Phylogenetic characterization of 16S rRNA gene clones from deep-groundwater microorganisms that pass through 0.2-micrometer-pore-size filters

Abstract

A total of 247 clones of 16S rRNA genes from microorganisms captured by 0.2- and 0.1-microm-pore-size filters from sedimentary and granite rock aquifers were amplified and yielded 37 operational taxonomic units (OTUs). Fifteen OTUs captured by 0.1-microm-pore-size filters were affiliated with the candidate divisions OD1 and OP11, representing novel lineages. On the other hand, OTUs captured by 0.2-microm-pore-size filters were largely affiliated with Betaproteobacteria.

FIG.1.

Neighbor-joining phylogenetic tree based on nearly complete 16S rRNA gene sequences from OTUs in the 0.2- and 0.1-μm-pore-size filter-captured groundwater fractions from sedimentary and granite rock aquifers in the Tono uranium mine. The 16S rRNA gene sequences of the Aquificales Aquifex aeolicus (AJ309733) and Hydrogenobacter hydrogenophilus (Z30242) were used as outgroups but were pruned from the tree. Yellow and light-blue backgrounds indicate the OTUs captured by 0.1- and 0.2-μm-pore-size filters, respectively. Black and red letters indicate the OTUs from sedimentary and granite rock aquifers, respectively. The OTUs written in both black and red are from both sedimentary and granite rock aquifers. Bootstrap values at branching nodes after 1,000 resamplings are represented by filled circles (>75%), open circles (75%>○>50%), and no circles (<50%). GNS, green nonsulfur bacteria.