018] [Accepted: 10/18/2021] [Indexed: 12/13/2022] Open
Abstract
Phosphorothioate (PT) modification by the dnd gene cluster is the first identified DNA backbone modification and constitute an epigenetic system with multiple functions, including antioxidant ability, restriction modification, and virus resistance. Despite these advantages for hosting dnd systems, they are surprisingly distributed sporadically among contemporary prokaryotic genomes. To address this ecological paradox, we systematically investigate the occurrence and phylogeny of dnd systems, and they are suggested to have originated in ancient Cyanobacteria after the Great Oxygenation Event. Interestingly, the occurrence of dnd systems and prophages is significantly negatively correlated. Further, we experimentally confirm that PT modification activates the filamentous phage SW1 by altering the binding affinity of repressor and the transcription level of its encoding gene. Competition assays, concurrent epigenomic and transcriptomic sequencing subsequently show that PT modification affects the expression of a variety of metabolic genes, which reduces the competitive fitness of the marine bacterium Shewanella piezotolerans WP3. Our findings strongly suggest that a series of negative effects on microorganisms caused by dnd systems limit horizontal gene transfer, thus leading to their sporadic distribution. Overall, our study reveals putative evolutionary scenario of the dnd system and provides novel insights into the physiological and ecological influences of PT modification.
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Affiliation(s)
- Huahua Jian
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Development Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
| | - Guanpeng Xu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Development Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Yi Yi
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Development Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Yali Hao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Development Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Yinzhao Wang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Development Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Lei Xiong
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, Wuhan, China
| | - Siyuan Wang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Development Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Shunzhang Liu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Development Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Canxing Meng
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Development Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Jiahua Wang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Development Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Yue Zhang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Development Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Chao Chen
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, Wuhan, China
| | - Xiaoyuan Feng
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Development Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- Simon F. S. Li Marine Science Laboratory, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Haiwei Luo
- Simon F. S. Li Marine Science Laboratory, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Hao Zhang
- Simon F. S. Li Marine Science Laboratory, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | | | - Lianrong Wang
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, Wuhan, China
| | - Zhijun Wang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Development Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Zixin Deng
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Development Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Xiang Xiao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Development Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China.
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50
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Liu Y, Demina TA, Roux S, Aiewsakun P, Kazlauskas D, Simmonds P, Prangishvili D, Oksanen HM, Krupovic M. Diversity, taxonomy, and evolution of archaeal viruses of the class Caudoviricetes. PLoS Biol 2021; 19:e3001442. [PMID: 34752450 PMCID: PMC8651126 DOI: 10.1371/journal.pbio.3001442] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 12/07/2021] [Accepted: 10/17/2021] [Indexed: 11/19/2022] Open
Abstract
The archaeal tailed viruses (arTV), evolutionarily related to tailed double-stranded DNA (dsDNA) bacteriophages of the class Caudoviricetes, represent the most common isolates infecting halophilic archaea. Only a handful of these viruses have been genomically characterized, limiting our appreciation of their ecological impacts and evolution. Here, we present 37 new genomes of haloarchaeal tailed virus isolates, more than doubling the current number of sequenced arTVs. Analysis of all 63 available complete genomes of arTVs, which we propose to classify into 14 new families and 3 orders, suggests ancient divergence of archaeal and bacterial tailed viruses and points to an extensive sharing of genes involved in DNA metabolism and counterdefense mechanisms, illuminating common strategies of virus-host interactions with tailed bacteriophages. Coupling of the comparative genomics with the host range analysis on a broad panel of haloarchaeal species uncovered 4 distinct groups of viral tail fiber adhesins controlling the host range expansion. The survey of metagenomes using viral hallmark genes suggests that the global architecture of the arTV community is shaped through recurrent transfers between different biomes, including hypersaline, marine, and anoxic environments.
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Affiliation(s)
- Ying Liu
- Institut Pasteur, Université de Paris, Archaeal Virology Unit, Paris, France
| | - Tatiana A. Demina
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Simon Roux
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Pakorn Aiewsakun
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- Department of Microbiology, Faculty of Science, Mahidol University, Bangkok, Thailand
- Pornchai Matangkasombut Center for Microbial Genomics, Department of Microbiology, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Darius Kazlauskas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Peter Simmonds
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - David Prangishvili
- Institut Pasteur, Université de Paris, Archaeal Virology Unit, Paris, France
- Ivane Javakhishvili Tbilisi State University, Tbilisi, Georgia
| | - Hanna M. Oksanen
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Mart Krupovic
- Institut Pasteur, Université de Paris, Archaeal Virology Unit, Paris, France
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