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Working Groups

Benthic Ecology

Hal Caswell, Lauren Mullineaux, Jesús Pineda
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Shallow water benthic ecology

Studies in Hal Caswell's laboratory apply matrix population models to the analysis of benthic populations in field, laboratory, and theoretical settings. Current projects include studies of the effects of pollutants on clam and polychaete populations, of the short-term dynamics of seeded scallop populations, and of the effects of recruitment variability on benthic population dynamics.

In the laboratory of Jesús Pineda, field, lab, and modeling techniques are used to understand the abundance and distribution of shallow water benthic species, with emphasis on hydrodynamic forcing on settlement and recruitment. Other work focuses on understanding the factors influencing the latitudinal and depth ranges of benthic species, and in particular, how hydrographic variability influences regional distribution and abundance.

Spatial patchiness and temporal variation in shallow benthic populations are often strongly influenced by local circulation and boundary layer flows. An ongoing research project in Lauren Mullineaux's lab focuses on the influence of coastal flows, particularly those generated by headlands or other topography, on the settlement patterns and post-settlement redistribution of bivalve species. These studies are complemented by flume experiments on interactions between burrowing behavior and the effect of these interactions on the resuspension and transport of juvenile bivalves.

Deep-sea benthic ecology

Many of the prominent benthic species living at hydrothermal vents exhibit strong zonation patterns that correspond to gradients in water temperature and chemistry. Manipulative field experiments conducted by Lauren Mullineaux's lab have recently demonstrated that zonal boundaries are not set solely by physiological tolerances and requirements of the species, but rather a combination of biological interactions and physical influences. This progression in our concept of community structure in vent communities is similar to the rapid advances brought about by manipulative experimentation in the rocky intertidal. (See also vent studies described in Larval Ecology section)


John Dacey, Stefan Sievert, Craig Taylor,John Waterbury
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Biogenic Trace Gases

Dacey's laboratory investigates the cycling of biogenic trace gases, particularly the radiatively important traces gases: dimethylsulfide (DMS) and methane. Dimethylsulfide studies focus on the concentration of the precursor of DMS in marine biota, and on the mechanisms for conversion of this precursor compound to DMS, such as zooplankton grazing, bacterial activity, and phytoplankton physiology. Research includes development of portable analytical equipment for rapid measurement of these labile compounds, since DMS concentration in seawater is highly variable in space and time. Methane studies focus on emissions from wetlands to the atmosphere. Particular emphases are the role of vascular plants as conduits for the emission of methane from sediments and the effect of rooted vegetation on rhizosphere processes and on marsh biogeochemistry in general. Recent work has addressed the influence of elevated atmospheric carbon dioxide on methane emission.

Coastal Studies

Matt Charette, Jeff Donnelly, Steve Elgar, Rob Evans, Rocky Geyer, Liviu Giosan, Charles Harvey, David Ralston, Britt Raubenheimer, Chris Reddy, Peter Traykovski
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Many coastal regions of the world have experienced unprecedented human development in the last 100 to 150 years. Much of this development is incompatible with the dynamic nature of the shoreline.

Understanding how coastal sedimentary systems function is critical if we are to effectively manage coastal resources. Predictions of accelerated sea-level rise and increased storm activity due to CO2-induced warming of the global climate system require understanding how sea level and storm activity

A group of Joint Program faculty, staff, and students focus on coastal research. Additionally, ties with other departments at WHOI (Marine Chemistry and Geochemistry, Applied Physics and Ocean Engineering) and MIT (Civil Engineering) as well as with colleagues in the U.S. Geological Survey strengthen the effort.

Researchers use a variety of techniques to study the coastal environment, including high-resolution geophysical tools (for example, high-resolution seismic reflection, electromagnetic mapping, ground penetrating radar (GPR)), sediment sampling and analysis, and the geochemical analysis of sediment and groundwater.

Environmental Toxicology

Neel AluruHal CaswellMark HahnJudy McdowellJohn Stegeman
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The ecological consequences of toxicants depend on how their effects on individual organisms are expressed at the level of the population. Demographic models provide a powerful tool for exploring these effects. Hal Caswell's group has studied this problem using matrix population models, addressing both the development of analytical methods (how to analyze experiments that measure the response of survival and reproduction to toxicants) and application of those methods to specific field and laboratory systems.

WHOI scientists are studying the impact of environmental contaminants on the health of marine organisms and ecosystems. Topics range from the ecology of coastal wetlands to physiological, biochemical, and molecular mechanisms of effects in vertebrate and invertebrate animals. Research in Mark Hahn's laboratory focuses on the halogenated aromatic hydrocarbons (dioxins, PCBs) and on receptors such as the aryl hydrocarbon receptor (Ah receptor) that mediate their action. Studies involve the characterization of receptor function in bony and cartilaginous fish, aquatic birds, and marine mammals.

Larval Ecology

Scott Gallager, Kirstin Meyer-Kaiser, Lauren MullineauxJesús Pineda
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Dispersal of larvae of benthic organisms living at deep-sea hydrothermal vents is essential for these species to maintain populations in the patchy, ephemeral vent environments. Lauren Mullineaux's lab is involved in collaborative field studies to investigate the physiological, behavioral and physical mechanisms that control dispersal to new or existing vent sites. These studies are part of the NSF-sponsored RIDGE LARVE (Larvae At Ridge VEnts) Project.

Marine Mammals

Mark BaumgartnerHal CaswellMark HahnDarlene KettenMichael MooreT. Aran Mooney, Michelle Shero, John Stegeman,  Peter Tyack,
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Study of Marine Mammal Auditory Systems

In Darlene Ketten's laboratory, studies are directed at understanding how the ears of marine animals, particularly whales and dolphins, are able to hear and use underwater sounds. Biomedical (CT and MRI) micro-imaging techniques are used to study auditory systems from a wide range of species and to produce mathematical and three-dimensional computer models of marine ears. The models allow us to estimate hearing abilities for rare and endangered species, like blue whales, that cannot be tested by normal methods. We also use computer simulations to determine how whale ears withstand rapid pressure changes during dives and how underwater noise affects hearing. Because of the close relationship between what an animal hears and the sounds it produces, work in this laboratory is linked closely with vocalization and behavioral research in the Tyack laboratory. Studies on stranded animals are tied also to research in Michael Moore's laboratory on the effects of pollutants and disease.

Acoustics and Behavior

Studies are conducted on acoustic behavior of a wide variety of species using hydrophone arrays and database organization of sound patterns. Surface and underwater activities of open ocean species, such as fin whales and sperm whales, are investigated with telemetry to follow details of dive profiles relative to water temperature, bottom topography and other environmental factors.

The WHOI cetacean group is determining how marine mammals learn and build individual vocalization patterns and is detailing the social behavior of these highly mobile, migratory animals. They also examine cetacean phylogeny, stock structure, and familial and kin relationships using population genetics methods.

One of the ongoing projects in the Tyack lab is the study of the foraging and acoustic behavior of wild bottlenose dolphins. Detailed feeding behaviors have been observed with an overhead video system, and acoustic activity has been recorded with this system as well as a non-invasively attached digital archival recording tag.

Pollution Effects

In the laboratory of Mark Hahn, the impact of chemical pollutants on marine mammals is being investigated through comparative studies on the biochemistry and molecular biology of the receptors and enzymes involved in toxic chemical action.

Population Dynamics

Quantifying the population dynamics of marine mammals is difficult because of the difficulty of collecting data on individual survival and fertility. In some cases, however, sufficient data have been obtained to permit the development of population models. Current studies on marine mammals by Hal Caswell include the development of stage-classified demographic models from photographic catalog data, assessment of the consequences of bycatch mortality in harbor porpoise, and general investigations of the use of population models in conservation biology.

Microbiology & Microbial Ecology

Craig TaylorJohn WaterburyStefan Sievert
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Microbial studies encompass the distribution, abundance, physiological status, and growth rates of these organisms as well as their symbiotic interactions, population diversity and dynamics, and biochemical adaptations. Molecular biological methods are increasingly applied to these areas of research. Other marine microbial studies include food-chain dynamics, production of bioactive compounds such as toxins and extracellular enzymes, and speciation and phylogeny. Some of the current research areas in microbiology include:

Microbial processes at hydrothermal vents

Bacterial chemosynthesis is the base of the food chain for the hydrothermal vent biota. The laboratory of Carl Wirsen and Stefan Sievert investigates the diversity of aerobic sulfide oxidizing bacteria and anaerobic, hyperthermophilic, sulfur reducing archaea, as well as their physiology, ecology and biotechnological applications.

Growth kinetics of oligotrophic marine bacteria

The bacterial turnover of dissolved organic matter in the world oceans is pivotal for the global carbon budget. A pressurized chemostat is used in the laboratory of Carl Wirsen and Stefan Sievert to measure metabolic activities of bacterial isolates that are adapted to high pressure, low temperature and low concentrations of organic substrates.

Characterization of the iron (Fe) scavenging systems employed by oligotrophic marine cyanobacteria.

In many oceanic regimes where Fe is thought to limit primary productivity, cyanobacteria are significant constituents of the phytoplankton community. Using genomic, proteomic, and genetic techniques work in the laboratory of Eric Webb is aimed at defining the mechanism employed by these cyanobacteria that allow them to thrive in Fe depleted regimes.

Modeling & Math

Hal CaswellCabell DavisMichael NeubertRubao Ji, Sam Laney
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WHOI biologists are using modeling, ecological theory, and state-of-the-art computer systems to examine the ecological processes that lead to the complex spatial and temporal patterns of organisms in the marine environment. The research focuses on population and community dynamics, life-history theory, and interactions of marine populations with the physical environment.

These studies are contributing also to an understanding of the demography of individual marine organisms, conservation biology, and the effects of pollutants on marine populations.

The laboratories of Hal Caswell and Michael Neubert are involved with studies that address the following issues:

1. Population modelling:

The development and analysis of matrix population models and their application in conservation biology and ecotoxicology. Stochastic matrix models and their sensitivity analysis. Bifurcation patterns in density-dependent matrix models in relation to life history structure.

2. Food web modelling:

Studies of the effects of population structure and nonlinearity on the dynamics of food webs and other ecological systems.

Molecular Biology

Rebecca GastJohn StegemanMark HahnStefan SievertLauren MullineauxAnn TarrantJohn WaterburyPeter TyackDon AndersonRob OlsonJudy Mcdowell,, Matt Johnson
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Molecular biology is an integrated and growing component of the research programs in the Biology Department at the Woods Hole Oceanographic Institution. Its powerful concepts and tools hold great promise for rapidly increasing knowledge of the phylogeny, biodiversity, ecology and population biology of marine organisms, their symbiotic interactions, and their biochemical, genetic and physiological adaptations to the ocean environment. WHOI biologists and affiliated scientists are using molecular approaches in coastal, open-ocean, deep-sea, and laboratory-based studies to explore a diverse array of biological oceanographic questions, ranging from the activities of individual organisms to the complex relationships of populations, communities and ecosystems.

Some of the areas where molecular approaches are being used by Biology Department staff include:

Microbial Ecology

Research in the laboratory of Rebecca Gast focuses on molecular phylogeny using srRNA gene sequences and the development of oligonucleotide probes for detection and identification of protists. These techniques are currently being developed and applied to Acanthamoeba and symbiotic algae in planktonic protists. Future research interests include the continued application of molecular biological techniques for the study of protist biodiversity and the identification of genes involved in the maintenance of symbiotic relationships between algae and planktonic marine invertebrates.

Chemical-Biological Interactions

The molecular mechanisms by which natural and man-made chemicals interact with vertebrate and invertebrate marine animals are being studied with biochemical, molecular and phylogenetic approaches. Work in the laboratory of John Stegeman focuses on the structure, function and regulation of cytochrome P450 enzymes and their role in cellular responses to chemical exposure. Research in Mark Hahn's laboratory is examining the comparative biochemistry and molecular biology of the aromatic hydrocarbon receptor, which mediates the biological activity of chlorinated hydrocarbon pollutants.

Deep-sea and Hydrothermal Vent Bacteria

Carl Wirsen and Stefan Sievert's group is using a combination of physiological and molecular approaches to study barophilic and psychrophilic deep-sea bacteria and to examine the diversity of microorganisms discovered at hydrothermal vents.

Larval Ecology and Dispersal

Research in Lauren Mullineaux's laboratory on organisms living in the patchy and ephemeral environments of seamounts and hydrothermal vents uses probes based on mitochondrial RNA sequences to identify larvae and gain population-level information about gene flow and geographic isolation.

Ecology of Marine Cyanobacteria and their Viruses

In the laboratory of John Waterbury, 23S rRNA sequence analysis and probes are being used to examine speciation and population ecology of cyanobacteria in the genus Synechococcus. The role of viruses in controlling Synechococcus populations is being examined with virus-specific antibodies.

Population Biology of Marine Mammals

Peter Tyack's group is using mitochondrial DNA sequences to elucidate the stock structure of pilot whales, with future studies planned for other species of toothed whales, including some that may be threatened by fishing activities.

Shellfish Diseases

The laboratory of Judy McDowell studies a leukemia-like neoplastic disease in soft-shell clams. Monoclonal antibodies specific to a cell-surface protein on neoplastic hemocytes allow early diagnosis of the disease, and a reverse transcriptase assay is being developed to evaluate viral replication as a causative factor.

Physiological Ecology of Phytoplankton

In the laboratory of Don Anderson, the dinoflagellates responsible for the harmful algal blooms known as "red tides" are

Physiology & Biogeochemistry

Mark HahnJudy McDowellJohn StegemanStefan Sievert, Ann Tarrant,  Matt Johnson,  T. Aran Mooney
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Shallow water benthic ecology

WHOI biologists are using a combination of traditional and modern approaches to investigate the comparative biochemistry and physiology of marine animals. Topics range from lipid metabolism and reproductive physiology to the regulation of gene expression and enzyme function. Studies involve a variety of taxonomic groups, including bivalve molluscs, crustaceans, teleost fish, elasmobranch fish, jawless fish, aquatic birds, and marine mammals.

Research in Mark Hahn's laboratory is aimed at understanding the function of biochemical pathways involved in chemical-biological interactions, especially ligand-receptor interactions, and the responses elicited by exposure to environmental contaminants and marine natural products. Research in John Stegeman's laboratory is focused broadly on the molecular basis underlying chemical-biological interactions and the effects of foreign chemicals on biota. This concerns effects in aquatic and terrestrial species, including humans. The work continues to center on the biochemistry and molecular biology of the cytochrome P450 enzymes, which are critical in chemical-biological interactions. The structure, function, regulation and evolution of these enzymes continue to be studied.

Overall objectives include:

1. Achieving a phylogenetic and mechanistic basis for predicting and evaluating chemical effects in many species.

2. Assessing the evolution of the P450 enzymes and their regulatory systems.

3. Establishing how ecological or environmental factors contribute to P450 gene diversity, by examining model systems from extreme environments.

4. Applying information and probes for P450 systems in assessing environmental exposure and effects in vertebrate animals.

Stegeman's laboratory is also investigating how chemicals affect cell proliferation, growth and differentiation, and the role of this process in chemically-induced diseases of marine species. Knowledge of the biochemistry of P450 enzymes, and the patterns of cell proliferation in growth and development, are being used to develop molecular markers of growth in vertebrates and invertebrates.

Phytoplanton Ecology

Don AndersonRubao JiMatthew JohnsonSam LaneyRob OlsonHeidi SosikCraig TaylorJohn Waterbury
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In the laboratory of Don Anderson, field and laboratory investigations of the causes and effects of toxic phytoplankton blooms ("red tides") in coastal waters focus on the physiology and genetics of the toxic algae.

In the laboratory of Robert Olson, research focuses on the physiological ecology of phytoplankton, especially through the analysis of individual cells using flow cytometry. Current studies include phytoplankton community structure and growth rates of particular groups of phytoplankton (through measurements of diel patterns in cell cycle events and cell size) in the Sargasso Sea, the equatorial Pacific and the Arabian Sea.

Research in Heidi Sosik's laboratory deals with phytoplankton photophysiology and bio-optical oceanography. Goals of the reasearch are to improve understanding of the effects of phytoplankton on ocean optical properties and to develop methods for the retrieval of information about phytoplankton from bio-optical measurements. Ongoing projects include work on optical modeling of primary production and studies of the optical and photosynthetic properties of phytoplankton under controlled conditions in the laboratory and under a wide range of natural environments. Specific emphasis is on the role of environmental factors in regulating the rate and distribution of primary production.

Current collaborative work between Olson and Sosik is focused on the application of individual particle techniques to provide insight into sources of variability in bulk optical and photosynthetic properties in the ocean. This includes measurement of photosynthetic efficiency of individual phytoplankton cells based on chlorophyll fluorescence assays and investigations of the effects of phytoplankton community composition and size structure on light absorption and scattering.