Single-cell genomics reveals metabolic strategies for microbial growth and survival in an oligotrophic aquifer

Abstract

Bacteria from the genus Pedobacter are a major component of microbial assemblages at Hanford Site (a largely decommissioned nuclear production complex) in eastern Washington state, USA, and have been shown to change significantly in abundance in response to the subsurface intrusion of Columbia River water. Here we employed single-cell genomics techniques to shed light on the physiological niche of these micro-organisms. Analysis of four Pedobacter single amplified genomes (SAGs) from Hanford Site sediments revealed a chemoheterotrophic lifestyle, with the potential to exist under both aerobic and microaerophilic conditions via expression of both aa3 -type and cbb3 -type cytochrome c oxidases. These SAGs encoded a wide range of both intra- and extracellular carbohydrate-active enzymes, potentially enabling the degradation of recalcitrant substrates such as xylan and chitin, and the utilization of more labile sugars such as mannose and fucose. Coupled to these enzymes, a diversity of transporters and sugar-binding molecules were involved in the uptake of carbon from the extracellular local environment. The SAGs were enriched in TonB-dependent receptors, which play a key role in uptake of substrates resulting from degradation of recalcitrant carbon. Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR)-Cas mechanisms for resisting viral infections were identified in all SAGs. These data demonstrate the potential mechanisms utilized for persistence by heterotrophic micro-organisms in a carbon-limited aquifer, and hint at potential linkages between observed Pedobacter abundance shifts within the 300 Area (in the south-eastern corner of the site) subsurface and biogeochemical shifts associated with Columbia River water intrusion.

Microbial mineral colonization across a subsurface redox transition zone

“…A recent single-cell genomic study of Pedobacter sp. present in 300 Area groundwater demonstrated the presence of a wide range of both intra and extracellular carbohydrate-active enzymes that may enable aerobic degradation of polymeric substrates as well as utilization of more labile sugars such as mannose and fucose ( Wilkins et al, 2014 ). Although only a few OTUs related to Pedobacter were present in our libraries, it seems reasonable to assume that the various heterotrophic taxa that colonized the minerals possessed analogous metabolic capabilities.…”

SAR202 Genomes from the Dark Ocean Predict Pathways for the Oxidation of Recalcitrant Dissolved Organic Matter

“…A full description of sorting, amplification, sequencing, assembly, and annotation is included in Text S1 in the supplemental material. Single-cell sorting, whole-genome amplification, PCR-based analyses, quality control, genome assemblies, and initial genome annotations were performed at the Bigelow Laboratory Single Cell Genomics Center ( http://scgc.bigelow.org ) ( 94 , 95 ). A total of five single-amplified genomes (SAGs) belonging to the SAR202 cluster were chosen for whole-genome sequencing and assembly based on multiple displacement amplification (MDA) and quantitative PCR (qPCR) kinetics, phylogenetic affiliation of small subunit rRNA genes, geographic location, and water depth, giving priority to SAGs that were closely related to the SAR202/SAR307 group III SAR202 clones from Giovannoni et al ( 10 , 12 ).…”

Comparative Single-Cell Genomics of Chloroflexi from the Okinawa Trough Deep-Subsurface Biosphere

“…Assembly was done using SPAdes v.3.0.0 ( 30 ). All contigs were compared to ensure no cross-contamination among SAGs and the NCBI nt database, which was followed by tetramer principal-component analysis as previously described ( 31 – 33 ). These analyses revealed no contamination.…”