Vertical stratification of subsurface microbial community composition across geological formations at the Hanford Site

Abstract

Microbial diversity in subsurface sediments at the Hanford Site 300 Area near Richland, Washington state (USA) was investigated by analysing 21 samples recovered from depths of 9-52 m. Approximately 8000 near full-length 16S rRNA gene sequences were analysed across geological strata that include a natural redox transition zone. These strata included the oxic coarse-grained Hanford formation, fine-grained oxic and anoxic Ringold Formation sediments, and the weathered basalt group. We detected 1233 and 120 unique bacterial and archaeal OTUs (operational taxonomic units at the 97% identity level) respectively. Microbial community structure and richness varied substantially across the different geological strata. Bacterial OTU richness (Chao1 estimator) was highest (> 700) in the upper Hanford formation, and declined to about 120 at the bottom of the Hanford formation. Just above the Ringold oxic-anoxic interface, richness was about 325 and declined to less than 50 in the deeper reduced zones. The deeper Ringold strata were characterized by a preponderance (c. 90%) of Proteobacteria. The bacterial community in the oxic sediments contained not only members of nine well-recognized phyla but also an unusually high proportion of three candidate divisions (GAL15, NC10 and SPAM). Additionally, 13 novel phylogenetic orders were identified within the Deltaproteobacteria, a clade rich in microbes that carry out redox transformations of metals that are important contaminants on the Hanford Site.

Comparison of bacterial and archaeal communities from different habitats of the hypogenic Molnár János Cave of the Buda Thermal Karst System (Hungary)

“…The sequence analysis of the representative molecular clones (selected by ARDRA grouping) resulted in the closest matches (with 87% to 99% sequence similarities) mainly to uncultured clone sequences from different environmental sources such as caves, thermal springs, soils, and sediments (Hansel et al, 2008;Lin et al, 2012;Ivanova et al, 2013).…”

Genome of Methanoregula boonei 6A8 reveals adaptations to oligotrophic peatland environments

“…For example, microbial diversity was shown to increase along a gradient from pH 4.2 in an ombrotrophic bog to 5.1 in a mesotrophic fen in Finland (Juottonen et al, 2005). Similarly, a fen in Minnesota was found to have higher diversity than that of a nearby bog (Lin et al, 2012). The genome of M. boonei harbours evidence of adaptation to a proton-rich, sodium-poor and potassium-poor environment, which may, in part, explain the cosmopolitan success of this and related organisms in acidic peat bogs.…”

Distribution of Microbial Biomass and Potential for Anaerobic Respiration in Hanford Site 300 Area Subsurface Sediment

“…To minimize the effects of inhibitors in assays, environmental DNA was diluted to 5 to 10% of the original concentrations, and duplicate wells each containing 2.5 l of diluted DNA were run for each sample. The results are reported as the relative abundance of gene copies, normalized to the total bacterial and archaeal 16S rRNA gene copy numbers as reported in Lin et al (28).…”