Biodiversity, community structural shifts, and biogeography of prokaryotes within Antarctic continental shelf sediment

Abstract

16S ribosomal DNA (rDNA) clone library analysis was conducted to assess prokaryotic diversity and community structural changes within a surficial sediment core obtained from an Antarctic continental shelf area (depth, 761 m) within the Mertz Glacier Polynya (MGP) region. Libraries were created from three separate horizons of the core (0- to 0.4-cm, 1.5- to 2.5-cm, and 20- to 21-cm depth positions). The results indicated that at the oxic sediment surface (depth, 0 to 0.4 cm) the microbial community appeared to be dominated by a small subset of potentially r-strategist (fast-growing, opportunistic) species, resulting in a lower-than-expected species richness of 442 operational taxonomic units (OTUs). At a depth of 1.5 to 2.5 cm, the species richness (1,128 OTUs) was much higher, with the community dominated by numerous gamma and delta proteobacterial phylotypes. At a depth of 20 to 21 cm, a clear decline in species richness (541 OTUs) occurred, accompanied by a larger number of more phylogenetically divergent phylotypes and a decline in the predominance of Proteobacteria. Based on rRNA and clonal abundance as well as sequence comparisons, syntrophic cycling of oxidized and reduced sulfur compounds appeared to be the dominant process in surficial MGP sediment, as phylotype groups putatively linked to these processes made up a large proportion of clones throughout the core. Between 18 and 65% of 16S rDNA phylotypes detected in a wide range of coastal and open ocean sediments possessed high levels of sequence similarity (>95%) with the MGP sediment phylotypes, indicating that many sediment prokaryote phylotype groups defined in this study are ubiquitous in marine sediment.

FIG. 1.

16S rDNA tree showing positions of mostly heterotrophic members of the gamma proteobacteria found within MGP sediment layers, including the AWS98-7e, B2M60, Oceanospirillum, Coxiella, Alteromonadaceae, and BPC036 phylotype groups.

FIG. 2.

16S rDNA tree showing positions of putatively sulfur-oxidizing and other members of the gamma proteobacteria and beta proteobacteria found within MGP sediment layers, including the BD3-6/JTB255, Ectothiorhodospiraceae, BD7-8, and JTB148/sva0091 phylotype groups.

FIG. 3.

16S rDNA tree showing positions of delta proteobacteria found within MGP sediment layers, including the JTB38/Clear-9, Myxobacteria, Desulfobacterium anilini, Desulfuromonas, Eel-TE1A4, BD1-2/sva0103, and Desulfobulbaceae phylotype groups.

FIG. 4.

16S rDNA tree showing positions of members of the Desulfosarcina group and of the genus Desulfobacula found within MGP sediment layers.

FIG. 5.

16S rDNA tree showing positions of members of the epsilon and alpha proteobacteria found within MGP sediment layers, including the Arcobacter, Thiomicrospira, Olavius losiae endosymbiont, JTB260, Amaricoccus, Ruegeria, JTB131, and Mertz cluster A phylotype groups.

FIG. 6.

16S rDNA tree showing positions of members of Acidobacteria and related lineages found within MGP sediment layers, including the NKB18 (OP8 group), SAR406, and NKB17/Sva0450 phylotype groups.

FIG. 7.

16S rDNA tree showing positions of members of the Flavobacteria, green sulfur bacteria, and spirochetes found within MGP sediment layers, including the Spirochaeta; Chlorobium-related; and flavobacterial JTB248/NB1-m, C. fermentans, Zobellia, Tenacibaculum-Polaribacter, and Cellulophaga-Psychroserpens groups. The latter three groups belong to the family Flavobacteriaceae.

FIG. 8.

16S rDNA tree showing positions of members of the Planctomycetales and relatives found within MGP sediment layers, including the Sva0500/BD2-18, Verrucomicrobium, ANAMMOX, BD2-16, and Pirellula phylotype groups.

FIG. 9.

16S rDNA tree showing positions of members of the gram-positive bacteria found within MGP sediment layers, including the JTB31/sva0389, PAUC43f/BD2-11, ACE-43, and BURTON-30 phylotype groups.

FIG. 10.

16S rDNA tree showing positions of members of the green non-sulfur bacteria found within MGP sediment layers, including the “Dehalococcoides” and BD3-16/PENDANT-37 phylotype groups.

FIG. 11.

16S rDNA tree showing positions of members of the OP11 group found within MGP sediment layers, including known reference clones from terrestrial and marine sediments.

FIG. 12.

16S rDNA tree showing positions of members of the Archaebacteria found within MGP sediment layers, including the pBRC84, ACE-6, PENDANT-33, CRA8-27cm, and marine group I phylotype groups.

FIG. 13.

Species richness estimate curves derived from 16S rDNA clone library data for 0- to 0.4-cm (•), 1.5- to 2.5-cm (▪), and 20- to 21-cm (□) MGP sediment layers. Error bars indicate 95% CIs.

FIG. 14.

Comparison between 16S rDNA library (percent of total clones) and rRNA hybridization (percent of universal rRNA) data for the abundances of various prokaryote groups in the MGP surface layer. RNA hybridization data are from reference . Error bars indicate standard deviations of means.