Members of the genus Pseudomonas are known to be widespread in hydrocarbon contaminated environments because of their remarkable ability to degrade a variety of petroleum hydrocarbons, including BTEX (benzene, toluene, ethylbenzene and xylene) compounds. During an enrichment investigation which aimed to study microaerobic xylene degradation in a legacy petroleum hydrocarbon-contaminated groundwater, a novel Gram-stain-negative, aerobic, motile and rod-shaped bacterial strain, designated as MAP12^T was isolated. It was capable of degrading benzene, toluene, meta- and para- xylene effectively under both aerobic and microaerobic conditions. The 16S rRNA gene sequence analysis revealed that strain MAP12^T belongs to the genus Pseudomonas, with the highest 16S rRNA gene similarity to Pseudomonas linyingensis LYBRD3-7^T (98.42%), followed by Pseudomonas sagittaria JCM 18195^T (98.29%) and Pseudomonas alcaliphila JCM 10630^T (98.08%). Phylogenomic tree constructed using a concatenated alignment of 92 core genes indicated that strain MAP12^T is distinct from any known Pseudomonas species. The draft genome sequence of strain MAP12^T is 4.36 Mb long, and the G+C content of MAP12^T genome is 65.8%. Orthologous average nucleotide identity (OrthoANI) and digital DNA–DNA hybridization (dDDH) analyses confirmed that strain MAP12^T is distinctly separated from its closest neighbors (OrthoANI < 89 %; dDDH < 36%). Though several members of the genus Pseudomonas are well known for their aerobic BTEX degradation capability, this is the first report of a novel Pseudomonas species capable of degrading xylene under microaerobic conditions. By applying genome-resolved metagenomics, we were able to partially reconstruct the genome of strain MAP12^T from metagenomics sequence data and showed that strain MAP12^T was an abundant member of the xylene-degrading bacterial community under microaerobic conditions. Strain MAP12^T contains ubiquinone 9 (Q9) as the major respiratory quinone and diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine as major polar lipids. The major cellular fatty acids of strain MAP12^T are summed feature 3 (C_16:1ω6c and/or C_16:1ω7c), C_16:0 and summed feature 8 (C_18:1ω6c and/or C_18:1ω7c). The results of this polyphasic study support that strain MAP12^T represents a novel species of the genus Pseudomonas, hence the name of Pseudomonas aromaticivorans sp. nov. is proposed for this strain considering its aromatic hydrocarbon degradation capability. The type strain is MAP12^T (=LMG 32466, =NCAIM B.02668).

The aim of the present study was to reveal how different microbial communities evolve in diesel fuel/crude oil-contaminated environments under aerobic and microaerobic conditions. To investigate this question, aerobic and microaerobic bacterial enrichments amended with a diesel fuel/crude oil mixture were established and analysed. The representative aerobic enrichment community was dominated by Gammaproteobacteria (64.5%) with high an abundance of Betaproteobacteriales (36.5%), followed by Alphaproteobacteria (8.7%), Actinobacteria (5.6%), and Candidatus Saccharibacteria (4.5%). The most abundant alkane monooxygenase (alkB) genotypes in this enrichment could be linked to members of the genus Rhodococcus and to a novel Gammaproteobacterium, for which we generated a high-quality draft genome using genome-resolved metagenomics of the enrichment culture. Contrarily, in the microaerobic enrichment, Gammaproteobacteria (99%) overwhelmingly dominated the microbial community with a high abundance of the genera Acinetobacter (66.3%), Pseudomonas (11%) and Acidovorax (11%). Under microaerobic conditions, the vast majority of alkB gene sequences could be linked to Pseudomonas veronii. Consequently, results shed light on the fact that the excellent aliphatic hydrocarbon degrading Rhodococcus species favour clear aerobic conditions, while oxygen-limited conditions can facilitate the high abundance of Acinetobacter species in aliphatic hydrocarbon-contaminated subsurface environments.

A floc-forming, Gram-stain-negative, petroleum hydrocarbon-degrading bacterial strain, designated Buc^T, was isolated from a petroleum hydrocarbon-contaminated site in Hungary. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain Buc^T formed a distinct phyletic lineage within the genus Zoogloea . Its closest relative was found to be Zoogloea caeni EMB43^T (97.2 % 16S rRNA gene sequence similarity) followed by Zoogloea oryzae A-7^T (95.9 %), Zoogloea ramigera ATCC 19544^T (95.5 %) and Zoogloea resiniphila DhA-35^T (95.4 %). The level of DNA–DNA relatedness between strain Buc^T and Z. caeni EMB43^T was 31.6 %. Cells of strain Buc^T are facultatively aerobic, rod-shaped, and motile by means of a polar flagellum. The strain grew at temperatures of 5–35 °C (optimum 25–28 °C), and at pH 6.0–9.0 (optimum 6.5–7.5). The predominant fatty acids were C_16 : 0, C_10 : 0 3-OH, C_12 : 0 and summed feature 3 (C_16 : 1ω7c and/or iso-C_15 : 0 2-OH). The major respiratory quinone was ubiquinone-8 (Q-8) and the predominant polar lipid was phosphatidylethanolamine. The genomic DNA G+C content was 63.2 mol%. On the basis of the chemotaxonomic, molecular and phenotypic data, isolate Buc^T is considered to represent a novel species of the genus Zoogloea , for which the name Zoogloea oleivorans sp. nov. is proposed. The type strain is Buc^T ( = DSM 28387^T = NCAIM B 02570^T).

Organisms of the candidate phylum Saccharibacteria have frequently been detected as active members of hydrocarbon degrading communities, yet their actual role in hydrocarbon degradation remained unclear. Here, we analyzed three enrichment cultures of hydrocarbon-amended groundwater samples using genome-resolved metagenomics to unravel the metabolic potential of indigenous Saccharibacteria. Community profiling based on ribosomal proteins revealed high variation in the enrichment cultures suggesting little reproducibility although identical cultivation conditions were applied. Only 17.5 and 12.5% of the community members were shared between the three enrichment cultures based on ribosomal protein clustering and read mapping of reconstructed genomes, respectively. In one enrichment, two Saccharibacteria strains dominated the community with 16.6% in relative abundance and we were able to recover near-complete genomes for each of them. A detailed analysis of their limited metabolism revealed the capacity for peptide degradation, lactate fermentation from various hexoses, and suggests a scavenging lifestyle with external retrieval of molecular building blocks. In contrast to previous studies suggesting that Saccharibacteria are directly involved in hydrocarbon degradation, our analyses provide evidence that these organisms can be highly abundant scavengers acting rather as organic carbon sinks than hydrocarbon degraders in these communities.