Microaerobic conditions caused the overwhelming dominance of Acinetobacter spp. and the marginalization of Rhodococcus spp. in diesel fuel/crude oil mixture-amended enrichment cultures

• Published in: Archives of microbiology 2020-03, Vol.202 (2), p.329-342
• Main Authors: Révész, Fruzsina, Figueroa-Gonzalez, Perla Abigail, Probst, Alexander J., Kriszt, Balázs, Banerjee, Sinchan, Szoboszlay, Sándor, Maróti, Gergely, Táncsics, András
• Format: Article
• Language: English
• Subjects: Abundance; Acinetobacter; Acinetobacter - classification; Acinetobacter - isolation & purification; Acinetobacter - metabolism; Actinobacteria - classification; Actinobacteria - isolation & purification; Actinobacteria - metabolism; Aerobic conditions; Aliphatic hydrocarbons; Alkane monooxygenase; Alkanes; AlkB gene; Alphaproteobacteria; Biochemistry; Biodegradation, Environmental; Biomedical and Life Sciences; Biotechnology; Cell Biology; Crude oil; Cytochrome P-450 CYP4A - genetics; Diesel; Diesel fuels; Ecology; Enrichment; Gammaproteobacteria; Gasoline - microbiology; Gene sequencing; Genomes; Genotype; Genotypes; Hydrocarbon-degrading bacteria; Hydrocarbons; Hydrocarbons - metabolism; Life Sciences; Metagenomics; Microbial activity; Microbial Ecology; Microbiology; Microorganisms; Oil pollution; Original Paper; Proteobacteria - classification; Proteobacteria - isolation & purification; Proteobacteria - metabolism; Pseudomonas; Pseudomonas - classification; Pseudomonas - isolation & purification; Pseudomonas - metabolism; Rhodococcus; Rhodococcus - classification; Rhodococcus - isolation & purification; Rhodococcus - metabolism; Saccharibacteria
• ISSN: 0302-8933; 1432-072X
• DOI: 10.1007/s00203-019-01749-2

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.