Journal Article

Long-read powered viral metagenomics in the oligotrophic Sargasso Sea

Cronin, Dylan R., Sullivan, Matthew B., Warwick-Dugdale, Joanna, Allen, Michael J., Parsons, Rachel J., Zayed, Ahmed A., Bell, Ashley, Temperton, Ben, Michelsen, Michelle L., Moore, Karen, Chittick, Lauren, Farbos, Audrey, Buchholz, Holger H., Tian, Funing, Bolanos, Luis M.

2024

Overview

Dominant microorganisms of the Sargasso Sea are key drivers of the global carbon cycle. However, associated viruses that shape microbial community structure and function are not well characterised. Here, we combined short and long read sequencing to survey Sargasso Sea phage communities in virus- and cellular fractions at viral maximum (80 m) and mesopelagic (200 m) depths. We identified 2,301 Sargasso Sea phage populations from 186 genera. Over half of the phage populations identified here lacked representation in global ocean viral metagenomes, whilst 177 of the 186 identified genera lacked representation in genomic databases of phage isolates. Viral fraction and cell-associated viral communities were decoupled, indicating viral turnover occurred across periods longer than the sampling period of three days. Inclusion of long-read data was critical for capturing the breadth of viral diversity. Phage isolates that infect the dominant bacterial taxa Prochlorococcus and Pelagibacter , usually regarded as cosmopolitan and abundant, were poorly represented. The Sargasso Sea is a natural laboratory for understanding future conditions of warmer oceans and associated nutrient limitation. Here, the authors combined short- and long-read sequencing to survey Sargasso Sea viral communities.

• Publisher: Nature Publishing Group UK,Nature Publishing Group,Nature Portfolio
• Subject: 45 / 45/22 / 45/23 / 45/77 / 631/114/2785 / 631/158/855 / 631/326/1321 / 704/158/855 / 704/829/826 / Bacteria - classification / Bacteria - genetics / Bacteria - isolation & purification / Bacteria - virology / Bacteriophages - classification / Bacteriophages - genetics / Bacteriophages - isolation & purification / Carbon / Carbon cycle / Community structure / Genome, Viral - genetics / Genomes / Humanities and Social Sciences / Metagenome - genetics / Metagenomics / Metagenomics - methods / Microbiota - genetics / Microorganisms / multidisciplinary / Oceans / Oceans and Seas / Phages / Phylogeny / Populations / Prochlorococcus - genetics / Prochlorococcus - virology / Representations / Science / Science (multidisciplinary) / Seawater - microbiology / Seawater - virology / Structure-function relationships / Surveys / Viruses