Genomic and physiological characterization of Novosphingobium terrae sp. nov., an alphaproteobacterium isolated from Cerrado soil containing a megasized chromid

Abstract

A novel bacterial strain, designated GeG2T, was isolated from soils of native Cerrado, a highly biodiverse savanna-like Brazilian biome. 16S rRNA gene sequence analysis of strain GeG2T revealed high sequence identity (100%) to the alphaproteobacterium Novosphingobium rosa, however, comparisons with N. rosa DSM7285T showed several distinctive features, prompting a full characterization of the new strain in terms of growth, morphology, biochemistry and, ultimately, its genome. GeG2T cells were Gram-stain negative bacilli, facultatively anaerobic, motile, positive for catalase and oxidase activities and for starch hydrolysis. Strain GeG2T presented planktonic-sessile dimorphism and cell aggregates surrounded by extracellular matrix and nanometric spherical structures were observed in liquid cultures, suggesting the production of exopolysaccharides (EPS) and outer membrane vesicles (OMVs). Whole genome assembly revealed four circular replicons: a 4.1 Mb chromosome, a 2.7 Mb extrachromosomal megareplicon and two plasmids (212.7 and 68.6 kb). The megareplicon contains few core genes and plasmid-type replication/maintenance systems, consistent with its classification as a chromid. Genome annotation shows a vast repertoire of carbohydrate active enzymes and genes involved in the degradation of aromatic compounds, highlighting the biotechnological potential of the new isolate obtained from Cerrado soils, especially regarding EPS production and biodegradation of recalcitrant compounds. Chemotaxonomic features, including polar lipid and fatty acid profiles, as well as physiological, molecular and whole genome comparisons showed significant differences between strain GeG2T and a N. rosa, clearly indicating that it represents a novel species, for which the name Novosphingobium terrae is proposed. The type strain is GeG2T (=CBMAI 2313T =CBAS 753T). IMPORTANCENovosphingobium is an alphaproteobacterial genus presenting diverse physiological profiles and broad biotechnological applications. However, many aspects regarding the biology of this important bacterial group remain elusive. A novel Novosphingobium strain was isolated from soils of Cerrado, an important Brazilian biome. Despite 100% 16S rRNA gene identity with Novosphingobium rosa, polyphasic characterizations, including physiological, chemotaxonomic, and whole genome- based analyses revealed significant differences between GeG2T and N. rosa DSM7285T, reinforcing resolution limitations in phylogenetic analysis based solely on 16S RNA and highlighting the importance of employing different approaches for the description of bacterial species. Using short and long read sequencing approaches, a high-quality fully resolved genome assembly was generated and one of the largest chromids reported to date was identified. A comprehensive characterization of environmental isolates allows us to better elucidate the diversity and biology of members of this bacterial group with potential biotechnological importance, guiding future bioprospecting efforts and genomic studies.