Phyllobacterium calauticae sp. nov. isolated from a microaerophilic veil transversed by cable bacteria in freshwater sediment

Abstract

Microaerophilic veils of swimming microorganisms form at oxic-anoxic interfaces, most commonly described in sediments where sulfide diffusing out from below meets oxygen diffusing in from the water phase. However, distinctive microaerophilic veils form even when there is a gap between the sulfide and O2 fronts, i.e., a suboxic zone, and suggest that the organisms inhabiting these veils can use electron donors other than sulfide. Suboxic zones are found for example in sediment where cable bacteria spatially separate sulfide and O2 by up to several centimetres. Here we describe the extraction of microorganisms from a microaerophilic veil that formed in cable-bacteria-enriched freshwater sediment using a glass capillary, and the subsequent isolation of a motile, microaerophilic, organoheterotrophic bacterium, strain R2-JL T , unable to oxidize sulfide. Based on phenotypic, phylogenetic, and genomic comparison, we propose strain R2-JL T as a novel Phyllobacterium species, P. calauticae sp. nov.. The type strain is R2-JL T (=LMG 32286 T =DSM 112555 T ). This novel isolate confirms that a wider variety of electron donors, including organic compounds, can fuel the activity of microorganisms in microaerophilic veils.

Genomic Insights into the Symbiotic and Plant Growth-Promoting Traits of “Candidatus Phyllobacterium onerii” sp. nov. Isolated from Endemic Astragalus flavescens

“…A general screening was carried out for genes essential for promoting plant growth under different stresses. Several genes related to iron uptake (17), nitrogen metabolism (8), virulence, disease and defence (32), membrane transport (54), stress response (50), and sulfur metabolism (18) were found in strain IY22 (Table S5). The variety of habitats indicates that Phyllobacterium has acquired an impressive aptitude for adapting to its surroundings.…”

Cable bacteria with electric connection to oxygen attract flocks of diverse bacteria

“…Genome sequencing and analysis of Acidovorax facilis DNA was extracted from Acidovorax facilis DSM 649 with the DNeasy PowerLyzer PowerSoil Kit (Qiagen), an Illumina library was prepared with the Nextera XT kit (Illumina), and the whole genome was sequenced on an Illumina MiSeq (see Lustermans et al 46 for details). Sequence quality was assessed using FastQC 36 before trimming with Trimmomatic 37 and assembly with SPAdes 47 .…”