Day 9: Science, refrigerated

 

Karyn in cold room 2

We’re coasting through tropical waters—the sun is bright, the sky is blue, and the temperature is balmy—but Karyn Rogers (above), a microbial geochemist from the Carnegie Institute of Washington, is bundled up in a thick sweatshirt, pants, and a wooly hat.

This is because Karyn spends much of her time processing samples in the cold room, a refrigerated mini-lab kept at a chilly 4 degrees C.

The foreboding entrance to the cold room.

The foreboding entrance to the cold room.

Why the cold room? Karyn and her collaborators are looking at redox (reduction/oxidation) chemistry in the water surrounding and inside of deep-sea microbial mats. Redox-sensitive chemical ions, like ferrous iron (Fe 2+), tend to react quickly with oxygen when brought to the surface, causing key information about the biogeochemical system to disappear. The cold temperature slows down these reactions, allowing Karyn to capture the chemistry in a state that’s as close to in situ conditions as possible.

The cold room: a little slice of the Arctic in the midst of the tropics.

The cold room: a little slice of the Arctic in the midst of the tropics.

Although previous research has addressed other components of water chemistry at hydrothermal vents, most studies don’t look at redox-sensitive chemistry in these deep-sea environments precisely because it’s so difficult to process before it reacts with oxygen in the air.  Samples come up from the seafloor in bulk rather than one at a time, meaning there’s always a mad rush to get everything processed before it’s too late.

Samples staying cool.

Samples staying cool.

But Karyn is willing to brave the cold temperatures and labor-intensive sample processing because redox chemistry is such a crucial component of the ecosystems that we’re here to study, where many of the microbes live by oxidizing ferrous iron from the hydrothermal vent waters. Karyn’s efforts (and heroic sacrifice of personal comfort) will help to develop a better understanding of the interplay between microbial diversity and geochemical diversity in extreme environments.

 

–Cat Wolner, NSF

 

Photo credits: Cat Wolner

Day 8: FeMO Deep

For Jason’s 3rd dive on this cruise (and 673rd dive ever), we’ve moved on from the hot hydrothermal pits, ledges and chimneys near the summit of Loihi Seamount to its colder, lower-most flanks. Generally referred to as “FeMO Deep” (for its discovery during the first Fe-Oxidizing Microbial Observatory expedition in 2006), this site is 5+ kilometers below the surface and characterized by ultra-diffuse hydrothermal flow. In other words, it’s really far away and not very warm. Sort of like visiting another planet.

A pillow basalt field at FeMO Deep.

A pillow basalt field at FeMO Deep.

But ultra-diffuse though the hydrothermal flow may be, it’s still enough to support microbial life. And not just a little life, either. Among the pillow basalts strewn about this otherworldly deep-sea landscape are microbial mat communities that range from patches a few centimeters thick to extensive jelly-like blankets up to 2 meters thick (maybe even more) and thousands of square meters wide.

Jason landing on a thick microbial mat.

Jason landing on a thick microbial mat.

Why are these extraordinary mats here? Are their presence and extent controlled thermally, geochemically, and/or by biological adaptation?  And how do these thick, iron- and manganese-rich mat environments get incorporated into the geologic record over long timescales? Could they be modern analogues for mineralogically similar geologic formations like jaspers and massive umber deposits? The samples we’re collecting at FeMO Deep will help us begin to address these questions.

Slurp sampling a thick, foam-like mat, revealing bright orange material underneath the black manganese outer crust.

Slurp sampling a thick, foam-like mat, revealing bright orange material underneath the black manganese outer crust.

In addition to syringe samples, we’ve been collecting scoops of mat and “slurp samples” (above), which are what they sound like: samples collected by slurping up large volumes of mat and water with a vacuum. Some slurp samples have been revealing color banding beneath the mat’s surface.

Jason prepares to submerge the nano stick, an electrochemical sensor, into the mat. It sunk in more than 60 cm.

Jason prepares to submerge the nano stick, an electrochemical sensor, into the mat. It sunk in more than 60 cm.

We’re collecting mat samples and electrochemical sensor data at both live mats and “moon mats”, or dead mats that are cold and cratered, like the surface of the moon. Why do some mats grow thick and wide, then die out? In this dynamic deep-sea environment, hydrothermal flow can be ephemeral, sometimes shutting off the energy supply in one place and turning it on in another.

The surface of the “moon mat”.

The surface of the “moon mat”.

All this fieldwork at FeMO Deep has kept us busy, but we still made time to look at some weird deep-sea creatures. Check out the bizarre purple tadpole-like fish spotted on the 8 pm–midnight watch—no one in the control van had ever seen one before.

What's that, a sea slug?

What’s that, a sea slug?

Nope, just a really weird fish.

Nope, it’s a really weird fish.

Here it is from above.

Here it is from above. Whoa.

Here it is head-on. Look at those crazy eyes.

Here it is head-on. Look at those crazy eyes.

–Cat Wolner, NSF

Photo credits: all photos from the Jason control van

Day 7: How and why? The Chan Lab investigates

A culturing station in the lab, with hand-knitted representation of Mariprofundus, a kind of Zetaproteobacteria that produces twisted iron oxide stalks (pink part) trailing behind the live cell (grey part). Knitting credit: Margo Haywood.

A microbe culturing station in the lab, with hand-knitted representation of Mariprofundus, a kind of Zeta that produces twisted iron oxide stalks (pink part) trailing behind the live cell (grey part). Knitting credit: Margo Haygood.

On this cruise to Loihi Seamount, the Chan lab–Prof. Clara Chan and PhD student Sean McAllister of U. Delaware, with collaborating post-doc Shingo Kato of RIKEN–is focused on the detailed evaluation of the structure and function of iron and sulfur oxidizing microorganisms (aka, they use iron and/or sulfur as their food source). We have spent many years at Loihi looking at the question of ‘who is there?’, and we have been able to sample these communities at increasingly smaller spatial scales. This trip, however, the Chan Lab focus is to connect the who with the how and why.

Shingo checks out Zetas under the microscope.

Shingo checks out Mariprofundus under the microscope.

How are they oxidizing iron; which genes are necessary for iron oxidation by the Zetaproteobacteria? We have some ideas about which genes are responsible for iron oxidation in acidic and near neutral freshwater systems, but so far there is very little know about iron oxidation in the marine environment.

Why is it that different Zetaproteobacteria form different iron oxide structures? Can we link these organisms to a specific niche such as a dependence on a particular chemical profile or a preferred location within the mat?

A micrograph of twisted iron oxide stalks produced by Zetas. Some Zetas produce a Y-shaped stalk instead; we could show you a micrograph of this different morphotype, but instead we’ll use interpretative dance.

A micrograph of twisted iron oxide stalks produced by Zetas.
Some Zetas produce a Y-shaped stalk; we could show you a micrograph of this different morphotype, but instead we’ll use interpretative dance.

We will try to answer these questions with various microbe cultivation strategies (including the cultivation of iron oxidizers that can also oxidize sulfur), in addition to active RNA transcript sequencing and the observation of mat formation in microslide enrichments.

–Sean McAllister, U. Delaware

Photo credits: Sean McAllister (top and middle), Clara Chan (bottom micrograph)

Day 6: Veil hunters

We use Jason to sample various sites underwater. Jason ops take place around the clock during a dive as we travel to various sites marked during previous research expeditions to Lō’ihi. During the day before yesterday’s 4:00 a.m. to 8:00 a.m. watch we found some gorgeous microbial mats and structures called chimneys, where active hydrothermal venting is occurring.

The first two hours of watch were spent searching for Marker 34, near an area of the seamount known as Hiolo South. We have marker locations stored in the navigation system onboard, but it can still take hours to locate a particular site. The sites being sampled during this expedition were last visited four years ago, and it’s challenging to predict how the landscape might have changed in that time. Sites are marked with painted numbers on bucket lids, and can be difficult to spot.

Marker 34

We thought Marker 34 was an eel on the rock before we got closer!

It does say 34 if you look closely!

It does say 34 if you look closely!

Once we find a site, we mark it in our navigation system and begin sampling. At Marker 34 we took temperature measurements and electrochemistry readings at sample sites and filled our bio mat sampler.

Temperature probe.

Temperature probe.

Electrochemistry wand.

Electrochemistry sensor.

Mat samples will later be brought on board for processing on the ship. Samples are dealt out to the various lab groups onboard, who then work to culture iron oxidizers, isolate genomic DNA, view samples under the microscope, fix them in glyceraldehyde and glycerol, and perform other shipside analyses. Any remaining mat sample is frozen at -80C for future use.

We’re very excited about the mats collected at Marker 34. These were very “fluffy” iron mats growing around a ledge above venting chimneys. We call these types of mats “veils” because of their light orange color. As we sampled, the veils peeled away, revealing darker, older mat material. These Marker 34 samples will be split into two groups—those collected on the ledge face, and those collected on the underside of the ledge.

Microbial mat described as a veil, with laser pointer from Jason. Distance between the two laser markers is 10cm.

Microbial mat described as a veil, with laser pointer from Jason. Distance between the two laser markers is 10cm.

The mat sampler.

The mat sampler on one of Jason’s arms.

Here the fluffy mat has peeled back, revealing the older and less active mat material.

Here the fluffy mat has peeled back, revealing the older and less active mat material.

Depending on the needs of the science team, we’ll return to Marker 34 and other sites to pursue additional samples, photo and video site surveys, and chemical analyses. In the meantime, Jason has been having some electrical problems and our second dive was terminated several hours early in order to avoid damaging the craft and our sampling equipment. Stand by for updates as we prepare for Jason dive #673!

-Kelsey Jesser, Western Washington University

Photo credits: all photos from the Jason control van

Day 5: First CTD cast

After experiencing some electrical problems last night, Jason II is back on deck for repairs. While we wait for the next dive, the geochemists on board are keeping themselves entertained with the CTD (below).

CTD alone

CTD is the abbreviated term for a sensor that measures conductivity (from which we can calculate salinity), temperature, and depth of seawater. It also measures the concentration of particles suspended in the water.

The sensor itself is mounted at the bottom of the frame pictured above. The rosette of bottles mounted on the frame are used to collect water samples to pair with the CTD measurements.

Here we are casting the CTD:

CTD cast

The CTD is gradually lowered deeper and deeper into the water, while the data it collects are streamed in real-time in the computer lab.

CTD data

Based on these data, we select depths at which to collect water samples on the way back up. As the CTD is slowly hoisted back up through the water column, a subset of bottles collects water at each selected sampling depth. The bottles are triggered to fill remotely from on board the ship.

The water samples and CTD data will help us better understand the characteristics of the hydrothermal plumes of water overlying Loihi Seamount. This will provide us with a broader physical and geochemical context for the fine-scale work that we’re doing at the hydrothermal vents, and tell us something about how Loihi relates to the surrounding ocean.

–Cat Wolner, NSF

 

Photo credits: Cat Wolner

Day 4: Spotlight on the Moyer Lab

Our fearless leader, Craig.

Our fearless leader, Craig.

Our Chief Scientist, Craig Moyer, is here with his Western Washington University lab group—Heather Fullerton (post-doc,) Kelsey Jesser (MS student), and Kevin Hager (undergrad)—to analyze Zeta DNA.

In Craig’s words, the Moyer Lab’s objectives for this cruise are all about microbial ecology across gradients—in particular, thermal and chemical gradients. How do microbial mat communities vary genetically with increasing distance from a hydrothermal vent, and with increasing depth in the interior of the mat? To answer these questions, the Moyer Lab is collecting mat samples (to be paired with temperature and electrochemical measurements) at fine spatial scales.

Collecting microbial mat samples in a cassette of syringes operated by one of Jason’s robotic arms.

Collecting microbial mat samples in a cassette of syringes gripped by one of Jason’s robotic arms.

Why fine-scale sampling? A risk in ecological studies is that preconceived sampling schemes can dictate the scale of community variability that we observe (e.g., if we chose to sample every 50 m, we could only see variability expressed at that scale or coarser—we might miss the natural scale of variability within the community). Fine-scale sampling helps to ensure that natural variability is more fully captured—or, to paraphrase Craig, it lets the microbes tell us what the scale of variability is.

Heather and Craig preparing miniature temperature recorders (MTRs) for deployment on the seafloor.

Heather and Craig preparing MTRs (miniature temperature recorders) for deployment on the seafloor.

The Moyer Lab is employing a suite of DNA analyses to investigate their mat samples. Heather is using a “shotgun sequencing” metagenomics approach to look at the Zetas’ functional genes  and determine how they vary spatially in the mat community. Kelsey is examining genes that control elemental cycling (e.g., oxygen, carbon, nitrogen).

In addition to mat sampling and DNA analyses, the Moyer lab’s objectives include photomosaic mapping with Sentry and Jason, plus aerial photodocumentation of Jason and elevator deployments using a remote-controlled micro-UAV (unmanned aerial vehicle) equipped with a camera.

Kevin's shirt says what we're all thinking.

Kevin’s shirt says what we’re all thinking.

Stay tuned to hear about what some of the other labs on board are doing.

–Cat Wolner, NSF

Photo credits: Clara Chan (top and 3rd), one of Jason’s cameras  (2nd), Cat Wolner (bottom)

Zetas up close

What do these thick iron mats look like under the microscope? Here are three characteristic structures made by various iron-oxidizing bacteria that we’ve collected at Lo’ihi in the past few days.

This sample was pulled from the fluffy “veil” that sometimes coats the wall of iron oxides. The tubular sheaths are formed by the bacteria cells as they grow. In fresh live cultures, bacterial cells can be seen lined up in a row within the walls of the sheaths.

J2-671-BM2-C-2013_03_20-40x032This next sample was taken from a deeper, and most likely older section of the mat. It contains twisted stalks. In the case of stalks, we find individual cells at one end, with the stalk streaming behind like a tail.

J2-671-BM2-A-2013_03_20-40x039We call the bacteria in the next image”Y-Guys” because of the branching patterns they make. You might find us doing the y-guy dance when we come across these guys under the microscope.

J2-672-S8-2013_03_20-40x017

Check back soon to hear more about the samples we’re collecting!

-Anna Leavitt, Bigelow

Photos: Anna Leavitt