Evaluating the aerobic xylene-degrading potential of the intrinsic microbial community of a legacy BTEX-contaminated aquifer by enrichment culturing coupled with multi-omics analysis: uncovering the role of Hydrogenophaga strains in xylene degradation

Abstract

To develop effective bioremediation strategies, it is always important to explore autochthonous microbial community diversity using substrate-specific enrichment. The primary objective of this present study was to reveal the diversity of aerobic xylene-degrading bacteria at a legacy BTEX-contaminated site where xylene is the predominant contaminant, as well as to identify potential indigenous strains that could effectively degrade xylenes, in order to better understand the underlying facts about xylene degradation using a multi-omics approach. Henceforward, parallel aerobic microcosms were set up using different xylene isomers as the sole carbon source to investigate evolved bacterial communities using both culture-dependent and independent methods. Research outcome showed that the autochthonous community of this legacy BTEX-contaminated site has the capability to remove all of the xylene isomers from the environment aerobically employing different bacterial groups for different xylene isomers. Interestingly, polyphasic analysis of the enrichments disclose that the community composition of the o-xylene-degrading enrichment community was utterly distinct from that of the m- and p-xylene-degrading enrichments. Although in each of the enrichments Pseudomonas and Acidovorax were the dominant genera, in the case of o-xylene-degrading enrichment Rhodococcus was the main player. Among the isolates, two Hydogenophaga strains, belonging to the same genomic species, were obtained from p-xylene-degrading enrichment, substantially able to degrade aromatic hydrocarbons including xylene isomers aerobically. Comparative whole-genome analysis of the strains revealed different genomic adaptations to aromatic hydrocarbon degradation, providing an explanation on their different xylene isomer-degrading abilities.

Microaerobic enrichment of benzene-degrading bacteria and description of Ideonella benzenivorans sp. nov., capable of degrading benzene, toluene and ethylbenzene under microaerobic conditions

“…According to previous studies, members of the genera Acidovorax and Pseudomonas occurred in benzene-, toluene-, and xylene-degrading enrichments as well (Révész et al 2020a ; Banerjee et al 2022 ). The genus Sediminibacterium and Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium have been also found to be present in petroleum-contaminated environments (Lindstrom et al 2003 ; Yessica et al 2013 ; Poi et al 2018 ; Banerjee et al 2022 ; Chen et al 2022 ). Members of the genus Xanthobacter are often used for biodegradation purposes, as they can play role in the degradation of chlorinated hydrocarbons, alkenes, cyclohexane and phenol as well (van Ginkel and de Bont 1986 ; Janssen et al 1989 ;; Trower et al 1985 ; Nagamani et al 2009 ).…”

“…Acidovorax genus related bacteria are frequently observed in petroleum hydrocarbon-contaminated environments (Singleton et al 2018;Révész et al 2020a,b), e.g., bacteria most closely related to Acidovorax defluvii and A. delafieldii were detected in BTEX-contaminated environments (Alfreider and Vogt 2007;Révész et al 2020a, b). According to previous studies, members of the genera Acidovorax and Pseudomonas occurred in benzene-, toluene-, and xylene-degrading enrichments as well (Révész et al 2020a;Banerjee et al 2022). The genus Sediminibacterium and Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium have been also found to be present in petroleum-contaminated environments (Lindstrom et al 2003;Yessica et al 2013;Poi et al 2018;Banerjee et al 2022;Chen et al 2022).…”

“…Paired-end fragment reads were generated on an Illumina MiSeq sequencer using MiSeq Reagent Kit v3 (600-cycle) by SeqOmics Biotechnology Ltd. (Mórahalom, Hungary). The raw sequencing data were analysed according to Banerjee et al ( 2022 ) to cluster sequences into OTUs and calculate the diversity of the samples using rarefaction curves. Read numbers were between 40 000 and 50 000 during the data processing performed by MiSeq SOP of mothur v1.41.1 (Schloss et al 2009 ; Kozich et al 2013 ).…”

Combined Omics Approach Reveals Key Differences between Aerobic and Microaerobic Xylene-Degrading Enrichment Bacterial Communities: Rhodoferax─A Hitherto Unknown Player Emerges from the Microbial Dark Matter

“…Genomic DNA from bacterial strains was isolated using the UltraClean Microbial DNA Kit (Qiagen) following the manufacturers' instructions. Subsequently, the 16S rRNA gene was amplified and sequenced using the method described by Banerjee et al 3 After Sanger sequencing, the nearly complete 16S rRNA gene sequences were analyzed using the EzTaxon server (www. ezbiocloud.…”

Isolation of Pseudomonas aromaticivorans sp. nov from a hydrocarbon-contaminated groundwater capable of degrading benzene-, toluene-, m- and p-xylene under microaerobic conditions

“…During investigation of microaerobic xylene-degrading bacterial community diversity of groundwater of a decade-old petroleum hydrocarbon-contaminated site at Siklos, Hungary ( Táncsics et al, 2013 ), by using selective enrichment method, strain MAP12 T was isolated and proved to be a yet undescribed lineage of the genus Pseudomonas . The Siklos site is an extensively studied, legacy hydrocarbon contaminated site of Hungary, which is predominantly contaminated by xylene ( Banerjee et al, 2022 ). The aim of this present study was to clarify the taxonomic status of this presumably novel member of the genus Pseudomonas using a polyphasic taxonomic approach, including whole genome sequencing, physiological, biochemical, and chemotaxonomic analyses.…”