Quantification of Cable Bacteria in Marine Sediments via qPCR

Abstract

Cable bacteria (Deltaproteobacteria, Desulfobulbaceae) are long filamentous sulfuroxidizing bacteria that generate long-distance electric currents running through the bacterial filaments. This way, they couple the oxidation of sulfide in deeper sediment layers to the reduction of oxygen or nitrate near the sediment-water interface. Cable bacteria are found in a wide range of aquatic sediments, but an accurate procedure to assess their abundance is lacking. We developed a qPCR approach that quantifies cable bacteria in relation to other bacteria within the family Desulfobulbaceae. Primer sets targeting cable bacteria, Desulfobulbaceae and the total bacterial community were applied in qPCR with DNA extracted from marine sediment incubations. Amplicon sequencing of the 16S rRNA gene V4 region confirmed that cable bacteria were accurately enumerated by qPCR, and suggested novel diversity of cable bacteria. The conjoint quantification of current densities and cell densities revealed that individual filaments carry a mean current of ∼110 pA and have a cell specific oxygen consumption rate of 69 fmol O 2 cell −1 day −1. Overall, the qPCR method enables a better quantitative assessment of cable bacteria abundance, providing new metabolic insights at filament and cell level, and improving our understanding of the microbial ecology of electrogenic sediments.

Using Oxidative Electrodes to Enrich Novel Members in the Desulfobulbaceae Family from Intertidal Sediments

“…In lab-cultured subtidal sediments collected from Aarhus Bay, Denmark, Ca. Electrothrix have comprised up to 8% of the total bacteria and up to 64% of the Desulfobulbaceae population [49]. In our samples, the relative abundance of Ca.…”

“…The dominant presence of the C1 taxa of the Desulfobulbaceae on the RA anodes also suggests that the above-sediment anode configuration of the RA reactor may favor the selection of microorganisms that can disperse through water and survive on the surface of an oxidative electrode (Figure 4). Several members in the Desulfobulbaceae family including CB can perform chemotaxis [6,49,50]. Other causes of differences in observed diversity indexes and microbial community compositions between RA and RB were likely the geochemical environment around the anodes and access to different forms of organic matter.…”

Fast-growing Arctic Fe–Mn deposits from the Kara Sea as the refuges for cosmopolitan marine microorganisms

“…The oxygenation of the bottom water in this deep part of the St. Anna Trough is driven by the cooling of oxygen-rich surface waters near the Novaya Zemlya archipelago and their further downwelling across the slope 58 . During the temporal decrease of oxygenation at this site, reduced sulfur species can be produced by sulfate-reducing bacteria of the Desulfobulbaceae , Desulfosarcinaceae and Desulfocapsaceae families, some of which were reported to establish single-species filamentous conductive structures (‘cables’), which couple the oxidation of sulfide in deeper sediment layers to the reduction of oxygen or nitrate near the sediment–water interface 70 .…”

Biogeochemical impacts of fish farming on coastal sediments: Insights into the functional role of cable bacteria

“…Indeed, sediments from LPP sites at 50 m distance, and to a lesser degree from SPP, showed a diversity and relative abundance of cable bacteria similar to that found in the lab incubations ( Figure 5D and Supplementary Table 4 ). In sediments with a clear e-SOx signature, cable bacteria can account for 0.6% up to 7% of the total 16S rRNA gene sequences, and as low as 0.2% in oxic layers or in suboxic sediment when the e-SOx signal is weakening ( Klier et al, 2018 ; Otte et al, 2018 ; Geelhoed et al, 2020 ; Dam et al, 2021 ; Liau et al, 2022 ). A recent study further shows a 10-fold higher percentage of cable bacteria sequences, when comparing DNA-based to RNA-based 16S rRNA genes in the same sediment sample ( Liau et al, 2022 ).…”

“…Total genomic DNA extraction was performed following the protocol of Zhou et al (1996) as amended and described in Geelhoed et al (2020). For field sediments, three depths were selected for DNA extraction: 0-0.5 cm (layer 1), 0.5-1 cm 10.3389/fmicb.2022.1034401 (layer 2), and 3.0-5.0 cm (layer 6).…”