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D M Karl

Publications and source records attributed to D M Karl.

At least 19 recordsLinked to original sources
PubMed2001

Unicellular cyanobacteria fix N2 in the subtropical North Pacific Ocean.

Fixed nitrogen (N) often limits the growth of organisms in terrestrial and aquatic biomes, and N availability has been important in controlling the CO2 balance of modern and ancient oceans. The fixation of atmospheric dinitrogen gas (N2) to ammonia is catalysed by nitrogenase and provides a fixed N for N-limited environments. The filamentous cyanobacterium Trichodesmium has been assumed to be the predominant oceanic N2-fixing microorganism since the discovery of N2 fixation in Trichodesmium in 1961 (ref. 6). Attention has recently focused on oceanic N2 fixation because nitrogen availability is generally limiting in many oceans, and attempts to constrain the global atmosphere-ocean fluxes of CO2 are based on basin-scale N balances. Biogeochemical studies and models have suggested that total N2-fixation rates may be substantially greater than previously believed but cannot be reconciled with observed Trichodesmium abundances. It is curious that there are so few known N2-fixing microorganisms in oligotrophic oceans when it is clearly ecologically advantageous. Here we show that there are unicellular cyanobacteria in the open ocean that are expressing nitrogenase, and are abundant enough to potentially have a significant role in N dynamics.

Atmosphere↗
PubMed2001

Archaeal dominance in the mesopelagic zone of the Pacific Ocean.

The ocean's interior is Earth's largest biome. Recently, cultivation-independent ribosomal RNA gene surveys have indicated a potential importance for archaea in the subsurface ocean. But quantitative data on the abundance of specific microbial groups in the deep sea are lacking. Here we report a year-long study of the abundance of two specific archaeal groups (pelagic euryarchaeota and pelagic crenarchaeota) in one of the ocean's largest habitats. Monthly sampling was conducted throughout the water column (surface to 4,750 m) at the Hawai'i Ocean Time-series station. Below the euphotic zone (> 150 m), pelagic crenarchaeota comprised a large fraction of total marine picoplankton, equivalent in cell numbers to bacteria at depths greater than 1,000 m. The fraction of crenarchaeota increased with depth, reaching 39% of total DNA-containing picoplankton detected. The average sum of archaea plus bacteria detected by rRNA-targeted fluorescent probes ranged from 63 to 90% of total cell numbers at all depths throughout our survey. The high proportion of cells containing significant amounts of rRNA suggests that most pelagic deep-sea microorganisms are metabolically active. Furthermore, our results suggest that the global oceans harbour approximately 1.3 x 10(28) archaeal cells, and 3.1 x 10(28) bacterial cells. Our data suggest that pelagic crenarchaeota represent one of the ocean's single most abundant cell types.

Archaea↗
PubMed2001

A novel method for the measurement of dissolved adenosine and guanosine triphosphate in aquatic habitats: applications to marine microbial ecology.

A novel method for the measurement of dissolved adenosine-5'-triphosphate and guanosine-5'-triphosphate (D-ATP and D-GTP, respectively) in marine and freshwater habitats was developed and applied to samples collected from the oligotrophic North Pacific Ocean. Both D-ATP and D-GTP are co-precipitated by authigenically formed Mg(OH)(2) and can be concentrated by factors greater than 200-fold, for subsequent measurement by the firefly luciferin-luciferase bioluminescence reaction. The detection limit for this method was 2-3 pmol ml(-1) of concentrated sample (equivalent to an in situ concentration of 10 pM) with a 5% precision at concentrations of 10 pmol ml(-1) or above.A significant positive correlation (P<0.001) was observed between particulate ATP (P-ATP) and D-ATP in water samples collected from Station ALOHA (22.75 degrees N, 158 degrees W; depth profiles 0-1000 m). The highest concentrations of dissolved nucleotides were found in the euphotic zone (0-175 m) below which the concentrations were low and relatively invariant. The dissolved nucleotide pools generally exceeded their corresponding particulate pools.Using radioisotopic tracer techniques and the new concentration method, turnover times for both particulate and dissolved nucleotides can be determined. The ability to measure concentrations and follow nucleotide tracers accurately in a very dilute environment provides a unique opportunity to address questions on microbial community metabolism, nutrient dynamics and energy flux.

Adenosine Triphosphate↗
PubMed2000

Phosphate depletion in the western North Atlantic Ocean.

Surface waters of the subtropical Sargasso Sea contain dissolved inorganic phosphate (DIP) concentrations of 0.2 to 1.0 nanomolar, which are sufficiently low to result in phosphorus control of primary production. The DIP concentrations in this area (which receives high inputs of iron-rich dust from arid regions of North Africa) are one to two orders of magnitude lower than surface levels in the North Pacific (where eolian iron inputs are much lower and water column denitrification is much more substantial). These data indicate a severe relative phosphorus depletion in the Atlantic. We hypothesize that nitrogen versus phosphorus limitation of primary production in the present-day ocean may be closely linked to iron supply through control of dinitrogen (N2) fixation, an iron-intensive metabolic process. Although the oceanic phosphorus inventory may set the upper limit for the total amount of organic matter produced in the ocean over geological time scales, at any instant in geological time, oceanic primary production may fall below this limit because of a persistent insufficient iron supply. By controlling N2 fixation, iron may control not only nitrogen versus phosphorus limitation but also carbon fixation and export stoichiometry and hence biological sequestration of atmospheric carbon dioxide.

Atlantic Ocean↗
PubMed1999

Microorganisms in the accreted ice of Lake Vostok, Antarctica.

Analysis of a portion of Vostok ice core number 5G, which is thought to contain frozen water derived from Lake Vostok, Antarctica (a body of liquid water located beneath about 4 kilometers of glacial ice), revealed between 2 x 10(2) and 3 x 10(2) bacterial cells per milliliter and low concentrations of potential growth nutrients. Lipopolysaccharide (a Gram-negative bacterial cell biomarker) was also detected at concentrations consistent with the cell enumeration data, which suggests a predominance of Gram-negative bacteria. At least a portion of the microbial assemblage was viable, as determined by the respiration of carbon-14-labeled acetate and glucose substrates during incubations at 3 degrees C and 1 atmosphere. These accreted ice data suggest that Lake Vostok may contain viable microorganisms.

Acetates↗
PubMed1996

A computer-simulated restriction fragment length polymorphism analysis of bacterial small-subunit rRNA genes: efficacy of selected tetrameric restriction enzymes for studies of microbial diversity in nature.

An assessment of 10 tetrameric restriction enzymes (TREs) was conducted by using a computer-simulated restriction fragment length polymorphism (RFLP) analysis for over 100 proximally and distally related bacterial small-subunit (SSU) rRNA gene sequences. Screening SSU rDNA clone libraries with TREs has become an effective strategy because of logistic simplicity, commercial availability, and economy. However, the rationale for selecting the type and number of TREs has not been systematically evaluated. Our objective was to identify the optimal combination of TREs for RFLP screening of cloned SSU rRNA genes from undefined bacterial clone libraries. After computer-simulated TRE digestion, the resultant fragments were categorized on the basis of the frequency of different restriction fragment size classes. Three groups of distribution patterns for the TREs were determined and further examined via graphical exploratory data analysis. The RFLP size-frequency distribution data for each group of enzymes were then used to infer phylogenetic relationships via the neighbor-joining method. The resulting bootstrap values and the correct placement of node bifurcations were used as additional criteria to evaluate the efficacy of the selected TREs. These RFLP data were compared with known phylogenetic relationships based on SSU rRNA sequence analysis as defined by the Ribosomal Database Project. A heuristic approach testing random combinations of TREs showed that three or more TRE combinations detected > 99% of the operational taxonomic units (OTUs) within the model data set. OTUs that remained undetected after three TRE treatments had a median sequence similarity of 96.1%. Of the 10 restriction enzymes examined, HhaI, RsaI, and BstUI (group 3) were the most efficacious at detecting and differentiating bacterial SSU rRNA genes on the basis of their ability to correctly classify OTUs. Group 3 TREs are therefore recommended for screening in studies using bacterial SSU rRNA genes as descriptors of in situ microbial diversity.

Computer Simulation↗
PubMed1996

The National Association of Marine Laboratories: a connected web for studying long-term changes in U.S. coastal and marine waters.

Long-term time-series measurements provide data that test specific hypotheses or suggest new avenues of study. Such studies are widely acknowledged as important for differentiating the influence of human activities from natural background variability. Several long-term research or monitoring programs are active in coastal and marine environments around the world and serve as models for development of new studies. The spatial array of U.S. coastal laboratories is suitable for resolving latitudinal trends and for many types of comparative studies. However, establishing a network of coastal laboratories focused on long-term monitoring and research problems presents special challenges in setting research priorities at appropriate scales, in data management, and in coordination of the scientific effort. The National Association of Marine Laboratories (NAML) is uniquely positioned to promote long-term studies among networks of its member institutions. The NAML can play an effective role in publicizing the importance of long-term studies, in providing access to expertise in this type of research, and in promoting its continuance for periods longer than the length of individual scientific careers.

Environmental Monitoring↗
PubMed1995

Phylogenetic diversity of the bacterial community from a microbial mat at an active, hydrothermal vent system, Loihi Seamount, Hawaii.

The phylogenetic diversity of small-subunit rRNA genes associated with the domain Bacteria was examined (by using previously defined operational taxonomic units [C. L. Moyer, F.C. Dobbs, and D. M. Karl, Appl. Environ. Microbiol. 60:871-879, 1994]; those for Pele's Vents Bacteria are hereafter abbreviated PVB OTUs) with samples from a microbial mat at an active, deep-sea hydrothermal vent system. A cluster of phylogenetically related PVB OTUs (OTUs 2, 3, 6, and 8) was closely affiliated with Thiovulum sp. contained within the epsilon subclass of the class Proteobacteria and accounted for 60.5% of the small-subunit rRNA bacterial clone library from Pele's Vents. A second, smaller cluster of PVB OTUs (OTUs 1 and 11) was closely affiliated with Xanthomonas sp., contained within the gamma subclass of the Proteobacteria and accounted for a total of 27.1% of the bacterial clone library. The remaining five PVB OTUs each accounted for 2.1% of the clones recovered and were affiliated with the following phylogenetic groups: PVB OTU 5 was a member of the Alteromonas group; PVB OTU 12 was a member of the Colwellia assemblage; PVB OTU 4 was loosely determined to be a member of the Thiothrix group, with the endosymbiotic bacteria from Bathymodiolus thermophilus and Calyptogena magnifica as the nearest relatives; PVB OTU 10B was a member of the Myxobacterium group; and PVB OTU 9A was a member of the Paraphyletic assemblage, with the Octopus Spring microbial mat type K clone as the closest known relative.(ABSTRACT TRUNCATED AT 250 WORDS)

Bacteria↗
PubMed1994

Estimation of diversity and community structure through restriction fragment length polymorphism distribution analysis of bacterial 16S rRNA genes from a microbial mat at an active, hydrothermal vent system, Loihi Seamount, Hawaii.

PCR was used to amplify (eu)bacterial small-subunit (16S) rRNA genes from total-community genomic DNA. The source of total-community genomic DNA used for this culture-independent analysis was the microbial mats from a deep-sea, hydrothermal vent system, Pele's Vents, located at Loihi Seamount, Hawaii. Oligonucleotides complementary to conserved regions in the 16S rRNA-encoding DNA (rDNA) of bacteria were used to direct the synthesis of PCR products, which were then subcloned by blunt-end ligation into phagemid vector pBluescript II. Restriction fragment length polymorphism patterns, created by using tandem tetrameric restriction endonucleases, revealed the presence of 12 groups of 16S rRNA genes representing discrete operational taxonomic units (OTUs). The rank order abundance of these putative OTUs was measured, and the two most abundant OTUs accounted for 72.9% of all of the 16S rDNA clones. Among the remaining 27.1% of the 16S rDNA clones, none of the 10 OTUs was represented by more than three individual clones. The cumulative OTU distribution for 48 bacterial 16S rDNA clones demonstrated that the majority of taxa represented in the clone library were detected, a result which we assume to be an estimate of the diversity of bacteria in the native hydrothermal vent habitat. 16S rDNA fingerprinting of individual clones belonging to particular OTUs by using an oligonucleotide probe that binds to a universally conserved region of the 16S rDNA fragments was conducted to confirm OTU specificity and 16S rDNA identity.

Bacteria↗
PubMed1993

Quantification of chemiluminescent DNA probes using liquid scintillation counting.

A novel method for quantifying chemiluminescent DNA probes is described. The method uses liquid scintillation counting to measure light emission from the alkaline phosphatase-catalyzed breakdown of the substrate PPD (3-(4-methoxyspiro[1,2-dioxetane-3,2'-tricyclo[3.3.1.1 (3.7[decan]- 4-yl)phenyl phosphate) on dot blot preparations. Serial dilutions of either pUC18 DNA or lambda DNA were hybridized with digoxigenin-labeled probes and detected using the method described. Light flux (luminescence) was linearly related to DNA concentration, typically with a coefficient of determination (r2) of 0.9 or better. Due to the stability of alkaline phosphatase and the long-lived luminescence of PPD in the Lumi-phos formulation, repetitive analyses of a given sample can be made for up to 20 h. The method can reliably detect 17 amol of DNA (30 pg pUC18DNA) with a coefficient of variation on replicate samples of 14%. Optimization experiments showed that 7% sodium dodecyl sulfate in the prehybridization and hybridization buffers resulted in the lowest background; the best combination of signal-to-noise ratio and reproducibility was obtained using Bio-Rad Zeta-Probe GT nylon membranes. Direct immersion of samples into a solution of substrate was found to give the most precise results and ensured that substrate limitation at high concentrations of alkaline phosphatase (i.e., higher DNA amounts) did not occur.

Adamantane↗
PubMed1991

Top predators in the Southern ocean: a major leak in the biological carbon pump.

Primary productivity in the Southern Ocean is approximately 3.5 gigatons of carbon per year, which accounts for nearly 15 percent of the global total. The presence of high concentrations of nitrate in Antarctic waters suggests that it might be possible to increase primary production significantly and thereby alleviate the net accumulation of atmospheric carbon dioxide. An analysis of the food web for these waters implies that the Southern Ocean may be remarkably inefficient as a carbon sink. This inefficiency is caused by the large flux of carbon respired to the atmosphere by air-breathing birds and mammals, dominant predators in the unusually simple food web of Antarctic waters. These top predators may transfer into the atmosphere as much as 20 to 25 percent of photosynthetically fixed carbon.

Animals↗
PubMed1990

Catabolism of tritiated thymidine by aquatic microbial communities and incorporation of tritium into RNA and protein.

The incorporation of tritiated thymidine by five microbial ecosystems and the distribution of tritium into DNA, RNA, and protein were determined. All microbial assemblages tested exhibited significant labeling of RNA and protein (i.e., nonspecific labeling), as determined by differential acid-base hydrolysis. Nonspecific labeling was greatest in sediment samples, for which >/=95% of the tritium was recovered with the RNA and protein fractions. The percentage of tritium recovered in the DNA fraction ranged from 15 to 38% of the total labeled macromolecules recovered. Nonspecific labeling was independent of both incubation time and thymidine concentration over very wide ranges. Four different RNA hydrolysis reagents (KOH, NaOH, piperidine, and enzymes) solubilized tritium from cold trichloroacetic acid precipitates. High-pressure liquid chromatography separation of piperidine hydrolysates followed by measurement of isolated monophosphates confirmed the labeling of RNA and indicated that tritium was recovered primarily in CMP and AMP residues. We also evaluated the specificity of [2-H]adenine incorporation into adenylate residues in both RNA and DNA in parallel with the [H]thymidine experiments and compared the degree of nonspecific labeling by [H]adenine with that derived from [H]thymidine. Rapid catabolism of tritiated thymidine was evaluated by determining the disappearance of tritiated thymidine from the incubation medium and the appearance of degradation products by high-pressure liquid chromatography separation of the cell-free medium. Degradation product formation, including that of both volatile and nonvolatile compounds, was much greater than the rate of incorporation of tritium into stable macromolecules. The standard degradation pathway for thymidine coupled with utilization of Krebs cycle intermediates for the biosynthesis of amino acids, purines, and pyrimidines readily accounts for the observed nonspecific labeling in environmental samples.

Journal Article↗
PubMed1986

Method for Assessing Heterogeneity in Turnover Rates within Microbial Communities.

A method is presented for determining both the average turnover rate and the standard deviation of the average turnover rate of the adenine nucleotide (AN) pool within a population of microorganisms. The method requires the calculation of the initial slope and curvature of a plot of AN specific activity versus time following the introduction of [H]adenine. An analysis of noise-corrupted data indicated that the method is capable of detecting a lack of uniformity in the turnover rate when the coefficient of variation of the turnover rate exceeds 39%. An analysis of field data revealed a significant lack of uniformity in the turnover rates of microbial communities in a marine sediment sample and freshwater pond but no significant nonuniformity in the turnover rates of microbial communities in a seawater sample and in a second freshwater pond. Although the method has been applied only to the analysis of AN turnover rates, it is applicable to any intracellular pool for which a suitable radioactive precursor exists.

Journal Article↗
PubMed1985

Influence of deep ocean sewage outfalls on the microbial activity of the surrounding sediment.

The microbial activity near two deep ocean sewage outfalls off the coast of the island of Oahu, Hawaii, was characterized. Water samples and sediment samples to a depth of 4.5 cm were analyzed from an area of approximately 4.5 x 10 m surrounding the outfalls. Although the effluent water at both sites exhibited heterotrophic activity that was 2 orders of magnitude greater than water from a control site, ambient water samples taken within 1 m of the discharge ports exhibited activity only twice that of the control water. The heterotrophic activity of the outfall sediment was only elevated above that of the control site for surface samples collected within 10 m of the outfall. Likewise, the rates of microbial nucleic acid synthesis and carbon production in the sediment were only elevated immediately adjacent to the outfalls. Total microbial biomass, as determined by the ATP content of the sediment, varied spatially but was generally elevated at the outfall sites. The specific growth rates calculated for the sediment microbial populations, however, were not greater at the outfall sites. At one site the rocks surrounding the diffuser pipe were covered with copious amounts of slime that appeared to be composed entirely of microbial cells and filaments. This microbial mat was extremely active with respect to heterotrophic activity and biomass production. Overall, it appears that the impact of the sewage discharge on the ambient seawater microbiota is slight and that the effect on the sediment microbiota is confined to an area immediately adjacent to the diffuser ports. In the sand itself, the effect is limited to the upper 2 cm at most.

Journal Article↗