Bigelow Laboratory for Ocean Sciences Annual Report 2007

Bigelow Laboratory for Ocean SciencesAnnual Report 2007

The ocean holdstremendous possibilitiesfor discovery—from newsources of energy tonew genetic pathwaysto health.More than two-thirds of our planet is blue ocean, a reality wesee time and again in images taken from space. It should thenbe no surprise that the network of life in the oceans has greatinfluence on the rest of the world, including the terrestrial ecosystemswe ourselves inhabit and depend upon for survival. As a society, we haveonly just begun to understand the magnitude and scope of this influence.The biogeochemical cycles of the oceans, and the life they nurture,are inextricably linked; how and why they persist and change are keyquestions that ocean science seeks to answer.The ocean holds tremendous possibilities for discovery—from newsources of energy to new genetic pathways to health. Advances inocean research and technology are offering us ways to improve thequality of our lives at the same time that we build an environmentallyresponsible future.Bigelow Laboratory for Ocean Sciences is known throughout theinternational scientific community for its independence, its spiritof collaboration, its entrepreneurship, and its creative energy. I amcommitted to carrying forward the vision of the Laboratory’s founders,Drs. Charles and Clarice Yentsch, by marshalling the outstandingmulti-disciplinary talent, the resolve, and the resources to do the job.I would like to pay tribute to my predecessor, Dr. Sandy Sage, whoenhanced the Laboratory’s reputation over the past eleven years.We must continue to explore the ocean from every conceivableperspective—from the genetic codes inside the smallest living cellsthat our novel molecular techniques reveal, to fieldwork in the extremeenvironments of the open ocean, to the analysis of detailed global imagesbrought to us by remote sensing satellites—and we must tell peopleeverywhere about the importance of what we are learning.I am both honored and delighted to have this opportunity to introducethe 2007 Annual Report for Bigelow Laboratory for Ocean Sciences, andproud to join this exceptional team of researchers at so pivotal a time inour planet’s environmental history.Graham Shimmield, Ph.D.Executive Director and PresidentFacing page: Photo courtesy of J. Goés.May 20, 2008

ContentsHow the Cause Works—The Global Reach of Microbial Oceanography ...................................... 4Research at Bigelow Laboratory for Ocean Sciences ranges from the study of singlecelledmicrobes to fieldwork on the open seas and analysis of satellite images of globalecosystems.This report focuses on our current research in microbial oceanography,within the overall global context of Bigelow Laboratory's programs. With advances ingenomic technologies, microbial oceanography is making it possible to understandthe enormous impact that the ocean has on global climate.Part I. Molecular Biology and Marine Microbial BiodiversityA Living Library—The Provasoli-Guillard National Centerfor Culture of Marine Phytoplankton ...................................................... 8Providing thousands of cultures for international scientific study and biomedical researchevery year, Bigelow Laboratory maintains the official national phytoplankton culture collectionof the United States. Now under the direction of Dr. Robert Andersen, the collection began asthe result of pioneering research by Dr. Robert Guillard.Marine Microbial DNA—One Cell at A Time ...................................... 11Marine microbes drive the world’s major biogeochemical cycles. Drs. Michael Sieracki andRamunas Stepanauskas have pioneered a method to analyze DNA in single marine microbialcells not grown in cultures, opening a new path to understanding much more about howbiodiversity functions in nature.Marine Virology—A New Universe of Possibilities .............................. 14Dr. William Wilson is investigating how viruses adapt to rapid changes in the oceanenvironment, and how those changes affect large-scale ecosystem processes in theseas. Dr. Susan Wharam’s research in phage therapy isolates marine viruses to testtheir ability to kill a number of disease-causing bacteria, avoiding the use of antibioticsand the associated problems of antibiotic resistance.Copepods and the Global Carbon Cycle ................................................ 17Combining small-scale fluid mechanics, neurophysiology, and animal behavior,invertebrate ecologist Dr. David Fields is examining the feeding and survival strategiesof copepods, the microscopic crustaceans that graze on phytoplankton and influencethe pathways by which carbon is transported to the deep ocean.Tracking Marine Life through Evolutionary Time................................ 18Dr. Hwan Su Yoon is studying when and how photosynthesis began on this planet byusing gene-sequencing technology to trace the evolutionary history of marine microorganisms.His research describes processes that continue to shape the way cells changeand evolve today.Part II. Ship’s Log, 2007: Research on the Open SeasAbrupt Climate Change—Evidence in the Arabian Sea ...................... 22Dr. Joaquim Goés is exploring the link between global warming, snow melt, and oceanproductivity in the Arabian Sea, documenting the significant effects of climate changeon phytoplankton production in a critical region of the world’s ocean.Changing Sea—Biological Productivityand Abundance in the Arctic Ocean ...................................................... 25The impact of climate change is more extreme in the high Arctic than anywhere else.Dr. Patricia Matrai is leading an investigation of the influence of biological productivitynear the ocean surface on the lower Arctic atmosphere; Dr. John Christensen’s polarresearch team is gathering baseline biomass data at various depths in the central ArcticOcean. These findings will allow scientists to predict future changes in the Arctic ecosystem.2Bigelow Laboratory for Ocean Sciences

Following Microbial Tracks in the South Atlantic .............................. 28Working in the ocean over the Patagonian Shelf, Dr. William Balch’s research team isinvestigating effects of ocean acidification on phytoplankton species that are vital in theglobal carbon cycle. Dr. Michael Sieracki is project leader for another team of BigelowLaboratory researchers using advanced cell-sorting technology to document phytoplanktondiversity in the largely unexplored subtropical ocean area between Brazil and Namibia.Forecasting Biological Productivity in the Northwest Atlantic .......... 33Dr. Richard Wahle’s research on benthic marine populations reflects large-scalechanges in ocean and atmospheric conditions in the Northwest Atlantic.Deep in the Pacific—Extremes of Life on the Loihi Seamount............ 35Dr. David Emerson’s research expeditions have taken him 16,000 feet down in deep-seasubmersibles to study bacteria living on the Loihi Seamount, an underwater volcano inthe Hawaiian archipelago. Part of a class of “extreme” microbes that use iron as an energysource, the bacteria may have influenced biogeochemistry early in the planet’s history.Part III. Ecosystem ModelingA Crucible for Multi-Disciplinary Ecosystem Modeling...................... 38Dr. Peter Larsen and a multi-disciplinary team of researchers have modeled the dynamicforces that drive and perpetuate the renowned biological productivity of Cobscook Bay.Their results provide a template for understanding energy and nutrient flows in a diversityof other marine ecosystems.From Biomolecules to Ecosystems—Organizing the Genomic Revolution .................................................... 39Bioinformatics combines molecular biology, mathematical modeling, and computersoftware design to study life at the biomolecular scale. Dr. David McClellan is usingbioinformatics to examine how ocean life is adapting to local and global climatechanges at the molecular level.Ocean Literacy—Telling the Story ............................................................ 40The need for public understanding of the ocean’s role in global environmentalsustainability has never been greater. Bigelow Laboratory has developed a seriesof programs and events to share its discoveries with audiences in the wider world.Glossary .................................................................................................... 42Selected Publications................................................................................ 44Message from the Chair ............................................................................ 46Trustees and Scientists.............................................................................. 47Financial Summary.................................................................................... 48Annual Report 20073

“How the Cause Works”Henry Bigelow steering the U.S. Bureau ofFisheries vessel Grampus, 1914. Courtesyof Woods Hole Oceanographic InstitutionArchives.The Global Reach ofMicrobial OceanographyThe founder of modern oceanscience, and the man afterwhom Bigelow Laboratoryfor Ocean Sciences was named, wasearly 20th-century oceanographerHenry Bryant Bigelow. He describedthe interconnected and largely undiscoveredrelationships betweenthe biological, chemical, and physicalsystems in the world’s oceansby saying that “nothing in the seafalls haphazard; if we cannot predict,it is because we do not knowthe cause, or how the causeworks.” Today, this visionary scientistis both an icon and inspirationfor the 21st-century researchers atBigelow Laboratory. His legacy isreflected in our focus on thedynamic biological, chemical, andphysical relationships that sustainlife in the oceans and their impacton the global environmentalprocesses upon which all lifedepends.The scope of research at BigelowLaboratory ranges from study ofthe genetic structure of phytoplanktonand other single-celledmicrobes to the relationshipbetween ocean ecosystems andglobal climate change. Ourscientists are exploring the biomolecularfoundations of life inthe world’s oceans and discoveringfundamental connections betweenthe biological productivity of theplanet’s ocean ecosystems andchanges in the global environmentas a whole. This report focuses onBigelow Laboratory’s burgeoningresearch focus on microbial oceanographywithin the broad globalcontext of our research programs.Microbial oceanography isthe study of microscopic marinelife—single-celled marine organisms,bacteria, and viruses—thatare essential to the functioningof the world’s oceans. Althoughmarine microbes exist in literallyastronomical abundance throughoutthe world’s oceans, the dynamicsthat drive this profusion oflife take place on an infinitesimalbiomolecular scale. But it is at thismicroscopic level that the vitalglobal processes of photosynthesis,the global carbon cycle, and theflow of nutrients through the foodweb begin.As a new and rapidly evolvingscientific field, microbial oceanographyis emerging from a synthesisof physical and chemical oceanography,marine ecology, physiology,and molecular genetics, offeringscientists an unprecedented opportunityto understand theliving world. Engineering advancesin genetic research have made itpossible to uncover the criticalrole that marine microbes havein biogeochemical processes thataffect all life—from global climateMarine Microbial Food WebThe “microbial food web” is the pathway in the marine food chain through which carbon is reintroduced to the marine ecosystem bybacteria that consume dissolved organic material. Microscopic marine organisms called protists consume the bacteria, which are theneaten by zooplankton. Since microbes are at the base of the marine food web, the microbial food web is vital to the total productivityof the oceans and plays a major role in how much organic carbon is transported to the sediments of the deep sea floor.4Bigelow Laboratory for Ocean SciencesNote: Words in bold italic type are defined in the glossary on p. 42.

The Global Carbon CycleCarbon is one of the basic elements of living plants and animals andis also found in decaying organic matter, and in fossil fuel deposits.Atmospheric carbon dioxide gas (CO 2 ) traps a portion of the sun’sheat, making the planet's atmosphere warmer than it would otherwisebe. Emissions of carbon dioxide have caused CO 2 levels in theatmosphere to increase by approximately 30% since the beginningof the Industrial Revolution in the 18 th century, a factor now recognizedto be a major cause of current global climate change.Scientists estimate that the amount of carbon in the world’soceans is at least ten times greater than on land, making the pathwayswithin the marine carbon cycle critically important to allglobal ecosystems. There is a continuous exchange occurringbetween CO 2 in the atmosphere and the reservoirs of carbon inthe oceans and on land. By far the largest carbon reservoir onthe planet is the deep ocean, which has a much slower rate ofexchange with the atmosphere, making it a net carbon “sink,”where CO 2 fixed during photosynthesis is transferred into longtermstorage. Understanding the biogeochemical role of marinemicrobes in the global carbon cycle is essential to addressingthe challenge of climate change.change, to the nature of the planet’sfood supply, to the future of evolutionitself.Natural ecosystems everywhereare responding to profound changesin the global environment. The roleof the oceans in stabilizing andsustaining life on our planet isbecoming increasingly clear, andthis knowledge has direct bearingon our lives. As we come to understandthe cause and how it works,we are empowered to face theenvironmental challenges andopportunities that will shape ourfuture. In the years ahead, oceanresearch will continue to be at theforefront of discovery, and it is fairto say that the more we know, themore there is to know. At Bigelow,this serves both as a scientificmandate and as a source of hope—for our planet and for our ability toco-exist with the natural world.Oceans cover 71% of the planet’s surface, and contain all but3% of the world’s water. They provide the only source ofprotein for over a billion people, directly influence globalweather patterns, and distribute solar energy throughoutthe world. Microscopic, single-celled marine phytoplanktongenerate over half of the oxygen we breathe, absorb half ofthe carbon dioxide in the atmosphere, and form the basis ofthe marine food web.PhotosynthesisPhotosynthesis is the process by whichphytoplankton, algae, some types ofbacteria, and higher plants use carbondioxide (CO 2 ) and water to convert lightenergy from the sun into storable chemicalenergy, releasing oxygen as a by-productof the reaction. Researchers believe thatphotosynthesis is responsible for generatingmost of the oxygen in our atmosphere.As a result of photosynthesis, phytoplanktonplay a crucial role in the major globalbiogeochemical cycles that regulate thecomposition of the oceans and atmosphere,and thus directly influence thehealth of the entire planet. Photo courtesyof NOAA.Annual Report 20075

Bigelow LaboratoryPART Ifor Ocean SciencesMolecular Biology andMarine MicrobialBiodiversity

A LIVING LIBRARY8Bigelow Laboratory for Ocean Sciences

The Provasoli-Guillard National Centerfor Culture of Marine PhytoplanktonExploring the abundance and diversity of theocean’s microbial universe has offered theresearchers at Bigelow Laboratory a glimpseof frontiers and possibilities that, until recently,we hardly knew existed. Discoveries areeverywhere; the challenge is to develop thetools and skills to know where to look, whatto make of the wealth of information we arediscovering, and how to understand the centralrole that ocean microbes play in the planet’sbiogeochemical processes.Above: Thalassiosira collected off the coastof Norway. Below: Odontella, resting on aCoscinodiscus cell. Scanning elecron microscopeimages by R. Andersen.An ever-growing sample ofmicrobial ocean life isbeing collected, saved, andnurtured in The Provasoli-GuillardNational Center for Culture ofMarine Phytoplankton (CCMP)at Bigelow Laboratory.The culture collection is literallya living library of resources availableto scientists everywhere. Thelargest such collection in the world,the CCMP is providing living cellsfor researchers to investigatemarine biodiversity’s potentialrole in helping to address a rangeof issues, from developing newsources of bioenergy, to managingthe harmful algal blooms that alterthe dynamics of ocean ecosystems.Complemented by collectionsin several other universities andinstitutions, the CCMP is thecentral source of marine phytoplanktoncultures for internationalscientific and commercial purposes.The CCMP is the official phytoplanktonculture collection of theUnited States. As a public researchasset and central repository forliving cultures of marine phytoplankton,the collection is continuallyexpanding. It currently holdsmore than 2,400 strains of phytoplanktonfrom the world’s oceans,and has supplied over 8,000cultures to scientists from a varietyof institutions and industries in thepast five years alone. An averageof ten cultures are shipped toresearchers from the CCMP everyday. Under the direction of Dr.Robert Andersen, the CCMP hasisolated and successfully culturednew strains of marine phytoplanktonfor experimentation in theareas of biotechnology and nanofabrication.The Center’s website(ccmp.bigelow.org) features imagesof many of the strains from itscollection, and offers on-lineInside the “Stacks”The CCMP holds its cultures in a base ofenriched seawater at five different temperatures(- 2°C, 4°C, 14°C, 20°C and 25°C)that represent a range of ocean environmentsranging from polar to tropicalregions. There are two culture chambersfor each environment, and three sets ofcultures are maintained for each phytoplanktonstrain. In addition, a completefourth set of the entire collection is keptin a separate building, providing back-upcultures as a safeguard against the possibilityof catastrophic loss. Strains are alsomaintained in frozen vials in two separatestorage tanks.Annual Report 20079

Making biofuel from oil in phytoplankton cells on a scale that could replace conventionalpetroleum-based fuels is a growing focus of research in the developmentof environmentally sustainable energy sources. As the world’s largest repository ofliving phytoplankton strains, Bigelow Laboratory is uniquely positioned to test anddevelop algal biofuel production technology. The photos above show two Cyclotellacryptica phytoplankton cells from the CCMP collection, taken at different focal planes.Arrows point to oil droplets inside each cell. Some algae strains are made up of asmuch as 50% oil.ordering services and informationabout growing and preserving itscultures.In addition to conducting researchon the evolutionary historyand structure of marine phytoplanktoncommunities, Andersenteaches a professional summertraining course in phytoplanktonculturing techniques at the CCMP.The Center also provides isolationand purification services, startercultures, strains with sequencedgenomes, kits with pre-mixedgrowth media and seawater, masscultures, and DNA extracts.The CCMP began as two privateculture collections maintained byphytoplankton physiologists Dr.Luigi Provasoli at Yale Universityand Bigelow Laboratory’s Dr.Robert R. L. Guillard, then atWoods Hole OceanographicInstitution. Their research onmarine phytoplankton flourishedas more strains were donated andcollected, but by 1980, the task ofmaintaining and working with thegrowing collection became too largefor a privately-based operation.The National Science Foundationprovided support to establish asingle, national collection formarine phytoplankton at BigelowLaboratory and named Guillardas the collection’s first director.In 1992, the United StatesCongress formally recognized theCCMP as a National Center andFacility (Public Law 102-587,In 1992, the United States Congress formally recognized theCCMP as a National Center and Facility (Public Law 102-587,Oceans Act of 1992). The Center was named in honor ofProvasoli and Guillard as a tribute to their pioneeringcontributions to marine phytoplankton research.Oceans Act of 1992). The Centerwas named in honor of Provasoliand Guillard as a tribute to theirpioneering contributions to marinephytoplankton research. NowScientist Emeritus, Guillard hascontinued his work at the CCMP asit evolved to incorporate advancesin electron microscopy and DNAanalysis, further strengtheningBigelow Laboratory’s researchemphasis on marine microbialoceanography.Robert A. Andersen, Ph.D.,Botany/Phycology,University of Arkansas,1981; M.A., AquaticBiology, St.Cloud StateCollege, 1972; B.S., Botany,North Dakota StateUniversity, 1970.Robert R.L. Guillard,Scientist Emeritus, Ph.D.,1954 and M.S., MicrobialEcology, Yale University,1951; B. S., Physics, CityCollege of New York, 1941.10Bigelow Laboratory for Ocean Sciences

MarineMicrobialDNAOne Cell at a TimeMarine microbes drive most ofthe biogeochemical cycles in theworld’s ocean, directly influencingthe ocean’s critical role in theglobal environment. However,the physiology and ecological rolesof most marine microbes are stillunknown. Genomic studies cangreatly reduce this knowledge gap,but thus far they have mostly beenlimited to the roughly 1% of oceanmicrobes that can be cultured inthe laboratory.

Single-cell DNA analysis is a major technological breakthrough in the study of microbial ecosystems in the ocean. Bigelow Laboratoryhas recently applied for a patent on this new method for genetic research.Piecing together the genetic“instructions” that drivemarine microbial processesis essential to understanding thefoundation and evolution of life inthe ocean environment, as well asto discovering potential practicalapplications of marine microbesfor human benefit.Drs. Michael Sieracki andRamunas Stepanauskas have developeda single-cell genomics (SCG)method, which, for the first time,allows researchers to obtain informationabout genes from individualmicrobial cells, without the need togrow them in cultures. BigelowLaboratory has applied for a patenton this breakthrough in singe-cellDNA analysis, and in the futurethis technology may make it possiblefor microbiologists to rapidlyand economically analyze thecomposition and biogeochemicalfunctions of marine microbesthroughout the world.Sieracki and Stepanauskas studybacterioplankton, the smallestorganisms in the ocean (0.2–0.6micrometers in diameter) andthey have pioneered a way tocombine the powerful capabilitiesof fluorescence-activated cellsorting with advanced molecularbiology techniques to analyzegenomes of individual unculturedmicrobial cells.Until now, most molecularstudies of uncultured marinemicroorganisms have relied onmethods that contributed enormouslyto understanding thebreadth of diversity among microorganismson the planet. However,these methods did not allowresearchers to see how variousMetagenomicsvs. Single-cell genomicsCommunityDNA(Figure 1)DNAextractionSingle cellgenomeamplificationand analysis12Bigelow Laboratory for Ocean Sciences

Microbial EnergyProteorhodopsins are light-sensitive proteinsthat convert sunlight into chemical energy,thought to provide a supplementary “charge” foras many as half of the bacteria living near thesurface of the ocean. The Sieracki-Stepanauskasteam discovered proteorhodopsin genes in twomarine microbes in their pilot genetic library.It is still unclear which other types of bacteriacarry proteorhodopsin genes, or whether allproteorhodopsins are involved in energy production.The team is currently collaboratingwith a group of molecular biologists at the U.S.Department of Energy Joint Genome Institute,using their new method to reconstruct thecomplete genomes of these bacteria. As moregenomes of proteorhodopsin-containingmicrobes are sequenced, it may eventuallybecome feasible to develop ways of harnessingproteorhodopsin’s photometabolic activityin the production of bioenergy, thereby reducingour dependence on fossil fuels. Photo courtesyof NOAA.genes interconnect to determinemetabolic pathways, or to assemblecomplete genomes for individualmicrobes.In the Human Genome Projectof the 1990s, for example, J. C.Venter and his colleaguessequenced genes in millions of random,short DNA fragments andthen assembled them, like a jigsawpuzzle, to recreate the genome.Venter’s group subsequently usedthis “metagenomic” approach duringa two-year ocean cruise to analyzeDNA from marine microbesaround the world. But the unanticipatedmagnitude of natural geneticdiversity in marine microbial communitiesproved too high to assembleindividual marine microbialgenomes, apart from a handful ofthe most common types.The SCG approach, on the otherhand, allows researchers to isolateindividual microbial cells directlyfrom the environment and accesstheir genetic information. SCGrelies on the separation of individualmicrobial cells by fluorescenceactivatedcell sorting, followed bya reaction that copies the cell’sgenome to produce enough DNAfor different genetic analyses (seeFig.1, p.12). Various DNA markershelp determine a cell’s identity andits biochemistry.SCG offers a practical alternativeto metagenomics for examiningDNA in marine microbes thatcannot be grown in cultures.Over the past year, Sieracki,Stepanauskas, and their researchteam have successfully completedthis process for fifty marine bacteriaand protists, taking the firststeps in creating a detailed geneticlibrary for the marine environment.Ramunas Stepanauskas,Ph.D., Limnology/Ecology,2000, and M.A., Limnology,1993, Lund University,Sweden; B.A., Limnology,Uppsala University,Sweden, 1993.Annual Report 200713

MARINE VIROLOGYA New Universe of PossibilitiesThe arrow points to a virus attached to an Emiliana huxleyi coccolithophore cell on the right. Thevirus particle is approximately 190 nm (nanometers) in diameter. (There are 1 million nanometersin a millimeter.) Scanning electron microscope image courtesy of K. Ryan, MBA, Plymouth, UK.14Bigelow Laboratory for Ocean Sciences

Marine viruses are the most abundant biologicalparticles in the ocean. With an estimated onemillion marine microbes in every teaspoon ofseawater, the amount of microscopic life in theocean can be overwhelming to imagine. Thereare a hundred million times more bacteria inthe ocean than stars in the known universe,and ten- to a hundred- times more marine virusesthan bacteria. On land, we usually associateviruses with damage and danger such as influenzaepidemics, viral pneumonia, and HIV disease,among a host of other critical problems. But inthe marine environment, scientists are findingthat viruses are crucial to biogeochemical cyclingin the sea.Billions upon billions ofmutations occur in marineviruses every hour, each ofwhich has the potential tocreate still another new virusand affect the metabolicprocesses at the foundationof marine ecosystems.As a leader in the rapidlyexpanding field of marinevirology, Dr. Willie Wilsonand a team of Bigelow Laboratoryscientists are conducting researchon the pathways by which virusesinfect marine microbes and influencethe dynamics of the marineenvironment and the globalclimate.Marine viruses are key to breakingdown phytoplankton and releasingorganic carbon, acting as “lubricants”for the microbial loop at thebase of the marine food web (seep.4). Without marine viruses, therewould be no rapid mechanism fordecomposing organic matter in theocean, and the seas would ultimatelyfill up with the same sort oforganic sludge that waste treatmentplants on land must process.Viruses are instrumental in controllingthe extent and duration ofphytoplankton blooms, influencingthe ability of phytoplankton to actas important carbon sinks in theglobal carbon cycle (see p.5). Upto a quarter of the carbon absorbed(or fixed) by phytoplankton is“shunted” into the dissolved organiccarbon pool by viruses. There arealso marine viruses that attack andeventually help to collapse harmfulphytoplankton blooms such asred tide.Marine viruses help determinenutrient content and species compositionthroughout the globalocean. Some marine viruses arebelieved to influence climatedirectly by causing the releaseof pulses of dimethyl sulfidegas, which contributes to cloudformation in the atmosphere.Viruses exist in a multitude ofshapes, sizes, and genetic types.Wilson and his fellow researchersare investigating a group of giantviruses, identifying them throughindividual DNA blueprints in theirgenes. By studying the diversity anddistribution of viruses and theirfunction in structuring microbialcommunities in different regions ofthe ocean, they are discovering howviruses adapt to rapid changes inAnnual Report 200715

Blue BiotechnologyFrom the perspective of marinebiotechnology, Dr. Susie Wharam seesthe ocean as a largely untapped naturalresource with the potential to solvea wide range of problems. Wilson’sDNA analysis of the giant E. huxleyivirus (see below) produced a trove ofnovel genes for Wharam to explore.As a molecular biologist, Wharam uses advanced DNAanalytical techniques to isolate and investigate genesfrom marine viruses and other marine organisms.Researchers are discovering how to use viruses to killharmful bacteria through an approach known as phagetherapy, considered to be a key emerging technologybecause it avoids the need for antibiotics and the problemsthat result when bacteria develop antibiotic resistance.Wharam and her research teamare currently conducting tests on theuse of marine viruses to fight specificdisease-causing bacteria in lobsterhatcheries. If these tests are successful,phage therapy in the future couldbenefit hatcheries and other aquacultureoperations by preventing orcontrolling disease outbreaks.Wharam is also interested in developing technologiesand new diagnostic tools that will improve detection ofmarine bacteria and viruses that affect human health.One of her goals is to design hand-held virus detectionkits that could be used for on-site testing of water availablefor recreation or shellfish harvesting.the marine environment and howthose changes affect ecosystemprocesses, natural selection, andspecies composition in the sea.Wilson and his team are demonstratingthat viruses have far-reachingeffects on the structure ofmarine microbial communities,nutrient and energy flows, andglobal climate. Billions upon billionsof mutations occur in marineviruses every hour, each of whichhas the potential to create stillanother new virus and affect themetabolic processes at the foundationof marine ecosystems.Besides the importance of theirrole in the global carbon cycle,marine viruses themselves are aIn the eye of a needle you could fit...100,000 viruses, 10,000 bacteria, 1,000phytoplankton, 100 amoeba, 10 copepodlegs, and 1 human eyelash.vast and constantly changing reservoirof unexplored and potentiallybeneficial genetic diversity. It isbecoming clear that marine virusesare at the center of the interrelateddynamics of ocean life and are keyto phytoplankton evolution, actingas vectors for gene transfer andfueling the evolutionary processesthat maintain high levels of marinebiodiversity on the planet.Most viruses are genetic “minimalists,”containing only a fewgenes, but Wilson and his colleagueshave succeeded in unravelingthe genetic code of the largestvirus known to attack algae todate—the 472-gene virus thatinfects Emiliana huxleyi, a speciesof phytoplankton that is a majorfocus of current research on globalclimate and biogeochemical cycles.Over 400 of these genes have nodatabase matches, making themcompletely new to science. Suchdegree of novelty provides a tantalizingglimpse of the potentialbenefits locked within, but manyof the gene secrets still remain amystery.Of the genes that did have databasematches there were severalsurprises, including compoundsthat could be developed for use inanti-aging and cancer-inhibitingtherapies. These genes have neverbeen found in a virus before—theyare more commonly seen in animaland plant cells. Understandingthese novel virus pathways will aidin the development of medicinesthat may help to limit life-threateningdiseases and slow the agingprocess.Susie Wharam, Ph.D.,Molecular Biology ofPlant/Pathogen Interactions,University of Warwick, UK,1992; B.S., MolecularBiology and Biochemistry,Durham University, UK,1988.Willie Wilson, Ph.D.,Marine Viruses, 1994 andM.S., CyanobacteriaGenetics, University ofWarwick, UK, 1991; B.S.,Marine Biology andBiochemistry, UniversityCollege of North Wales,Bangor, UK, 1990.16Bigelow Laboratory for Ocean Sciences

Copepods and theGlobal Carbon CycleCopepods, a group of small aquatic microorganisms,have profound effects both on the ocean’sfisheries and on the accumulation of greenhousegases in the atmosphere. They consume approximately80-90% of the organic carbon produced bymarine algae, using some to grow and reproduceand packaging the remainder into pellets that sinkto the bottom of the ocean.Each year copepods providefood for commercially andecologically importantspecies such as fish and whales,and reduce atmospheric carbondioxide by exporting carbon tothe deep ocean.Copepods are the most numerousmulti-cellular invertebrateanimals on the planet, with numbersapproaching 10 21 individuals.There are more copepods on theplanet than there are insects, andthey have roughly the same biomassas would 600 billion humansput together. They are found inboth fresh and salt water systems,inhabiting waters from the poles tothe equator and from the surface tothe bottom of the ocean. Marinecopepods primarily feed by grazingon phytoplankton and consumingseveral kinds of microscopicanimals. Despite being tiny(between 0.1–10 mm in size), theirnumbers make them the dominantconsumers of the ocean’s biologicalproduction, fundamentally affectingthe fate of the fixed organic carbonin the ocean and the global carboncycle as a whole (see p.5).Dr. David Fields and his researchteam are investigating how copepodsfind their food and escapefrom potential predators. Combiningsmall-scale fluid mechanics,neurophysiology, and animal behavior,much of this work has focusedon how copepods are able to detectmechanical and chemical signalsin their environment. Little is currentlyknown about the sensorysystems of copepods, but the enormousdiversity of their sensorystructures provides an ideal modelsystem for understanding howthese relatively simple, but important,marine invertebrates pick upand process sensory information.A copepod is adorned withnumerous sensors throughout itsbody. Fields’s team is studying howthe architecture of copepod sensorysystems affects what these animalseat, what predators they can detect,and ultimately where they arefound within the global ocean.In a recent joint project with theMassachusetts Institute ofTechnology, Fields and his colleaguesmodeled the fluid dynamicssurrounding the individual sensoryhairs that these animals use toperceive their environment.Top: The female Temora longicornis(1.1 mm) swimming through the watercolumn is searching for food (phytoplankton)and detecting predators usingchemical and mechanical sensors on herantennae.Bottom: A scanning electron microscope(SEM-800X) photograph of the antenuleof Gaussia priceps. G. Priceps is a deep-seacopepod captured 2,100 feet below theocean’s surface off the coast of Hawaii.Photos by D. Fields.Understanding the small-scalemechanics, structure, and “tuning”of these sensors may provideanswers to how these organisms,and the marine life that dependson them for food, are distributedon a global scale.David Fields, Ph.D.,Oceanography 1996,and M.S., CoastalOceanography 1991,State University of NY-Stony Brook; B.S., Biology,University of Utah, 1986.Annual Report 200717

Tracking Marine Lifethrough Evolutionary TimeOften depicted as a vigorous ever-branching tree,life evolved through innumerable microscopicmoments of genetic chance—each creating thepossibility for a new way to go about living; fora different path to survival; for another branch.By deciphering the genetic signatures of marinemicrobes, researchers are discovering seismicmoments in the history of nature that reach backto the roots of life itself.18Bigelow Laboratory for Ocean Sciences

The protist Paulinella chromatophora is aspecies of amoeba that has evolved theability to use plastids for photosynthesis.Dr. Hwan Su Yoon’sresearch has uncoveredone such moment overone and half billion years ago—thepoint at which bacteria took thefirst steps toward becoming plants,and photosynthesis began to fuel anexplosion of new life on this planet.Yoon’s work is central to the growingscientific focus on the evolutionarybiology of marine life, andon what that history can teach usabout biological processes at workin the ocean today.The transition from the bacterialstage of life to more organized, single-celledlife forms, and then onto the legions of complex multicellularorganisms that includeus, involved a biological processknown as endosymbiosis. This vitalstep consisted of the capture of onetype of bacterial cell by another,but, rather than being consumedas food, the engulfed bacteriumbecame a tiny organ, or organelle,with a specialized function insideits “host” cell. One function, criticallyimportant for the rest of us,was harnessing the sun’s energythrough photosynthesis, and wasperformed by bacteria that hadbeen engulfed by other bacteria,becoming a category of organellescalled plastids. Molecular biologistsconsider plastids to be “the powerhousesof primary productivity” inthe plant kingdom.The single-celled phytoplanktonthat drift in the open oceans andthe more complex, multi-cellularmarine algae we can see growing incoastal waters all contain plastidsthat are essential to their survival.Yoon is investigating the way photosynthesisfirst developed inmarine algae by studying the evolutionof plastids inside individualalgal cells. He uses advanced genesequencing techniques to identifythe evolutionary connectionsamong living cells, and analyzesthe molecular structure of fossilcells to piece together informationabout how plastids originallyevolved. His findings show thatplastids were initially formed whena single-celled blue-green alga capableof bacterial photosynthesis wascaptured by another single-celledorganism and became “enslaved”as a permanent organelle. By tracingthousands of genetic sequencesfound in algae backwards throughtime—a cellular forensics of sort—Yoon and fellow scientists havefound evidence that photosynthesisby plastids began on the planetapproximately 1.6 billion years ago.As more and more genes aresequenced, researchers are discoveringsome of the pathways by whichplastids diversified and diverged asdifferent groups of algae evolved,eventually branching out to developnew and more specialized functionsin the cells of higher plants. Yoonand his research team are creatingan increasingly accurate evolutionarytime-line connecting endosymbiosisand plastid evolution withthe genetic diversity that continuesto shape ocean ecosystems today.Hwan Su Yoon, Ph.D.,Botany, 1999; M.S., Biology,1994; and B.S., Biology,Chungnam NationalUniversity, Korea, 1992.Annual Report 200719

Indicates focus of major research cruise.

Bigelow LaboratoryPART IIfor Ocean SciencesShip’s Log, 2007Research on the Open Seas

Abrupt Climate ChangeEvidence in the Arabian SeaIn March 2007, Dr. Joaquim Goésand Dr. Helga Gomes received athree-year, $1.18 million NationalAeronautics and Space Administration(NASA) grant, bringing aninternational team of atmosphericand ocean scientists together inthe field to measure the effects ofglobal climate change on phytoplanktonblooms in the ArabianSea. The team is using satelliteimaging and direct sea sampling toinvestigate how global warming isaffecting marine life in the ArabianSea, increasing greenhouse gasesin the atmosphere, and changingdrought and flood patterns oversouthwestern Asia—an area thatis home to more than a third ofthe world’s human population.

(Figure 1)WinterSummerDifferences in temperature between land and ocean drive the Asian monsoon. During the winter in South Asia (upper left), warmair over the Arabian Sea rises, drawing cold air from the land to the north. In summer (upper right), after much of the snow melts,the land warms more than the ocean, and the wind direction reverses. (Maps by Robert Simmon, based on data provided by BigelowLaboratory.)The Arabian Sea has givenresearchers at BigelowLaboratory a window ontothe dramatic consequences of globalclimate change for marineecosystems. Over the past sevenyears, the western half of theArabian Sea has witnessed recordincreases in phytoplankton blooms,triggered by the rapid decline andmeltdown of winter snow oversouthwest Asia and the Himalayas.Goés and his research team arestudying the connection betweenchanging weather patterns andocean processes in this 1.5 millionsquare mile area of the IndianOcean, amassing concrete evidenceabout the effects of abrupt climatechange on phytoplankton blooms.Goés began the study by usingremote sensing data from NASAEarth Observing Satellites to measurechlorophyll, sea-surface temperatures,and nitrate concentrationsthroughout the Arabian Sea (seeFig.3, p.24). He first observed signsof unusually high levels of nutrientupwelling in satellite images thatshowed massive increases in nitrateconcentrations (a major nutrientsource for phytoplankton).Findings also showed a 350%increase in chlorophyll concentrationsover the past seven years—reflecting an enormous increasein phytoplankton growth. Overall,the data show that phytoplanktonblooms—once a healthy source offood for the area’s fisheries—areoccurring on such a scale and withsuch intensity, that upon death anddecay, they are using up oxygenin the waters below the surface.This is causing a shift in speciescomposition, and declining levelsof phytoplankton biodiversity inthe Arabian Sea ecosystem. Reportsof fish kills from lack of dissolvedoxygen in these waters are further% Changein snowcoverextent(Figure 2) Average snow cover, 1967–present.Across Eurasia, snow cover (red line) hasdropped significantly since the late 1990s.Warming temperatures are most likely toblame. Lack of snow allows the land surfaceto heat up more in the summer, andthe widening temperature contrastbetween land and ocean in the summerstrengthens the monsoon. (Graph byRobert Simmon, based on data providedby Bigelow Laboratory.)1975 1980 1985 1990 1995 2000YearAnnual Report 200723

(Figure 3)Nitrate concentrations from August 2002, with blue indicating low levels and lightgreen signifying high levels. (Map by Robert Simmon, based on data provided by H.Gomes, Bigelow Laboratory.)evidence of a spreading “dead zone”in which biological productivity isvirtually gone.The problem is made worse bythe fact that lack of dissolved oxygenin the water fosters the growthof a type of bacteria that releasesnitrous oxide, a greenhouse gasthat is a significantly greater contributorto atmospheric warmingthan carbon dioxide. Increasinglevels of nitrous oxide are essentiallyadding “fuel to the fire” that hasalready warmed the Eurasian landmass 50% more than the averageglobal temperature increase of1.3°F. over the past century. (Since1979, overall temperatures on landhave been going up by nearly half adegree per decade, almost twice asfast as ocean temperatures havebeen rising.)Located in the northwest part ofthe Indian Ocean between Arabiaand western India, the ArabianSea has historically had a uniquemonsoon cycle, with reversingwinds that create both winter andsummer monsoon seasons, causinga strong upwelling of nutrientsthat nourish seasonal phytoplanktonblooms. The extent of winterand spring snow cover over theEurasian land mass, and the heatreleased during spring, have amajor impact on the land-seathermal gradient that drivesthe monsoons. These yearly, seasonallyreversing monsoons (seeFig.1, p.23) in turn drive one of themost energetic ocean current systemsin the world, causing thegreatest seasonal variability of phytoplanktonobserved in any oceanbasin. The Arabian Sea is the onlyocean system that fully reverses itscirculation on a semi-annual basis.The extreme seasonality of theArabian Sea’s circulation and itsoverlying wind field arise from theheating and cooling temperaturecontrasts between the Tibetanplateau of the Indian subcontinentand the large volume of ocean surroundingit. The plateau heats upin spring, producing low pressureover the region. Meanwhile, highpressure prevails over the ocean,causing winds to flow northwards.This strong surface wind reaches36 knots (over 40 miles per hour)or more during July, pulling deep,nutrient rich waters to the surfaceto fuel phytoplankton growth. Thiswater is then replaced by deeper,cold water welling up from belowthat is rich in dissolved nutrients,which nourish phytoplankton asthey photosynthesize and grow.The reverse is true in winter.Although these are regular andpredictable events, monsoonintensity from year to year is governedby the amount of snow andice on the plateau. In years ofreduced snow and ice, heat inspring and summer warms the landfaster, creating a large contrastbetween the pressure over land andocean and resulting in a strongersummer monsoon.Since 1999, there has been anabrupt decline in the amount ofannual winter snowfall in theHimalayan-Tibetan mountains onthe eastern side of the Arabian Sea(see Fig.2, p.23), which has shiftedweather patterns and intensifiedthe monsoon winds in the westernpart of the sea. Year after year,rapidly declining snow cover in themountains has led to ever-warmerconditions on land. This hasstrengthened the southwest monsoonwinds and caused strongernutrient upwelling from the coolerwaters of the western coast, triggeringincreasingly massive phytoplanktonblooms.Joaquim I. Goés, Ph.D.,Ocean Biochemistry, NagoyaUniversity, Japan, 1996;M.S., Marine Microbiology,1985 and B.S., Botany/Zoology, 1980, BombayUniversity, India.24Bigelow Laboratory for Ocean Sciences

ChangingSeaBiologicalProductivity andAbundance in theArctic OceanThe Arctic climate is changingrapidly—averaged over anarea north of 60° N, warmingis approximately twice theglobal average. PerennialArctic sea-ice cover is diminishing,glaciers are retreating,and areas of permafrost arebecoming smaller. All of thisimpacts the special ecologyof the Arctic, but it also haspotential consequences forglobal climate.

Curious visitors to the air andwater sampling activities of CruiseAOE-01, Icebreaker Oden, 89° N.Photos on pp. 25–27 courtesy of P. Matrai.Because the impact of globalenvironmental changes ismore extreme in the Arcticthan anywhere else, the marineecosystem of the Arctic Ocean, particularlythe role of phytoplanktonin the biological productivity ofthe region, has become a focus ofresearch about changing conditionsthere and how they affect the restof the planet.The biological productivity ofphytoplankton depends upon ongoinginteractions between thebiology and chemistry of theworld’s oceans. Phytoplanktonbloom and thrive because of theirability to use sunlight for photosynthesis.As a consequence, theyprovide food for other formsof ocean life, fueling the vast,multi-dimensional predator-preyfood web of the sea. Phytoplanktonare directly involved in the cyclingof chemical compounds throughthe marine environment and theexchange of gases at the interfacebetween the ocean and the loweratmosphere. These processes arecritical to the overall global ecosystemdynamics that regulate andsustain life.Dr. Patricia Matrai is currentlycollaborating with a team ofO(cean)-Buoyresearchers on a multi-institutionalproject to synthesize existingknowledge about biological productivityin the Arctic Ocean. She andher colleagues are studying primaryproductivity through a combinationThe International Polar Year (IPY) is a major scientific campaign focusing onthe Arctic and the Antarctic. The largest polar research program in history, it isco-sponsored by the World Meteorological Organization and the InternationalCouncil for Science. IPY is scheduled to run from March 2007 to March 2009,and is the beginning of a new era in polar science.Dr. Matrai (right) is participating in the International Polar Year programthrough her work on O-Buoy, a three-year project with a team of scientists fromthe United States, Canada, and Germany. They will design and deploy a series ofautonomous ice-tethered buoys with chemical sensors to monitor the atmosphericchemistry over the Arctic Ocean. Similar measurements have been made inlandand along the coast, but O-Buoy is the first time scientists will continuously studythe chemistry of the Arctic atmosphere by monitoring the frozen ocean surface.Each buoy will have an on-board computer controlling its instruments and sendingdata to satellites for transmission back to the lab. Researchers expect that theO-Buoy Project will begin years of measurements for ozone, carbon dioxide, andother atmospheric chemicals above the Arctic Ocean that are key indicators ofpollution, mercury deposition, and greenhouse gas emissions.26Bigelow Laboratory for Ocean Sciences

of historical direct measurements,nutrient budgets, and remotesensing. By looking at the biologyof the Arctic Ocean from multipledimensions they are modeling howclimate change and its impact onsea-ice cover is affecting phytoplanktonpopulations in the region.Nutrient Flow in Arctic WatersThe water that carries dissolvednutrients vital for phytoplanktongrowth through the central ArcticOcean basin is influenced by twostrong continental shelf currentsalong the Alaska coastline and theBering Sea. Dr. John Christensen isproject leader for two NationalScience Foundation-funded polarresearch teams compiling yearroundbaseline data about this biologicallyproductive ocean area.The researchers are using nutrientanalyzers on moorings positioned inshelf break regions to assess cyclesof nitrate concentration and phytoplanktonabundance. Working atthe North Pole EnvironmentalObservatory, Christensen and histeam are investigating whether theedges of the shelf break in theArctic Ocean function as upwellingsites for nutrient-rich deeper watersfrom the surrounding Chukchi andBeaufort Seas. Helicopter surveysare helping to identify areas wherestrong currents influence temperature,subsurface nutrient content,and phytoplankton abundance atdifferent depths in advance of thespring phytoplankton bloom. Thereis very little baseline biological dataavailable from this region, and theresults of this project are providingessential information about theArctic Ocean ecosystem and how itis responding to changing climateconditions.Patricia Matrai, Ph.D.,Biological Oceanography,1988, and M.S., Oceanography,1984, ScrippsInstitution of Oceanography,University of California, SanDiego; B.S., Marine Biology,1981, Universidad deConcepción, Concepción,Chile.John Christensen, Ph.D.,Chemical Oceanography,1981 and M.S., ChemicalOceanography, Universityof Washington, 1974; B.A.,Chemistry, NorthernArizona University, 1971.Annual Report 200727

Following Tracksin the South AtlanticEvery year, the ocean over thePatagonian Shelf off the coast ofArgentina turns brilliant turquoiseas a teeming population of phytoplanktoncalled coccolithophorescreates one of the SouthernHemisphere’s largest algal blooms.Dr. Barney Balch is the projectleader of a major National ScienceFoundation grant to study theecological factors regulating Emilianahuxleyi, the coccolithophoreresponsible for this massive bloom.His team is studying the role ofcoccolithophores in absorbing carbonfrom seawater and their significantimpact on the global carbon cycle.

Microscopic Emiliana huxleyi coccolithophore cells cover themselves withhighly-reflective limestone (calcium carbonate) platelets called coccoliths.When this single-celled phytoplankton species blooms, the coccolithsreflect sunlight back out to space, instead of absorbing light and raisingthe temperature of the water. Emiliana huxleyi blooms turn vast areas ofthe ocean a milky turquoise color that is clearly seen in satelliteimages from space. These images are scanning electron micrographsof Emiliana huxleyi cells taken by Dr. Dolors Blasco, Institute de Cienciasdel Mar, Barcelona, Spain.Since the beginning of theindustrial revolution in the18 th century, the ocean hasbecome about 26% moreacidic (with more than halfof that change in just thelast decade).Scientists have lacked evenbasic knowledge about thephytoplankton ecology of thePatagonian shelf and how environmentalchanges affect the blooms.Balch’s project is the first multidisciplinary,ship-based investigationof these massive blooms, andit will allow researchers to build oninformation that, until now, hasbeen based almost exclusively onbloom studies in the NorthernHemisphere.Using a combination of underway,satellite, and direct sampling,the Patagonian expedition is documentingthe factors regulating thedistribution of the coccolithophoreblooms. The results will be integratedwith data that Balch andhis research team have gatheredover thousands of nautical mileson previous research cruises, refiningestimates of phytoplankton productivityand other hydrographic,chemical, and optical properties ofocean ecosystems. By calibratingmeasurements at sea with satelliteimages of ocean reflectance, seasurface temperature, and light,Balch and his colleagues are able tointerpret remote sensing satellitedata about long-term changes in theocean environment in the contextof increasing levels of atmosphericcarbon dioxide and associatedglobal climate changes.The coccolithophore Emilianahuxleyi belongs to a category ofsingle-celled phytoplankton thattake up dissolved carbon in theprocess of covering themselveswith tiny plates or scales madefrom calcium carbonate (CaCO 3 ).The CaCO 3 plates create patches ofcolor in the ocean that can extend200,000 square miles or more andcan be easily seen from satellites.Facing page: Coccolithophore bloom(turquoise color) cradling the FalklandIslands, Patagonian Shelf. (NASA photo.)Annual Report 200729

Bigelow Laboratory’s portable researchunit is equipped for installation and useon oceanographic vessels and ships ofopportunity (ferries, cargo ships, etc.)around the world.Calcium carbonate is among themost common minerals found inthe ocean and is the compoundmany marine organisms need tomake shells. Coral reefs are madealmost entirely from CaCO 3 , asare the White Cliffs of Dover. Theamount of CaCO 3 that can befound in ocean water is directlytied to the acidity of the marineenvironment.Starting in 1994, researchershave documented a continuousincrease in the acidity of oceanwater. Since the beginning ofthe industrial revolution in the18 th century, the ocean has becomeabout 26% more acidic (with morethan half of that change occurringin just the last decade).Balch and his colleagues areinvestigating the effect that thisincreasing ocean acidity is havingon marine organisms’ ability tomake CaCO 3 shells. In sufficientlyacidic conditions, CaCO 3 in shellsmay even dissolve, leaving organismswithout their natural defensefrom predators.Ocean acidification also hasthe potential to affect a muchbroader suite of physiologicalprocesses in plankton that arenot directly tied to CaCO 3 production,such as photosynthesisand respiration. Increased aciditywould also alter the natural chemicalequilibrium that existsbetween CO 2 and other dissolvedcarbon forms in seawater, fundamentallychanging the chemistryof the sea.The information obtained on thePatagonian Shelf cruise is criticalfor modeling complex biogeochemicalprocesses that regulate phytoplanktonproduction and the globalcarbon cycle. This study will providethe first detailed analysis ofthe coccolithophores in this enormousarea of the ocean.William “Barney” Balch,Ph.D., Scripps Institutionof Oceanography, 1985;B.A. Biology, CornellUniversity, 1980.30Bigelow Laboratory for Ocean Sciences

Brazil to NamibiaThe South Atlantic TransectScientists predict that “desertlike”areas of the ocean withrelatively low biological productivitywill expand as a result ofthe warming climate, particularlyin the marine ecosystems of subtropicalgyres such as the SouthAtlantic Ocean. Understanding thedynamics of phytoplankton communitiesand the biogeochemicalprocesses at work in the huge physicalexpanse of these areas will helpresearchers assess the magnitude oftheir effect on global climate.At the end of 2007, Dr. MichaelSieracki and a team of Bigelowresearchers embarked on a fourweekoceanographic researchexpedition between Brazil andNamibia to investigate thebiochemistry and phytoplanktonecology of this vast and largelyunexplored area of the SouthR/V Knorr. Owned by the U.S. Navy and operated by Woods Hole OceanographicInstitution for the ocean research community. Photo by M. Sieracki.Atlantic. Taking 12-hour shifts tobe able to work 24 hours of everyday aboard ship, the team examinedthe structure, dynamics, and statusof phytoplankton communitiesalong a transect from the SouthAtlantic subtropical gyre to thebiologically rich waters of theBenguela upwelling off the coastof Namibia on the African continent.In December 2007, Dr. Sieracki led a teamof scientists from Bigelow Laboratory ona research cruise to investigate the biologicalcharacteristics of these nutrientrichwaters as part of a month-long studyof the largely unexplored South AtlanticOcean between Brazil and Namibia.Phytoplankton bloom off Namibia,November 8, 2007. National Aeronauticsand Space Administration (NASA),MODIS Image.Annual Report 200731

Along the South Atlantic transect, looking west. Photo by M. Sieracki.Sieracki and his research teaminstalled state-of-the art, high-speedfluorescence-activated cell sortingtechnology on board the R/V Knorrin order to analyze phytoplanktonproductivity and nutrient requirementsfor a myriad of phytoplanktonspecies collected along thetransect. Dozens of species werealso collected for deposit inBigelow Laboratory’s growingphytoplankton culture collection(see p. 9, Provasoli-GuillardNational Center for the Cultureof Marine Phytoplankton).Comparing the measurementsthat Sieracki and his researchersmade across the South Atlantic gyrewith their subsequent analysis ofthe rich plankton community of theBenguela upwelling will strengthenour ability to evaluate phytoplanktonproductivity from remotesensing satellite images.Marine sulfur compounds producedby phytoplankton eventuallyeither enter the atmosphere asdimethylsufide gas, or are routedinto the marine microbial foodweb (see p.4). Results of the team’sshipboard investigation of thesecompounds will allow climatemodelers to more fully understandwhat the ocean’s biogeochemicalresponse to climate warming willbe in the future.Michael Sieracki, Ph.D.,Biological Oceanography,1985 and M.S. 1980,Microbiology, University ofRhode Island; B.A. 1977,Biological Sciences,University of Delaware.32Bigelow Laboratory for Ocean Sciences

Forecasting BiologicalProductivity in theNorthwest AtlanticThe Gulf Stream and the Labrador Current meetover the coastal shelf waters of New Englandand Atlantic Canada, resulting in the steepestnorth-south thermal gradient in ocean temperaturein the world. Historically, the biologicalrichness of this active mixing zone gave riseto some of the world’s most productive fishinggrounds. But the region’s most iconic species,including lobster and cod, are increasinglythreatened by human activity. Dr. RichardWahle’s research combines oceanography,experimental ecology, and fisheries scienceto evaluate and predict the consequences ofnatural processes and human impacts on thedistribution and abundance of key species in thebenthic communities of the Northwest Atlantic.Dr. Wahle’s research team with the benthic sled used in camera surveys of deep sea redcrab off the southern New England shelf break. Photo by R. Wahle.

Wahle and his researchteam study the criticallinks between life stagesof benthic ocean species, from theirbeginnings as fertilized eggs, to initialdays as free-floating planktoniclarvae, to life as reproductive adultson the sea floor. A critical time forlobsters, for example, occurs justafter the larval stage, when juvenilessettle to nursery habitat onthe bottom and begin to grow. Thenumber of individuals that successfullymakes this transition eachyear is vital to determining thenumber of adults entering the fisherybetween five and nine yearslater.With initial funding from theNational Science Foundation(NSF) and National Oceanic andAtmospheric Administration(NOAA), Wahle and his colleagueshave developed techniques for settlementmonitoring by diver-basedsuction sampling. Modeling larvaltransport and monitoring settlementsuccess are essential toolsin forecasting trends in lobsterpopulations.Much of this long-term monitoringis being continued by participatingstates and provinces fromRhode Island to Nova Scotia, withBigelow Laboratory as the centralclearinghouse for data and analysis.Rick Wahle conducting sea urchin population surveys in the Gulf of Maine.Photo by Hoyt Peckham.Wahle’s team has subsequentlydeveloped “passive post-larvalcollectors,” making it possible forthe first time to obtain lobstersettlement data at depths beyondthe limits of scuba diving. Fundedby NOAA’s Northeast Consortium,this deep-water project is openinga window on the poorly understoodrelationship between thermalstratification of the water columnand benthic settlement patterns.The collaboration has widenedto include several Canadian andEuropean researchers, expandingthe scope of study beyond lobstersettlement to evaluate patterns oftrans-Atlantic benthic biodiversity.Wahle’s work is also providinga better understanding of howdepletion of sea urchin and deep-sea red crab adults by harvestingmay compromise individualspawning success and diminishthe abundance of their larvae.Results of the team’s monitoring,modeling, and field experimentshave allowed researchersto identify separate “geographies”for pre- and post-settlementprocesses, in which the role ofocean and atmosphere interactionson one hand, and disease, predation,and competition on the other,ultimately determine regionaldifferences in population size.New funding from the NationalAeronautics and Space Administration(NASA) is allowing Wahleand his collaborators to investigatehow these patterns are being affectedby changing climate conditions.2007 Northeast Climate Impacts AssessmentDr. Wahle was a contributing author on the Marine Sector Team of theNortheast Climate Impacts Assessment (NECIA) report, developed by fiftyindependent experts and the Union of Concerned Scientists, and released inthe summer of 2007. The report was based on cumulative, multi-disciplinaryresearch findings about the continuing effects of global warming on thenortheastern region of the Western Hemisphere. Wahle’s research is part ofthe NECIA’s assessment of the impact of climate change on marine life.Rick Wahle, Ph.D.,Zoology, University ofMaine, 1990; M. S.,Biology, San Francisco StateUniversity, 1982; B. A.,Zoology, University of NewHampshire, 1977.34Bigelow Laboratory for Ocean Sciences

Deep in the PacificExtremes of Life on the Loihi SeamountBiogeochemical interactions in the prehistoricseas were vastly different from the naturalprocesses of life in most of the ocean today.Exploring deep reaches of the ocean floor,scientists have discovered hydrothermalvents and seeps in the Earth’s crust wherethose ancient processes are still continuing.The microbial life that flourishesin these extreme environmentsoffers clues aboutthe role of ocean microbes in theplanet’s early geochemistry.Microbes may have been directlyinvolved in the creation of bandediron formations—the world’s primarysource of iron ore—as well ashaving had a central part in theevolution of the global ecosystemas a whole.Compared to the abundant diversityof life in the ocean’s water column,conditions at deep-sea ventstend to be quite extreme, favoringhighly specialized microbes knownas extremophiles. Vents wherethere is very little oxygen and lotsof iron are an ideal habitat for ametabolically extreme group ofiron-eating bacteria that are distinguishedby their ability to convertiron molecules into food energy.These bacteria can live literally byeating nails and producing rust asby-product of their metabolism.Microbial ecologist Dr. DavidEmerson has used deep-sea submersiblesmore than three milesbelow the surface of the PacificOcean to explore iron oxidation inbiological systems associated withdeep-sea venting and lava flowsat the base of the Loihi Seamount,Iron-oxide structures at Loihi, 3,600 feetbelow the surface. Photo by D. Emerson.Bathymetry of the Loihi Seamount.Close-up of filamentous bacterial mats.Courtesy of Clara Chan.Hawaii’s youngest underwater volcano.His expeditions are part ofa novel deep-sea iron microbialobservatory project, known asFeMO (Iron Microbial Observatoryat Loihi Volcano).Emerson and his research teamhave discovered an entirely newclass of marine bacteria, includingorganisms called Mariprofundusferrooxydans, which grow in thickfilamentous mats around the volcano’scaldera and hydrothermalvents. Investigation of the geneticstructure and physiology of theselife forms has begun to reveal themechanisms by which they metabolizeiron and survive where othermicrobes cannot exist.Emerson and his colleaguesare analyzing the genomes andphysiology of these newly describedmicrobes to determine their possibleuse in nanotechnology andother applications. For example,they may be quite effective atremoval of both organic and inorganicpollutants for environmentalclean-up. Other investigations arealso underway to assess the rolethat iron-oxidizing bacteria may beable to play in climate change byacting as a potentially significantglobal carbon sink.David Emerson, Ph.D.,Microbiology, CornellUniversity, 1989; B.A.,Human Ecology, Collegeof the Atlantic, 1981.Annual Report 200735

Bigelow LaboratoryPART IIIfor Ocean SciencesEcosystem Modeling

A Crucible for Multi-DisciplinaryEcosystem ModelingLocated on the international borderbetween the United States andCanada at the mouth of the Bayof Fundy, Cobscook Bay has beenthe site of extraordinary biologicalrichness for millennia, providinghabitat for the highest level of biodiversitynorth of the tropics.The bay is a geologicallycomplex estuary characterizedby large tides and tidalpools, fog, and significant nutrientinput. In recent decades, areas ofthe bay have been proposed for aseries of industrial projects includingsites for liquefied natural gasterminals, oil refineries, tidal powergeneration, and aquaculture.Scientists have found 900 speciesof marine invertebrates living inthe bay, and estimate a total speciesdiversity of over 1,500. Funded by amajor, multi-year grant to TheNature Conservancy from theAndrew W. Mellon Foundation, theCobscook project brought togetherresearchers from diverse ocean sciencedisciplines to investigate howthis spectacular combination ofspecies richness and biological productivitydeveloped and how it continues,in great part, to exist today.An estuarine and coastal benthicecologist at Bigelow Laboratory, Dr.Peter Larsen has been a member ofthe Cobscook research team sinceit began its work. More than twoCobscook Bay.Google Earthimage.dozen scientists, Nature Conservancystaff, and Cobscook area communitymembers synthesized whatwas already known about the bayand undertook new research tomodel the flow of energy and nutrientsthrough the estuary. Theystudied physical, chemical, geological,and biological processes,including phytoplankton andmacroalgal productivity, waterquality, habitat characteristics,and hydrodynamics in order todescribe the forces that drive andperpetuate the bay’s biological productivity.Key among their findingsis the fact that, when the myriadinputs into this unique biologicalsystem are translated into equivalentunits of energy, tidal energyand circulation emerge as thedominant physical forces at workwithin the ecosystem.Because of its unique convergenceof natural features andprocesses, the bay has becomean extremely valuable “provingground” for modeling naturalenergy flows, as well as for evaluatingthe energy impacts of existingand proposed human activities,such as the potential environmentaleffects of tidal power development.Larsen is now expandingthe Cobscook model to make thisapproach transferable to estuarineand marine ecosystem modeling inother coastal regions.Peter F. Larsen, Ph.D.,Marine Science, College ofWilliam and Mary, 1974;M.S., Zoology, 1969 andB.A., Zoology, Universityof Connecticut, 1967.38Bigelow Laboratory for Ocean Sciences

From Biomolecules to EcosystemsOrganizing the Genomic RevolutionA major research focus of marine evolutionarybiology includes identifying the mechanismsby which adaptation takes place at the cellularlevel, the actual genetic pathways that createnew approaches to survival in the face of environmentalchange. Bioinformatics is a computationalapproach to biology that combines molecular biologyand mathematical modeling with computersoftware design to investigate this and otherquestions at the biomolecular level.Dr. David McClellan isdeveloping biological andcomputational approachesfor the study of molecular adaptation,a field of research that investigatesthe molecular mechanismsbehind a wide range of biologicalphenomena—from drug and vaccineresistance in viruses and bacteria,to the effects of global and localclimate change on humans andother organisms. He is developinganalytical methodology and computersoftware, and working incollaboration with other researchersat Bigelow Laboratory andaround the world to characterizeadaptation in a variety of organisms,including worms, copepods,wasps, agricultural crops, lizards,whales, and humans.Molecular adaptation is usuallya consequence of changes in geneticcodes for proteins, which result indifferent levels of fitness in termsof an organism’s chances to surviveand reproduce. Bioinformaticsprovides a means for scientists toexamine adaptation at the molecularlevel and uncover informationabout the molecular sequenceswithin the specific amino acidsthat form the building blocks ofproteins. For example, McClellanis currently using bioinformaticsto study the molecular adaptationsthat allowed copepod species (seep.17) to make the evolutionarytransition from fresh water to saltwaterhabitats.The ability to find and use suchdata is helping researchers identifyand categorize the causes of adaptation.This, in turn, is making itpossible to visualize where andhow evolution is occurring at themolecular level, determine the relativechronology of evolutionarychanges in different species overtime, and begin to model possibleevolutionary changes in the future.The emergence of bioinformaticsas a new field of study was in largepart a response to the flood of informationfrom recent major advancesin genomic research. By applyingthe power of database developmentand software design to the resultsBouquet of Corallium with deep purpleTrachythela octocoral. Mountains in theSea Expedition, 2004. Photo courtesy ofNOAA Office of Ocean Exploration, Dr. LesWatling, Chief Scientist, University ofMaine.of empirical research, bioinformaticsis enabling scientists to understandand integrate biological systemsat vastly different hierarchicallevels, from molecules andmicrobes to entire ecosystems.David McClellan, Ph.D.,Biological Sciences,Louisiana State University,1999; M. S., Zoology, 1994and B.S., Zoology, BrighamYoung University, 1992.Annual Report 200739

Ocean LiteracyTelling the StoryThe research programs at Bigelow Laboratorycontinually expand our understanding of oceansystems and their importance to global environmentalsustainability. Bigelow scientists arecommitted to sharing their discoveries witheducators, students, and the public through avariety of programs. The need to communicatethis knowledge to the wider world has neverbeen greater.Foundations of Marine ScienceAseries of upper undergraduate and graduate level courses knownas Foundations of Marine Science is taught at the Laboratory byBigelow scientists, often in collaboration with guest lecturersfrom other institutions. Course content changes regularly and is basedon current research projects, giving students the experience of directlycontributing to ongoing investigations. Recent courses include:Photo by Bruce Wood.PhytoplanktonCulturing TechniquesDrs. Robert Andersen and MichaelSieracki teach at the Labratory’sProvasoli-Guillard National Centerfor Culture of Marine Phytoplankton.(See p.9.) Their phytoplanktonculturing course is designed forgraduate students, faculty members,and aquaculturists; and covers basicas well as advanced techniques forisolating, growing, and cryopreservingmarine phytoplankton. Studentsuse fluorescence-activated cellsorting to isolate and purify culturestrains, and conduct cryopreservationlaboratory exercises.Physical-Biological Interactionsin the PlanktonDr. David Fields and two colleaguesfrom the Danish Fisheries ResearchInstitute and Texas A&MUniversity have collaborated toteach Physical-BiologicalInteractions in the Plankton—asmall-scale fluid dynamics coursethat examines the miniature worldof plankton and the physical andchemical characteristics that affecttheir feeding, encounter rates,and perception within the marineenvironment.40Bigelow Laboratory for Ocean Sciences

Agouron Hawaii Summer CourseIn the summer of 2007, Dr. Michael Sieracki joined a team of internationalexperts in marine microbiology, microbial ecology, and biogeochemistrywho gathered at the University of Hawaii to teach an intensive eightweekgraduate course on microbial oceanography. Sponsored by theAgouron Institute, the course brought students from seven countriestogether to explore the essential role of marine microbes in the ecologyand biogeochemistry of ocean ecosystems. The course included a 10-daycruise with Sieracki aboard the 186-foot Navy catamaran R/V Kilo Moana,giving students hands-on experience with the research tools used toexplore fundamental concepts in microbiology and oceanography.Photo by M. Sieracki.High School Research, for RealCafé ScientifiqueEvery year, Bigelow Laboratorybrings sixteen high school juniorsfrom Maine together for a weeklongmarine science researchinternship. The program was begunby Bigelow researcher MaureenKeller to provide a real-world oceanresearch experience for studentswho have demonstrated enthusiasmand aptitude for science. It isdesigned to encourage careers inocean science and to furtherenhance young people’s interestPhoto by Bruce Wood.in science in general. The programcombines laboratory workshops andfield studies with a day-longresearch cruise. Working directlywith scientists, students conductfield sampling in a variety ofmarine environments, and usestate-of-the-art instrumentation forsubsequent data analysis. The weekincludes discussion of science andpublic policy, scientific ethics, andcareer directions.Since the beginning of theLaboratory’s residency on theMaine coast, Bigelow scientistshave given talks for the generalpublic, following the example ofthe Laboratory’s founders Drs.Charles and Clarice Yentsch.Drawing an enthusiastic audiencefor many years, these have beeninformal gatherings and seminars toshare scientific findings and theresults of the latest ocean researchprojects with people of all backgroundsand professions. TheLaboratory’s summer lecture seriesrecently took on the new title ofCafé Scientifique, based on themodel of the international CaféScientifique movement begun inGreat Britain in the mid-1990s.Over 150 cafés have been organizedall over the world and are activelypromoting public engagement withscience. Recent Bigelow LaboratoryCafé Scientifique topics haveincluded the connection betweensea ice, clouds, and phytoplankton;ocean bacteria; the InternationalPolar Year; red tides; and climatechange.Annual Report 200741

Glossaryantibiotic resistance—a type of drugresistance in which a microbe has evolvedthe ability to withstand the effects of anantibiotic.bacterioplankton—the bacterial portionof the plankton (see phytoplankton,below). Photosynthetic bacteria aremajor contributors to ocean’s biologicalproductivity.biological productivity—nature’s abilityto reproduce and regenerate living matter,defined as the rate at which organicmatter is produced.benthic—living on or in the bottom ofbodies of water.coccolithophore—a type of phytoplankton(single-celled marine plant) that livesin large numbers throughout the upperlayers of the ocean. Coccolithophoressurround themselves with microscopicplates called coccoliths that are madeof limestone (calcite). Individual coccolithophoresare commonly smaller than20 micrometers across and are oftenenclosed by over 30 plates.endosymbiosis—a relationship betweentwo organisms in which one (the endosymbiont)lives inside the body of theother (the host).fluorescence-activated cell sorting—a specialized type of flow cytometry,which is a technique for counting, examining,and sorting microscopic particlessuspended in a stream of fluid.Fluorescence-activated cell sorting usesthe light scattering and fluorescentcharacteristics of biological cells to sortthem one cell at a time. This techniquerapidly records fluorescent signals fromindividual cells, as well as making itpossible to physically separate cells ofparticular research interest.genome—a complete genetic sequenceof an organism that is encoded in the DNAon one set of chromosomes.greenhouse gas—any gas that absorbsinfra-red radiation from the sun, trappingheat in the atmosphere. Greenhousegases include water vapor, carbon dioxide(CO 2 ), methane (CH 4 ), nitrous oxide (N 2 O),halogenated fluorocarbons (HCFCs),ozone (O 3 ), perfluorinated carbons (PFCs),and hydrofluorocarbons (HFCs).gyre—a giant, circular, oceanic surfacecurrent.invertebrate—an animal without aninternal skeleton made of bone. Morethan 97% of the known animal speciesin the world are invertebrates.monsoon—a seasonal prevailing windthat lasts for several months.nutrient budget—a description of themeasure of input and outflow of elementsthrough various parts of an ecosystem.organelle—a specialized subunit inside acell that performs a specific function andis separately enclosed within its ownmembrane.phage therapy—the therapeutic useof viruses known to kill bacteria as atreatment for bacterial infections.phytoplankton—the plant componentof the suspended or floating microscopicanimals, plants, and bacteria in the oceanthat are collectively called plankton.Composed mostly of single-celled algaeand bacteria, phytoplankton carry outphotosynthesis and are at the base of themarine food chain. Most phytoplanktonspecies are too small to be individuallyseen with the unaided eye.phytoplankton bloom—phytoplanktonblooms occur when, under favorableconditions, phytoplankton rapidlyincrease in numbers. An example isthe annual springtime bloom in theNorthwest Atlantic that begins whensunlight and wind-mixed nutrientsbecome readily available in theupper ocean.plastids—organelles that are found inthe cells of plants and algae, and arethe site of manufacture and storage ofimportant chemical compounds used bythe cell. Plastids often contain pigmentsused in photosynthesis, and the typesof pigments present can change ordetermine the cell’s color.protists—a collective term for singlecelledorganisms, including single-celledalgae, whose cells have a nucleus, butwhich are not considered animals, plants,or fungi.remote sensing—the scientific techniqueor process of gathering data or imagesfrom a distance, as from satellites oraircraft.sequencing genes—assembling a successionof letters representing the primarystructure of a DNA molecule or strand,with the capacity to carry information.shelf break—the region of the oceanfloor where the continental shelf andcontinental slope meet. This is where themore gently-shelving region of the seabed adjacent to a land mass abruptlyslopes more steeply down towards theocean depths, commonly around 200meters (approximately 656 feet).strains—cell lines cloned from a singlespecimen in order to perpetuate it.thermal gradient—the rate of temperaturechange with distance. For example,the ocean’s layers of water have differenttemperatures, decreasing with depth fromthe warmer surface to the cold, deepregions near the ocean floor.upwelling—the transport of deepwater to shallow levels of the ocean.The upwelling of nutrient-rich water isoften responsible for driving biologicalproductivity in the ocean and is largelycontrolled by winds.42Bigelow Laboratory for Ocean SciencesFacing page: Emiliana huxleyi coccolithophore cells. Scanning electronmicrographs courtesy of the Belgian Federal Science Policy Office.

Selected PublicationsAllen, M.J, J.M. Martinez, D.C. Schroeder,P.J. Somerfield, and W.H.Wilson. 2007.Use of microarrays to assess viral diversity:from genotype to phenotype.Environmental Microbiology. 9(4) 971–982.Andersen, R.A. 2007. MolecularSystematics of the Chrysophyceae andSynurophyceae. Pp. 283–311 in Unravelingthe Algae: The Past, Present and Future ofAlgal Systematics, J.Lewis and J. Brodie,eds. Taylor and Francis, Boca Raton, FL.Andersen, R.A. 2007. Heterokontophyta:Synurophyceae. Pp. 235–254 In Algae ofAustralia: Introduction. P.M. McCarthy andA.E.Orchard, eds. ABRS, Canberra, CSIROPublishing, Melbourne.Baer, K. and D.A. McClellan. 2007.Molecular coevolution of the vertebratecytochrome c1 and Rieske iron sulfur proteinsin the cytochrome bc1 complex.International Journal of BioinformaticsResearch and Applications 3:456–470.Balch,W.M., J.J. Vaughn, J.I.Goés, J.F.Novotny, D.T. Drapeau, E.S.Booth,and C.L. Vining. 2007. Bio-opticalconsequences of viral infection ofphytoplankton: I. Experiments with thecyanobacterium, Synechococcus sp.Limnology and Oceanography52:727–738.Balch,W.M., D.T. Drapeau, B.C. Bowler,and E.S.Booth. 2007. Prediction of pelagiccalcification rates using satellite measurements.Deep-Sea Research II (ChapmanCalcification Conference Special Volume).Vol. 54, no. 5–7, Pp. 478–495DOI:10.1016/J.DSR2.2006.12.006.Balch,W.M. 2007. Coccolithophores andthe “sea of milk.” In Our Changing Planet:The View From Space. M.King, C. Parkinson,K. Partington and R. Williams, eds.Cambridge University Press. Cambridge,U.K.Benfield M. C., P. Grosjean, P. Culverhouse,X. Irigoien, M.E. Sieracki, A. Lopez-Urrutia,H.G. Dam, Q. Hu, C.S. Davis, A. Hansen,C.H. Pilskaln, E. Riseman, H. Schultz, P.E.Utgoff, G. Gorsky. 2007. RAPID: Research onAutomated Plankton Identification.Oceanography 20:12–26.Benavides, E., R. Baum, D.A. McClellan, andJ.W. Sites. 2007. Molecular phylogeneticsof the lizard genus Microlophus(Squamata: Tropiduridae): Aligning andretrieving indel signal from nuclearintrons. Systematic Biology 56:776–797.Berelson, W.M., W.M. Balch, R. Najjar, R.A.Feely, C. Sabine, and K. Lee. 2007. Relatingestimates of CaCO 3 production, exportand dissolution in the water column tomeasurements of CaCO 3 rain into sedimenttraps and dissolution on the seafloor: A revised global carbonate budget.Global Biogeochemical Cycles. 21, GB1024,DOI:10.1029/2006GB002803Carroll, H.D., M.T.W. Ebbert, M. Clement,Q.O. Snell, W.A. Beckstead, T.D. O’Connor,and D.A. McClellan. 2007. DNA alignmentbenchmark based on tertiary structureof encoded proteins. Bioinformatics23:2648–2649.Chamala, S., W.A. Beckstead, M.J. Rowe,and D.A.McClellan. 2007. Evolutionaryselective pressure on three mitochondrialSNPs in consistent with their influenceon metabolic efficiency in Pima Indians.International Journal of BioinformaticsResearch and Applications 3:504–522.Cleland D., K. Jastrzembski, E. Stamenova,J. Benson, C. Catranis, D. Emerson, andB. Beck. 2007. Growth characteristicsof microorganisms on commerciallyavailable animal-free alternatives totryptic soy medium. Journal ofMicrobiological Methods. 69:345–352.Ebbert, M.T.W., T.D. O’Connor, W.A.Beckstead, M.J. Clement, and D.A.McClellan. 2007. Pharmacogenomics:Analyzing SNPs in the CYP2D6 geneusing amino acid properties. InternationalJournal of Bioinformatics Research andApplications 3:471–479.Eckard R.S., P.J. Hernes, B.A. Bergamaschi,R. Stepanauskas, and C. Kendall. 2007.Landscape scale controls on the vascularplant component of dissolved organiccarbon across a freshwater delta.Geochemica et Cosmochemica Acta71:5968–5984.Emerson, D., J.A. Rentz, T.G. Lilburn, R.E.Davis, H. Aldrich, C. Chan, and C.L. Moyer.2007. A novel lineage of proteobacteriainvolved in formation of marine Feoxidizingmicrobial mat communities .PLOSOne. 2(8): e667. doi:10.1371/journal.pone.0000667Emerson, D., and J. Tang. 2007. Media andNutrition. In Manual of Methods for Generaland Molecular Microbiology, 3rd Edition.C.A. Reddy, et al [eds.] American Society ofMicrobiology Press. pp 200–214.Evans, C., S.V. Kadner, L.J. Darroch, W.H.Wilson, P. Liss, and G. Malin. 2007. Therelative significance of viral lysis andmicrozooplankton grazing as pathwaysof dimethylsulfoniopropionate (DMSP)cleavage: An Emiliania huxleyi culturestudy. Limnology and Oceanography52:1036–1045.Fields, D.M. , M.J. Weissburg, and H.Browman. 2007. Chemoreception in thesalmon louse Lepeophtheirus salmonis: anelectrophysiology approach. Disease ofAquatic Organisms 78:161–168.Fogarty, Incze, Wahle, and Mountain,2007. Marine Center White Paper, Unionof Concerned Scientists Northeast ClimateImpacts Assessment synthesis report,Global Environmental Program, UCS,Cambridge, MA.Hackett, J.D., H.S.Yoon, N.J. Butterfield,M.J. Sanderson, and D.Bhattacharya. 2007.Plastid endosymbiosis: sources and timingof the major events. In Evolution of PrimaryProducers in the Sea, P. Falkowski and A.Knoll, eds. Academic Press. Pp109–133.Hoef-Emden, K., F.C. Küpper. and R.A.Andersen. 2007. Meeting Report: SloanFoundation Workshop to ResolveProblems Relating to the Taxonomy ofMicroorganisms and to CultureCollections Arising from the BarcodingInitiatives; Portland ,ME, November 6-7,2006. Protist 158:135–137.44Bigelow Laboratory for Ocean Sciences

Kegel, J., M.J. Allen, K. Metfies, W.H.Wilson,D. Wolf-Gladrow, and K. Valentin. 2007.Pilot study of an EST approach of thecoccolithophorid Emiliania huxleyi duringa virus infection. Gene 406: 209–216Kimmance, S.A., W.H.Wilson, and S.D.Archer. 2007. Modified dilution techniqueto estimate viral versus grazing mortalityof phytoplankton: limitations associatedwith method sensitivity in natural waters.Aquatic Microbial Ecology, 49(3), 207–222.Llewellyn, C.A., C. Evans, R.L. Airs, I. Cook,N. Bale, and W.H. Wilson. 2007. Theresponse of carotenoids and chlorophyllsduring virus infection of Emiliania huxleyi(Prymnesiophyceae). Journal of ExperimentalMarine Biology and Ecology.344(1), 101–112Lohr, J., C.B. Munn,. and W.H.Wilson.2007. Characterisation of a Latent ViruslikeInfection of Symbiotic Zooxanthellae.Applied and Environmental Microbiology73:2976–2981.Matondkar, S.G.P., H. Gomes, S.G. Parab,S. Pednekar and J.I.Goés. 2007.Phytoplankton diversity, biomass, andproduction. In The Mandovi and ZuariEstuaries. S.R. Shetye, M. Dileep Kumar,and D. Shankar, eds. Pp. 99–104 . NationalInstitute of Oceanography, India.Martinez, J.M., D.C. Schroeder, A. Larsen, G.Bratbak, and W.H.Wilson. 2007.Molecular Dynamics of Emiliania huxleyiand Cooccurring Viruses during TwoSeparate Mesocosm Studies. Applied andEnvironmental Microbiology 73: 554–562Matrai,P.A., M. Vernet, and P. Wassmann.2007. Relating temporal and spatial patternsof DMSP in the Barents Sea tophytoplankton biomass and productivity,Journal of Marine Systems 67(1-2): 87–101.Matrai,P.A., L. Tranvik, C. Lek, and J. Knulst.2007. Are high Arctic microlayers a potentialsource of aerosol organic precursors?Marine Chemistry 108:109–122.Neubauer, S.C., G. E. Toledo-Durán,D.Emerson, J.P.Megonigal. 2007.Returning to their roots: Iron-oxidizingbacteria enhance short-term plaque formationin the wetland-plant rhizosphere.Geomicrobiology Journal 24:65–73.O’Donnell, K.P., R.A.Wahle, M.J.Dunnington, and M. Bell. 2007. Spatiallyreferenced trap arrays detect sedimentdisposal impacts in a New Englandestuary. Marine Ecology Progress Series348: 249–260.Porter, M., T. Cronin, D.A. McClellan, andK. A. Crandall. 2007. Molecular characterizationof crustacean visual pigments andthe evolution of pancrustacean opsins.Molecular Biology and Evolution24:253–268.Poulton, A. J., T.R. Adey, W.M. Balch,and P.M. Holligan. 2007. Relating coccolithophorecalcification rates tophytoplankton community dynamics:regional differences and implicationsfor carbon export. Deep-Sea Research II(Chapman Calcification Conference-Special Volume). Vol. 54, no. 5–7, pp.538-557.Rentz, J.A., C. Kraiya, G.W. Luther III, andD. Emerson. 2007 Control of ferrous ironoxidation within circumneutral microbialiron mats by cellular activity and autocatalysis.Environmental Science andTechnology 41:6048–6089.Roden, E. R. and D. Emerson. 2007.Microbial Metal Cycling in AquaticEnvironments. Manual of EnvironmentalMicrobiology, 3rd Ed. American Societyof Microbiology Press. Washington, D.C.pp, 540–562.Roesler, C. S. and E. Boss. 2007. In situmeasurement of the inherent opticalproperties (IOPs) and potential for harmfulalgal bloom (HAB) detection and coastalecosystem observations, Chapter 5. InReal-Time Coastal Observing Systems forEcosystem Dynamics and Harmful AlgalBlooms: Thoery, Observation and Modeling.M. Babin, J J. Cullen, and C.S. Roesler, eds.UNESCO Series Monographs onOceanographic Methodology.Saunders. G.W. and R.A.Andersen. 2007.Heterokontophyceae: Pelagophyceae.Pp.228-234. In Algae of Australia:Introduction. P.M. McCarthy and A.E.Orchard, eds. ABRS, Canberra, CSIROPublishing, Melbourne.Selgrath, J., K. Hovel,and R.A.Wahle. 2007.Effects of habitat edges on Americanlobster abundance & survival. Journal ofExperimental Marine Biology and Ecology353: 253–264Steele, J.H., J.S. Collie, J.J. Bisagni, D.J.Gifford, M.J. Fogarty, J.S. Link, B.K. Sullivan,M.E. Sieracki, A.R. Beet, D.G. Mountain,E.G. Durbin, D. Palka, W.T. Stockhausen.2007 Balancing end-to-end budgets ofthe Georges Bank ecosystem. Progress inOceanography. 74:423–448.Stepanauskas, R. and M.E. Sieracki.2007. Matching phylogeny and metabolismin the uncultured marine bacteria,one cell at a time. Proceedings of theNational Academy of Sciences of the UnitedStates of America 104:9052–9057.Weiss, J.V., J.A. Rentz, T. Plaia, S.C. Neubauer,M.M. Floyd, T. Lilburn, C. Bradburne, J.P.Megonigal, and D. Emerson. 2007.Identification of diverse neutrophilic Fe(II)-oxidizing bacteria isolated from therhizosphere of wetland plants anddescription of Ferritrophicum radicicolagen. nov. sp. nov., and Sideroxydanspaludicola sp.nov. GeomicrobiologyJ. 24:559-570.Wharam,S.D., M.J. Hall, and W.H.Wilson.2007. Detection of virus mRNA withininfected host cells using an isothermalnucleic acid amplification assay: marinecyanophage gene expression withinSynechococcus sp. Virology Journal 4:52.Williamson, P., R.A.Andersen, and F.C.Küpper. 2007. Why every protist needs abarcode. Microbiology Today 34(1):46–47.Yoon,H.S., J.D. Hackett, S. Li, A. Reyes-Prieto, S.E. Rümmele, and D. Bhattacharya.2007. Phylogenomic analysis supportsthe association of “Rhizaria” with chromalveolatesand the monophyly of cryptophytesand haptophytes. Molecular Biologyand Evolution 24:1702–1713.This is a selected list of 2007 publicationsin which Bigelow scientists (in bold) areauthors.Annual Report 200745

Understanding the ocean’srole within the vast naturalcycles that support theworld’s ecosystems is ofparamount importance tothe quality of our lives andto the generations who willlive on this planet after us.This is one of the most excitingperiods in the thirtyfouryear history of BigelowLaboratory for Ocean Sciences. Ourresearchers are working on the frontiersof scientific inquiry to develop,test, and patent new technologies tostudy microbial oceanography andglobal ocean systems in ways thathave never been possible before.Bigelow Laboratory is drawingoutstanding scientists from allover the world to study the globalocean. Five new senior researchersjoined the science staff in 2007, furtherbroadening our programs andstrengthening opportunities forinterdisciplinary collaboration.Donna Cheney, Sandy Sage, andGraham Shimmield.Their work and vision are an integral part of our plans for building thenew, high technology center we will need to support global oceanographicresearch in the twenty-first century.As this report goes to press, Bigelow Laboratory is welcomingDr. Graham Shimmield as its new Executive Director. Dr. Shimmield isan international leader in ocean science, and part of a multi-disciplinary,collaborative research focus on oceans and global climate change.Dr. Shimmield has come to Bigelow Laboratory from the ScottishAssociation for Marine Sciences and the Dunstaffnage MarineLaboratory, which flourished under his direction by doubling itsscientific staff, increasing annual research revenues six-fold, andbuilding a major research facility.In the past year, we have also celebrated the contributions ofDr. Louis “Sandy” Sage, who retired from his eleven-year tenure asExecutive Director in July 2007. This report is a testament to hisleadership in bringing Bigelow Laboratory into the vanguard of internationalocean research.Our society is becoming increasingly aware of the significant effect thatclimate change is having on the global processes that sustain life. Understandingthe ocean’s role within the vast natural cycles that support theworld’s ecosystems is of paramount importance to the quality of our livesand to the generations who will live on this planet after us. The scientificresearch underway at Bigelow Laboratory has direct bearing on thedecisions, challenges, and opportunities that will determine our environmentalfuture.Donna Lee Cheney, ChairBoard of TrusteesMay 20, 200846Bigelow Laboratory for Ocean Sciences

Trustees and ScientistsBOARD OF TRUSTEESDonna Lee Cheney, ChairRichard ChapinDavid M. CoitRobert E. HealingStephen L. MalcomRichard A. MorrellHelen A. NortonWalter M. NortonBarbara Reinertsen, Vice ChairNeil RoldeRichard J. RubinEXECUTIVE DIRECTOR AND PRESIDENTGraham B. Shimmield, Ph.D.Michael E. Sieracki, Ph.D.,Interim DirectorPRESIDENT EMERITUSLouis E. Sage, Ph.D.DISTINGUISHED FOUNDERSCharles S. Yentsch, Ph.D.Clarice M. Yentsch, Ph.D.SCIENCE STAFFRobert A. Andersen, Ph.D.William M. Balch, Ph.D.Wendy Korjeff Bellows, B.A.Charlene E. Bergeron, B.S.Emily S. Booth, B.S.Bruce C. Bowler, M.S.Jeffrey F. Brown, A.A.S.John P. Christensen, Ph.D.Terry L. Cucci, M.S.David T. Drapeau, M.S.David Emerson, Ph.D.David M. Fields, Ph.D.Ilana Gilg, M.S.Joaquim I. Goes, Ph.D.Helga do R. Gomes, Ph.D.Robert R.L. Guillard, Ph.D.Jane Heywood, Ph.D.Peter Foster Larsen, Ph.D.Patricia A. Matrai, Ph.D.David A. McClellan, Ph.D.Elise Olson, M.S.Nicole J. Poulton, Ph.D.Carlton D. Rauschenberg, M.S.Tracey S. Riggens, B.S.Kristen Roberts, B.S.Julianne P. Sexton, B.A.Michael E. Sieracki, Ph.D.Ramunas Stepanauskas, Ph.D.Benjamin Tupper, M.S.Richard A. Wahle, Ph.D.Christine Woll, B.S.Susan D. Wharam, Ph.D.William H. Wilson, Ph.D.Hwan Su Yoon, Ph.D.HONORARY TRUSTEESMarylouise Tandy CowanDavid Hibbs DonnanEdgar T. Gibson, M.D.James F. JaffrayW. Redwood Wright, Ph.D.TRUSTEES EMERITISpencer ApollonioThomas A. Berry, Esq.Christopher FlowerRussell W. JeppesenJames G. McLoughlinCampbell B. Niven*Jefferson D. Robinson, III* deceasedPhoto courtesy of the Census of Marine Life.Annual Report 200747

Summary Financial StatementsStatement of Activities and Changes in Net Assets(For fiscal years ended June 30) 2007 2006 2005Operating ActivitiesOperating Revenue and SupportGrants and contracts for research and education $ 4,317,915 $ 3,980,906 $ 3,614,363Other revenue, including course fees 637,691 533,852 723,263Growth fund assets released from restrictions 360,202 0 0Contributions to annual fund 206,942 197,276 174,166Total Operating Revenue and Support 5,522,750 4,712,034 4,511,792Operating ExpensesResearch and education 5,005,089 4,594,254 4,508,603Unallocated management and general 497,014 433,470 364,742Development 90,553 71,185 90,150Total Operating Expenses 5,592,656 5,098,909 4,963,495Change in Net Assets from Operating Activities (69,906) (386,875) (451,703)Non-Operating Revenue and SupportContributions to growth fund 362,750 1,100,000 1,535,143Gain on sale of land 0 0 1,554,151Grants for purchase of equipment 239,290 992,191 477,529Growth fund assets released from restrictions (360,202) 0 0Change in Net Assets from Non-Operating Activities 241,838 2,092,191 3,566,823Total Change in Net Assets 171,932 1,705,316 3,115,120Statement of Financial Position(At June 30) 2007 2006 2005AssetsCash $ 254,395 $ 213,044 $ 448,674Investments 2,599,931 2,933,632 1,736,786Property and equipment, net 5,082,443 4,955,469 4,124,373Other 1,620,585 1,140,107 1,282,088Total Assets 9,557,354 9,242,249 7,591,921Liabilities and Net AssetsLiabilities 482,381 339,207 394,195Net AssetsUnrestricted 5,608,787 5,315,578 5,171,684Temporarily restricted 3,267,231 3,390,816 1,831,415Permanently restricted 198,944 196,639 194,627Total Net Assets 9,074,962 8,903,042 7,197,726Total Liabilities and Net Assets 9,557,343 9,242,249 7,591,921Bigelow Laboratory for Ocean Sciences was formed in 1974. Bigelow is a Maine nonprofit public benefit corporation and is qualified as a tax exempt organization under Sec. 501(c)(3)of the Internal Revenue Code. The Laboratory’s financial statements for fiscal years 2005, 2006, and 2007 were audited by Macdonald Page Schatz Fletcher & Co. The summary financialstatements shown here are derived from the audited financial statements. Amounts shown in this summary as growth funds released from restrictions reflect contributions intended tosupport the recruitment and startup costs of new senior research scientists. Copies of the audited financial statements are available on request from: Director of Finance, BigelowLaboratory for Ocean Sciences, P.O. Box 475, West Boothbay Harbor, ME 04575; or by email to: finance@bigelow.org48Bigelow Laboratory for Ocean Sciences

Satellite view of a phytoplankton bloomin the Black Sea. Photo courtesy of NASA.Written by Tatiana Brailovskaya, M.S.Design by Mahan Graphics, Bath, Maine.Unless otherwise noted, all photos are fromBigelow Laboratory for Ocean Sciences.Bigelow scientist and on-site laboratoryphotographs by Buddy Doyle.Cover: NASA photo.Cert no. SGS-COC-003679

Bigelow Laboratory for Ocean SciencesPO Box 475 • 180 McKown Point RoadWest Boothbay Harbor, ME 04575 USAwww.bigelow.org • 207.633.9600