Vertical shifts in the microbial community structure of organic-rich Namibian shelf sediments

Abstract

This study investigates the diversity and abundance of bacteria in organic-rich Namibian shelf sediments from two sampling stations, using the 16S rRNA library approach and Catalyzed Reporter Deposition Fluorescent in situ Hybridization (CARD-FISH). Six clone libraries were constructed. Clone libraries were dominated by Delta-proteobacteria (up to 48%) and Gamma-proteobacteria (up to 98%). Bacteroidetes were dominant in the clone library of the top 6 cm (up to 17%), while actinobacteria dominated at a depth of 10 to 12 cm (up to 34%). Sequences that were related to bacteria with hydrolytic and fermenting abilities include members from the Gamma-proteobacteria, Bacteroidetes, Actinobacteria, and Acidobacteria. Cloned sequences within the Delta-proteobacteria affiliates to sulfate reducing bacteria, including Desulfarculaceae, Desulfobacteraceae, Desulfobulbaceae,and Desulfuromonadales and were detected throughout the sediment. The two sampling stations differed in microbial diversity with a higher diversity prevailing at the station with higher metabolic rates for organic matter decomposition. At both sampling stations a shift in microbial community composition with depth was observed and is explained by gradients in organic substrate availability within the sediment, which affects the life strategies adopted by bacteria, resulting in niche diversification and ultimately affects bacterial community composition and structure throughout the sediment depth. Key words: Namibia, upwelling, microbial, diversity, abundance.