Prokaryotic metabolic activity and community structure in Antarctic continental shelf sediments

Abstract

The prokaryote community activity and structural characteristics within marine sediment sampled across a continental shelf area located off eastern Antarctica (66 degrees S, 143 degrees E; depth range, 709 to 964 m) were studied. Correlations were found between microbial biomass and aminopeptidase and chitinase rates, which were used as proxies for microbial activity. Biomass and activity were maximal within the 0- to 3-cm depth range and declined rapidly with sediment depths below 5 cm. Most-probable-number counting using a dilute carbohydrate-containing medium recovered 1.7 to 3.8% of the sediment total bacterial count, with mostly facultatively anaerobic psychrophiles cultured. The median optimal growth temperature for the sediment isolates was 15 degrees C. Many of the isolates identified belonged to genera characteristic of deep-sea habitats, although most appear to be novel species. Phospholipid fatty acid (PLFA) and isoprenoid glycerol dialkyl glycerol tetraether analyses indicated that the samples contained lipid components typical of marine sediments, with profiles varying little between samples at the same depth; however, significant differences in PLFA profiles were found between depths of 0 to 1 cm and 13 to 15 cm, reflecting the presence of a different microbial community. Denaturing gradient gel electrophoresis (DGGE) analysis of amplified bacterial 16S rRNA genes revealed that between samples and across sediment core depths of 1 to 4 cm, the community structure appeared homogenous; however, principal-component analysis of DGGE patterns revealed that at greater sediment depths, successional shifts in community structure were evident. Sequencing of DGGE bands and rRNA probe hybridization analysis revealed that the major community members belonged to delta proteobacteria, putative sulfide oxidizers of the gamma proteobacteria, Flavobacteria, Planctomycetales, and Archaea. rRNA hybridization analyses also indicated that these groups were present at similar levels in the top layer across the shelf region.

FIG. 1.

(A) Cell biomass (▪) and bacterial direct count (□) estimates for MGP sediment cores at different depths. (B) Aminopeptidase (substrate, l-leucine-4-methylcoumarinyl-7-amide) activity in MGP sediment cores at different depths. (C) Chitinase (substrate, 4-methylumbelliferyl-β-d-glucosaminide dihydrate) activity in MGP sediment cores at different depths. (D) Temperature range for aminopeptidase (▪) and chitinase (□) activities in MGP sediment grabs. All values are averages and standard deviations from five sediment samples.

FIG. 2.

Phylogram based on 16S rRNA gene sequences for MGP isolates (in boldface) obtained from MPN trays and from samples directly plated onto SWN agar. Strains isolated from samples incubated under anaerobic conditions are indicated by the suffix AN. GenBank accession numbers are indicated in parentheses after the sequence name.

FIG. 3.

Comparison of PLFA profiles in MGP sediment cores (n = 5) at depths of 0 to 1 and 13 to 14 cm. Error bars indicate standard deviations.

FIG. 4.

DGGE gel showing distribution of bacterial 16S rRNA gene fragments in a variety of Antarctic sediment samples. Lanes A to E, MGP samples at a 1- to 2-cm depth; lane F, Burton Lake, Vestfold Hills; lane G, control DNA. Black bars at the left of DGGE bands indicate which bands were sequenced. Bands sequenced are enumerated in descending order and correspond to the MGP band numbers shown in Fig. 7.

FIG. 5.

DGGE gel showing distribution of bacterial 16S rRNA gene fragments within a MGP sediment core (10GC01). Lane designations are by sample depth: A, 2 to 4 cm; B, 4 to 6 cm; C, 6 to 8 cm; D, 8 to 10 cm; E, 10 to 12 cm; F, 14 to 16 cm; G, 16 to 18 cm; H, 18 to 20 cm. Lane I, control.

FIG. 6.

Principal-coordinate plots showing the similarity of patterns of prominent DGGE bands in MGP sediment at various depths and in comparison to other Antarctic sediment samples. The threeseparate plots show different combinations of the first three eigenvectors. Symbols: ▪, 2- to 4-cm depth; •, 4 to 6 cm; ▴, 6 to 8 cm; ⧫, 8 to 10 cm; □, 10 to 12 cm; ○, 12 to 14 cm; ▵, 14 to 16 cm; ◊, 18 to 20 cm; +, Burton Lake; ✻, O'Briens Bay.

FIG. 7.

Phylogenetic tree based on 16S rRNA gene sequences of DGGE fragments from MGP sediments. The band numbers correspond to bands indicated by black bars in Fig. 4. GenBank accession numbers are indicated in parentheses after the sequence name.