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

Abstract

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.

Effect of oxygen limitation on the enrichment of bacteria degrading either benzene or toluene and the identification of Malikia spinosa (Comamonadaceae) as prominent aerobic benzene-, toluene-, and ethylbenzene-degrading bacterium: enrichment, isolation and whole-genome analysis

“…Although these strains did not harbour subfamily I.2.C-type C23O gene, this lineage of the genus Pseudomonas seems to be adapted to microaerobic environments. Earlier we have observed the dominance of these bacteria in microaerobic, crude oil/gasoline mixture–degrading enrichment cultures (Benedek et al 2018 ; Révész et al 2020 ), and it was reported that P. extremaustralis preferably degrades alkanes under microaerobic conditions (Tribelli et al 2018 ).…”

“…The sampled biofilm continuously developed on the stainless steel surface of a submersible pump, which was part of a pump-and-treat system operating at the contaminated site. In previous enrichment studies, this continuously emerging biofilm was successfully used to study the biodegradation of petroleum hydrocarbons under microaerobic conditions (Benedek et al 2018 ; Révész et al 2020 ). Members of the class Gammaproteobacteria overwhelmingly dominated the bacterial community of the newly sampled biofilm material (47% of 16S rDNA sequence reads) (Online Resource 1 , Fig.…”

“…The metagenome-assembled genome of this bacterium contained genes encoding the benzylsuccinate synthase, which is the key enzyme of anaerobic toluene degradation and known to be highly oxygen sensitive (Leuthner et al 1998 ). Members of genera Simplicispira and Acidovorax are frequently observed in oxygen-limited, petroleum hydrocarbon–degrading enrichment cultures (Keller et al 2018 ; Révész et al 2020 ); therefore, their role in the degradation can be also assumed.…”

Aerobic and oxygen-limited naphthalene-amended enrichments induced the dominance of Pseudomonas spp. from a groundwater bacterial biofilm

“…Interestingly, under full aerobic conditions, no hydrocarbon degradation occurred (Tribelli et al 2018). Moreover, Révész et al (2019) also found the dominance of P. extremaustralis/P. veronii lineage-related bacteria in diesel fuel/crude oil mixture-amended enrichment cultures.…”

Low-Temperature Biosurfactants from Polar Microbes

“…While both genera are commonly found in hydrocarbon-contaminated environments, hydrocarbon substrates have only been shown to enrich and select for different Psychrobacter phylotypes [68][69][70]. Janthinobacteria, on the other hand, are believed to tolerate petroleum hydrocarbon toxicity rather than using oil components as carbon sources [71], although, indirect measurements (i.e., community structure analysis of contaminated soils based on 16S rRNA genes) hint at their hydrocarbon degrading capabilities [72,73]. Likewise, the petroleum hydrocarbon degradation activity of S. quinivorans, which was most closely related to Serratia sp.…”