2018 Cruise - JC165

Molecular ecology at PAP

This is my fourth PAP cruise, and it has been a great trip. During this cruise, I have been collecting samples from the amphipod trap, the CTD, the megacore, and the trawl. I am a molecular ecologist, which means that I use molecules like DNA to make inferences about ecology. Every living organism, from microbes to humans has DNA, which is the molecule that encodes the information that the organism uses to grow from an egg to an adult and that the organism eventually passes on to its own offspring. It is a combination of the transmission of this molecule between generations from parent to offspring and the fact that every time it is replicated, the copy contains small differences from the original molecule that allows us to use it to infer properties of the ecology of a species.

For example, we can use DNA to track the movement of individuals between populations, to identify new species, or to reconstruct the evolutionary history of groups of animals. We can determine the DNA sequence of whole genomes, like those of bacteria, that tell us what types of compounds the bacteria might be able to consume. We can use the bits of DNA shed into the environment, like a forensic detective, to detect the presence of animals even if we haven’t observed them directly. We will be using all of these approaches on the samples that we collected this trip.

We collect water samples with the CTD throughout the water column, from the surface to just a few meters off of the seafloor, and we filter those samples to collect any material as small as 0.2 microns (about 1/200th the width of a human hair). The filter traps most bacteria and any larger material, from which we extract DNA and find out its sequence. From this information, we can tell what species are in the water that we collected and how those species change by depth, by the time of year, or over many years. We can tell what types of microbes are responsible for breaking down various compounds to help us understanding how photosynthetically produced carbon at the surface is turned back into carbon dioxide as it sinks through the water column.

Figure 1. Holothurians observed during the HyBIS dive.

We also extract DNA from the sediments samples that we collect with the megacore to find out which species are in the sediment and how diverse the sediment microbial communities are. We can determine how microbial communities are changing in the sediment in response to varying amounts of food arriving from the surface and what role they play in the energy budget for larger members of benthic communities. Even though microbes represent the vast majority of genetic diversity on our planet, we understand less about their ecological roles, because we cannot culture most microbes in the lab. Applying genetic and genomic tools to these environmental samples helps us to understand their roles in these ecosystems, even though we can’t culture them in the lab.

Every year we sort and preserve animals from the trawl and the amphipod traps for DNA analysis. We look for new species among the samples that we collect. This past year, using a combination of morphological analysis and DNA methods on samples that we collected on previous cruises, Tammy Horton (who curates the Discovery Collection at NOC) and I have found a new species of amphipod at PAP, even though researchers have been visiting the site for over 30 years. We will continue to search for new species in the samples that we collected this year.

Our target species from the trawl this year were the holothurians (sea cucumbers). Holothurians are some of the most numerous animals that we find at PAP. But we were not just interested in the sea cucumbers themselves. We were specifically going after the microbes in their guts. We dissected the gut contents out of individuals belonging to the 8 species that we came across this year, building up our collection from the previous two cruises. Our objective is to describe the microbial communities that live in the guts of these holothurians and to determine what roles the microbes play in helping the host species digest the material that they come across in the different ecological niches that they occupy. We want to know if there are any microbes that only occur in specific holothurian species and if these microbes help the host by specializing on specific types of compounds. By comparing the microbes in the water column, the sediment, and the dominant grazers in this environment, we will have a better understanding of how carbon and other nutrients flow through these ecological systems.

diversity of holothurians
Figure 2. Diversity of holothurians collected from the trawls.

The association of holothurians and their microbiomes begs the question: Are the holothurians cleverly taking advantage of the microbes’ diverse genetic metabolic repertoire to extract more energy from the environment, or have the microbes co-opted the holothurians as convenient vehicles to transport them efficiently to their preferred resources?


Written by Rob Young

2018 Cruise - JC165

Imaging the sea bed

Yesterday we completed the third successful deployment of the HyBIS system (Hydraulic Benthic Interactive Sampler). HyBIS is one of several underwater vehicles operated by the National Oceanography Centre to study deep-ocean seabed environments. It consists of a stain-less steel frame that carries several underwater cameras designed to observe the environment and to monitor the vehicle’s operating systems, which include a steering unit with two propellers and a complex array of telemetry, hydraulic, and electrical systems. This includes a special ultra-Short baseLine (USBL) beacon that helps map the HyBIS position as we survey. Additional ocean bottom sensors and sampling devices can be attached to the frame, depending on the aims of the mission.

Figure 1_HyBIS on deck
Figure 1. HyBIS on deck the RRS James Cook. The remotely controlled submersible system is deployed over the starboard side of the ship. Energy is supplied from a high-voltage power source on the vessel via an umbilical cable. The vehicle’s systems are designed to operate at depths of up to 6000 metres. Images of the seabed are captured with the downward facing camera.
Figure 2_Image display
Figure 2. Imaging the deep. Left: A large computer screen in the ship’s observation lab allows the scientists and crew to watch real-time video from the HyBIS Ultra-High Definition camera system. Right: Typical still image from the PAP abyssal plain showing the soft seabed. Video is recorded continuously and still images are typically taken every 5 seconds.  

During this year’s PAP cruise, HyBIS is deployed to collect seafloor images from the abyssal plain and, if possible, from abyssal hills. We use the image data to study the larger invertebrates that live on the seafloor such as sponges, anemones, worms and echinoderms. We call this group of organisms benthic megafauna. Back ashore, we will be counting the number and types of the organisms on the photographs to describe the diversity and the composition of the species assemblages.

We will also be measuring the body size of the organisms to estimate the mass of the living megafauna (biomass). We will be using the biomass data together with the physical and chemical data that we collect at PAP to assess the links between surface carbon production, sinking carbon fluxes (marine snow) to the seabed (food supply) and deep-ocean biomass distributions (food demand). We will also be comparing this year’s observations with image data collected in previous years to assess how the megafaunal communities at PAP are changing over time and to help answering questions about impacts of climate change on ocean carbon budgets and deep-ocean food webs.


Figure 3a
Figure 3. Examples of benthic sea cucumbers observed during the first two dives of HyBIS in water depths of about 4850 meters



Figure 3b
Figure 4. Examples of benthic megafauna observed during the first two dives of HyBIS.


Figure 3c
Figure 5. Examples of Lebensspuren (life traces) that can be seen on the seabed of the Porcupine Abyssal Plain. Left: Central mound surrounded by several small depressions possibly created by one or more acorn worms (Enteropneusta). Right: Central burrow hole with radial extending feeding tracks likely created by an annelid worm. 


Written by Simone Pfeifer