Laboratory for Microbial Oceanography
in the School of Ocean and Earth Science and Technology at the University of Hawai'i at Manoa

Present & Past Research Projects

Simons Collaboration on Ocean Processes and Ecology (SCOPE)

D. Karl and E. V. Armbrust (co-Directors)
Status: Currently funded through 2023

Life on Earth most likely originated as microorganisms in the sea. Over the past 3.5 to 4 billion years, microbes have shaped and defined Earth's biosphere, and have created conditions that allowed the evolution of more complex life. Today, microbes are the 'unseen majority' of organisms that inhabit and sustain all of Earth's habitats, including marine environments.

Microbes capture solar energy, catalyze key biogeochemical transformations of important elements, produce and consume greenhouse gases, and compose the base of the marine food web. Yet our understanding of the fundamental principles that determine the distribution, composition and function of microorganisms in the sea remains incomplete. Much of our understanding about the structure and dynamics of microbial assemblages has been qualitative, descriptive and contributed by a single individual or small teams of investigators working within a discipline.

Now, with a concerted cross-disciplinary effort by a team of scientists working in a well-described ocean ecosystem, the possibility of using a quantitative theoretical framework to interpret microbial community dynamics in the context of new field observations and experimental results is within reach. The time is right to achieve a more comprehensive, qualitative, quantitative and theoretical understanding of marine microbial community structure, function and activities in the sea.

The Simons Collaboration on Ocean Processes and Ecology (SCOPE), funded by the Simons Foundation, will establish a collaborative effort that will measure, model and experimentally manipulate a complex system representative of a broad swath of the North Pacific Ocean. This collaboration aims to advance our understanding of the biology, ecology and biogeochemistry of microbial processes that dominate Earth's largest biome: the global ocean. A multidisciplinary team of scientists who share a common interest in microbial oceanography have committed to partner in a meaningful collaboration that will begin to address some of the long-standing scientific challenges and previously unattainable research goals of that discipline. Specifically, SCOPE will conduct highly resolved spatial and temporal analyses over multiple levels of biological organization at a representative ocean benchmark, Station ALOHA, located in the North Pacific Subtropical Gyre (NPSG).

The central mission of SCOPE is to measure, model and predict the pathways and exchanges (inputs and outputs) of energy and matter within and between specific microbial groups and their environment at relevant spatial and temporal scales, from surface waters to the deep sea (more than 4 km in depth) at Station ALOHA. A central premise of SCOPE is that we must study the ocean ecosystem in situ, at a variety of levels of biological organization (e.g., genetic, biochemical, physiological, biogeochemical and ecological), and at highly resolved, nested scales of space and time in order to fully describe and model it.

Hawaii Ocean Time-series (HOT)

A. White (P.I.), D. Karl and J. Potemra (co- P.I.s)
Status: Currently funded through 2023

Systematic, long-term time-series studies of selected aquatic and terrestrial habitats have yielded significant contributions to earth and ocean sciences through the characterization of climate trends. Important examples include the recognition of acid rain (Hubbard Brook long- term ecological study), documentation of increasing carbon dioxide (CO2) in the earth's atmosphere (Mauna Loa Observatory, Hawaii) and the description of large scale ocean- atmosphere climate interactions in the equatorial Pacific Ocean (Southern Oscillation index).

Long time-series observations of climate-relevant variables in the ocean are extremely important, yet they are rare. Repeated oceanographic measurements are imperative for an understanding of natural processes or phenomena that exhibit slow or irregular change, as well as rapid event-driven variations that are impossible to document reliably from a single field expedition. Time-series studies are also ideally suited for the documentation of complex natural phenomena that are under the combined influence of physical, chemical and biological controls. Examination of data derived from the few long-term oceanic time-series that do exist provides ample incentive and scientific justification to establish additional study sites.

The role of the oceans in climate variability is primarily in sequestering and transporting heat and carbon. Both can be introduced into the ocean in one place, only to return to the atmosphere, at a subsequent time, possibly at a far removed location. While both heat and carbon can be exchanged with the atmosphere only carbon is lost to the seafloor through sedimentation. The oceans are known to play a central role in regulating the global concentration of CO2 in the atmosphere. It is generally believed that the world ocean has removed a significant portion of anthropogenic CO2 added to the atmosphere, although the precise partitioning between the ocean and terrestrial spheres is not known.

The cycling of carbon within the ocean is controlled by a set of reversible, reduction- oxidation reactions involving dissolved inorganic carbon (DIC) and organic matter with marine biota serving as the critical catalysts. Detailed information on the rates and mechanisms of removal of DIC from the surface ocean by biological processes, the export of biogenic carbon (both as organic and carbonate particles) to the ocean's interior, and the sites of remineralization and burial are all of considerable importance in the carbon cycle. The continuous downward flux of biogenic materials, termed the "biological pump", is a central component of all contemporary studies of biogeochemical cycling in the ocean and, therefore, of all studies of global environmental change.

During the embryonic phase of ocean exploration more than a century ago, it was realized that a comprehensive understanding of the oceanic habitat and its biota required a multidisciplinary experimental approach and extensive field observations. Progress toward this goal has been limited by natural habitat variability, both in space and time, and by logistical constraings of ship-based sampling. Consequently, our current view of many ocmplex oceanographic processes is likely biased. The synoptic and repeat perspective that is now available from research satellites is expected to improve our understanding of oceanic variability despite certain limitations.

In 1988, two deep ocean time-series hydrostations were established with support from the U.S. National Science Foundation (NSF): one in the western North Atlantic Ocean near the historical Panulirus Station (Bermuda Atlantic Time-series Study [BATS]) and the other in the subtropical North Pacific Ocean near Hawaii (Hawaii Ocean Time-series [HOT]). These programs were established and are currently operated by scientist at Bermuda Biological Station for Research and the University of Hawaii, respectively.

The primary research objective of the initial 5-year phase of HOT (1988-1993) was to design, establish and maintain a deep-water hydrostation as a North Pacific oligotrophic ocean benchmark for observing and interpreting physical and biogeochemical variability. The design included repeat measurements of a suite of core parameters at approximately monthly intervals, compilation of the data and rapid distribution to the scientific community. The establishment of the HOT program study site Sta. ALOHA (A Long-term Oligotrophic Habitat Assessment) also provides an opportunity for visiting colleagues to conduct complementary research, a deep-water laboratory for the development and testing of novel methodologies and instrumentation, and a natural laboratory for marine science education and interlaboratory comparison experiments. Since 1993, HOT program scientists have been engaged in field testing of several interrelated hypotheses derived from observations made during phase I of the program. The measurement program is expected to extend into the next century.

A special volume of Deep-Sea Research published in spring 1996 focuses on oceanic time-series research at Hawaii and Bermuda. A paper published in that volume, "The Hawaii Ocean Time-series (HOT) Program: Background, rationale and field implementation" by D. Karl and R. Lukas presents a detailed history and prospectus of the HOT program research effort.

Center for Microbial Oceanography: Research and Education (C-MORE)

D. Karl (P.I.), E. DeLong, P. Chisholm and J. Zehr (co- P.I.s)
Status: Completed 2016

Microorganisms are the foundation of life and are key to Earth's habitability and sustainability. In open ocean ecosystems, planktonic microbes dominate the living biomass, harvest light energy, produce organic matter and the oxygen we breathe, and facilitate the storage, transport, and turnover of key bioelements. Their metabolic activities and specific growth rates are also responsible for the production and consumption of most of Earth's greenhouse gases. As microbiologist Louis Pasteur noted more than a century ago, "The very great is accomplished by the very small." To gain a full understanding of contemporary and probable future states of marine ecosystems, we need to understand the genetic basis of marine microbe biogeochemistry and ocean processes, and their response to climate change. Because of recent developments in molecular-based biotechnologies and their application to marine ecosystems, we are poised for rapid advances in our understanding of the integrated relationships among the previously isolated disciplines of genomics, biogeochemistry and ecology in the sea. The Earth's inhabitants need solutions to the global scale issues concerning the impact of the burgeoning human population, and this will require a comprehensive understanding of ocean habitat variability and biodynamics, including prognostic modeling of future ecosystem states. Without this information, we are at risk of making grievous mistakes in management and policy decisions that impact the current and future health of our ecosystems and all that they support. Furthermore, we need to communicate this information to others and include it in contemporary academic and community informal educational programs to increase public awareness about the importance of the research and to contribute to personal career choices, accountability and policymaking.

We propose to establish the Center for Microbial Oceanography: Research and Education (C-MORE) that will facilitate broad based research on marine microorganisms across geographical, disciplinary, and cultural boundaries. The proposed Center will be the entity to establish, monitor and manage the research, broker partnerships, conduct a comprehensive education and outreach program and facilitate the formative and summative evaluation necessary to obtain and apply the comprehensive new information about microbial life in the sea. The Center will bring together knowledgeable teams of scientists, educators and community members who otherwise do not have the opportunity to communicate, collaborate or design creative solutions to long-term ecosystem scale problems, and whose collective expertise will synergistically advance microbial oceanography beyond what an ensemble of individual researchers and teachers could accomplish. The Center will facilitate a range of activities, from genomics to instrument/sensor development for remote sensing, to mesocosm experimentation, to ecosystem modeling and, most importantly, integration of results from these diverse approaches. We believe the only way to achieve these interactions, and catalyze new transdisciplinary connections on large problems in a sustained effort, is under the auspices of a Science and Technology Center.

The establishment of C-MORE will provide novel and leveraged opportunities to enhance the coherent physical and biogeochemical datasets now being collected in the North Pacific Subtropical Gyre (NPSG) and in Monterey Bay. This will facilitate, largely for the first time, comprehensive cell-to-ecosystem-to-biome level analyses of key marine habitats and the populations that reside within them. This ecosystem scale of synthesis of the disciplines of oceanography, microbiology and systems ecology will lead to the design and implementation of whole ecosystem-scale perturbation/manipulation experiments that will serve to test meaningful hypotheses linking ecological structure to function. Ultimately, it will require unique opportunities and training like those proposed for C-MORE to lead the next generation of scientists, educators and policy makers on the path to describing new ways for understanding and managing the global marine ecosystem. Without a Center structure, it is doubtful that integrated research on this scale could ever be achieved.

Multi-disciplinary Ocean Sensors for Environmental Analyses and Networks (MOSEAN)

D. Karl (P.I.)
Status: Completed 2007

The U.H. component of MOSEAN (Multi-Disciplinary Ocean Sensors for Environmental Analysis and Networks) will support research at the HALE-ALOHA mooring site near 22 45N, 158W. In conjunction with ship-based research at Station ALOHA, supported through independent NSF grants to D. M. Karl and R. B. Lukas, we will provide calibration data for the inorganic carbon system, chlorophyll dissolved gases, nutrients and primary production. The direct support provided through MOSEAN will be used to hire personnel for selected biochemical analyses, for at-sea sampling and for the maintenance of the HALE ALOHA mooring. The MOSEAN program will benefit from in kind donations of existing mooring equipment (including a 3-m surface buoy with met tower, dual acoustic releases) and mooring instruments valued at over $150,000. The UH-MOSEAN activities will complement other planned Hawaii Ocean Time-series including field tests of a new solar autonomous underwater vehicle (S-AUV) with D. R. Blidberg and a cabled bottom observatory that is currently under review at NSF for funding consideration (F. Duennebier, P.I.)

PARtnership for ADvancing Interdiscipinary Global Models (PARADIGM)

D. Karl (P.I. of Hawaii component)
Status: Completed 2007

Work Statement

David Karl is a microbiological oceanographer with extensive experience with at-sea observations and experimentation. Karl will participate in PARADIGM as a source of knowledge and expertise for the North Pacific Ocean, especially the North Pacific Subtropical Gyre habitat, including various aspects of microbial community structure and function, ecophysiology, and ecosystem responses to climate variations. For the past 13 years, Karl has led the biogeochemical component of the HOT program and through this effort has maintained a globally accessible high quality data base on various relevant biogeochemical parameters. He has also contributed to the development of several new biogeochemical paradigms, especially involving nutrient dynamics, ecological stoichiometry and climate-driven regime shifts in the North Pacific. In addition to HOT, Karl is a team member of the Long-Term Ecological Research (LTER) study of coastal biogeochemical dynamics in the Antarctic Peninsula and of a recently funded Biocomplexity project to investigate Fe-N2 fixation P interactions. He will leverage the intellectual assets of his laboratory to supplement the data synthesis and modeling work in PARADIGM. Karl will participate directly in Tasks 1.1, 2.1, 3.1, 3.3 and 5.5, as detailed below.

Task 1.1: Generalized Community Ecological-Biogeochemical Module. In collaboration with Abbott, Doney, Follows, McGillicuddy and Smith, Karl will assist in the conceptualization and evaluation of new models. Novel concepts (e.g., non-Redfield stoichiometry) and metabolic proceses (e.g. photoheterotrophy) will be used to construct a meaningful representation of the emergent biocomplexity of ecosystem processes.

Task 2.1: Data Mining and Synthesis Program. In collaboration with Ducklow and others, in years 1-2 of the PARADIGM project, Karl will collate and certify existing North Pacific biogeochemical data sets, mostly from Climax, PRPOOS, ADIOS and VERTEX research programs. Most of these data are not currently available via NODC. These historical data sets will be invaluable for testing hypotheses about short-term and long-term ecosystem change. This data archaeology or data mining effort will be coupled to a data accessibility program which will provide synthesized ready-to-use summaries of primary production, nutrients and export fluxes. The user-friendly HOT-DOGS program will be further enhanced to provide ready access to these data products, and will provide one-stop shopping for biogeochemical analyses of the North Pacific Subtropical Gyre, Earths largest biome.

Task 3.1: Exploring the Background State Hypothesis. Karl will collaborate with Cullen, Denman and Ducklow to formulate and parameterize a new model of the microbial (both autotrophic and heterotrophic) background state. The focus of Karls efforts will be on subtropical and Southern Ocean ecosystems. Trophic interactions including symbioses, syntrophy, mixotrophy and other partitioning of the ecosystem resources will be explored. This work will begin in year 3 and continue to the end of the PARADIGM project.

Task 3.2: Nutrient Ratios Multiple Limitations Functional Groups. As stated in the text, The Redfield ocean is on its last legs as a construct for biogeochemical modeling. Karl has already contributed data and interpretations to the next generation paradigm. He will continue to do so, working closely with Abbott and Denman to translate concepts into new models. Once developed, the models will be tested using the extensive data sets that are already available, or recently mined, from the North Pacific Ocean (see Task 2.1).

Task 3.3: Complex Emergent Behavior Regime Shifts. Beyond regime shifts, Karl and colleagues have hypothesized domain shifts wherein the structure of photoautotrophic community oscillates or changes unidirectionally from eukaryote dominance to prokaryotes, with numerous attendant biogeochemical consequences from fishery yields to net carbon sequestration. Karl will work closely with the PARADIGM team of biogeochemical modelers on these matters of great ecological impact and global biogeochemical significance.

Task 5.1: Biogeochemical Regional Models of Subtropical Gyres (HOT and BATS). Karl has labored at sea during the past 13 years to assemble a coherent set of biogeochemically relevant core measurements at Station ALOHA. The analyses of these time-series data have completely changed our view of these low nutrient habitats. What remains to be discovered and understood are the detailed mechanisms behind the seasonal and aperiodic variations in primary production and carbon export and the selection pressures that drive the observed changes in microbial community structure. Karl, working with most of the PARADIGM team, will be the ombudsman for HOT including, but not limited to, the facilitator for data accessibility, information exchange and data interpretations.

Biocomplexity: Collaborative Research: Oceanic N2 Fixation and Global Climate

A. Michaels and D. Capone (P.I.s), A. Subramaniam, E. Boyle, D. Karl, E. Carpenter, R. Siefert, S. Doney, D. Siegel, N. Mahowald, D. Sigman, and G. Haug (co- P.I.s)
Status: Completed 2004

Oceanic nitrogen fixation has recently been identified as a significant part of the oceanic nitrogen (N) cycle and may directly influence the rate of sequestration of atmospheric CO2 in the oceans by providing a new source of N to the upper water column. The prokaryotic micro-organisms that convert N2 gas to reactive N are a unique subcomponent of planktonic ecosystems and exhibit a variety of complex dynamics including the formation of microbial consortia and symbioses and, at times, massive blooms. Accumulating evidence indicates that iron availability may be a key controlling factor for these planktonic marine diazotrophs. The primary pathway of iron delivery to the upper oceans is through dust deposition.

N2 fixers may therefore be directly involved in global feedbacks with the climate system and these feedbacks may also exhibit complex dynamics on many different time-scales. The hypothesized feedback mechanism will have the following component parts: The rate of N2 fixation in the worlds oceans can have an impact on the concentration of the greenhouse gas, carbon dioxide (CO2), in the atmosphere on time-scales of decades (variability in surface biogeochemistry) to millennia (changes in the total nitrate stock from the balance of N2 fixation and denitrification). Carbon dioxide concentrations in the atmosphere influence the climate. The climate system, in turn, can influence the rate of N2 fixation in the oceans by controlling the supply of iron on dust and by influencing the stratification of the upper ocean. Humans also have a direct role in the current manifestation of this feedback cycle by their influence on dust production, through agriculture at the margins of deserts, and by our own production of CO2 into the atmosphere. The circular nature of these influences can lead to a feedback system, particularly on longer time-scales.

We will study each of the components of this system and then to model the hypothesized feedback processes. Because of the interaction of the various parts of this system, keyed around the unique behavior and biogeochemistry of the prokaryotic microorganisms that can fix N2, this feedback loop should exhibit complex behaviors on a variety of time-scales. In this proposed research, we will conduct a targeted series of experiments and field observations to understand and parameterize each of the pieces of this global process including the direct control of marine N2 fixation by dust deposition. This understanding will then feed a modeling process that examines the complex dynamics of this system on time-scales of years to millennia. The modeling process will be evaluated by comparison with data on the time-dependent behavior of ocean biogeochemistry as available from ocean time-series studies and sediment cores.

Coupled Intensification of N and P Cycles in the Subtropical North Pacific Ocean

D. Karl (P.I.), K. Björkman (co- P.I.)
Status: Completed 2002

This project seeks fundamental information on the interactions between nitrogen (N) and phosphorus (P) in the oligotrophic North Pacific Ocean, and their relationships to rates and mechanisms of ecosystem production and export. The research is guided by the following general hypothesis: Climate-related shifts in the structure of the epipelagic habitat have selected for N2-fixing bacteria, resulting in a coupled intensification of N and P cycling rates which has forced the system from N- to P-limitation with numerous ecological and biogeochemical consequences. This hypothesized shift from N-to-P limitation has affected community structure, rates of gross primary production and export, and the elemental (C, N, P) stoichiometry of dissolved and particulate matter pools. We will conduct a series of field and laboratory experiments designed to evaluate several ecological predictions of this coupled intensification model of nutrient dynamics in the North Pacific Subtropical Gyre with a primary focus on P pool dynamics. The field research will be conducted at Sta. ALOHA (22 45N, 158W) and will complement the ongoing Hawaii Ocean Time-series (HOT) core measurement program. These efforts will focus on: (1) dissolved inorganic P uptake and remineralization rates, (2) dissolved organic P pool production rates, chemical characterizations and bioavailability and (3) physiological and biochemical assessments of Trichodesmium and Prochlorococcus. Knowledge derived from this project will be used to refine our understanding of the oligotrophic North Pacific ecosystem and to predict the response of oceanic habitats to environmental variability and global climate change.

Palmer Long-Term Ecological Research (PAL-LTER) Project

R.C. Smith (P.I.), K. Baker, W. Fraser, E. Hofmann, D. Karl, J. Klinck, L. Quetin, R. Ross, W. Trivelpiece and M. Vernet (co-P.I.s)
Status: Completed 2002

This is a multidisciplinary, multi-investigator project to investigate ecosystem dynamics in Antarctica. A central tenet of the PAL-LTER project is that the annual advance and retreat of sea ice is a major physical determinant of spatial and temporal variability and change in the antarctic marine ecosystem from total annual primary and export production to breeding success in seabirds. Numerous interrelated hypotheses are currently under investigation. PAL-LTER is one of 18 separate LTER programs around the globe with common research objectives, methoeds and scientific motivations. A comprehensive summary of the PAL-LTER program has recently appeared (Smith et al. 1995, Oceanography 8: 77-86).

Within PAL-LTER, our group "Coupled Ocean-ice Linkages and Dynamics (COLD)" has focused our research on the topics of microbiology and carbon flux. Microorganisms, including unicellular algae, bacteria, viruses, protozoans and small metazoans, are vital components of Southern Ocean habitats. They are largely responsible for the production and decomposition of organic matter, for the primary uptake and regeneration of inorganic nutrients and for export of carbon and energy to intermediate ocean depths. Furthermore, microbial growth and metabolism can have a profound effect on seawater pH and redox state and, therefore can influence the distribution, speciation and availability of certain elements and compounds. Consequently, field data both on individual groups of microorganisms and on the complex interactions among them are necessary for a complete assessment of the role of marine microorganisms on both local and global environments.

Our COLD program research can be broadly divided into several separate but related topics: (1) dissolved inorganic carbon and dissolved organic carbon pool dynamics, (2) bacterial biomass and activity distributions, and controls on bacterial growth and (3) particle sedimentation and export production. These interrelated studies will be used to gain a general understanding of carbon and energy flux through the microbial food web and subsequently to higher trophic levels. As such, they are a central component of the overall PAL-LTER program objectives.

LTER Cross-site Comparison: Microbial Loop Dynamics and Regulation of Bacterial Physiology in Subtropical and Polar Marine Habitats

D. M. Karl (P.I.)
Status: Completed 2002

The microbial loop has been shown to play an important role in marine and freshwater plankton ecosystems in all climatic zones. Our research in two contrasting habitats: an Antarctic coastal/shelf/oceanic ecosystem and a subtropical oceanic ecosystem, have shown significant differences in the ecological role of the microbial loop and the physiology of bacterioplankton. These two habitats are isolated from input of terrestrially derived organic matter and so provide excellent opportunities to study bacterial metabolism of autochthonous organic matter of phytoplankton origin. Strong contrasts in plankton community parameters (high vs. low inorganic nutrients, large vs. small phytoplankton, metazoan vs. protozoan grazers, large percentage of photosynthetic production respired by animals vs. by bacteria and protozoa) make these two sites ideal for this comparison. This study will be embedded within ongoing programs at each of these two sites (US-JGOFS Hawaii Ocean Time-series in the North Pacific and Palmer LTER in Antarctica) that provide both logistical support and supporting data on a wide range of hydrographic, chemical and biological parameters, with extensive documentaiton of spatial and temporal variation. Preliminary field results show that bacterial communities in these two areas are physiologically distinct, that bacterial physiology is regulated by the structure of the microbial community and particularly by grazer recycling of nitrogen, that organic compounds rare in seawater, especially histidine, play a large role in regulation of bacterial ectoenzyme expression, and that photolysis of dissolved organic matter by solar ultraviolet radiation also plays a role in regulation of bacterial ectoenzymes. More thorough investigation of these phenomena in ecologically distinct microbial communities will facilitate understanding of the complex interactions between bacterioplankton and the rest of the microbial community.