Collaborative research: revealing RNA virus and host population dynamics across marine oxygen minimum zones

Bigelow Laboratory for Ocean Sciences received a $630,848 Project Grant from the National Science Foundation's Division of Ocean Sciences under the Geosciences program (CFDA 47.050), awarded September 1, 2025, with completion targeted for August 31, 2028. This collaborative research initiative delivers fundamental scientific discoveries regarding RNA (ribonucleic acid) virus populations and their host dynamics within marine oxygen minimum zones—regions experiencing expanding oxygen depletion due to warming ocean temperatures. The project leverages a unique collection of microbial and viral samples from three of the world's largest oxygen-depleted marine systems (Eastern Tropical North Pacific, Eastern Tropical South Pacific, and Bay of Bengal) to uncover previously undiscovered RNA virus populations and establish virus-host connections using state-of-the-art computational workflows and novel characterization techniques.

The award supports the generation of peer-reviewed scientific research findings and datasets that advance understanding of microbial process controls in oxygen-depleted waters, with particular focus on how viral infections impact these critical ecosystems and associated biogeochemical cycles affecting nitrous oxide and methane production. Additionally, the project integrates educational components through undergraduate internship programs that provide students with hands-on research experience in coding, data science, genomics, and molecular biology—skills essential for biotechnology and environmental forecasting careers. This integrated research and workforce development approach directly supports the Geosciences program's mission to strengthen the national scientific enterprise through fundamental knowledge expansion of Earth's integrated systems and student training initiatives.

Abstract

Warmer ocean temperatures are leading to expanding oxygen loss within earth?s oceans, negatively impacting global fisheries. Microbial processes exacerbate ocean deoxygenation and in low oxygen conditions facilitate the production of gases, including nitrous oxide and methane, that can have feedbacks on atmospheric and ocean chemistry. Despite the significant role of microbes, little is known about controls on microbial processes within oxygen-depleted marine waters, including the impact of viral infection. Such information is critical to accurately forecast the impact of ocean deoxygenation. This project uncovers previously undiscovered populations of RNA viruses present and active within marine oxygen-depleted systems and connects them to hosts through leveraging a one-of-a-kind collection of microbial and viral samples sourced from three of the largest marine oxygen-depleted systems on earth. The project incorporates immersive educational programs into the research workflow through undergraduate internships leading to CO-authorship on scientific manuscripts and presentations at scientific conferences. Student interns are gaining valuable experience carrying out research that involves learned skills in coding, data science, genomics and molecular biology, skills required for future careers in biotechnology and forecasting. This project applies state-of-the-art computational workflows and develops new techniques to discover and characterize RNA viruses within a multidimensional sample collection originating from research expeditions to the eastern tropical north pacific, eastern tropical south pacific and the BAY of bengal. Identical sampling protocols were followed to collect nucleic acids from the viral, microbial and particle/eukaryotic size fractions from 6 to 12 depths from the oxygen-depleted water columns at two stations per expedition. Rnaseq data sets derived from these samples are used for RNA virus discovery and characterization. Metagenome assembled genomes, single amplified genomes and 18S and 16S rrna libraries from the same locations are used to identify bacterial, archaeal and eukaryotic populations. RNA viruses are then connected to potential hosts using several different computational approaches. The project then maps RNA virus and host distributions across depths, between size fractions and across geographic locations. With this approach, the project 1) discovers RNA virus diversity in previously unexplored locations, 2) identifies universal trends in RNA virus diversity and dynamics in relation to potential host populations, 3) identifies novel virus-host interactions, and 4) compares trends across geographically distant low oxygen systems to identify relationships between RNA viruses, microbial hosts and shifting biogeochemical conditions. This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the foundation's intellectual merit and broader impacts review criteria.- subawards are not planned for this award.