In this study, we conducted a genome-wide comparative analysis of a former Rhodobacter sphaeroides strain EBL0706, which is now recorded as Luteovulum sphaeroides EBL0706. The genome of EBL0706 was compared with that of Luteovulum azotoformans ATCC 17025, Luteovulum azotoformans KA25, and Luteovulum sphaeroides 2.4.1. The average nucleotide identity (ANI), tetra nucleotide signatures (Tetra), digital DNA–DNA hybridization (dDDH) values, comparative genome, and phylogenetic analysis proposed that EBL0706 is a strain of Luteovulum azotoformans. Functional annotations identified a total of 4034 protein-coding genes in the genome of EBL0706, including a complete photosynthetic gene cluster. This study provides genomic molecular verification for the strain EBL0706 to be reclassified to Luteovulum azotoformans.

Farmland-oilfield mixed areas are fragile ecosystems that require dynamic remediation to counteract the undesirable impact of energy development. Practicable assessment methods are pivotal to a fast and accurate evaluation of the in situ bioremediation process. Petroleum pollutants impose component-dependent effects on autochthonous microbiota before and after remediation. Here, the predicted functional response of soil microbiomes to petroleum pollutants was analyzed in a historically polluted farmland-oilfield mixed area from the perspective of developing a set of feasible biomarkers for immediate post-bioremediation evaluation. An array of microbial, genetic, systematic, and phenotypic biomarkers was proposed. Our results showed that the biomarkers could proxy the stage of the bioremediation multidimensionally. We argue that functional diversity should be considered together with microbial community dynamic to evaluate the restoration status of the microbial communities in petroleum-contaminated farmland-oilfield mixed environments.

Petroleum contamination poses a serious threat to human health and ecosystems worldwide, and microbially driven natural attenuation is an effective approach for accelerating hydrocarbon removal. Species of the genus Rhodococcus are recognized for their ability to degrade long chain petroleum hydrocarbons. However, their physiological traits and degradation mechanisms under alkaline conditions remain insufficiently understood. In this study, soil samples were collected from the Dagang oilfield in Tianjin, China, and Rhodococcus sp. A17 was isolated as an active indigenous strain for genomic and physiological characterization under high pH petroleum degradation conditions. The results showed that strain A17 grew optimally at 30 °C, pH 9.0, and 2% salinity. Petroleum hydrocarbon degradation reached 67.8% within 72 h, with a degradation half life of 34.2 h. Genome sequencing identified 18 oxygenase related genes involved in alkane degradation, including alkB, cytochrome P450 monooxygenases, and the long chain alkane monooxygenase ladA, together with four antibiotic resistance genes. Metabolite analysis suggested that alkane degradation might proceed via terminal and subterminal oxidation pathways. Overall, these findings indicate that Rhodococcus sp. A17 exhibits multiple adaptive traits that support its potential application in the bioremediation of petroleum contaminated alkaline environments.