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

Abstract

The primary aims of this present study were to evaluate the effect of oxygen limitation on the bacterial community structure of enrichment cultures degrading either benzene or toluene and to clarify the role of Malikia-related bacteria in the aerobic degradation of BTEX compounds. Accordingly, parallel aerobic and microaerobic enrichment cultures were set up and the bacterial communities were investigated through cultivation and 16S rDNA Illumina amplicon sequencing. In the aerobic benzene-degrading enrichment cultures, the overwhelming dominance of Malikia spinosa was observed and it was abundant in the aerobic toluene-degrading enrichment cultures as well. Successful isolation of a Malikia spinosa strain shed light on the fact that this bacterium harbours a catechol 2,3-dioxygenase (C23O) gene encoding a subfamily I.2.C-type extradiol dioxygenase and it is able to degrade benzene, toluene and ethylbenzene under clear aerobic conditions. While quick degradation of the aromatic substrates was observable in the case of the aerobic enrichments, no significant benzene degradation, and the slow degradation of toluene was observed in the microaerobic enrichments. Despite harbouring a subfamily I.2.C-type C23O gene, Malikia spinosa was not found in the microaerobic enrichments; instead, members of the Pseudomonas veronii/extremaustralis lineage dominated these communities. Whole-genome analysis of M. spinosa strain AB6 revealed that the C23O gene was part of a phenol-degrading gene cluster, which was acquired by the strain through a horizontal gene transfer event. Results of the present study revealed that bacteria, which encode subfamily I.2.C-type extradiol dioxygenase enzyme, will not be automatically able to degrade monoaromatic hydrocarbons under microaerobic conditions.

Hydrogenophaga aromaticivorans sp. nov., isolated from a para-xylene-degrading enrichment culture, capable of degrading benzene, meta- and para-xylene

“…Regarding metabolic potentials of strain D2P1 T it was found that it had a phenol-degradation gene cluster in its genome encoding for a multicomponent phenol-hydroxylase system and for a complete meta-cleavage pathway (data not shown). This cluster was most probably responsible for the benzene-degrading ability of strain D2P1 T , similarly as it was reported in the case of other members of the family Comamonadaceae [14]. Regarding the p-and m-xylene-degrading ability of strain D2P1 T , a large gene cluster (~28 kbp) was found encoding for all of the genes (e.g.…”

“…The Siklós site is one of the best-characterized petroleum hydrocarbon contaminated environment in Hungary (45° 51′ 25.8″ N 18° 17′ 32.3″ E) [13], contaminated mainly with xylenes. To isolate strain D2P1 T , a fully aerobic (~7–8 mg l −1 dissolved O 2 ) enrichment was set up in 100 ml crimp-top serum bottles, which contained 45 ml of a mineral salt medium supplemented with vitamins (MSV medium) as described earlier [14], 5 ml groundwater sample and 1 mM para -xylene as sole source of carbon and energy. After consecutive seven transfers, 1 ml enrichment culture was serially diluted with 0.85 % (w/v) sterile saline solution.…”

“…BTEX compounds (benzene, toluene, ethylbenzene, o -, m - and p -xylenes) degradation by D2P1 T under aerobic condition was also investigated, considering that strain D2P1 T was isolated from a BTEX-contaminated environment. The experiment was performed in triplicates of 100 ml crimp-top serum bottles with 50 ml of MSV medium [14] containing an individual BTEX compound at a concentration of 5 mg l −1 . Serum bottles were inoculated with 100 µl suspensions (OD 600 0.5) of D2P1 T cells and incubated in a rotary shaker at 25 °C and 150 r.p.m.…”

Saccharibacteria as Organic Carbon Sinks in Hydrocarbon-Fueled Communities

“…Oxic enrichment cultures were set up in triplicates, named AER1, AER2, and AER3, using 45 mL of freshwater media dispensed in 100 mL crimp-sealed serum bottles ( Révész et al, 2020a ). Biofilm samples were collected from a gasoline contaminated groundwater well ( Benedek et al, 2016 ), of which 1 g (wet weight) was mixed with 99 mL of physiological saline solution.…”

Table_1.xlsx

“…Oxic enrichment cultures were set up in triplicates, named AER1, AER2, and AER3, using 45 mL of freshwater media dispensed in 100 mL crimp-sealed serum bottles (Révész et al, 2020a). Biofilm samples were collected from a gasoline contaminated groundwater well (Benedek et al, 2016), of which 1 g (wet weight) was mixed with 99 mL of physiological saline solution.…”