Paenarthrobacter sp. GOM3 Is a Novel Marine Species With Monoaromatic Degradation Relevance

Abstract

Paenarthrobacter sp. GOM3, which is a strain that represents a new species-specific context within the genus Paenarthrobacter, is clearly a branched member independent of any group described thus far. This strain was recovered from marine sediments in the Gulf of Mexico, and despite being isolated from a consortium capable of growing with phenanthrene as a sole carbon source, this strain could not grow successfully in the presence of this substrate alone. We hypothesized that the GOM3 strain could participate in the assimilation of intermediate metabolites for the degradation of aromatic compounds. To date, there are no experimental reports of Paenarthrobacter species that degrade polycyclic aromatic hydrocarbons (PAHs) or their intermediate metabolites. In this work, we report genomic and experimental evidence of metabolic benzoate, gentisate, and protocatechuate degradation by Paenarthrobacter sp. GOM3. Gentisate was the preferred substrate with the highest volumetric consumption rate, and genomic analysis revealed that this strain possesses multiple gene copies for the specific transport of gentisate. Furthermore, upon analyzing the GOM3 genome, we found five different dioxygenases involved in the activation of aromatic compounds, suggesting its potential for complete remediation of PAH-contaminated sites in combination with strains capable of assimilating the upper PAH degradation pathway. Additionally, this strain was characterized experimentally for its pathogenic potential and in silico for its antimicrobial resistance. An overview of the potential ecological role of this strain in the context of other members of this taxonomic clade is also reported.

Definition of the Metagenomic Profile of Ocean Water Samples From the Gulf of Mexico Based on Comparison With Reference Samples From Sites Worldwide

“…Notably, the results related to the presence of enzymes involved in oil degradation are consistent with previous works of our own and other groups that investigated the Mexican exclusive economic zone and identified oil-degrading microorganisms derived from 16S amplicon analysis (Fernanda Sánchez-Soto Jiménez et al, 2018;Godoy-Lozano et al, 2018;Hernández-López et al, 2019;Moreno-Ulloa et al, 2019;Raggi et al, 2020;Ramírez et al, 2020); isolated fractions related to petroleum (Moreno-Ulloa et al, 2019); isolated consortia and species capable of degrading petroleum under aerobic and anaerobic conditions (Muriel-Millán et al, 2019;Curiel-Maciel et al, 2021;Rosas-Díaz et al, 2021); and characterized petroleum-degrading enzymes (Rodríguez-Salazar et al, 2020), even in regions with no evidence of anthropogenic perturbation. A recent review illustrated the distribution of bacteria in the water column and sediments of the Mexican exclusive economic zone of the GoM (Rodríguez-Salazar et al, 2021).…”

Oil-degrading bacterial consortium from Gulf of Mexico designed by a factorial method, reveals stable population dynamics

“…GOM3 strain was isolated with phenanthrene as the sole carbon source but exhibited higher growth rates with monoaromatics. This strain was reported as a monoaromatic degrader (Rosas-Dıáz et al, 2021), but it can degrade other complex PAHs present in light crude oil (Supplementary Figure S3). This is consistent with the presence of cytochrome P450 monooxygenase (PF00067) in its genome (GenBank accession number GCA_018215265.1), which has been related to the degradation of alkanes and of pyrene and phenanthrene compounds (Zhou et al, 2020).…”

“…One of them was identified as Paenarthrobacter sp. GOM3 and was found to be a monoaromatic degrader (Rosas-Dıáz et al, 2021). The second one, isolated from asphalt marine sediments, was Halopseudomonas aestusnigri GOM5 (Rojas-Vargas et al, 2022).…”

“…Sediment samples were added to mineral medium (MM) composed of (g•L -1 ): Na 2 SO 4 0.183; CaCl 2 0.073; NH 4 Cl 0,267; MgCl 2 •6H 2 O 0.16; NaMoO 4 •2H 2 O 0.0002; FeSO 4 0.005; NaCl 11.68; K 2 HPO 4 0.8; KH 2 PO 4 0.2; and supplemented with HCs such as kerosene, phenanthrene or oil petroleum as the sole carbon and energy source. Bacterial isolates were plated in LB agar (Bertani, 2004) or EDM agar (Rosas-Dıáz et al, 2021). Three additional strains were isolated from sediment samples collected in the coastal area of Rosarito Port, Baja California, in the MPO (Silva-Jimeńez et al, 2018) (Table 1).…”

“…From marine sediment samples collected in an area of 200,000 km 2 , and using high throughput sequencing, we have identified at least 450 genera belonging to the bacterial baseline (Godoy-Lozano et al, 2018;Raggi et al, 2020). In addition to this effort, we have isolated some bacterial strains from the GoM (Muriel-Millań et al, 2019;Muriel-Millań et al, 2021;Rodrıǵuez-Salazar et al, 2021;Rosas-Dıáz et al, 2021;Rojas-Vargas et al, 2022) and from the Northwest region of the Mexican Pacific Ocean (MPO) (Silva-Jimeńez et al, 2018). These strains were isolated from water column and sediment samples collected at locations where crude oil was reported to be present; as such, we expect to find HC degraders among them, which could potentially be used to design a promising bacterial consortium for HC bioremediation in seawater.…”