Fingerprinting Microbial Assemblages from the Oxic/Anoxic Chemocline of the Black Sea

Abstract

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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