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David M Karl

Publications and source records attributed to David M Karl.

13 recordsLinked to original sources
PubMed2006

Community genomics among stratified microbial assemblages in the ocean's interior.

Microbial life predominates in the ocean, yet little is known about its genomic variability, especially along the depth continuum. We report here genomic analyses of planktonic microbial communities in the North Pacific Subtropical Gyre, from the ocean's surface to near-sea floor depths. Sequence variation in microbial community genes reflected vertical zonation of taxonomic groups, functional gene repertoires, and metabolic potential. The distributional patterns of microbial genes suggested depth-variable community trends in carbon and energy metabolism, attachment and motility, gene mobility, and host-viral interactions. Comparative genomic analyses of stratified microbial communities have the potential to provide significant insight into higher-order community organization and dynamics.

Amino Acid Sequence↗
PubMed2006

Reduced mixing generates oscillations and chaos in the oceanic deep chlorophyll maximum.

Deep chlorophyll maxima (DCMs) are widespread in large parts of the world's oceans. These deep layers of high chlorophyll concentration reflect a compromise of phytoplankton growth exposed to two opposing resource gradients: light supplied from above and nutrients supplied from below. It is often argued that DCMs are stable features. Here we show, however, that reduced vertical mixing can generate oscillations and chaos in phytoplankton biomass and species composition of DCMs. These fluctuations are caused by a difference in the timescales of two processes: (1) rapid export of sinking plankton, withdrawing nutrients from the euphotic zone and (2) a slow upward flux of nutrients fuelling new phytoplankton production. Climate models predict that global warming will reduce vertical mixing in the oceans. Our model indicates that reduced mixing will generate more variability in DCMs, thereby enhancing variability in oceanic primary production and in carbon export into the ocean interior.

Biomass↗
PubMed2005

Genomic perspectives in microbial oceanography.

The global ocean is an integrated living system where energy and matter transformations are governed by interdependent physical, chemical and biotic processes. Although the fundamentals of ocean physics and chemistry are well established, comprehensive approaches to describing and interpreting oceanic microbial diversity and processes are only now emerging. In particular, the application of genomics to problems in microbial oceanography is significantly expanding our understanding of marine microbial evolution, metabolism and ecology. Integration of these new genome-enabled insights into the broader framework of ocean science represents one of the great contemporary challenges for microbial oceanographers.

Ecosystem↗
PubMed2005

Marine phosphate oxygen isotopes and organic matter remineralization in the oceans.

We show that the isotopic composition of oxygen (delta18O) in dissolved inorganic phosphate (Pi) reveals the balance between Pi transport and biological turnover rates in marine ecosystems. Our delta18Op of Pi (delta18Op) measurements herein indicate the importance of cell lysis in the regeneration of Pi in the euphotic zone. Depth profiles of the delta18Op in the Atlantic and Pacific Oceans are near a temperature-dependent isotopic equilibrium with water. Small deviations from equilibrium below the thermocline suggest that P remineralization in the deep ocean is a byproduct of microbial carbon and energy requirements. However, isotope effects associated with phosphohydrolase enzymes involved in P remineralization are quite large and could potentially lead to significant disequilibration of Pi oxygen. The observed near equilibration of deep water Pi likely calls for continued slow rates of microbial uptake and release of Pi and/or extracellular pyrophosphatase-mediated oxygen exchange between water and Pi along the deep water flow path.

Biological Transport↗
PubMed2005

Carbon mass balance methodology to characterize the growth of pigmented marine bacteria under conditions of light cycling.

A carbon mass balance methodology employing minimal measurements was applied to heterotrophic and photoheterotrophic marine bacteria grown under constant dilution and exposed to 12-h intervals of light or darkness. Carbon mass balance calculations using measurements taken every 3 h closed to within 93-103% using dissolved organic carbon, biomass carbon and CO2 production data only, indicating that background interference from dissolved inorganic carbon variations in the amended seawater medium was not significant. Neither strain was observed to sustain a net CO2 fixation using paramagnetic measurement of oxygen uptake rates (OUR), indicating a need for more sensitive on-line measurement techniques for OUR. Photoheterotrophic growth demonstrated lower carbon-mole biomass yields (0.41+/-0.026 vs. 0.64+/-0.013 mol mol(-1)) despite higher specific glucose uptake rates (0.025 vs. 0.02 mol mol(-1) h(-1)), suggesting that bioreactor-based study of marine bacteria can present growth modes that are different from those encountered in the marine environment.

Biomass↗
PubMed2005

Temporal patterns of nitrogenase gene (nifH) expression in the oligotrophic North Pacific Ocean.

Dinitrogen (N(2))-fixing microorganisms (diazotrophs) play important roles in ocean biogeochemistry and plankton productivity. In this study, we examined the presence and expression of specific planktonic nitrogenase genes (nifH) in the upper ocean (0 to 175 m) at Station ALOHA in the oligotrophic North Pacific Ocean. Clone libraries constructed from reverse-transcribed PCR-amplified mRNA revealed six unique phylotypes. Five of the nifH phylotypes grouped with sequences from unicellular and filamentous cyanobacteria, and one of the phylotypes clustered with gamma-proteobacteria. The cyanobacterial nifH phylotypes retrieved included two sequence types that phylogenetically grouped with unicellular cyanobacteria (termed groups A and B), several sequences closely related (97 to 99%) to Trichodesmium spp. and Katagnymene spiralis, and two previously unreported phylotypes clustering with heterocyst-forming nifH cyanobacteria. Temporal patterns of nifH expression were evaluated using reverse-transcribed quantitative PCR amplification of nifH gene transcripts. The filamentous and presumed unicellular group A cyanobacterial phylotypes exhibited elevated nifH transcription during the day, while members of the group B (closely related to Crocosphaera watsonii) unicellular phylotype displayed greater nifH transcription at night. In situ nifH expression by all of the cyanobacterial phylotypes exhibited pronounced diel periodicity. The gamma-proteobacterial phylotype had low transcript abundance and did not exhibit a clear diurnal periodicity in nifH expression. The temporal separation of nifH expression by the various phylotypes suggests that open ocean diazotrophic cyanobacteria have unique in situ physiological responses to daily fluctuations of light in the upper ocean.

Animals↗
PubMed2004

Light dependence of [3H]leucine incorporation in the oligotrophic North Pacific ocean.

The influence of irradiance on bacterial incorporation of [(3)H]leucine was evaluated at Station ALOHA in the oligotrophic North Pacific subtropical gyre. Six experiments were conducted on three cruises to Station ALOHA to examine how [(3)H]leucine incorporation varied as a function of irradiance. Two experiments were also conducted to assess the photoautotrophic response to irradiance (based on photosynthetic uptake of [(14)C]bicarbonate) in both the upper and lower photic zones. Rates of [(3)H]leucine incorporation responded to irradiance in a photosynthesis-like manner, increasing sharply at low light and then saturating and sometimes declining with increasing light intensity. The influence of irradiance on bacterial growth was evaluated in both the well-lit (5 to 25 m) and dimly lit regions of the upper ocean (75 to 100 m) to determine whether the bacterial response to irradiance differed along the depth-dependent light gradient of the photic zone. [(3)H]leucine incorporation rates were analyzed with a photosynthesis-irradiance model for a quantitative description of the relationships between [(3)H]leucine incorporation and irradiance. Maximum rates of [(3)H]leucine incorporation in the upper photic zone increased 48 to 92% relative to those of dark-incubated samples, with [(3)H]leucine incorporation saturating at light intensities between 58 and 363 micromol of quanta m(-2) s(-1). Rates of [(3)H]leucine incorporation in the deep photic zone were photostimulated 53 to 114% and were susceptible to photoinhibition, with rates declining at light intensities of >100 micromol of quanta m(-2) s(-1). The results of these experiments revealed that sunlight directly influences bacterial growth in this open-ocean ecosystem.

Bacteria↗
PubMed2003

Proteorhodopsin genes are distributed among divergent marine bacterial taxa.

Proteorhodopsin (PR) is a retinal-binding bacterial integral membrane protein that functions as a light-driven proton pump. The gene encoding this photoprotein was originally discovered on a large genome fragment derived from an uncultured marine gamma-proteobacterium of the SAR86 group. Subsequently, many variants of the PR gene have been detected in marine plankton, via PCR-based gene surveys. It has not been clear, however, whether these different PR genes are widely distributed among different bacterial groups, or whether they have a restricted taxonomic distribution. We report here comparative analyses of PR-bearing genomic fragments recovered directly from planktonic bacteria inhabiting the California coast, the central Pacific Ocean, and waters offshore the Antarctica Peninsula. Sequence analysis of an Antarctic genome fragment harboring PR (ANT32C12) revealed moderate conservation in gene order and identity, compared with a previously reported PR-containing genome fragment from a Monterey Bay gamma-proteobacterium (EBAC31A08). Outside the limited region of synteny shared between these clones, however, no significant DNA or protein identity was evident. Analysis of a third PR-containing genome fragment (HOT2C01) from the North Pacific subtropical gyre showed even more divergence from the gamma-proteobacterial PR-flanking region. Subsequent phylogenetic and comparative genomic analyses revealed that the Central North Pacific PR-containing genome fragment (HOT2C01) originated from a planktonic alpha-proteobacterium. These data indicate that PR genes are distributed among a variety of divergent marine bacterial taxa, including both alpha- and gamma-proteobacteria. Our analyses also demonstrate the utility of cultivation-independent comparative genomic approaches for assessing gene content and distribution in naturally occurring microbes.

Antarctic Regions↗
PubMed2003

Climate-driven changes to the atmospheric CO2 sink in the subtropical North Pacific Ocean.

The oceans represent a significant sink for atmospheric carbon dioxide. Variability in the strength of this sink occurs on interannual timescales, as a result of regional and basin-scale changes in the physical and biological parameters that control the flux of this greenhouse gas into and out of the surface mixed layer. Here we analyse a 13-year time series of oceanic carbon dioxide measurements from station ALOHA in the subtropical North Pacific Ocean near Hawaii, and find a significant decrease in the strength of the carbon dioxide sink over the period 1989-2001. We show that much of this reduction in sink strength can be attributed to an increase in the partial pressure of surface ocean carbon dioxide caused by excess evaporation and the accompanying concentration of solutes in the water mass. Our results suggest that carbon dioxide uptake by ocean waters can be strongly influenced by changes in regional precipitation and evaporation patterns brought on by climate variability.

Atmosphere↗
PubMed2002

Nutrient dynamics in the deep blue sea.

For more than a century, oceanographers have studied the interactions between the photosynthetic production of organic matter and nutrient dynamics in the sea. This research has been field-oriented and transdisciplinary, occurring at the intersections of research in microbiology, physics, analytical chemistry, cell physiology and ecology. The global database derived from this collective effort established a sound scientific understanding of nutrient dynamics and the vital role of microorganisms, both autotrophic and heterotrophic, in the coupled organic-matter production and decomposition cycles in the sea. However, novel approaches used over the past two decades, including new designs for field experiments, repeat field observations and remote-sensing capabilities, together with updated methods of sample analysis, have led to a revolution in our thinking about the mechanisms and controls of nutrient dynamics in the deep blue sea. Contemporary paradigms bear only partial resemblance to the dogma of the past, and are likely to evolve further as new data and new ideas are presented for open discussion and debate.

Climate↗