Microbial Countdown

No matter how early you start planning for an expedition like this, the pace gets hectic as departure approaches. Here’s a story of those weeks and months recounted by a member of the Microbe Team who has arrived at Palmyra.

by Katie Barott, member of the Microbe Team

The clear waters of Kingman Reef—under a breaking wave. Photograph by Jen Smith.

Preparing for a cruise like this is an enormous undertaking. Viewed from the outside, chaos would undoubtedly be the go-to word. For weeks leading up to departure our team is in a constant state of, at best, controlled chaos, which slides into outright madness for the days just before our main shipping dates and our own travel dates as we scramble to handle every last minute item. During the early stages of planning for this trip (months ago), we flesh out our main scientific questions and goals, then design the experiments that we hope to carry out to answer those questions. At this point everyone is eager and excited. Since the logistics haven’t yet been fully considered, we are sure we can accomplish about a million different things, far more than in practicality we’ll have enough time, space, money, supplies, and manpower to do.
Once our main objectives are set, we go through several rounds of calculating what supplies we’ll need. For the Microbe Team, these essentials include much standard microbiology equipment, such as filters to capture bacteria and viruses, sterile containers of various types, and numerous pumps for collecting seawater. Although filtering water to collect the microbes therein seems simple enough, we have come up with three different ways to do this, ranging from the traditional to the innovative and maybe slightly crazy. The traditional approach uses vacuum pumps to pull reef water through filters or peristaltic pumps to move the water through tubing and cylindrical inline filters. Our own home-made filtration rigs use compressed air from a scuba tank to push water from collection bottles (niskins) through a variety of different inline filters. We’ve also designed our own system for deploying manual bilge pumps underwater to collect water from directly above the corals.

Each of these methods requires a different mechanical setup, and since we will be on a ship thousands of miles from the nearest hardware store, scientific supply center, or machine shop, we are bringing at least two of everything. The number of filters we can bring and the number of hours it takes to complete each filtration is one of the main factors limiting how much we can do while at sea. To make the best of this, we make repeated rounds of calculations to estimate how many filters and how much time will be needed for each experiment. Each time we decide to add some other experiment to the schedule, we have to prioritize, sometimes limiting the number of replicates we can do or coming up with alternate methods.

Murky microbial waters above an algae-dominated reef at Christmas Island. Photograph by Jen Smith.

Out of about 10 people that work regularly in the Rohwer lab at SDSU, three of us will be on the cruise. For the others, these weeks are a struggle as they try to maintain the normal daily operations in the lab, working around the massive piles of supplies that we accumulate in advance of being shipped. Not only do we take up a lot of space, but we also take with us several important tools that the entire lab uses regularly. For example, as a microbiology lab, we rely on microscopy for much of what we do. Unfortunately for those left behind, we will be taking the microscopes with us, leaving them to scrounge others around the university to use. In order to get the microscopes to sea, they must be carefully dismantled and boxed. Microscopes are delicate (and expensive) instruments that in most labs are treated with only the utmost care and respect, certainly never stuffed into a cooler and shipped to the tropics where the heat and humidity are infamous for destroying equipment. However, we will need our microscopes to complete our work, so we pack them off to the ship. On board, they will be unloaded and reassembled in one of the make-shift microscopy stations that we establish scattered about the ship, as we commandeer any “unused” space we can find, space such as the common rooms or someone’s sleeping cabin. We expect teasing complaints from the less equipment-heavy teams (the fish, in particular) about how we are cluttering their ship with all of our extravagant stuff.

The bottom line is that we have to make do with whatever gear we managed to get onboard. Any supplies that were forgotten, replacements will have to be fashioned on board, or an alternate method improvised that doesn’t require the missing item, or the project jettisoned. Given the mountain of supplies that did make it, we will have enough to keep us busy for at least the month we will be at sea, likely enough for a couple more if we were somehow granted more days on the reefs.