Depth profile of sulfate-reducing bacterial ribosomal RNA and mercury methylation in an estuarine sediment

Abstract: The community structure of complex anaerobic microbial communities has been difficult to elucidate because of an inability to cultivate most of the contributing populations. In this study, the distribution of sulfate-reducing bacteria (SRB) in anaerobic sediments was determined using oligonucleotide probes complementary to the 16S ribosomal RNAs of major phylogenetic groups. Sediment cores were collected from Santa Rosa Sound in northwest Florida, and sectioned by depth into 1 to 2 cm fractions. Nucleic acids were extracted from each fraction and hybridized with the SRB-specific ribosomal RNA probes. SRB ribosomal RNAs accounted for almost 5% of the microbial community ribosomal RNA pool in the 3–4 cm depth fraction and were dominated by Desulfovibrionaceae ribosomal RNA. The SRB ribosomal RNA peak coincided with mercury methylation, an activity attributed to SRB. Profiles of the ribosomal RNAs indicate that SRB populations in sediments are stratified by depth.     

The preferred electron acceptor of Desulfovibrio desulfuricans CSN

Abstract: The sulfate-reducing bacterium Desulfovibrio desulfuricans strain CSN (DSM 104) oxidized H₂ with thiosulfate, sulfate, sulfite, nitrite, nitrate and oxygen with rates increasing (in the order listed) from 20 to 525 nmol H₂ min⁻¹ mg⁻¹ protein. Nitrate reduction was induced by nitrate or limiting concentrations of sulfate during growth, while all other activities were constitutive. Oxygen prevented reduction of all other electron acceptors, while nitrate and nitrite blocked the reduction of the sulfur compounds. In the presence of H₂ and reduced sulfur compounds, H₂ was the preferred electron donor. The cells oxidized thiosulfate or sulfite coupled to the reduction of nitrate to ammonia. This represents a novel type of metabolism connecting the sulfur and nitrogen cycles. It is concluded that oxygen is the preferred electron acceptor of D. desulfuricans . Sulfate reduction in oxic environments must be due to different organisms or mechanisms.     

Survival of sulfate-reducing bacteria in oxic surface sediment of a seawater lake

Abstract Microhabitats and survival of sulfate-reducing bacteria (SRB) in an oxic surface sediment of a seawater lake were examined. The size of fractionation of the sediment suspension showed that most of SRB were associated with sediment particles larger than 10 μm. The D values (time in h required to destroy 90% of the initial viable population) for SRB in the whole sediment suspension and for SRB i n the < μ m and the < 5 μ m fractions were, respectively, 23.7, 10 and 4 when the SRB were exposed to air. Survival of the FeS-associated Desulfovibrio desulfuricans ( D value, 9.3) was higher than that of the free-living ones ( D value, 1.8). These results show that particle-associated SRB are more protected against oxygen than free-living ones in oxic sediments.     

Occurrence of two l-threonine (l-serine) dehydratases in the thermophile Chloroflexus aurantiacus

The thermophilic phototrophic prokaryote, Chloroflexus aurantiacus was shown to contain high constitutive l-threonine (l-serine) deaminating activity. Separation of cellular proteins by DE 52-cellulose chromatography and by polyacrylamide gel electrophoresis with subsequent activity staining of the gels yielded two bands, one representing an isoleucine-sensitive, the other one an isoleucine-insensitive form of l-threonine dehydratase. Both enzymes had a molecular weight of 120,000 but were distinguished by their different affinities to the two substrates, l-threonine and l-serine.Abbreviations SDH l-serine dehydratase - TDH l-threonine dehydratase     

Acetate oxidation to CO2 in anaerobic bacteria via a novel pathway not involving reactions of the citric acid cycle

In several sulfate-reducing bacteria capable of complete oxidation of acetate (or acetyl CoA), the citric acid cycle is not operative. No 2-oxoglutarate dehydrogenase activity was found in these organisms, and the labelling pattern of oxaloacetate excludes its synthesis via 2-oxo-glutarate. These sulfate-reducers contained, however, high activities of the enzymes carbon monoxide dehydrogenase and formate dehydrogenase and catalyzed an isotope exchange between CO₂ and the carboxyl group of acetate (or acetyl CoA), showing a direct C-C-cleavage of activated acetic acid. These findings suggest that in the investigated sulfate-reducers acetate is oxidized to CO₂ via C₁ intermediates. The proposed pathway provides a possible explanation for the reported different fluoroacetate sensitivity of acetate oxidation by anaerobic bacteria, for mini-methane formation, as well as for the postulated anaerobic methane oxidation by special sulfate-reducers.     

Purification and partial characterization of ad(−)-lactate dehydrogenase fromDesulfovibrio desulfuricans (ATCC 7757)

Summary A membrane-boundd(–)-lactate dehydrogenase (LDH), an important enzyme in carbon and energy metabolism in sulfate-reducing bacteria of the genusDesulfovibrio, was solubilized from the membrane fraction ofDesulfovibrio desulfuricans (ATCC 7757). The enzyme was purified 84-fold to a final specific activity of 525 nmol DCPIP-reduced/min/mg protein by ammonium sulfate precipitation, chloroform extraction, gel filtration with Sephadex G-150, and hydrophobic column chromatography withN-octylamine Sepharose 4B. The enzyme eluted off a Sephacryl S-300 column as a single peak with a molecular weight of 400 000±40 000 Da. Denaturing gel electrophoresis showed it to be composed of 5 protein bands. The oxidized and dithionite reduced spectra of LDH resembles the spectra ofc-type cytochromes found inDesulfovibrio species. The addition of lactate to LDH resulted in a partially reduced spectrum. The flavin/cytochromec/non-heme iron content per 400 000 Da LDH molecular weight was found to be 11.64.5. The LDH activity was specific ford(–)-lactate and had aK _m ford(–)-lactate of 4.3×10^–4 M. The pH optimum was between 6.5 and 8.5.     

Amino acid cost and codon-usage biases in 6 prokaryotic genomes: a whole-genome analysis

For most prokaryotic organisms, amino acid biosynthesis represents a significant portion of their overall energy budget. The difference in the cost of synthesis between amino acids can be striking, differing by as much as 7-fold. Two prokaryotic organisms, Escherichia coli and Bacillus subtilis, have been shown to preferentially utilize less costly amino acids in highly expressed genes, indicating that parsimony in amino acid selection may confer a selective advantage for prokaryotes. This study confirms those findings and extends them to 4 additional prokaryotic organisms: Chlamydia trachomatis, Chlamydophila pneumoniae AR39, Synechocystis sp. PCC 6803, and Thermus thermophilus HB27. Adherence to codon-usage biases for each of these 6 organisms is inversely correlated with a coding region's average amino acid biosynthetic cost in a fashion that is independent of chemoheterotrophic, photoautotrophic, or thermophilic lifestyle. The obligate parasites C. trachomatis and C. pneumoniae AR39 are incapable of synthesizing many of the 20 common amino acids. Removing auxotrophic amino acids from consideration in these organisms does not alter the overall trend of preferential use of energetically inexpensive amino acids in highly expressed genes.     

Reduction of molybdate by sulfate-reducing bacteria

Molybdate is an essential trace element required by biological systems including the anaerobic sulfate-reducing bacteria (SRB); however, detrimental consequences may occur if molybdate is present in high concentrations in the environment. While molybdate is a structural analog of sulfate and inhibits sulfate respiration of SRB, little information is available concerning the effect of molybdate on pure cultures. We followed the growth of Desulfovibrio gigas ATCC 19364, Desulfovibrio vulgaris Hildenborough, Desulfovibrio desulfuricans DSM 642, and D. desulfuricans DSM 27774 in media containing sub-lethal levels of molybdate and observed a red-brown color in the culture fluid. Spectral analysis of the culture fluid revealed absorption peaks at 467, 395 and 314 nm and this color is proposed to be a molybdate–sulfide complex. Reduction of molybdate with the formation of molybdate disulfide occurs in the periplasm D. gigas and D. desulfuricans DSM 642. From these results we suggest that the occurrence of poorly crystalline Mo-sulfides in black shale may be a result from SRB reduction and selective enrichment of Mo in paleo-seawater.