Uncultivated Viral Populations Dominate Estuarine Viromes on the Spatiotemporal Scale

Sun, Mengqi; Zhan, Yuanchao; Marsan, David; Páez-Espino, David; Cai, Lanlan; Chen, Feng

doi:10.1128/msystems.01020-20

Uncultivated Viral Populations Dominate Estuarine Viromes on the Spatiotemporal Scale

Journal Article · Tue Mar 16 00:00:00 EDT 2021 · mSystems

DOI:https://doi.org/10.1128/msystems.01020-20· OSTI ID:1904067

^[1]; Zhan, Yuanchao ^[2]; Marsan, David ^[2]; Páez-Espino, David ^[3]; Cai, Lanlan ^[4]; ^[2]

University of Maryland, College Park, MD (United States). Center for Environmental Science; OSTI
University of Maryland, College Park, MD (United States). Center for Environmental Science
USDOE Joint Genome Institute (JGI), Berkeley, CA (United States); Mammoth Biosciences, Inc., South San Francisco, CA (United States)
Xiamen University (China)

Viruses are ubiquitous and abundant in the oceans, and viral metagenomes (viromes) have been investigated extensively via several large-scale ocean sequencing projects. However, there have not been any systematic viromic studies in estuaries. Here, we investigated the viromes of the Delaware Bay and Chesapeake Bay, two Mid-Atlantic estuaries. Deep sequencing generated a total of 48,190 assembled viral sequences (>5 kb) and 26,487 viral populations (9,204 virus clusters and 17,845 singletons), including 319 circular viral contigs between 7.5 kb and 161.8 kb. Unknown viruses represented the vast majority of the dominant populations, while the composition of known viruses, such as pelagiphage and cyanophage, appeared to be relatively consistent across a wide range of salinity gradients and in different seasons. A difference between estuarine and ocean viromes was reflected by the proportions of Myoviridae, Podoviridae, Siphoviridae, Phycodnaviridae, and a few well-studied virus representatives. The difference in viral community between the Delaware Bay and Chesapeake Bay is significantly more pronounced than the difference caused by temperature or salinity, indicating strong local profiles caused by the unique ecology of each estuary. Interestingly, a viral contig similar to phages infecting Acinetobacter baumannii (“Iraqibacter”) was found to be highly abundant in the Delaware Bay but not in the Chesapeake Bay, the source of which is yet to be identified. Highly abundant viruses in both estuaries have close hits to viral sequences derived from the marine single-cell genomes or long-read single-molecule sequencing, suggesting that important viruses are still waiting to be discovered in the estuarine environment.

View Accepted Manuscript (DOE)

Research Organization:: USDOE Joint Genome Institute (JGI), Berkeley, CA (United States)

Sponsoring Organization:: USDOE; National Science Foundation (NSF); China Scholarship Council Fellowship; Ratcliffe Environmental Entrepreneurial Fellowship

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 1904067

Journal Information:: mSystems, Journal Name: mSystems Journal Issue: 2 Vol. 6; ISSN 2379-5077

Publisher:: American Society for MicrobiologyCopyright Statement

Country of Publication:: United States

Language:: English

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