An Anthropocentric View of the Virosphere-Host Relationship

Rodrigues, Rodrigo Araújo Lima; Andrade, Aron José Pazin de; Boratto, Paulo Victor de Miranda; Trindade, Giliane de Souza; Kroon, Erna Geessien; Abrahão, Jônatas Santos

doi:10.3389/fmicb.2017.01673

Cited by 29 publications

(21 citation statements)

References 59 publications

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“…The advent of “omics” technologies has fueled more intensive efforts to assess global viral diversity, especially in marine environments [ 3 , 4 , 5 , 6 , 7 ]. However, despite the substantial increase in virus sampling, our picture of the virosphere remains largely restricted to bacteria, some animal lineages and plants [ 8 , 9 , 10 , 11 , 12 ]. Clearly, such a sampling bias also impacts our understanding of the fundamental patterns and processes of virus evolution.…”

Section: Introductionmentioning

confidence: 99%

Metatranscriptomic Identification of Diverse and Divergent RNA Viruses in Green and Chlorarachniophyte Algae Cultures

Charon

Marcelino

Wetherbee

et al. 2020

Viruses

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Our knowledge of the diversity and evolution of the virosphere will likely increase dramatically with the study of microbial eukaryotes, including the microalgae within which few RNA viruses have been documented. By combining total RNA sequencing with sequence and structural-based homology detection, we identified 18 novel RNA viruses in cultured samples from two major groups of microbial algae: the chlorophytes and the chlorarachniophytes. Most of the RNA viruses identified in the green algae class Ulvophyceae were related to the Tombusviridae and Amalgaviridae viral families commonly associated with land plants. This suggests that the evolutionary history of these viruses extends to divergence events between algae and land plants. Seven Ostreobium sp-associated viruses exhibited sequence similarity to the mitoviruses most commonly found in fungi, compatible with horizontal virus transfer between algae and fungi. We also document, for the first time, RNA viruses associated with chlorarachniophytes, including the first negative-sense (bunya-like) RNA virus in microalgae, as well as a distant homolog of the plant virus Virgaviridae, potentially signifying viral inheritance from the secondary chloroplast endosymbiosis that marked the origin of the chlorarachniophytes. More broadly, these data suggest that the scarcity of RNA viruses in algae results from limited investigation rather than their absence.

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Section: Introductionmentioning

confidence: 99%

Metatranscriptomic Identification of Diverse and Divergent RNA Viruses in Green and Chlorarachniophyte Algae Cultures

Charon

Marcelino

Wetherbee

et al. 2020

Viruses

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“…Clinically important phages infecting different gammaproteobacterial species, including, e.g., Escherichia spp. and Pseudomonas spp., are among the most well-studied phage-host systems in the world (21). However, in marine environments, phages infecting Gammaproteobacteria have received less attention, and research has been focused mainly on phages infecting Pseudoalteromonas (22–24) or Vibrio (13, 25, 26).…”

Section: Introductionmentioning

confidence: 99%

Genomic and Seasonal Variations among Aquatic Phages Infecting the Baltic Sea GammaproteobacteriumRheinheimerasp. Strain BAL341

Nilsson

Fridlund

et al. 2019

Appl Environ Microbiol

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Knowledge in aquatic virology has been greatly improved by culture-independent methods, yet there is still a critical need for isolating novel phages to identify the large proportion of “unknowns” that dominate metagenomes and for detailed analyses of phage-host interactions. Here, 54 phages infecting Rheinheimera sp. strain BAL341 (Gammaproteobacteria) were isolated from Baltic Sea seawater and characterized through genome content analysis and comparative genomics. The phages showed a myovirus-like morphology and belonged to a novel genus, for which we propose the name Barbavirus. All phages had similar genome sizes and numbers of genes (80 to 84 kb; 134 to 145 genes), and based on average nucleotide identity and genome BLAST distance phylogeny, the phages were divided into five species. The phages possessed several genes involved in metabolic processes and host signaling, such as genes encoding ribonucleotide reductase and thymidylate synthase, phoH, and mazG. One species had additional metabolic genes involved in pyridine nucleotide salvage, possibly providing a fitness advantage by further increasing the phages’ replication efficiency. Recruitment of viral metagenomic reads (25 Baltic Sea viral metagenomes from 2012 to 2015) to the phage genomes showed pronounced seasonal variations, with increased relative abundances of barba phages in August and September synchronized with peaks in host abundances, as shown by 16S rRNA gene amplicon sequencing. Overall, this study provides detailed information regarding genetic diversity, phage-host interactions, and temporal dynamics of an ecologically important aquatic phage-host system. IMPORTANCE Phages are important in aquatic ecosystems as they influence their microbial hosts through lysis, gene transfer, transcriptional regulation, and expression of phage metabolic genes. Still, there is limited knowledge of how phages interact with their hosts, especially at fine scales. Here, a Rheinheimera phage-host system constituting highly similar phages infecting one host strain is presented. This relatively limited diversity has previously been seen only when smaller numbers of phages have been isolated and points toward ecological constraints affecting the Rheinheimera phage diversity. The variation of metabolic genes among the species points toward various fitness advantages, opening up possibilities for future hypothesis testing. Phage-host dynamics monitored over several years point toward recurring “kill-the-winner” oscillations and an ecological niche fulfilled by this system in the Baltic Sea. Identifying and quantifying ecological dynamics of such phage-host model systems in situ allow us to understand and study the influence of phages on aquatic ecosystems.

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“…A volume of 45 µl hybridization mixture was used, with a final gene probe concentration of 330 pg µL -1 (30 pg µL -1 for each polynucleotide) and rRNA probe final concentration of 1 pmol µL -1 . In the hybridization chamber, 30…”

Section: Virus-targeted Genomefish Of Msi Biofilmsmentioning

confidence: 99%

“…The knowledge gap on archaeal viruses is fostered by a lack of their genome entries in public databases [28], missing marker genes for viruses [29] and a bias towards viruses related to economical, medical or biotechnological activities [30]. In addition, only ~150 archaeal viruses have been isolated and described to date [31].…”

Section: Introductionmentioning

confidence: 99%

Genome-informed microscopy reveals infections of uncultivated carbon-fixing archaea by lytic viruses in Earth’s crust

Rahlff

Turzynski

Esser

et al. 2020

Preprint

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The continental subsurface houses a major portion of life’s abundance and diversity, yet little is known about viruses infecting microbes that reside there. Here, we used a combination of metagenomics and genome-informed microscopy to show that highly abundant carbon-fixing organisms of the uncultivated genus Candidatus Altiarchaeum are frequent targets of previously unrecognized viruses in the deep subsurface. Analysis of CRISPR spacer matches displayed resistances of Ca. Altiarchaea against eight predicted viral clades, which showed genomic relatedness across continents but little similarity to previously identified viruses. Based on metagenomic information, we tagged and imaged a putatively viral genome rich in protospacers using fluorescence microscopy. Virus-targeted genomeFISH revealed a lytic lifestyle of the respective virus and challenges previous predictions that lysogeny prevails as the dominant viral lifestyle in the subsurface. CRISPR development over time and imaging of 18 samples from one subsurface ecosystem suggest a sophisticated interplay of viral diversification and adapting CRISPR-mediated resistances of Ca. Altiarchaeum. We conclude that infections of primary producers with lytic viruses followed by cell lysis potentially jump-start heterotrophic carbon cycling in these subsurface ecosystems.

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An Anthropocentric View of the Virosphere-Host Relationship

Cited by 29 publications

References 59 publications

Metatranscriptomic Identification of Diverse and Divergent RNA Viruses in Green and Chlorarachniophyte Algae Cultures

Metatranscriptomic Identification of Diverse and Divergent RNA Viruses in Green and Chlorarachniophyte Algae Cultures

Genomic and Seasonal Variations among Aquatic Phages Infecting the Baltic Sea GammaproteobacteriumRheinheimerasp. Strain BAL341

Genome-informed microscopy reveals infections of uncultivated carbon-fixing archaea by lytic viruses in Earth’s crust

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