Indications for a genetic basis for big bacteria and description of the giant cable bacterium Candidatus Electrothrix gigas sp. nov.

Abstract

Bacterial cells can vary greatly in size, from a few hundred nanometers to hundreds of micrometers in diameter. Filamentous cable bacteria also display substantial size differences, with filament diameters ranging from 0.4 to 8 µm. We analyzed the genomes of cable bacterium filaments from 11 coastal environments of which the resulting 23 new genomes represent 10 novel species-level clades of Candidatus Electrothrix and two clades that putatively represent novel genus-level diversity. Fluorescence in situ hybridization with a species-level probe showed that large-sized cable bacteria belong to a novel species with the proposed name Ca . Electrothrix gigas. Comparative genome analysis suggests genes that play a role in the construction or functioning of large cable bacteria cells: the genomes of Ca . Electrothrix gigas encode a novel actin-like protein as well as a species-specific gene cluster encoding four putative pilin proteins and a putative type II secretion platform protein, which are not present in other cable bacteria. The novel actin-like protein was also found in a number of other giant bacteria, suggesting there could be a genetic basis for large cell size. This actin-like protein (denoted big bacteria protein, Bbp) may have a function analogous to other actin proteins in cell structure or intracellular transport. We contend that Bbp may help overcome the challenges of diffusion limitation and/or morphological complexity presented by the large cells of Ca . Electrothrix gigas and other giant bacteria. IMPORTANCE In this study, we substantially expand the known diversity of marine cable bacteria and describe cable bacteria with a large diameter as a novel species with the proposed name Candidatus Electrothrix gigas. In the genomes of this species, we identified a gene that encodes a novel actin-like protein [denoted big bacteria protein (Bbp)]. The bbp gene was also found in a number of other giant bacteria, predominantly affiliated to Desulfobacterota and Gammaproteobacteria, indicating that there may be a genetic basis for large cell size. Thus far, mostly structural adaptations of giant bacteria, vacuoles, and other inclusions or organelles have been observed, which are employed to overcome nutrient diffusion limitation in their environment. In analogy to other actin proteins, Bbp could fulfill a structural role in the cell or potentially facilitate intracellular transport.

A model analysis of centimeter-long electron transport in cable bacteria

“…15 Thicker cable bacteria simply embed more parallel fibers in the cell envelope ( N F ranges from 15 to 75 15 ). Here, we adopt N F = 60 as a reference value, which is a characteristic value for Electrothrix gigas , the larger strain of cable bacteria 29 that was used in our electrical characterization experiments.…”

Closing the genome of unculturable cable bacteria using a combined metagenomic assembly of long and short sequencing reads

“…Each available cable bacteria genome [30,41,75] was evaluated for genome completeness using CheckM v1.2.2 with the preset --lineage_wf [66]. To determine the 'single genes' of Ca.…”

“…Electrothrix genomes have been generated from a single cable bacterium filament using whole-genome amplification and subsequent short-read sequencing (Fig. 3a) [30,75]. However, this approach has resulted in assemblies that consist of many contigs (73 to 489 contigs for 6 draft genomes, as reported in [75].…”

“…Electrothrix previously described, and also larger than available Ca. Electronema genomes [30,41,75] (Fig. S4).…”

“…Cable bacteria can be found globally in freshwater and saltwater sediments [25][26][27], and when active, their electrogenic metabolism exerts a large impact on the geochemistry of the sediments, as it strongly influences the cycling of sulfur, iron and phosphorus [28,29]. Currently, all cable bacteria are classified into two candidate genera: Candidatus Electronema, typically found in freshwater environments, and Candidatus Electrothrix, typically found in saltwater environments [30,31].…”