Genomic and Metabolic Insights into Denitrification, Sulfur Oxidation, and Multidrug Efflux Pump Mechanisms in the Bacterium Rhodoferax sediminis sp. nov.

Abstract

This genus contains both phototrophs and nonphototrophic members. Here, we present a high-quality complete genome of the strain CHu59-6-5 T , isolated from a freshwater sediment. The circular chromosome (4.39 Mbp) of the strain CHu59-6-5 T has 64.4% G+C content and contains 4240 genes, of which a total of 3918 genes (92.4%) were functionally assigned to the COG (clusters of orthologous groups) database. Functional genes for denitrification (narGHJI, nirK and qnor) were identified on the genomes of the strain CHu59-6-5 T , except for N 2 O reductase (nos) genes for the final step of denitrification. Genes (soxBXAZY) for encoding sulfur oxidation proteins were identified, and the FSD and soxF genes encoding the monomeric flavoproteins which have sulfide dehydrogenase activities were also detected. Lastly, genes for the assembly of two different RND (resistance-nodulation division) type efflux systems and one ABC (ATP-binding cassette) type efflux system were identified in the Rhodoferax sediminis CHu59-6-5 T . Phylogenetic analysis based on 16S rRNA sequences and Average Nucleotide Identities (ANI) support the idea that the strain CHu59-6-5 T has a close relationship to the genus Rhodoferax. A polyphasic study was done to establish the taxonomic status of the strain CHu59-6-5 T . Based on these data, we proposed that the isolate be classified to the genus Rhodoferax as Rhodoferax sediminis sp. nov. with isolate CHu59-6-5 T .

Bolstering fitness via opportunistic CO2fixation: mixotroph dominance in modern groundwater

“…Organisms affiliated with Burkholderiales, related to the key mixotrophic taxa in our groundwater microcosms, were found to have the highest abundance of RuBisCO-encoding transcripts at our groundwater site [14]. For taxa like Polaromonas, Dechloromonas, Hydrogenophaga, and Rhodoferax, the ability for sulfur oxidation has been suggested based on genomic evidence [60][61][62][63].…”

“…Under such conditions, the ability to use inorganic electron donors would be an advantageous part of the survival strategy. For various facultative autotrophic taxa from clusters II to IV, including Polaromonas, Dechloromonas, Hydrogenophaga, and Rhodoferax, the ability for sulfur oxidation has been suggested based on genomic evidence (Kämpfer et al, 2005;Mattes et al, 2008;Salinero et al, 2009;Jin et al, 2020). However, chemolithoautotrophic growth on reduced sulfur compounds has not been observed for these genera in pure culture so far.…”

“…Organisms most closely related to Burkholderiales spp., the key mixotrophic taxa in our groundwater microcosms, gave rise to the geatest number of RuBisCO-encoding transcripts in a previous study at our groundwater site 17 . For taxa like Polaromonas , Dechloromonas , Hydrogenophaga , and Rhodoferax spp., the ability to oxidize sulfur has been posited based solely on genomic evidence 60–63 . Hitherto, chemolithoautotrophic growth on reduced sulfur compounds has not been observed from any of these genera in pure culture.…”

Nitrogen Removal by an Anaerobic Iron-Dependent Ammonium Oxidation (Feammox) Enrichment: Potential for Wastewater Treatment

“…Similarly, Albidiferax ferrireducens, previously recognized as Rhodoferax ferrireducens [38], is classified as a FeRM (iron-reducing microorganism). Therefore, it grows in Fe(III)-rich environments, and reduces it to ferrous iron [39,40]. At the same time, Ferrovum myxofaciens uses only ferrous iron as electron donor, and oxygen as electron acceptor.…”

Complete Genome Sequence of Rhodoferax sp. Strain BAB1, Isolated after Filter Sterilization of Tap Water

“…The genus Rhodoferax represents rod-shaped or curved ( 1 ) Gram-negative bacteria, currently encompassing eight named species ( 1 – 8 ). Whereas characterized Rhodoferax species have been isolated from freshwater, sewage, and sediment ( 1 , 5 , 6 ), we repeatedly isolated strain BAB1 from previously filter-sterilized (0.22-μm pore size) tap water.…”