Diverse uncultivated ultra-small bacterial cells in groundwater

Abstract

Bacteria from phyla lacking cultivated representatives are widespread in natural systems and some have very small genomes. Here we test the hypothesis that these cells are small and thus might be enriched by filtration for coupled genomic and ultrastructural characterization. Metagenomic analysis of groundwater that passed through a B0.2-mm filter reveals a wide diversity of bacteria from the WWE3, OP11 and OD1 candidate phyla. Cryogenic transmission electron microscopy demonstrates that, despite morphological variation, cells consistently have small cell size (0.009 ± 0.002 mm 3 ). Ultrastructural features potentially related to cell and genome size minimization include tightly packed spirals inferred to be DNA, few densely packed ribosomes and a variety of pili-like structures that might enable inter-organism interactions that compensate for biosynthetic capacities inferred to be missing from genomic data. The results suggest that extremely small cell size is associated with these relatively common, yet little known organisms.

Aquifer environment selects for microbial species cohorts in sediment and groundwater

“…Organisms at high abundance in groundwater samples from the CSP and GW2011 sites cluster by filter pore size, and hence, cell size (purple nodes, Figure 2). The small-celled candidate phyla organisms enriched on the 0.1 mM filters have restricted metabolisms, lacking many core metabolic and biosynthetic pathways (Wrighton et al, 2012;Luef et al, 2015). The members of these candidate phyla radiations are predicted to rely on their surrounding microbial community for nutrients, cofactors and other compounds, forming syntrophic or even obligate symbiotic relationships (Kantor et al, 2013).…”

“…(B) AAC site: sediment incubated in a groundwater well prior to an acetate amendment experiment (Kantor et al, 2013;Handley et al, 2014). (C) GW2011 site: groundwater filtrate ('A') obtained prior to an acetate amendment experiment (Luef et al, 2015).…”

New CRISPR–Cas systems from uncultivated microbes

“…1, Extended Data Table 1). These bacteria typically have small cell sizes, very small genomes and a limited biosynthetic capacity 6,30-32 , indicating they are most likely symbionts 6,[30][31][32][33] . The ~1,200 aa Cas protein, which we named CasY, appears to be part of a minimal CRISPR-Cas system that includes Cas1 and a CRISPR array (Fig.…”

Microbiology: lessons from a first attempt at Lake Ellsworth

“…In future, the issue of drill water filtration needs to be looked at carefully, with additional backup and potentially more rigorous pre-filters. In any case, a potentially serious issue with sub 0.2 µm cell filtrate has recently emerged after Luef et al [58] recently suggested that small cells of less than 0.2 µm might be enriched by filtration. …”