It's the Little Things: Studying Marine Microbes

Nastassia Patin, Ph.D., is a CIMAS postdoctoral researcher at the Southwest Fisheries Science Center, where she studies water samples from the California Current.

Most of us intuitively know that global climate and life in the ocean are intricately connected. Less appreciated, perhaps, is a crucial link between them: single-celled microbial organisms (Bacteria and Archaea). Marine microbes produce much of the oxygen in our atmosphere via photosynthesis, cycle crucial nutrients like nitrogen and phosphorous, and form the base of the food web that leads all the way to the largest animals on Earth.

Until relatively recently, the way we studied marine bacteria was by growing them in the lab. Today, thanks to the technological revolution in DNA sequencing, we can study entire microbial communities, or “microbiomes,” using only environmental DNA (“eDNA”) from seawater. Computational tools that rely on biological principles and complex statistics are used to assemble short sequences of DNA into longer sequences, like the pieces of a puzzle.

This process, known as metagenomics, tells us both who is there (taxonomy) and what they are doing (biochemical function). It is one flavor in the suite of molecular data collectively known as ‘Omics, which also includes RNA (metatranscriptomics), small molecules (metabolomics), and proteins (metaproteomics), among others. ‘Omics data, and particularly metagenomics, have revealed incredible new diversity in the Tree of Life, and altered our understanding of how microbes grow and evolve in the ocean.

However, collecting marine microbial communities in situ remains a major challenge. The moment water is put in a bottle and transported to a lab, its microscopic life begins to change. Filtration to capture cells and the extraction of DNA from those cells further alter the native community. Moreover, oceanographic ship time is increasingly limited and wet lab facilities vary among vessels, leading to wide variability in how studies are performed.

A new NOAA collaboration with the Monterey Bay Aquarium Research Institute (MBARI) aims to overcome some of these challenges with two autonomous systems combined into one. The first is a system capable of filtering and preserving a sample in situ – the Environmental Sample Processor (ESP). The second is an underwater drone capable of travelling over 1000 miles at up to 300 meters depth - the Long Range Autonomous Underwater Vehicle (LRAUV). With an ESP on an LRAUV, eDNA samples can be collected over space and time in situ, without the disturbance required by traditional bottle sampling. The sampling is automated, providing a standard and repeatable protocol. Finally, the carbon footprint and human labor required for robotic sampling are vastly lower than those of ship-based methods.

MBARI boat
The LRAUV-ESP autonomous sampler was developed at the Monterey Bay Aquarium Research Institute.


At the Southwest Fisheries Science Center in La Jolla, CA, I am comparing the quantity and quality of manually collected eDNA with eDNA provided by the LRAUV-ESP. I am interested in how such robots can expand the spatial and temporal scale of sampling marine microbiomes and open new frontiers for the study of oceanographic processes. Further, the eDNA collected on the filters can also be analyzed for megafauna like fish and whales. This will allow a microbiologist to connect the base of the food web to commercially important species. Visual surveys at sea require tremendous amounts of labor and ship time; such long, costly, and imprecise missions could ultimately be replaced by eDNA sampling.

We face a future where it is crucial that we understand how life in the sea responds to changes in climate. Underwater robots that both expand our sampling capability and reduce costs and emissions are a promising new frontier for NOAA. I look forward to sharing our findings and hope they will help guide the future of eDNA sampling in the ocean!

February 26, 2021