Identification and characterization of o-xylene-degrading Rhodococcus spp. which were dominant species in the remediation of o-xylene-contaminated soils

Influence of growth substrate and contaminant mixtures on the degradation of BTEX and MTBE by Rhodococcus rhodochrous ATCC strain 21198

The degradation of the prevalent environmental contaminants benzene, toluene, ethylbenzene, and xylenes (BTEX) along with a common co-contaminant methyl tert-butyl ether (MTBE) by Rhodococcus rhodochrous ATCC Strain 21198 was investigated. The ability of 21198 to degrade these contaminants individually and in mixtures was evaluated with resting cells grown on isobutane, 1-butanol, and 2-butanol. Growth of 21198 in the presence of BTEX and MTBE was also studied to determine the growth substrate that best supports simultaneous microbial growth and contaminants degradation. Cells grown on isobutane, 1-butanol, and 2-butanol were all capable of degrading the contaminants, with isobutane grown cells exhibiting the most rapid degradation rates and 1-butanol grown cells exhibiting the slowest. However, in conditions where BTEX and MTBE were present during microbial growth, 1-butanol was determined to be an effective substrate for supporting concurrent growth and contaminant degradation. Contaminant degradation was found to be a combination of metabolic and cometabolic processes. Evidence for growth of 21198 on benzene and toluene is presented along with a possible transformation pathway. MTBE was cometabolically transformed to tertiary butyl alcohol, which was also observed to be transformed by 21198. This work demonstrates the possible utility of primary and secondary alcohols to support biodegradation of monoaromatic hydrocarbons and MTBE. Furthermore, the utility of 21198 for bioremediation applications has been expanded to include BTEX and MTBE.

Enrichment cultivation of VOC-degrading bacteria using diffusion bioreactor and development of bacterial-immobilized biochar for VOC bioremediation

Volatile organic compounds (VOCs) have been globally reported at various sites. Currently, limited literature is available on VOC bioremediation using bacterial-immobilized biochar (BC-B). In this study, multiple VOC-degrading bacteria were enriched and isolated using a newly designed diffusion bioreactor. The most effective VOC-degrading bacteria were then immobilized on rice husk-derived pristine biochar (BC) to develop BC-B. Finally, the performances of BC and BC-B for VOCs (benzene, toluene, xylene, and trichloroethane) bioremediation were evaluated by establishing batch microcosm experiments (Control, C; bioconsortium, BS; pristine biochar, BC; and bacterial-immobilized biochar, BC-B). The results revealed that the newly designed diffusion bioreactor effectively simulated native VOC-contaminated conditions, easing the isolation of 38 diverse ranges of VOC-degrading bacterial strains. Members of the genus Pseudomonas were isolated in the highest (26.33%). The most effective bacterial strain was Pseudomonas sp. DKR-23, followed by Rhodococcus sp. Korf-18, which degraded multiple VOCs in the range of 52-75%. The batch microcosm experiment data showed that BC-B remediated the highest >90% of various VOCs, which was comparatively higher than that of BC, BS, and C. In addition, compared with C, the BS, BC, and BC-B microcosms abundantly reduced the half-life of various VOCs, implying a beneficial impact on the degradation behavior of VOCs. Altogether, this study suggests that a diffusion bioreactor system can be used as a cultivation device for the isolation of a wide range of VOC-degrading bacterial strains, and a compatible combination of biochar and bacteria may be an attractive and promising approach for the sustainable bioremediation of multiple VOCs.

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

Among monoaromatic hydrocarbons, xylenes, especially the ortho and para isomers, are the least biodegradable compounds in oxygen-limited subsurface environments. Although much knowledge has been gained regarding the anaerobic degradation of xylene isomers in the past 2 decades, the diversity of those bacteria which are able to degrade them under microaerobic conditions is still unknown. To overcome this limitation, aerobic and microaerobic xylene-degrading enrichment cultures were established using groundwater taken from a xylene-contaminated site, and the associated bacterial communities were investigated using a polyphasic approach. Our results show that the xylene-degrading bacterial communities were distinctly different between aerobic and microaerobic enrichment conditions. Although members of the genus Pseudomonas were the most dominant in both types of enrichments, the Rhodoferax and Azovibrio lineages were only abundant under microaerobic conditions, while Sphingobium entirely replaced them under aerobic conditions. Analysis of a metagenome-assembled genome of a Rhodoferax-related bacterium revealed aromatic hydrocarbon-degrading ability by identifying two catechol 2,3-dioxygenases in the genome. Moreover, phylogenetic analysis indicated that both enzymes belonged to a newly defined subfamily of type I.2 extradiol dioxygenases (EDOs). Aerobic and microaerobic xylene-degradation experiments were conducted on strains Sphingobium sp. AS12 and Pseudomonas sp. MAP12, isolated from the aerobic and microaerobic enrichments, respectively. The obtained results, together with the whole-genome sequence data of the strains, confirmed the observation that members of the genus Sphingobium are excellent aromatic hydrocarbon degraders but effective only under clear aerobic conditions. Overall, it was concluded that the observed differences between the bacterial communities of aerobic and microaerobic xylene-degrading enrichments were driven primarily by (i) the method of aromatic ring activation (monooxygenation vs dioxygenation), (ii) the type of EDO enzymes, and (iii) the ability of degraders to respire utilizing nitrate.

Biodegradation of naphthalene, BTEX, and aliphatic hydrocarbons by Paraburkholderia aromaticivorans BN5 isolated from petroleum-contaminated soil

To isolate bacteria responsible for the biodegradation of naphthalene, BTEX (benzene, toluene, ethylbenzene, and o-, m-, and p-xylene), and aliphatic hydrocarbons in petroleum-contaminated soil, three enrichment cultures were established using soil extract as the medium supplemented with naphthalene, BTEX, or n-hexadecane. Community analyses showed that Paraburkholderia species were predominant in naphthalene and BTEX, but relatively minor in n-hexadecane. Paraburkholderia aromaticivorans BN5 was able to degrade naphthalene and all BTEX compounds, but not n-hexadecane. The genome of strain BN5 harbors genes encoding 29 monooxygenases including two alkane 1-monooxygenases and 54 dioxygenases, indicating that strain BN5 has versatile metabolic capabilities, for diverse organic compounds: the ability of strain BN5 to degrade short chain aliphatic hydrocarbons was verified experimentally. The biodegradation pathways of naphthalene and BTEX compounds were bioinformatically predicted and verified experimentally through the analysis of their metabolic intermediates. Some genomic features including the encoding of the biodegradation genes on a plasmid and the low sequence homologies of biodegradation-related genes suggest that biodegradation potentials of strain BN5 may have been acquired via horizontal gene transfers and/or gene duplication, resulting in enhanced ecological fitness by enabling strain BN5 to degrade all compounds including naphthalene, BTEX, and short aliphatic hydrocarbons in contaminated soil.

o-Xylene removal using one- and two-phase partitioning biotrickling filters: steady/transient-state performance and microbial community

In this study, one- and two-phase partitioning biotrickling filters (1P-BTF and 2P-BTF, respectively) inoculated with a pre-acclimated mixed culture were examined for the removal of hydrophobic and refractory o-xylene. A small fraction of silicone oil (5% v/v) was added as a non-aqueous phase. Due to the presence of silicone oil, the 2P-BTF exhibited superior performance and stability for o-xylene biodegradation at steady and transient operations. Higher macro-kinetic constants for o-xylene removal by the Michaelis-Menten model were obtained for the 2P-BTF with a saturation constant of 0.396 g m^-3 and a maximum elimination capacity of 105.7 g m^-3 h^-1. The enhancement of removal performance for the 2P-BTF was supported by dominant specialized microorganisms with o-xylene biodegradability. The diversity of microbial community was influenced by the presence of silicone oil. This study demonstrated that a BTF with 5% of silicone oil could be applied for the treatment of hydrophobic and refractory volatile organic compounds. It also provided valuable information for better understanding the relationship between microbial community and removal performance using two-phase partitioning bioreactors.

Benzene Degradation by a Variovorax Species within a Coal Tar-Contaminated Groundwater Microbial Community

Investigations of environmental microbial communities are crucial for the discovery of populations capable of degrading hazardous compounds and may lead to improved bioremediation strategies. The goal of this study was to identify microorganisms responsible for aerobic benzene degradation in coal tar-contaminated groundwater. Benzene degradation was monitored in laboratory incubations of well waters using gas chromatography mass spectrometry (GC-MS). Stable isotope probing (SIP) experiments using [¹³C]benzene enabled us to obtain ¹³C-labled community DNA. From this, 16S rRNA clone libraries identified Gammaproteobacteria and Betaproteobacteria as the active benzene-metabolizing microbial populations. Subsequent cultivation experiments yielded nine bacterial isolates that grew in the presence of benzene; five were confirmed in laboratory cultures to grow on benzene. The isolated benzene-degrading organisms were genotypically similar (>97% 16S rRNA gene nucleotide identities) to the organisms identified in SIP experiments. One isolate, Variovorax MAK3, was further investigated for the expression of a putative aromatic ring-hydroxylating dioxygenase (RHD) hypothesized to be involved in benzene degradation. Microcosm experiments using Variovorax MAK3 revealed a 10-fold increase in RHD (Vapar_5383) expression, establishing a link between this gene and benzene degradation. Furthermore, the addition of Variovorax MAK3 to microcosms prepared from site waters accelerated community benzene degradation and correspondingly increased RHD gene expression. In microcosms using uninoculated groundwater, quantitative (q)PCR assays (with 16S rRNA and RDH genes) showed that Variovorax was present and responsive to added benzene. These data demonstrate how the convergence of cultivation-dependent and -independent techniques can boost understandings of active populations and functional genes in complex benzene-degrading microbial communities.

IMPORTANCE

Benzene is a human carcinogen whose presence in contaminated groundwater drives environmental cleanup efforts. Although the aerobic biodegradation of benzene has long been established, knowledge of the identity of the microorganisms in complex naturally occurring microbial communities responsible for benzene biodegradation has evaded scientific inquiry for many decades. Here, we applied a molecular biology technique known as stable isotope probing (SIP) to the microbial communities residing in contaminated groundwater samples to identify the community members active in benzene biodegradation. We complemented this approach by isolating and growing in the laboratory a bacterium representative of the bacteria found using SIP. Further characterization of the isolated bacterium enabled us to track the expression of a key gene that attacks benzene both in pure cultures of the bacterium and in the naturally occurring groundwater microbial community. This work advances information regarding the documentation of microbial processes, especially the populations and genes that contribute to bioremediation.

Comparative transcriptomics elucidates adaptive phenol tolerance and utilization in lipid-accumulating Rhodococcus opacus PD630

Lignin-derived (e.g. phenolic) compounds can compromise the bioconversion of lignocellulosic biomass to fuels and chemicals due to their toxicity and recalcitrance. The lipid-accumulating bacterium Rhodococcus opacus PD630 has recently emerged as a promising microbial host for lignocellulose conversion to value-added products due to its natural ability to tolerate and utilize phenolics. To gain a better understanding of its phenolic tolerance and utilization mechanisms, we adaptively evolved R. opacus over 40 passages using phenol as its sole carbon source (up to 373% growth improvement over wild-type), and extensively characterized two strains from passages 33 and 40. The two adapted strains showed higher phenol consumption rates (∼20 mg/l/h) and ∼2-fold higher lipid production from phenol than the wild-type strain. Whole-genome sequencing and comparative transcriptomics identified highly-upregulated degradation pathways and putative transporters for phenol in both adapted strains, highlighting the important linkage between mechanisms of regulated phenol uptake, utilization, and evolved tolerance. Our study shows that the R. opacus mutants are likely to use their transporters to import phenol rather than export them, suggesting a new aromatic tolerance mechanism. The identified tolerance genes and pathways are promising candidates for future metabolic engineering in R. opacus for improved lignin conversion to lipid-based products.

Enhanced biofilm production by a toluene-degrading Rhodococcus observed after exposure to perfluoroalkyl acids

This study focuses on interactions between aerobic soil-derived hydrocarbon degrading bacteria and a suite of perfluorocarboxylic acids and perfluoroalkylsulfonates that are found in aqueous film-forming foams used for fire suppression. No effect on toluene degradation rate or induction time was observed when active cells of Rhodococcus jostii strain RHA1 were exposed to toluene and a mixture of perfluoroalkyl acids (PFAAs) including perfluorooctanoic acid (PFOA) and perfluorooctanesulfonate (PFOS) at concentrations near the upper bounds of groundwater relevance (11 PFAAs at 10 mg/L each). However, exposure to aqueous PFAA concentrations above 2 mg/L (each) was associated with enhanced aggregation of bacterial cells and significant increases in extracellular polymeric substance production. Flocculation was only observed during exponential growth and not elicited when PFAAs were added to resting incubations; analogous flocculation was also observed in soil enrichments. Aggregation was accompanied by 2- to 3-fold upregulation of stress-associated genes, sigF3 and prmA, during growth of this Rhodococcus in the presence of PFAAs. These results suggest that biological responses, such as microbial stress and biofilm formation, could be more prominent than suppression of co-contaminant biodegradation in subsurface locations where poly- and perfluoroalkyl substances occur with hydrocarbon fuels.

Deepening TOL and TOU catabolic pathways of Pseudomonas sp. OX1: cloning, sequencing and characterization of the lower pathways

Pseudomonas sp. OX1 is able to metabolize toluene and o-xylene through the TOU catabolic pathway, whereas its mutant M1 strain was found to be able to use m- and p-xylene as carbon and energy source, using the TOL catabolic pathway. Here we report the complete nucleotide sequence of the phe lower operon of the TOU catabolic pathway, and the sequence of the last four genes of the xyl-like lower operon of the TOL catabolic pathway. DNA sequence analysis shows the gene order within the operons to be pheCDEFGHI (phe operon) and xyl-likeQKIH (xyl-like operon), identical to the order found for the isofunctional genes of meta operons in the toluene/xylene pathway of TOL plasmid pWW0 from Pseudomonas putida mt-2 and the phenol/methylphenol pathway of pVIl50 from Pseudomonas sp. CF600. The nucleotide and the deduced amino acid sequences are homologous to the equivalent gene and enzyme sequences from other Pseudomonas meta pathways. Recombinant 2-hydroxymuconic semialdehyde dehydrogenase (HMSD) and 2-hydroxymuconic semialdehyde hydrolase (HMSH), coded by pheCD genes, respectively, and ADA and HOA enzymes from both phe and xyl operons were expressed in E. coli and steady-state kinetic analysis was carried out. The analysis of the kinetic parameters of HMSD and HMSH showed that the enzymes from Pseudomonas sp. OX1 are more specialized to channel metabolites into the two branches of the lower pathway than homologous enzymes from other pseudomonads. The kinetics parameters of recombinant ADA from phe and xyl-like operon were found to be similar to those of homologous enzymes from other Pseudomonas strains. In addition, the enzyme from xyl-like operon showed a substrate affinity three times higher than the enzyme from phe operon.

Characterization of indigenous Rhodococcus sp. 602, a strain able to accumulate triacylglycerides from naphthyl compounds under nitrogen-starved conditions

An indigenous bacterium (strain 602) isolated in this study from a polluted soil sample collected in Patagonia (Argentina) was investigated in relation to its metabolic responses under unbalanced growth conditions. This strain was identified as Rhodococcus sp. by molecular analyses. Strain 602 showed the ability to degrade a wide range of compounds and to synthesize triacylglycerols under nitrogen-limiting conditions. Cells were also able to accumulate triacylglycerols during cultivation on naphthalene and naphthyl-1-dodecanoate. Triacylglycerols produced by resting cells in the presence of naphthyl-1-dodecanoate contained only short-chain length fatty acids (from C(8) to C(12)), suggesting an initial attack of the substrate by an esterase releasing 1-naphthol and dodecanoic acid, which was subsequently degraded by beta-oxidation. On the other hand, naphthalene seemed to be degraded by a mono-oxygenase yielding 1-naphthol, which was then transformed to 4-hydroxy-1-tetralone and to other possible metabolic intermediates. On the basis of the results obtained, a pathway involved in the metabolism of both aromatic compounds under nitrogen starvation by strain 602 is proposed. The results also demonstrated that Rhodococcus sp. 602 maintains its metabolic activity even in the absence of a nitrogen source. Intracellular triacylglycerols may help cells to maintain their catabolic activities under these growth-restricting conditions.

Degradation of a mixture of hydrocarbons, gasoline, and diesel oil additives by Rhodococcus aetherivorans and Rhodococcus wratislaviensis

Two strains, identified as Rhodococcus wratislaviensis IFP 2016 and Rhodococcus aetherivorans IFP 2017, were isolated from a microbial consortium that degraded 15 petroleum compounds or additives when provided in a mixture containing 16 compounds (benzene, toluene, ethylbenzene, m-xylene, p-xylene, o-xylene, octane, hexadecane, 2,2,4-trimethylpentane [isooctane], cyclohexane, cyclohexanol, naphthalene, methyl tert-butyl ether [MTBE], ethyl tert-butyl ether [ETBE], tert-butyl alcohol [TBA], and 2-ethylhexyl nitrate [2-EHN]). The strains had broad degradation capacities toward the compounds, including the more recalcitrant ones, MTBE, ETBE, isooctane, cyclohexane, and 2-EHN. R. wratislaviensis IFP 2016 degraded and mineralized to different extents 11 of the compounds when provided individually, sometimes requiring 2,2,4,4,6,8,8-heptamethylnonane (HMN) as a cosolvent. R. aetherivorans IFP 2017 degraded a reduced spectrum of substrates. The coculture of the two strains degraded completely 13 compounds, isooctane and 2-EHN were partially degraded (30% and 73%, respectively), and only TBA was not degraded. Significant MTBE and ETBE degradation rates, 14.3 and 116.1 mumol of ether degraded h(-1) g(-1) (dry weight), respectively, were measured for R. aetherivorans IFP 2017. The presence of benzene, toluene, ethylbenzene, and xylenes (BTEXs) had a detrimental effect on ETBE and MTBE biodegradation, whereas octane had a positive effect on the MTBE biodegradation by R. wratislaviensis IFP 2016. BTEXs had either beneficial or detrimental effects on their own degradation by R. wratislaviensis IFP 2016. Potential genes involved in hydrocarbon degradation in the two strains were identified and partially sequenced.

Application of aerobic microorganisms in bioremediation in situ of soil contaminated by petroleum products

Aerobic microorganisms able to biodegrade benzene, toluene, ethylbenzene, xylene (BTEX) have been isolated from an area contaminated by petroleum products. The activity of the isolated communities was tested under both laboratory and field conditions. Benzene, toluene, ethylbenzene and xylene were added to the cultures as the sole carbon source, at a concentration of 500 mg/L. In batch cultures under laboratory conditions, an 84% reduction of benzene, 86% of toluene and 82% of xylene were achieved. In cultures with ethylbenzene as the sole carbon source, the reduction was around 80%. Slightly lower values were observed under field conditions: 95% reduction of benzene and toluene, 81% of ethylbenzene and 80% of xylene. A high biodegradation activity of benzene (914 microM/L/24h), toluene (771 microM/L/24h), xylene (673 microM/L/24h) and ethylbenzene (644 microM/L/24h) was observed in the isolated communities.

Biodegradation potential of the genus Rhodococcus

A large number of aromatic compounds and organic nitriles, the two groups of compounds covered in this review, are intermediates, products, by-products or waste products of the chemical and pharmaceutical industries, agriculture and the processing of fossil fuels. The majority of these synthetic substances (xenobiotics) are toxic and their release and accumulation in the environment pose a serious threat to living organisms. Bioremediation using various bacterial strains of the genus Rhodococcus has proved to be a promising option for the clean-up of polluted sites. The large genomes of rhodococci, their redundant and versatile catabolic pathways, their ability to uptake and metabolize hydrophobic compounds, to form biofilms, to persist in adverse conditions and the availability of recently developed tools for genetic engineering in rhodococci make them suitable industrial microorganisms for biotransformations and the biodegradation of many organic compounds. The peripheral and central catabolic pathways in rhodococci are characterized for each type of aromatics (hydrocarbons, phenols, halogenated, nitroaromatic, and heterocyclic compounds) in this review. Pathways involved in the hydrolysis of nitrile pollutants (aliphatic nitriles, benzonitrile analogues) and the corresponding enzymes (nitrilase, nitrile hydratase) are described in detail. Examples of regulatory mechanisms for the expression of the catabolic genes are given. The strains that efficiently degrade the compounds in question are highlighted and examples of their use in biodegradation processes are presented.