DNA extraction from coral reef sediment bacteria for the polymerase chain reaction.

A rapid and effective method for the direct extraction of high molecular weight amplifiable DNA from two coral reef sediments was developed. DNA was amplified by the polymerase chain reaction (PCR) using 16S rDNA specific primers. The amplicons were digested with HaeIII, HinP1I and MspI and separated using polyacrylamide gel electrophoresis and silver staining. The resulting amplified ribosomal DNA restriction analysis (ARDRA) patterns were used as a fingerprint to discern differences between the coral reef sediment samples. Results indicated that ARDRA is an effective method for determining differences within the bacterial community amongst different environmental samples.

Nitrogen fixation in sediments and the rhizosphere of the seagrassZostera capricorni.

Rates of nitrogen fixation in seagrass beds (Zostera capricorni) were determined with(15)N and reduction of acetylene in intact cores of sediment and seagrass. There was good agreement in the results from the two techniques, with a molar ratio of 3∶1.9 ethylene: ammonia produced. Fixed nitrogen was rapidly utilized by the plants, with significant amounts of(15)N found in the roots and rhizomes and 50% of fixed(15)N apparently translocated to the leaves. Rates of fixation were high in summer (25 to 40 mg N m(-2) day(-1)) and lower in winter (10 mg N m(-2) day(-1)) and were estimated to supply between one-third and one-half of the nitrogen requirements of the seagrass. Rates of nitrogen fixation were greater in the light than in the dark, and in cores of intact seagrass than in defoliated cores, indicating that the bacteria were dependent on organic compounds secreted by the plants.

Effects of patch scale on density-dependence and species-dependence in two host-parasitoid systems.

Data from two host-parasitoid communities were analyzed to ascertain whether patch scale affected the kinds of correlations existing between 1) spatial differences in host density and the intensity of parasitism (density-dependence) and 2) number of species of parasitoids and the intensity of parasitism (species-dependence). We concluded that parasitization rates are usually independent of both host density and number of parasitoid species present regardless of patch scale. Therefore, the responses of parasitoids to host density and the addition of parasitoid species to a community are equally unpredictable in outcome.

Thrombospondin in essential thrombocythemia.

Essential thrombocythemia is a myeloproliferative disorder characterized by frequent bleeding and thrombotic complications. On a molecular level, two abnormalities of platelet thrombospondin have been identified: abnormal glycosylation of the intact 185,000-dalton chain has been detected and a shortened form of the thrombospondin chain is present. We have used two monoclonal antibodies and Lens culinaris lectin to probe the structure of thrombospondin in the platelets from three patients with essential thrombocythemia; one patient with polycythemia vera and two patients with secondary thrombocytosis. The presence of abnormal thrombospondin fragments with molecular weights of 160,000 and 30,000 was detected in the intact platelets and in the supernatant from thrombin-treated platelets, in all of the individuals except one of the secondary thrombocytosis patients. Monoclonal antibody binding studies indicate that both fragments are produced by proteolysis at a single site, which results in the removal of a 30,000-dalton fragment from the NH2-terminal. Lens culinaris lectin-binding studies revealed that some of the carbohydrate moieties of thrombospondin are near this cleavage site. The results are consistent with the hypothesis that the abnormal thrombospondin fragments observed under conditions of increased platelet production are due to increased susceptibility to proteolysis which, in turn, may be due to defective glycosylation.

Bacterial productivity in ponds used for culture of penaeid prawns.

The quantitative role of bacteria in the carbon cycle of ponds used for culture of penaeid prawns has been studied. Bacterial biomass was measured using epifluorescence microscopy and muramic acid determinations. Bacterial growth rates were estimated from the rate of tritiated thymidine incorporation into DNA. In the water column, bacterial numbers ranged from 8.3×10(9) 1(-1) to 2.57×10(10) 1(-1) and production ranged from 0.43 to 2.10 mg Cl(-1) d(-1). In the 0-10 mm zone in sediments, bacterial biomass was 1.4 to 5.8 g C m(-2) and production was 250 to 500 mg C m(-2) d(-1). The results suggested that most organic matter being supplied to the ponds as feed for the prawns was actually being utilized by the bacteria. When the density of meiofauna increased after chicken manure was added, bacterial biomass decreased and growth rates increased.

Microbial biomass and productivity in seagrass beds.

Different methods for measuring the rates of processes mediated by bacteria in sediments and the rates of bacterial cell production have been compared. In addition, net production of the seagrass Zostera capricorni and bacterial production have been compared and some interrelationships with the nitrogen cycle discussed. Seagrass productivity was estimated by measuring the plastochrone interval using a leaf stapling technique. The average productivity over four seasons was 1.28 +/- 0.28 g C m-2 day-1 (mean +/- standard deviation, n = 4). Bacterial productivity was measured five times throughout a year using the rate of tritiated thymidine incorporated into DNA. Average values were 33 +/- 12 mg C m-2 day-1 for sediment and 23 +/- 4 for water column (n = 5). Spatial variability between samples was greater than seasonal variation for both seagrass productivity and bacterial productivity. On one occasion, bacterial productivity was measured using the rate of 32P incorporated into phospholipid. The values were comparable to those obtained with tritiated thymidine. The rate of sulfate reduction was 10 mmol SO4(-2) m-2 day-1. The rate of methanogenesis was low, being 5.6 mg CH4 produced m-2 day-1. A comparison of C flux measured using rates of sulfate reduction and DNA synthesis indicated that anaerobic processes were predominant in these sediments. An analysis of microbial biomass and community structure, using techniques of phospholipid analysis, showed that bacteria were predominant members of the microbial biomass and that of these, strictly anaerobic bacteria were the main components. Ammonia concentration in interstitial water varied from 23 to 71 micromoles. Estimates of the amount of ammonia required by seagrass showed that the ammonia would turn over about once per day. Rapid recycling of nitrogen by bacteria and bacterial grazers is probably important.

Quantitative determination of microbial activity and community nutritional status in estuarine sediments: evidence for a disturbance artifact.

In estuarine sediments with a high degree of vertical heterogeneity in reduced substrate and terminal electron acceptor concentrations, the method of exposure of the microbiota to labeled substrates can introduce a "disturbance artifact" into measures of metabolic activity. The detection of this artifact is based on quantitative measurement of the relative rates of incorporation of [14C]acetate into phospholipid fatty acids (PLFA) and endogenous storage lipid, poly-beta-hydroxyalkanoate (PHA). Previous studies have shown that PLFA synthesis measures cellular growth and that PHA synthesis measures carbon accumulation (unbalanced growth). The "disturbance artifact" of exposure to [14C]acetate was demonstrated by comparing injection of a core with the usual or pore-water replacement or slurry techniques. Only injection of labeled substrate allowed detection of preassay disturbance of the sediment with a garden rake. The raking increased PLFA synthesis with little effect to differences in concentration or distribution of [14C]acetate in the 10-min incubation. Bioturbation induced by sand dollar feeding in estuarine sediment could be detected in an increased PLFA/PHA ratio which was due to decreased PHA synthesis if the addition of labeled substrate was by the injection technique. Addition of labeled precursors to sediment by slurry or pore-water replacement induces greater disturbance artifacts than injection techniques.

Validity of the tritiated thymidine method for estimating bacterial growth rates: measurement of isotope dilution during DNA synthesis.

The rate of tritiated thymidine incorporation into DNA was used to estimate bacterial growth rates in aquatic environments. To be accurate, the calculation of growth rates has to include a factor for the dilution of isotope before incorporation. The validity of an isotope dilution analysis to determine this factor was verified in experiments reported here with cultures of a marine bacterium growing in a chemostat. Growth rates calculated from data on chemostat dilution rates and cell density agreed well with rates calculated by tritiated thymidine incorporation into DNA and isotope dilution analysis. With sufficiently high concentrations of exogenous thymidine, de novo synthesis of deoxythymidine monophosphate was inhibited, thereby preventing the endogenous dilution of isotope. The thymidine technique was also shown to be useful for measuring growth rates of mixed suspensions of bacteria growing anaerobically. Thymidine was incorporated into the DNA of a range of marine pseudomonads that were investigated. Three species did not take up thymidine. The common marine cyanobacterium Synechococcus species did not incorporate thymidine into DNA.

Effects of therapy with cholestyramine on progression of coronary arteriosclerosis: results of the NHLBI Type II Coronary Intervention Study.

In the National Heart, Lung and Blood Institute Type II Coronary Intervention Study, patients with Type II hyperlipoproteinemia and coronary artery disease (CAD) were placed on a low-fat, low-cholesterol diet and then were randomly allocated to receive either 6 g cholestyramine four times daily or placebo. This double-blind study evaluated the effects of cholestyramine on the progression of CAD as assessed by angiography. Diet alone reduced the low-density lipoprotein cholesterol 6% in both groups. After randomization, low-density lipoprotein cholesterol decreased another 5% in the placebo group and 26% in the cholestyramine-treated group. Coronary angiography was performed in 116 patients before and after 5 years of treatment. CAD progressed in 49% (28 of 57) of the placebo-treated patients vs 32% (19 of 59) of the cholestyramine-treated patients (p less than .05). When only definite progression was considered, 35% (20 of 57) of the placebo-treated patients vs 25% (15 of 59) of the cholestyramine-treated patients exhibited definite progression; the difference was not statistically significant. However, when this analysis was performed with adjustment for baseline inequalities of risk factors, effect of treatment was more pronounced. Of lesions causing 50% or greater stenosis at baseline, 33% of placebo-treated and 12% of cholestyramine-treated patients manifested lesion progression (p less than .05). Similar analyses with other end points (percent of baseline lesions that progressed, lesions that progressed to occlusion, lesions that regressed, size of lesion change, and all cardiovascular end points) all favored the cholestyramine-treated group, but were not statistically significant. Thus, although the sample size does not allow a definitive conclusion to be drawn, this study suggests that cholestyramine treatment retards the rate of progression of CAD in patients with Type II hyperlipoproteinemia.

National Heart, Lung, and Blood Institute type II Coronary Intervention Study: design, methods, and baseline characteristics.

The Type II Coronary Intervention Study (Type II Study) is a double-blind, randomized, placebo-controlled clinical trial conducted by the Division of Intramural Research of the National Heart, Lung, and Blood Institute of Bethesda, Maryland. The study was designed to evaluate the 5-year treatment effect of cholestyramine on low density lipoprotein (LDL) cholesterol and on lesions in the coronary arteries. One hundred forty-three patients with Type II hyperlipoproteinemia (elevated LDL cholesterol) and coronary artery disease (CAD) were entered into the study between 1972 and 1976. Patients were stratified by sex and extent of coronary disease as defined angiographically and were randomly allocated to a daily dosage of 24 g cholestyramine and diet (treatment group) or placebo and diet (control group). Changes in the coronary arteries were evaluated by sequential coronary angiography carried out before and after five years of treatment. This report describes the trial design and baseline characteristics of the study patients.

Ultrastructure of bacteria and the proportion of Gram-negative bacteria in marine sediments.

Bacteria in sediments from the surface aerobic layer (0-1 cm) and a deeper anaerobic layer (20-21 cm) of a seagrass bed were examined in section by transmission electron microscopy. Bacteria with a Gram-negative ultrastructure made up 90% of bacteria in the surface layer, and Gram-positive bacteria comprised 10%. In the anaerobic zone, Gram-negative bacteria comprised 70% and Gram-positive bacteria 30% of the bacterial population. These differences were highly significant and support predictions of these proportions made from muramic acid measurements and direct counting with fluorescence microscopy. Most cells were enveloped in extracellular slime layers or envelopes, some with considerable structural complexity. The trophic value to animals of these envelopes is discussed. A unique organism with spines was observed.

Improved method using muramic acid to estimate biomass of bacteria in sediments.

A method, which depends on the measurement of muramic acid content to estimate bacterial biomass, has been improved in sensitivity by two orders of magnitude. It is now applicable to any aquatic sediment, whereas previously it was mainly useful in the analysis of gut contents of deposit-feeding animals. Reduced NAD, a product of the oxidation of d-lactate derived from muramic acid, is assayed using bacterial luciferase. The amount of muramic acid in a number of terrestrial and marine bacteria was measured, and found to be lower than that obtained with the previous, less specific, assay procedure. The muramic acid content of a blue-green alga has been measured, thus allowing blue-green algae to be taken into account when estimating bacterial biomass. Experimental evidence is presented which shows that muramic acid in cell wall fragments of bacteria is rapidly degraded by microorganisms in a marine sediment.

A method for estimating the biomass of bacteria in aquatic sediments and its application to trophic studies.

A method is described for estimating the biomass of bacteria in aquatic sediments by an enzymic measurement of D-lactic acid derived from hydrolysis of muramic acid. A correlation is shown between muramic acid and biomass. The Gram-negative rod bacteria contain about 20 µg muramic acid/mg carbon whereas the Gram-negative or Gramvariable pleomorphic and Gram-positive bacteria contain about 100 µg muramic acid/mg carbon. Thus to measure biomass, the relative proportions of these bacteria in the population must be measured. The method is limited at present to sediments in which the biomass of blue-green algae is insignificant compared to bacteria. It is particularly suited to measuring the biomass of bacteria in sediments ingested by animals. This is illustrated by analysis of the gut contents of two deposit-feeders, a mullet (Mugil cephalus) and a prawn (Metapenaeus bennettae), in which it is shown that bacteria are an important component of their diet.