Viral Communities of Shark Bay Modern Stromatolites

White, Richard Allen; Wong, Hon L.; Ruvindy, Rendy; Neilan, Brett A.; Burns, Brendan P.

doi:10.3389/fmicb.2018.01223

Title: Viral Communities of Shark Bay Modern Stromatolites

Journal Article · 12 June 2018 · Frontiers in Microbiology

DOI: https://doi.org/10.3389/fmicb.2018.01223 · OSTI ID:1728612

White, Richard Allen ^[1]; Wong, Hon L. ^[2]; Ruvindy, Rendy ^[2]; Neilan, Brett A. ^[2]; Burns, Brendan P. ^[2]

Washington State Univ., Pullman, WA (United States); Univ. of New South Wales, Sydney, NSW (Australia); RAW Molecular Systems (RMS) LLC, Spokane, WA (United States)
Univ. of New South Wales, Sydney, NSW (Australia)

Single stranded DNA viruses have been previously shown to populate the oceans on a global scale, and are endemic in microbialites of both marine and freshwater systems. We undertook for the first time direct viral metagenomic shotgun sequencing to explore the diversity of viruses in the modern stromatolites of Shark Bay Australia. The data indicate that Shark Bay marine stromatolites have similar diversity of ssDNA viruses to that of Highbourne Cay, Bahamas. ssDNA viruses in cluster uniquely in Shark Bay and Highbourne Cay, potentially due to enrichment by phi29-mediated amplification bias. Further, pyrosequencing data was assembled from the Shark Bay systems into two putative viral genomes that are related to Genomoviridae family of ssDNA viruses. In addition, the cellular fraction was shown to be enriched for antiviral defense genes including CRISPR-Cas, BREX (bacteriophage exclusion), and DISARM (defense island system associated with restriction-modification), a potentially novel finding for these systems. This is the first evidence for viruses in the Shark Bay stromatolites, and these viruses may play key roles in modulating microbial diversity as well as potentially impacting ecosystem function through infection and the recycling of key nutrients.

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Research Organization:: Pacific Northwest National Laboratory (PNNL), Richland, WA (United States)

Sponsoring Organization:: Australian Research Council (ARC); USDOE

Grant/Contract Number:: AC05-76RL01830

OSTI ID:: 1728612

Report Number(s):: PNNL-SA-123161

Journal Information:: Frontiers in Microbiology, Journal Name: Frontiers in Microbiology Vol. 9; ISSN 1664-302X

Publisher:: Frontiers Research FoundationCopyright Statement

Country of Publication:: United States

Language:: English

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Genomic characteristics and environmental distributions of the uncultivated Far-T4 phages Roux, Simon; Enault, François; Ravet, Viviane Frontiers in Microbiology, Vol. 6 https://doi.org/10.3389/fmicb.2015.00199	journal	March 2015
Metagenomic analysis reveals that modern microbialites and polar microbial mats have similar taxonomic and functional potential White, Richard Allen; Power, Ian M.; Dipple, Gregory M. Frontiers in Microbiology, Vol. 6 https://doi.org/10.3389/fmicb.2015.00966	journal	September 2015
Metagenomic Analysis Suggests Modern Freshwater Microbialites Harbor a Distinct Core Microbial Community White, Richard Allen; Chan, Amy M.; Gavelis, Gregory S. Frontiers in Microbiology, Vol. 6 https://doi.org/10.3389/fmicb.2015.01531	journal	January 2016
Release and bioavailability of C, N, P Se, and Fe following viral lysis of a marine chrysophyte Gobler, Christopher J.; Hutchins, David A.; Fisher, Nicholas S. Limnology and Oceanography, Vol. 42, Issue 7 https://doi.org/10.4319/lo.1997.42.7.1492	journal	November 1997
Towards quantitative viromics for both double-stranded and single-stranded DNA viruses Roux, Simon; Solonenko, Natalie E.; Dang, Vinh T. PeerJ, Vol. 4 https://doi.org/10.7717/peerj.2777	journal	January 2016
Benchmarking viromics: an in silico evaluation of metagenome-enabled estimates of viral community composition and diversity Roux, Simon; Emerson, Joanne B.; Eloe-Fadrosh, Emiley A. PeerJ, Vol. 5 https://doi.org/10.7717/peerj.3817	journal	January 2017

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The Complete Genome and Physiological Analysis of the Eurythermal Firmicute Exiguobacterium chiriqhucha Strain RW2 Isolated From a Freshwater Microbialite, Widely Adaptable to Broad Thermal, pH, and Salinity Ranges White, Richard Allen; Soles, Sarah A.; Gavelis, Greg Frontiers in Microbiology, Vol. 9 https://doi.org/10.3389/fmicb.2018.03189	journal	January 2019
Applying Genome-Resolved Metagenomics to Deconvolute the Halophilic Microbiome Uritskiy, Gherman; DiRuggiero, Jocelyne Genes, Vol. 10, Issue 3 https://doi.org/10.3390/genes10030220	journal	March 2019
Comparative metagenomics of microbial mats from hypersaline lakes at Rottnest Island (WA, Australia), advancing our understanding of the effect of mat community and functional genes on microbialite accretion Mendes Monteiro, Juliana; Vogwill, Ryan; Bischoff, Karl Limnology and Oceanography, Vol. 65, Issue S1 https://doi.org/10.1002/lno.11323	journal	January 2020
Applying Genome-Resolved Metagenomics to Deconvolute the Halophilic Microbiome Uritskiy, Gherman; DiRuggiero, Jocelyne Genes, Vol. 10, Issue 3 https://doi.org/10.3390/genes10030220	journal	March 2019

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