The vertical distribution of bacteriochlorophyll a, the numbers of infrared fluorescent cells, and the variable fluorescence signal at 880 nanometers wavelength, all indicate that photosynthetically competent anoxygenic phototrophic bacteria are abundant in the upper open ocean and comprise at least 11% of the total microbial community. These organisms are facultative photoheterotrophs, metabolizing organic carbon when available, but are capable of photosynthetic light utilization when organic carbon is scarce. They are globally distributed in the euphotic zone and represent a hitherto unrecognized component of the marine microbial community that appears to be critical to the cycling of both organic and inorganic carbon in the ocean.

During the past few years Archaea have been recognized as a widespread and significant component of marine picoplankton assemblages and, more recently, the presence of novel archaeal phylogenetic lineages has been reported in coastal marine benthic environments. We investigated the relative abundance, vertical distribution, phylogenetic composition, and spatial variability ofArchaea in deep-sea sediments collected from several stations in the Atlantic Ocean. Quantitative oligonucleotide hybridization experiments indicated that the relative abundance of archaeal 16S rRNA in deep-sea sediments (1500 m deep) ranged from about 2.5 to 8% of the total prokaryotic rRNA. Clone libraries of PCR-amplified archaeal rRNA genes (rDNA) were constructed from 10 depth intervals obtained from sediment cores collected at depths of 1,500, 2,600, and 4,500 m. Phylogenetic analysis of rDNA sequences revealed the presence of a complex archaeal population structure, whose members could be grouped into discrete phylogenetic lineages within the two kingdoms, Crenarchaeota and Euryarchaeota. Comparative denaturing gradient gel electrophoresis profile analysis of archaeal 16S rDNA V3 fragments revealed a significant depth-related variability in the composition of the archaeal population.

Seven strains of marine aerobic anoxygenic phototrophs belonging to the genus Erythrobacter were isolated. The strains were characterized regarding their physiological and biochemical properties, 16S rDNA and pufM gene sequences, morphological features, substrate preference, as well as pigment and lipid composition. All strains had functional type-2 reaction centers containing bacteriochlorophyll, served by small, light-harvesting complex 1, and were photosynthetically competent. In addition, large pools of carotenoids were found, but only some of the accessory pigments transfer energy to the reaction centers. All of the isolates were facultative photoheterotrophs. They required an organic carbon substrate for growth; however, they are able to supplement a significant fraction of their metabolic requirements with photosynthetically derived energy.

The discovery of hyperthermophilic microorganisms and the analysis of hyperthermostable enzymes has established the fact that multisubunit enzymes can survive for prolonged periods at temperatures above 100°C. We have carried out homology-based modeling and direct structure comparison on the hexameric glutamate dehydrogenases from the hyperthermophiles Pyrococcus furiosus and Thermococcus litoralis whose optimal growth temperatures are 100°C and 88°C, respectively, to determine key stabilizing features. These enzymes, which are 87% homologous, differ 16-fold in thermal stability at 104°C. We observed that an intersubunit ion-pair network was substantially reduced in the less stable enzyme from T. litoralis, and two residues were then altered to restore these interactions. The single mutations both had adverse effects on the thermostability of the protein. However, with both mutations in place, we observed a fourfold improvement of stability at 104°C over the wild-type enzyme. The catalytic properties of the enzymes were unaffected by the mutations. These results suggest that extensive ion-pair networks may provide a general strategy for manipulating enzyme thermostability of multisubunit enzymes. However, this study emphasizes the importance of the exact local environment of a residue in determining its effects on stability.

o C e a N i C S P r e a D i N g C e N t e r P r o C e S S e S | ridge 2000 P r o g r a M r e S e a r C h is currently a notable lack of process-oriented studies that would allow an assessment of the larger role of these ecosystems in global biogeochemical cycles. By combining the presently available powerful "omic" and single-cell tools with thermodynamic modeling, experimental approaches, and new in situ instrumentation to measure rates and concentrations, it is now possible to bring our understanding of these truly fascinating ecosystems to a new level and to place them in a quantitative framework and thus a larger global context.

Biomass samples from the Black Sea collected in 1988 were analyzed for SSU genes from Bacteria and Archaea after 10 years of storage at ؊80°C. Both clonal libraries and direct fingerprinting by terminal restriction fragment length polymorphism (T-RFLP) analyses were used to assess the microbial community. Uniform and discrete depth distributions of different SSU phylotypes were observed. However, most recombinant clones were not restricted to a specific depth in the water column, and many of the major T-RFLP peaks remain uncharacterized. Of the clones obtained, an -Proteobacteria and a Pseudoalteromonas-like clone accounted for major peaks in the fingerprint, while deeply branching lineages of ␣-and ␥-Proteobacteria were associated with smaller peaks. Additionally, members were found among both the ␦-Proteobacteria related to sulfate reducers and the Archaea related to phylotypes from the ANME groups that anaerobically oxidize methane.The Black Sea is the largest surface-exposed, permanently anoxic basin on this planet. In this area, the high intensity of photosynthetic primary production in the surface waters, the associated flux of organic carbon, and the shallow sill depth has led to the development and maintenance of the largest, stable oxic/anoxic interface on the planet (3). This interface, or chemocline (defined by the first appearance of hydrogen sulfide in the water column) is located at 81 to 99 m depth (3, 16). A 20-to 30-m-deep suboxic layer depleted in both O 2 and H 2 S overlies the sulfide zone (16). The stratified water column in the Black Sea is believed to host more active and diverse microbial assemblages than anywhere else in the pelagic ocean (14). As such, the Black Sea is an excellent model system for studying oxic/anoxic interfaces, essentially stretching a chemocline normally encountered on the submillimeter scale over tens of meters.Although other oxic/anoxic regions exist and reports of molecular characterization of microbial communities from the Cariaco Trench (23) or sedimentary systems (12,22,40,42) have been published, few systematic profiles of the transition between oxic and anoxic bacterial communities beyond a domain-or group-specific approach have been reported. The purpose of this study was to characterize the Bacteria and Archaea populations in the Black Sea at a species-specific level and to correlate the vertical distribution of the various prokaryotic plankton with the profiles of terminal electron acceptors that occur throughout the oxic/anoxic chemocline. To this end, we conducted culture-independent studies on samples collected from the Black Sea water column during the 1988 oceanographic expedition. Terminal restriction fragment length polymorphism (T-RFLP) analysis (1) was performed on samples between 10 and 500 m depth to characterize the microbial assemblages, using the 16S ribosomal RNA genes (20). Discrete bacterial communities were seen corresponding to the aerobic zone, the high-nitrate zone, the sulfate-reducing zone, and the anoxic deep waters. This research ...

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Autotrophic carbon fixation was characterized in representative members of the three lineages of the bacterial phylum Aquificae. Enzyme activity measurements and the detection of key genes demonstrated that Aquificae use the reductive tricarboxylic acid (TCA) cycle for autotrophic CO(2) fixation. This is the first time that strains of the Hydrogenothermaceae and 'Desulfurobacteriaceae' have been investigated for enzymes of autotrophic carbon fixation. Unexpectedly, two different mechanisms of citrate cleavage could be identified within the Aquificae. Aquificaceae use citryl-CoA synthetase and citryl-CoA lyase, whereas Hydrogenothermaceae and 'Desulfurobacteriaceae' use ATP citrate lyase. The first mechanism is likely to represent the ancestral version of the reductive TCA cycle. Sequence analyses further suggest that ATP citrate lyase formed by a gene fusion of citryl-CoA synthetase and citryl-CoA lyase and subsequently became involved in a modified version of this pathway. However, rather than having evolved within the Aquificae, our phylogenetic analyses indicate that Aquificae obtained their ATP citrate lyase through lateral gene transfer. Aquificae play an important role in biogeochemical processes in a variety of high-temperature habitats. Thus, these findings substantiate the hypothesis that autotrophic carbon fixation through the reductive TCA cycle is widespread and contributes significantly to biomass production particularly in hydrothermal habitats.