Day 12: The Emerson Lab–cassettes, cultures, and interconnections

mat sampler close up

Dave Emerson (Bigelow Laboratory for Ocean Sciences) is a Loihi veteran. He and Craig Moyer have been coming here for decades to investigate the microbial ecosystems of the seamount. Over the years, Dave and his collaborators have gotten a pretty good sense of who lives at Loihi (microbially speaking), so now the focus is on getting a more detailed, fine-scale picture to help place the iron-oxidizing Zetas in a functional and evolutionary context.

Anna prepping the mat sampler.

Anna prepping the mat sampler.

The new tool that’s helping to make this possible is the mat sampler (sometimes called the cassette sampler) that we’ve been featuring so much on this blog. Previously, sampling technology was limited to scoops and vacuum slurps (pretty much what they sound like)—techniques that pick up a lot of biomass but don’t allow for any assessment of fine-scale details. Initial attempts to sample microbial mats with syringes revealed that communities could vary substantially on the scale of centimeters—a much finer scale than what a scoop or a slurp could capture. But individual syringes were difficult to operate with the ROV Jason’s robotic arms.

So Dave pursued funding with Chip Breier of Woods Hole Oceanographic Institution to develop the mat sampler, which involves a cassette of 6 syringes, each with a separate nozzle to avoid cross-contamination. The cassettes journey to the seafloor by elevator or in Jason’s science basket.

magnet wand cassette

When it’s time to sample, the Jason pilot picks up a cassette using a magnetized wand gripped with one of the vehicle’s arms (above). The pilot uses the wand to position the nozzles, but the syringes themselves are operated remotely by a tablet computer. The pilot and the tablet user work as a team to get a sample of microbial mat into each syringe.

Emerson Lab post-doc Erin Field is using samples collected in the cassettes for single cell genomics, meaning that she’s isolating individual Zeta cells and amplifying their DNA so that she can sequence it. The results will be tied in with metagenomics from the Moyer Lab in order to relate individual microbe metabolisms to the functional capacity of the whole microbial community—in other words, tying the individual to the group.

slide trap - anna credit

Along with the mat sampler, the Emerson Lab is making use of slide traps (above and below). Inside the plastic housings are glass microscope slides positioned to collect microbes on their surfaces.

Slide traps deployed on a deep-sea ridge.

Slide traps deployed on a deep-sea ridge.

When the slides are retrieved, technician Anna Leavitt views them under the microscope to observe the Zeta-created mat structures in their intact form—something that’s difficult to preserve with other sampling devices.

Micrograph of iron oxide structures produced by Zetas.

Micrograph of iron oxide structures produced by
Zetas.

Post-doc Jarrod Scott is developing node networks that show how different microbe populations found at Loihi are interconnected with one another (below). The node (dot) size indicates the abundance of a given species; the length of the line between two nodes indicates how closely two species are associated.

One of Jarrod’s node networks showing associations between different species of microbes found at Loihi. Individual species are represented by nodes (dots); associations are represented by lines.

The Emerson Lab is also continuing ongoing efforts to culture Zetas. This is a tricky, iterative process that involves creating Loihi-like micro-habitats in the lab and tweaking them to encourage different types of Zetas to grow. The electrochemical data that the Glazer Lab has been collecting on this cruise will help to better define the chemical and thermal niches in which different kinds of Zetas grow best, facilitating the Emerson Lab’s efforts to culture a wider variety of Zeta species.

By understanding Zetas, the Emerson Lab and their collaborators on this cruise are pushing forward our understanding of life on Earth, and maybe even beyond. Zetas are potentially ancient organisms that are highly evolved for using iron as an energy supply, and may be analogues for life in extreme, iron-rich environments on other planets. As Dave says, Zetas may be tiny, but they’re worthy of interest: they’ve been around for a long time and they may once have been among the most dominant life forms on Earth.

–Cat Wolner, NSF

For more on this, see Dave’s essay on orders of magnitude and interconnections in the study of Zetas.

Image credits: Anna Leavitt (top and fourth photo, micrograph), Jason Sylvan (second photo), Jarrod Scott (node network graphic); subsurface photos from the Jason control van

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