Genomic insights into a novel species Rhodoferax aquaticus sp. nov., isolated from freshwater

Abstract

A novel non-phototrophic member of the genus Rhodoferax was obtained from freshwater. The purpose of this study was to analyse the genome of a nonphototrophic strain and propose a new species based on its phylogenetic, genomic, physiological and chemotaxonomic characteristics. The results of phylogenetic analysis based on 16S rRNA gene sequences supports that the strain, designated Gr-4T, has a close relationship to the genus Rhodoferax . The observed average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) values between strain Gr-4T and its closest related strains were 72.3–74.6 % and 21.9–22.8 %, respectively. These values were much lower than the species separation thresholds for ANI or dDDH of 95–96 and 70 %, respectively, and in fact fall in the intergeneric range. Strain Gr-4T does not contain RuBisCO-related genes, but does contain GS/GOGAT pathway-related genes enabling nitrate ammonification. A polyphasic study and a genomic-level investigation were done to establish the taxonomic status of strain Gr-4T. Based on the phylogenetic, genomic and physiological differences, it is proposed that the isolate be classified to the genus Rhodoferax as Rhodoferax aquaticus sp. nov. with isolate Gr-4T (=KCTC 32394T=JCM 19166T) as the type strain.

Charakterisierung von mikrobiellen Biofilmen aus Tunnelwässern

“…Die Gruppe "A + H" bezeichnet solche, die in Bezug auf die Energiequelle autotroph sind (Mn, Fe, S, H 2 ), aber als C-Quelle organische Substanz benötigen. Genannt seien hier die Gattungen Sulfuritalea, Rhodoferax, Hydrogenophaga und Leptothrix [13][14][15]. Bei den Heterotrophen sind in allen Proben Vertreter der Familie der Caulobacteraceae vorhanden, das sind Bakterien, die typischerweise in aquatischen Habitaten anzutreffen sind.…”

“…The group "A + H" designates those that are autotrophic in relation to the energy source (Mn, Fe, S, H 2 ) but, as a source of carbon, require organic matter. This includes the genera Sulfuritalea, Rhodoferax, Hydrogenophaga and Leptothrix [13][14][15]. As far as the heterotrophs are concerned, representatives of the family Caulobacteraceae are present in all samples, and these bacteria are typically found in aquatic habitats.…”

Rhodoferax potami sp. nov. and Rhodoferax mekongensis sp. nov., isolated from the Mekong River in Thailand

“…The functional annotation of protein-coding CDS was performed using eggNOG-mapper version 2 with the eggNOG 5.0 database [39]. The genomic DNA sequences and protein annotations of the reference genomes, namely R. bucti KCTC 62564 T (NCBI assembly: GCA_005876985.1) [7] and R. aquaticus KCTC 32394 T (NCBI assembly: GCA_006974105.1) [11], were downloaded from the NCBI Assembly database.…”

“…At the time of writing, eight species of the genus Rhodoferax with validly published names (including synonyms) have been identified according to the List of Prokaryotic names with Standing in Nomenclature (LSPN) [8]. Among these species, seven type strains of species of the genus Rhodoferax have been identified in freshwater and sediment environments [7,[9][10][11][12][13][14], whereas one type strain was isolated from sludge during wastewater treatment [6]. Some species of the genus Rhodoferax have shown potential for biotechnological applications.…”

Rhodoferax lithotrophicus sp. nov., a neutrophilic iron-oxidizing and -reducing bacterium isolated from iron-rich freshwater sediments

“…The genus Rhodoferax belonging to the family Comamonadaceae was proposed in 1991 [1]. It contains the type species Rhodoferax fermentans [1] and nine validly published species, i.e., Rhodoferax antarcticus [2], Rhodoferax aquaticus [3], Rhodoferax bucti [4], Rhodoferax ferrireducens [5], Rhodoferax lacus [6], Rhodoferax saidenbachensis [7], Rhodoferax sediminis [8], Rhodoferax mekongensis and Rhodoferax potami [9]. In addition, two species names, ‘ Rhodoferax koreense’ [10] and ‘ Rhodoferax jenense ,’ [11] have been reported, but not yet validly published in accordance with the International Code of Nomenclature of Prokaryotes.…”