Relative abundance of 'Candidatus Tenderia electrophaga' is linked to cathodic current in an aerobic biocathode community

Abstract

Biocathode microbial communities are proposed to catalyse a range of useful reactions. Unlike bioanodes, model biocathode organisms have not yet been successfully cultivated in isolation highlighting the need for culture-independent approaches to characterization. Biocathode MCL (Marinobacter, Chromatiaceae, Labrenzia) is a microbial community proposed to couple CO₂ fixation to extracellular electron transfer and O₂ reduction. Previous metagenomic analysis of a single MCL bioelectrochemical system (BES) resulted in resolution of 16 bin genomes. To further resolve bin genomes and compare community composition across replicate MCL BES, we performed shotgun metagenomic and 16S rRNA gene (16S) sequencing at steady-state current. Clustering pooled reads from replicate BES increased the number of resolved bin genomes to 20, over half of which were > 90% complete. Direct comparison of unassembled metagenomic reads and 16S operational taxonomic units (OTUs) predicted higher community diversity than the assembled/clustered metagenome and the predicted relative abundances did not match. However, when 16S OTUs were mapped to bin genomes and genome abundance was scaled by 16S gene copy number, estimated relative abundance was more similar to metagenomic analysis. The relative abundance of the bin genome representing 'Ca. Tenderia electrophaga' was correlated with increasing current, further supporting the hypothesis that this organism is the electroautotroph.

Figure 1

Relative abundance of 20 resolved dominant ray‐metabat case 1b bin genomes to each other classified by AMPHORA2 (i.e. Sphingomonadaceae should be Kordiimonadaceae as noted in the main text). Unresolved bin genomes are assumed to make up < 1% of the Biocathode MCL community in each reactor as bin genomes shown here make up at least 1% relative abundance. Short contigs that were not binned may belong to identified bin genomes but were not clustered do to cut‐off value. Sample IDs are for each individual bioelectrochemical system (BES).

Figure 2

Relative abundance estimated for bin genomes from each replicate bioelectrochemical system (BES) representing (A) Marinobacter spp., (B) Labrenzia sp. and (C) ‘Ca. Tenderia electrophaga’ using read counts associated with OTUs linked to longer 16S sequences or generated by whole‐genome shotgun (WGS) sequencing and resolved by ray‐metabat case 1b (BES key: 1 = 1031813, 2 = 2021213, 3 = 2031813, 5 = 3042313, 6 = 4021213, 7 = 4032113, 8 = 4040813).

Figure 3

Correlation of per cent abundance of (A) Marinobacter spp. (combined bin genomes) and the order Chromatiales (representing ‘Ca. Tenderia electrophaga’) to absolute current, as well as (B) Labrenzia sp. and the order Sphingomonadales (Kordiimonadales) using read counts associated with OTUs linked to longer 16S sequences or generated by whole‐genome shotgun (WGS) sequencing and resolved by ray‐metabat case 1b (BES key: 1 = 1031813, 2 = 2021213, 3 = 2031813, 5 = 3042313, 6 = 4021213, 7 = 4032113, 8 = 4040813).