Sampling Microbial Muck

July 5, 2010-

Hansen and Brady (in canoe) get a precarious assist from Collins as they struggle to push their canoe through a several-meter-wide rim of deep, sticky mud surrounding Deer lake. Their goal: to collect water samples from the center of the lake. Credit: Henry Bortman

On my last day with folks from PLRP, I went on a road trip to the Cariboo Plateau lakes with Allyson Brady, the acting principal investigator for PLRP 2010; Eric Collins, a post-doctoral fellow; and Jennifer Hansen, a laboratory assistant. All three are or have been connected with Greg Slater’s group at McMaster University. Slater, who has been a leading member of the PLRP team for several years, was home this year with a newborn son.

The Cariboo Plateau lakes are a group of small lakes that dot the landscape in a region near Pavilion Lake. The three we visited are quite unlike Pavilion, however: They’re shallow, highly alkaline (think baking soda dissolved in water, so everything it splatters on, your clothes, your hands, your face, turns slimy when wet, and crusty when dry), and they’re surrounded by noxious, sucking mud that makes entering and exiting them in a canoe a serious challenge.

The mud contains a large amount of microbial slime, a mix of living organisms and the rotting cellular carcasses of dead ones. I didn’t quite get clear on which of the two, the living or the dead, was responsible for the general stench. There was something disturbingly familiar about the smell. It took me a while to identify it, but it finally clicked: Old Bay gone bad. (For those of you who’ve never dined along the Maryland coast, Old Bay is a spice mixture liberally used to flavor the state crustacean, the blue crab. Having grown up in Maryland, I’ve always been a fan of crab à la Old Bay, but after visiting the Cariboo Plateau, I may reconsider.)

The day began with a protracted effort to lash the 10-foot-long canoe to the uncooperatively small roof rack of a rented SUV. We rewarded our success with a stop at the Cordial Restaurant in Clinton, British Columbia, apparently an initiation rite for PLRP visitors to the Cariboo Plateau. The Cordial is known for its pancakes. Very large, very thick pancakes. You have two choices: eat the whole thing, or face public humiliation. I was cautioned the night before to eat a light dinner, advice which I ignored (there was fruit cobbler for dessert). Nevertheless, I did finish my pancake. With bacon. Just for the record.

Back on shore, Hansen labels a bottle of hard-won lake water that she and Brady had retrieved. Credit: Henry Bortman

First up was a lake unofficially dubbed “Probe” Lake (researchers lost a scientific probe there some years back). After a ride down a twisting one-lane dirt logging road, the canoe juddering somewhat uncertainly on the roof, we arrived. The challenge at Probe Lake is the quarter-mile portage from the road to the canoe-launching point along the shore. Once you’re there, though, the mud barrier surrounding the lake is relatively narrow.

Here, Brady and Hansen paddled out in the canoe to collect lake water. Meanwhile Collins waded out into the muck and scooped up a few choice gobs of slime, sealing them into various-sized jars and tubes for later distribution to analytical laboratories. His sampling tool, affectionately called Mat Sampler 3000 (a reference to the rubbery mat-like structures built by some microbes), was a six-foot-long hollow PVC pipe. Lashed to one end of the pipe with electrical tape was a cutoff Nalgene bottle, holes drilled in its bottom. Brady explained later that they had found its component parts in a basement some years ago. “It does what it needs to do,” she said. You gotta love the duct-tape culture of field science.

This same basic scenario, two people heading out into the lake in the canoe for water samples while the third person stayed near shore and scooped up slime, was repeated at lakes number two and three. But each lake had its particular charm.

Lake number two, referred to as Deer Lake, is much closer to the road than Probe Lake, so minimal portage is required. But it wins the prize hands-down for widest mud apron.

Brady wades into the shallow waters of Probe Lake, armed with her trusty Mat Sampler 3000, to obtain samples of microbial mat. Not shown: she’s standing calf-deep in mud. Credit: Henry Bortman

Last year, the PLRP team built a walkway there of downed tree limbs, hauled to the lakeshore from the nearby woods, so that they can get the canoe close enough to the water to have any hope of paddling it though the muck. This year, the water level of the lake was lower than last year, so the walkway had to be extended several feet.

Employing the word “paddling” to describe the propulsion of the canoe through the mud is a bit misleading. What happened was this: Brady and Hansen got in the canoe with paddles, while Collins stood at the end of the makeshift walkway, one hand on the stern, the other outstretched for balance. Brady and Hansen plunged their paddles into the muck and pushed with all their might, while Collins gave an extra little shove from the edge of the walkway, the total effort moving the canoe perhaps a few inches. Then Brady and Hansen struggled to extract their paddles from the viscous muck, trying to avoid, in the process, pulling their boat back towards shore. (You know, that pesky action-reaction thing.) This went on for about ten minutes, although after the first two rounds the canoe was out of Collins’s reach, so Brady and Hansen had to traverse the last few feet on their own.

Finally, Brady and Hansen went sailing off into clear water, all 15 cm of it, while Collins squatted on the end of the walkway, scooping up handfuls of mud, sniffing each handful in turn (the particular mix of noxious gasses given off by each handful holds clues to which types of microbes reside within), and occasionally stuffing a handful into a collection jar. He did this, by the way, not in knee-high boots like a normal, sensible person, but in sandals. He did wear the requisite purple nitrile gloves, but that was to protect the microbes from being contaminated by him, not the other way around.

When we finished up at Deer Lake, I asked Brady what the particular distinguishing characteristic was of the third lake, officially named Goodenough Lake,. “Bugs,” she said. I’ll leave that to your imagination. Suffice it to say that a week later I was still nursing a scab from the worst of my mosquito bites.

Forgoing the use of the Mat Sampler 3000, Collins gets down and dirty with a handful of lakeshore mud, performing a sniff test before deciding to add it to his collecting jar. Note the footwear. Credit: Henry Bortman

I suppose you want to know why they go to all this trouble. Here’s the Cliff’s Notes version. The Cariboo Lakes help put Pavilion Lake in context because, as Brady said, “The [Cariboo] mats are full of carbonate,” as are the microbialite structures at Pavilion Lake. But unlike at Pavilion Lake, in the Cariboo Plateau lakes, “they’re not forming microbialites. Either there’s a missing factor, or something’s inhibiting them.”

Brady and Hansen are interested in how the water chemistry of various lakes affects the microbial communities that live there, which in turn may determine whether or not microbialites form. They are also hoping to pinpoint biomarkers, chemical signatures that can be used as unambiguous indicators of biology at work. That work is focused on carbon isotopes and lipids. Collins is conducting a broad-scale DNA analysis of the microbial populations in Pavilion and other nearby lakes.

As a parting image, picture this scene: Collins and I are sitting in a filthy canoe on Deer Lake, in very shallow water, the surface of the stinking microbial mats mere inches below us. I’m paddling around, gently so as not to stir up too much muck, which would interfere with his sampling efforts, and he’s leaning over the edge of the canoe, on the lookout. Every once in a while, he gets excited because he’s seen a glob of green gunk (it mostly ranges from dirty pink to brown). So I plunge my paddle into the muck to hold the canoe steady while he scoops up the green stuff with the Mat Sampler 3000.

In this idyllic setting I ask him, “Which do you like better, collecting or taking stuff back to the lab and analyzing it?”

“I really like collecting,” he says with a grin. “But the problem is, if you’re just collecting, you never actually find out any answers.”