A large number of today's drugs are based on natural products that have been discovered from terrestrial and marine microbes. The University of Michigan's David Sherman is working to discover new potential drugs for infectious diseases and cancer by harnessing the tremendous capabilities of microorganisms to create complex molecules with the potential for use as new therapeutic treatments. To that end, he collects samples from a range of habitats; back in his lab in the Life Sciences Institute he then isolates and analyzes the natural chemical compounds made by microorganisms.
An experienced diver, Sherman has led expeditions to Papua New Guinea, Panama, the Caribbean and various parts of Costa Rica, collecting samples and building a chemical library at the Center for Chemical Genomics, which is housed at U-M's Life Science Institute. At the end of May, he and a team of scientists headed to Isla del Coco, a protected island off the Pacific coast of Costa Rica. This is his diary of the expedition.
May 31 to June 1 — The Crossing
Ever since watching “Jurassic Park” for the first time 20 years ago, I have wondered about the “Cocos,” where parts of the movie were filmed. A UNESCO World Heritage Site with 2,000 foot cliffs rising out of the eastern Pacific ocean, Isla del Coco's remote beauty and remarkable biodiversity beckons visitors to its waters and land.
Now, after eight years of working as a PI as well as program director of the Costa Rica international cooperative biodiversity (ICBG) group, I can stop wondering. Our group of six scientists— second-year medicinal chemistry graduate student Matt Okoneski and me from the University of Michigan and four of my colleagues from the Costa Rica National Biodiversity Institute (aka, INBio)—have completed the 36-hour crossing from Puntarenas, Costa Rica on the M/V Undersea Hunter, a 120-foot boat.
The constant drone of the engine and rolling and rocking of the boat has ended, and we sit in the calm, clear waters of Chatham Bay. Various members of our expedition sit in the galley sipping hot coffee as the sun rises over the horizon. This is the smaller of two ranger stations on the Cocos Islands.
Our project focuses on developing natural-product drug discovery and bioenergy resources from Costa Rican microbiota. This has resulted in more than 35,000 semi-fractionated extracts from marine and terrestrial microorganisms that are being screened for therapeutic potential in the LSI Center for Chemical Genomics on a regular basis. We have found exciting compounds with antibiotic, antiviral, antimalarial, anticancer and other biological activities. Our ICBG is in its second cycle of funding support through the NIH Fogarty International Center. Resources come through a consortium of federal agencies including the NIH (NIGMS, NCI), the NSF, USDA, NOAA and DOE.
The constant drone of the engine and rolling and rocking of the boat has ended, and we sit in the calm, clear waters of Chatham Bay. Various members of our expedition sit in the galley sipping hot coffee as the sun rises over the horizon. We are anchored several hundred meters offshore in view of a small structure just off the beach in a grove of trees. This is the smaller of two ranger stations on the Cocos Islands.
Before heading out for our first dive to collect sediments and marine invertebrates, we will take a small boat over to meet with the rangers, and to show them our long-sought permits to collect in the waters and on the island this World Heritage conservation zone. The process of requesting and obtaining permits took more than two years, was delayed by a change in government, and was finalized in early 2013.
Later this morning we will be performing final checks on our equipment and will discuss dive site options with our guide, who has extensive knowledge and experience in the waters around the island. We will spend the first four days (Sunday through Wednesday) diving, then transfer for two days of collections on the island, and then move back to the boat for two final days of diving before returning to the mainland.
Breakfast, 7 a.m.: muesli-type cereals, tropical fruits (pineapple, papaya, watermelon), scrambled eggs, gallo pinto (traditional beans and rice).
At 8:30 a.m. our group heads to Wafer Bay to find the main ranger station. It is a substantial complex with administrative offices, cabins for volunteers and a lodge. As you walk from the shore to meet the ranger, you immediately notice a huge storage facility with hundreds of bags of confiscated fishing nets, taken by the rangers on daily patrols of the island waters, and a stack of clear plastic boxes filled with thousands of fishhooks that were removed from the lines and netting. This is evidence of the non-stop battle with illegal fishing boats that threaten this unusual environmental conservation zone and marine natural park, which extends 22.2 km from the Isla del Coco shoreline
A heartbreaking documentary film made a few years ago shows the devastation wrought by illegal fishing and shark finning in this area, primarily from Asian countries, and how difficult it is to stop their activities. There remains an insatiable demand for shark fin soup, and populations worldwide are in serious decline. Let’s hope we see some reef sharks on our first dive! After about an hour speaking with the ranger and checking documents, we are proclaimed good to go, with a limit of 2,000 samples collectively from marine and terrestrial areas.
First dive, Chatham Bay Reef
The first dive of any expedition is the “checkout” dive. We make sure our equipment is working properly, and that buoyancy is acceptable based on the thickness of the wetsuit and salt content of the ocean. Bouyancy is important because it is critical to control your ability to float above the reef to avoid crashing down on the sensitive corals. It also enables you hover and collect over sandy areas instead of setting down and risk disturbing an animal (e.g., ray) that is hidden and might have a toxic venom.
I decided to wear a 5/7 mm wetsuit as opposed to my normal 3 mm version due to some discussion of steep thermoclines. This meant I would need 18 lbs of weight in my integrated belt compared to my typical load of 14 lbs Although it was a perfect amount of weight, the 5/7 mm wetsuit was overkill for the water temperature on this dive, which was about 50 feet in a beautiful coral field.
There was a tiger shark siting and many white tip reef sharks amid thousands of King Angelfish, Panamic Sergeant Major fish, Hawkfish, Wrasses of many types, Parrotfish, Guineafowl pufferfish, thousands of Blue-and-Gold Snappers and others. We collected 160 sediment samples between the four expedition divers— the first from such a large distance away from mainland Costa Rica.
Lunch, 1:30 p.m.: Fish, sauteed vegetables, green salad.
Second dive, Manuelita Coral Garden
Totally awesome dive! Clear visibility, with fish that were fearless and numerous beyond my 36 years of experience. Swimming in schools of blue-and-gold snappers that were so thick you could not see through them. Also, striation of different schools, one layer over another in dense lines. White tip reef sharks were lazily swimming by, or resting on the sandy bottom. Found some cyanobacteria, and also collected about 160 sediment samples. A most memorable and remarkable dive.
June 3, 2013
First dive, “Dirty Rock” dive site
84 foot maximum depth. Collected ~110 samples after steep drop to bottom at about 80-85 feet. Within minutes we were along the reef wall, with hammerhead sharks circling in a school along with tuna, jacks and other fish. These were large sharks, with many white tip sharks of varying sizes as well. Consumed nitrox more rapidly than I would prefer but got the samples and avoided undo distraction by the large animals. An inspiring site and rare in the diving world to witness this activity.
Second dive, Punta Maria
Galapagos shark cleaning station, 112 foot depth in very heavy current. We had to descend along the anchor line and hold on to lateral rope to avoid being swept away. Landed on sandy bottom where we collected 110 total sediment samples for 10-15 minutes, then proceeded through large crevasse to open area at about 85 feet where huge Galapagos sharks were circling while being cleaned of parasites by smaller fish. These were much larger than the hammerheads we saw on the previous dive. My dive computer insisted that I ascend to maintain non-decompression diving parameters so I was hovering above the group that was 20 feet below. (I was watching the sharks carefully, but they were—fortunately—ignoring me). We then converged and ascended for a 5-minute stop at 15-20 while hanging on TIGHTLY to the anchor line. Surfaced and returned to the boat quickly as surface waters were quite choppy.
Third dive, Weston Bay Coral Garden, Islas Pajara
Two of the park rangers joined us for this dive to make sure that our collection technique was acceptable (fortunately we passed the test!). This site is a protected area that requires scientific permits to enter and dive. It exceeded expectations with respect to coral health, density and diversity.
We dropped down to the reef at about 40 feet and then descended to 65 feet to a sandy bottom, where we collected about 140 sediment samples. White tip sharks were scattered on the sandy bottom area and large fish schools were swimming about. After about 30 minutes we passed across the flat bottom to a vertical wall with dense coverage of invertebrates, and to our delight, at about 40 feet significant coverage of cyanobacteria. We feverishly collected as much as possible in the remaining time before ascending to our five-minute safety stop at ~15 feet. Incredible activity, and fish life including an orange frog fish, lone hammerhead that meandered by during our ascent, numerous white tip sharks and eels. We should return to collect more cyanos.
June 4, 2013
First dive (Juan Bautista, on south side of the island)
This part of the island is highly exposed and rarely suitable for diving. However, we set out to see for ourselves—with strong rain and heavy seas—to test the waters, so to speak. Fortunately, the weather calmed as soon as we entered the water, and what I thought was going to be a difficult, high-surge dive turned into a surprisingly calm experience. Sediments and some cyanos were readily obtained in the rocky reef with sandy patches. Lots of fish throughout, and a couple of young white tip sharks during the ascent. Boat re-entry was straightforward. The sun peaked through the heavy clouds and a wonderful waterfall cascaded down the cliffs. Palm trees growing out of the bare rock high up the cliff are a mysterious presence juxtaposed against the cloud forest as an ever-present impenetrable wall. We stopped at a small island to snorkel and check out the presence of cyanobacteria in remarkably clear waters close to shore.
Second dive, Punta Ulloa
This was an easy 60 minute, 40-45 foot dive in calm waters with sandy patches and coral. About a dozen white tip sharks (especially smaller ones) were cruising the entire period of collection, seemingly curious about what we were up to and approaching within a meter or two before turning away. Sediments and some cyanobacteria were found as well (perhaps enough for DNA isolation, and culturing, but not direct organic extract).
Third dive, Weston Bay Coral Garden, Islas Pajara wall mount
Late in our dive to the Weston Bay Coral Garden yesterday, [June 3, dive 3] we reached the vertical wall and realized that it was rich in cyanobacteria extending down to at least 70 feet, and we planned to return to the wall for a focused effort to obtain significant cyanobacterial cell mass for culture, direct extraction of natural products, and DNA isolation/metagenomic sequencing.
This vertical wall face with remarkably little current reaches to the sea floor at about 100 feet (bottom) and extends beyond the water surface to the top of a small pinnacle about 100 feet skyward. Our boat came right up to the edge of the wall (literally one meter away) so we had just enough room to backward-roll into the water, drop to our desired depth (we started at 40 feet) and then work down and across collecting cyanobacterial mats along the way (we were still finding rich mats of cyanos at 70-80 feet; which is rare for these photosynthetic microbes).
Our team of four (Brian, Frank, Matt and I) worked this area for about an hour and obtained a total of 500 gms semi-dry cell weight of material. This provides a good perspective of how much effort is required to collect reasonable amounts of this macroscopic, filamentous bacterium. Coverage included the edges of live and dead coral, rocks and seemingly all other substrates. I was so focused on a narrow view range that I started to reach toward a large eel concealed in a wall crevasse. Fortunately, I realized before going too far that I better move on.
June 5, 2013
Beetle collection, lichen hunting on Islas del Coco; “Aguirre, The Wrath of God” trek from Wafer Bay to Chatham Bay
We spent Wednesday on the island collecting Passalid beetles as well as finding lichens for isolation of their cyanobacterial partners. Our interest is to study the beetle gut microbiome, and through metagenomic DNA sequencing of the microbial consortium, to identify enzymes involved in production of secondary metabolites with biological activity. This ‘genomes to natural products’ approach is an important next step in accessing the broad chemical diversity that exists within unculturable bacteria and fungi that make up the vast majority of the microbial world. We also want to mine the sequencing data for gene products that are able to degrade cellulose, with longer-term bioenergy-related applications.
Getting to the island involves a short trip in the skiff to Wafer Bay, where the main ranger station is. Several failed attempts have been made over the past several hundred years to set up a permanent human presence on this remote piece of land. Feral pigs, deer and rats mill around the hardwood structure and the surrounding field. It looks like a summer camp. Within the complex is a main lodge, dining area, kitchen, small rooms with bunk beds and three stand alone cabins from the park administration and head rangers. There is also an open air work-out room with spinning bike, elliptical and various rudimentary weight machines and free weights.
There is a constant mist, sometimes changing over to a heavier rain, with clouds hiding some of the higher elevations on the island (2,000 feet above sea level). Our plan was to collect beetles in two areas using trails that lead to the highest peak, as well as on a trail that leads straight up and over a ridge that provides walking access from Wafer Bay to Chatham Bay (a 2.5km trail leading to a smaller ranger station on the edge of the rocky beach).
Our INBio beetle expert and a long-time parataxonomist, both with years of field experience, joined us. They handled large machetes and axes like we handle a fork and knife. They had spent the last two days at the higher elevations searching in vain for beetles and were clearly frustrated and dismayed by their lack of success. Now, with our group of six and a treacherous muddy trail full of exposed roots and rocks, we decided to focus on the lower elevation areas.
To collect beetles, you carefully slice into a fallen, decaying log and locate the beetle “galleries." We had success in our first log, and during the day we had continued success at the lower elevations, eventually gathering enough material for all of the experiments planned over the coming year. Many adults, larvae at various stages (there are three), and some eggs were collected into plastic containers along with plenty of the gallery wood from where we found the original family. We carried these in our backpacks over the 2.5km trail—fortunately, there were rope-hand ladders to protect against falls and to facilitate the ascent on the nearly vertical trail. The descent was equally dangerous, if not more so, as the saturated ground and algae-covered rocks made every surface slippery. We finally made it down and met the two rangers who graciously shared hot café negro before we were picked up by our boat waiting off-shore. A fantastic collection day!
June 6, 2013
First dive, Viking Rock
Big current, hammerhead schools viewed from below, Galapagos sharks, and rays. Dropped down reef wall to collect sediments and search for cyanobacteria. Found typical red algae on wall but no clear sign of cyano populations. Viewed numerous passes of hammerheads that were ~20 feet above and away from the wall, both individuals and large school, as well as several rounds of Galapagos sharks (84 feet, 51 minutes). White tip sharks pass within inches of us during collection as I look toward the blue.
Second dive, Islas Manuelita
Another reef wall where we descended to collect sediments and searched for cyanobacteria. Rising surge and currents hampered collections due to effects of storm building in Gulf of Mexico. High current, reduced visibility, hammerheads and white tips (104 feet, 45 minutes).
Third dive, Silverado
Sediments and more cyanobacterial “puffballs” than other sites. This is an important find and we will attempt to culture, extract directly and isolate DNA. Balance disturbing underwater surge, poor visibility, huge marble ray resting on sandy bottom at the edge of the rocky reef. Tiger shark also appeared fleetingly, but very difficult to see due to deteriorating conditions (39 feet, 54 minutes). Huge spiny urchins congregated on the sandy bottom of the reef, which had clearly been degraded by el Nino cold water upwelling. Appeared similar to entire reef in Islas Mercielago in Guanacaste. Fortunately, most of Isla del Coco reefs remain in excellent condition with good health, little bleaching or destruction.
June 7, 2013
Wafer Bay Ranger Station
At 6:45 a.m. we traveled by boat from Chatham Bay to Wafer Bay so I could give an International Cooperative Biodiversity Group presentation and general overview and objectives for our current expedition to the rangers, staff and volunteers at this uniquely fragile UNESCO World Heritage Site. Knowing there will be a LCD projector and screen at the ranger station, I packed up my computer (wrapped in two layers of plastic bags), laser pointer and Mac adapter.
Although it is possible at high tide to drive the boat right up to the dock, the timing did not work out (high tide was coming up but had a long way to go), so we had to leave the boat at a suitable distance to avoid damaging the engine propellers on the rocky bottom. I jumped with the group out of the boat and waded onto shore with the backpack over my head and water up to my waist. We walked the 100 meters or so to the main lodge, I set up within minutes, and delivered the presentation barefoot, soaked from the waist down, and in 100 percent humidity. I would have felt drier under water. My half-hour presentation stretched to one hour with simultaneous translation from English to Spanish (a first for me), and some excellent question from the participants. The head ranger was especially enthusiastic about opportunities to discover new medicines and enzymes for bioenergy applications and wanted to know how they could help move our project forward in our absence. There was also lots of discussion about intellectual property, benefit sharing, obtaining permits, the drug discovery process and challenges. This was a terrific experience and I hope we can conduct these talks on future expeditions in Costa Rica.
Dive 1, Chatham Bay
Obtained sediments on this dive, but high surge and poor visibility made collecting cyanos difficult
Dive 2, Dirty Rock
Huge currents and surge along with schools of hammerheads. Early in the dive I was drawn rapidly down to 80 feet and worked out of current to calmer location against the wall. We saw wave after wave of large hammerheads. We could only safely collect sediments as surge made the wall treacherous.
June 8, 2013
Dive 1, Wafer Bay Point North A
Good sediment location in sandy areas within the coral. This 7 a.m. event was the most spectacular dive of the expedition, with superbly clear visibility, no surge or current and huge schools of reef fish with packs of hammerheads lumbering by every few minutes—all against the backdrop of a splendid coral garden. This was the “aquarium plus hammerheads” dive. Our divemaster, who has been working in Isla del Coco for years, had only been to this location twice because of the strict requiements for scientific permits to access the site. The scene was probably no different than several hundred years ago when the first explorers discovered this remote land. To see this health coral reef environment changes your life.
Dive 2, Wafer Bay Point North B
Similar location to A, but by this time the weather had picked up and made visibility significantly poorer. We still saw plenty of fish and hammerheads but much more difficult. Collected sediments only.
Dive 3, Silverado
We collected more "puffball" cyanos at this site. We used our microscope on board the ship to confirm that they were a unique cyanobacteria, not a red algae.
This was our final dive. When we were done it was time to rinse equipment, pack up and head back to the mainland and Puntarenas.
We had smooth seas the entire way back to the mainland. Then it was time to unpack the source materials, barcode and enter them into the INBio database, then transfer them to my lab in the Life Sciences Institute at Michigan. We anticipate the exciting new microbial diversity and biologically active natural products that will come from these unique samples.
In collaboration with my colleagues at Michigan, INBio, HMS and the Center for Chemical Genomics, we look forward to conducting many high throughput screens on new disease targets as a first step on the long road to drug and molecular probe development.