Research
University of North Carolina at Charlotte
microbial oceanography • computational biology • metagenomics
Carbon cycling at deep-sea hydrothermal vents
Sampling deep-sea microbial communities using ROV (remotely-operated vehicle) Jason aboard the R/V (research vessel) Thompson in summer 2022.
Live display, from the control van of ROV Jason, of hydrothermal vents at Axial Seamount in the Juan de Fuca Ridge off the Oregon coast.
Exploratory metagenomic studies can uncover unprecedented microbial diversity, but linking genomic diversity to function remains a challenge our field. DNA-SIP combines metagenomics with stable isotope probing to link novel microbial diversity to their impacts on biogeochemical cycling. The lab is collaborating with the Woods Hole Oceanographic Institution and Lawrence Livermore National Laboratory conducting and analyzing the first DNA-SIP experiments to probe the carbon cycling activity of both cells and viruses in productive deep-sea hydrothermal vents. This ongoing project is an opportunity to explore a new approach that combines metagenomics, microscopy, and NanoSIMS to study microbial carbon cycling in the deep sea.
Biogeochemical and ecological impacts of viral parasites
Contemporary metagenomic approaches, such as hybrid short- and long-read sequencing, have potential to reveal novel classes of lifeforms in natural microbial communities, such as virus-induced mobile genetic elements (“viral parasites”). While viruses depend on cellular host metabolism to synthesize DNA and structural proteins for reproduction, viral parasites are mobile genetic elements that lack most viral genes required for producing viruses. Instead, these free-loaders parasitize viral particles by replacing another virus's DNA with their own (right). In collaboration with University of Hawai'i, Nanopore, and Wellesley, we reported the first observation of viral parasites in the wild, and discovered that 0.6% of viral particles in the open ocean (that's 104 -105/mL!) contain parasitic rather than viral DNA. This project combines short- and long-read metagenomics with field sampling to address these questions.
How might they impact the rate of viral production and carbon transformation from cells to organic matter?
What role do they play in the sustainability of marine communities, e.g. though horizontal gene transfer, virulence and disease, and virus-host interactions (is "the enemy of my enemy my friend"?)
Viral parasites are mobile genetic elements that reside in cellular genomes. These elements cannot mobilize (hop from cellular host to another) without the presence of another "helper virus". When this helper virus infects the cell, the parasite hijacks the virus's replicative machinery, replacing viral DNA with its own.