C R Young
This is my 5th consecutive year as a member of the science team for the PAP research cruise. Every year, I collect various types of samples for genetic analysis. I collect water samples from the CTD Niskin bottles, sediment samples from the megacorer, and preserve samples of organisms from the trawl. We preserve these samples, usually by freezing at -80C, for processing back at the National Oceanography Centre.
Our focus is on the ecology and evolution of the organisms that we find here. We study a broad range of organisms by applying a variety of genetic, genomic, and computational biology tools. By sequencing the genes and genomes of larger animals like sea cucumbers, molluscs, and crustaceans, we can identify new species, tell how these species are related to one another, how they move between populations, and even which of their genes have been affected by natural selection in the past. By bulk sequencing whole communities of microscopic organisms like bacteria, we can understand how they are contributing to the cycling of organic material and what roles they play in the benthic food web.
My group has been studying environmental microbiology at PAP over the past several years. We have generated data from hundreds of water and sediment samples, and we have even described the gut microbiomes of many of the species of sea cucumbers that we find here. All of this data together will help us to understand the ecological roles of these different types of microbes. Usually, we collect the samples to be process back home, but this year we tried something new.
This year, I brought aboard a graduate student that I’m co-advising under the NEXUS doctoral training program, Robyn Samuel, to help with the sample processing. Robyn has been filtering the water samples from the CTD and extracting DNA from these samples. We collect water from various depths and study the microbial communities by sequencing their genomes. This year we are performing our genomic sequencing on board the ship using a MinION sequencer. This is a genomic sequencer that plugs into a USB port on your computer that can generate information from billions of nucleotides (the building blocks of DNA) in a sample over the course of a couple of days. It works by drawing a single strand of DNA from the sample through a nanopore and measuring the electrical current that passes through the pore. The temporal variation in electrical signal as the DNA molecule is drawn through the nanopore is then translated into DNA sequence by software using sophisticated machine-learning algorithms such as deep-neural nets. This near real-time data allows us to understand the composition of our samples while we are still at sea, and we can adjust our sampling strategy based on what we see in the sample.
(Left) MinION genome sequencer (Right) Inside of the MinION sequencer showing the flowcell into which the sample is loaded.
Applying these technologies at PAP are a first step towards our ultimate goal of performing sequencing on observatory assets like the mooring our on autonomous underwater vehicles. Like our environmental sensors that continuously send real-time data back to NOC without having to have scientists at sea making the measurements, one day we hope to be beaming genomic data back, allowing us to monitor microbial communities from shore all year around. For example, we can visually detect blooms of the coccolithophore E. huxleyi from space [their calcium carbonate scales (coccoliths) make up the white cliffs of the southern UK], but we cannot see all of the other microorganisms associated with these blooms. Coupling satellite imagery of surface blooms with real-time genetic data would allow us to better understand the ecology of these and other surface events. We know even less about microorganisms in the deep-sea, and these technologies will allow us to construct a better picture of the dynamics of these enigmatic communities.
Whether we are measuring ecological dynamics on the scale of hours or decades, at the surface or 4800m below in the sediments, the value of long-term observatories such as PAP is all about temporal dynamics. We visit PAP once a year, and have done so for over 30 years. We hope to use technology to eventually generate continuous ecological data during the times of the year that we aren’t able to be out here on the ship. There is immense scientific value generated by sustained ocean observatories that allow us to understand how our oceans are changing on a decadal scale, and our efforts to expand the data the PAP-SO generates to include microbial genomics will undoubtedly generate new (and likely unforeseen) insights over the next 30.