Abstract
Rapid industrial and societal developments have led to substantial increases in the use and exploitation of petroleum, and petroleum hydrocarbon pollution has become a serious threat to human health and the environment. Polycyclic aromatic hydrocarbons (PAHs) are primary components of petroleum hydrocarbons. In recent years, microbial remediation of PAHs pollution has been regarded as the most promising and cost-effective treatment measure because of its low cost, robust efficacy, and lack of secondary pollution. Rhodococcus bacteria are regarded as one of main microorganisms that can effectively degrade PAHs because of their wide distribution, broad degradation spectrum, and network-like evolution of degradation gene clusters. In this review, we focus on the biological characteristics of Rhodococcus; current trends in PAHs degradation based on knowledge maps; and the cellular structural, biochemical, and enzymatic basis of degradation mechanisms, along with whole genome and transcriptional regulation. These research advances provide clues for the prospects of Rhodococcus-based applications in environmental protection.
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Data availability
All data was collected from NCBI database and WoSCC database; data can be provided on request.
References
Ahmad M, Wang PD, Li JL et al (2021) Impacts of bio-stimulants on pyrene degradation, prokaryotic community compositions, and functions. Environ Pollut 289:117863. https://doi.org/10.1016/j.envpol.2021.117863
Ahmed RZ, Ahmed N (2016) Isolation of Rhodococcus sp. CMGCZ capable to degrade high concentration of fluoranthene. Water Air Soil Poll 227:162. https://doi.org/10.1007/s11270-016-2857-4
Akhtar N, Ghauri MA, Anwar MA et al (2015) Phylogenetic characterization and novelty of organic sulphur metabolizing genes of Rhodococcus spp. (Eu-32). Biotechnol Lett 37:837–847. https://doi.org/10.1007/s10529-014-1736-6
Anno FD, Rastelli E, Sansone C et al (2021) Bacteria, fungi and microalgae for the bioremediation of marine sediments contaminated by petroleum hydrocarbons in the omics era. Microorganisms 9:1695. https://doi.org/10.3390/microorganisms9081695
Anokhina TO, Esikova TZ, Gafarov AB et al (2020) Alternative naphthalene metabolic pathway includes formation of ortho-phthalic acid and cinnamic acid derivatives in the Rhodococcus opacus strain 3D. Biochemistry (Moscow) 85:355–368. https://doi.org/10.1134/S0006297920030116
Araki N, Niikura Y, Miyauchi K et al (2011) Glucose-mediated transcriptional repression of PCB/biphenyl catabolic genes in Rhodococcus jostii RHA1. J Mol Microb Biotech 20:53–62. https://doi.org/10.1159/000323509
Auffret M, Labbé D, Thouand G et al (2009) Degradation of a mixture of hydrocarbons, gasoline, and diesel oil additives by Rhodococcus aetherivorans and Rhodococcus wratislaviensis. Appl Environ Microb 75:7774–7782. https://doi.org/10.1128/AEM.01117-09
Bajaj S, Singh DK (2015) Biodegradation of persistent organic pollutants in soil, water and pristine sites by cold-adapted microorganisms: mini review. Int Biodeter Biodegr 100:98–105. https://doi.org/10.1016/j.ibiod.2015.02.023
Barbosa F, Jr-Rocha BA, Souza MCO et al (2023) Polycyclic aromatic hydrocarbons (PAHs): updated aspects of their determination, kinetics in the human body, and toxicity. J Toxicol Env Heal B 26:28–65. https://doi.org/10.1080/10937404.2022.2164390
Bej AK, Saul D, Aislabie J (2000) Cold-tolerant alkane-degrading Rhodococcus species from Antarctica. Polar Biol 23:100–105. https://doi.org/10.1007/s003000050014
Bequer-Urbano S, Albarracín VH, Ordoñez OF et al (2013) Lipid storage in high-altitude Andean Lakes extremophiles and its mobilization under stress conditions in Rhodococcus sp. A5, a UV-resistant actinobacterium. Extremophiles 17:217–227. https://doi.org/10.1007/s00792-012-0508-2
Bisht S, Pandey P, Bhargava B et al (2015) Bioremediation of polyaromatic hydrocarbons (PAHs) using rhizosphere technology. Braz J Microbiol 46:7–21. https://doi.org/10.1590/S1517-838246120131354
Bourguignon N, Isaac P, Alvarez H et al (2014) Enhanced polyaromatic hydrocarbon degradation by adapted cultures of actinomycete strains. J Basic Microb 54:1288–1294. https://doi.org/10.1002/jobm.201400262
Boyd C, Larkin MJ, Reid KA et al (1997) Metabolism of naphthalene, 1-naphthol, indene, and indole by Rhodococcus sp. strain NCIMB 12038. Appl Environ Microb 63:151–155. https://doi.org/10.1128/AEM.63.1.151-155.1997
Bukliarevicha HA, Charniauskayaa MI, Akhremchukb AE et al (2019) Effect of the structural and regulatory heat shock proteins on hydrocarbon degradation by Rhodococcus pyridinivorans 5Ap. Microbiol 88:573–579. https://doi.org/10.1134/S0026261719050023
Cai QH, Zhang BY, Chen B et al (2016) Biosurfactant produced by a Rhodococcus erythropolis mutant as an oil spill response agent. Water Qual Res J Can 51:97–105. https://doi.org/10.2166/wqrjc.2016.025
Chang JS, Cha DK, Radosevich M et al (2020) Different bioavailability of phenanthrene to two bacterial species and effects of trehalose lipids on the bioavailability. J Environ Sci Heal A 55:326–332. https://doi.org/10.1080/10934529.2020.1712176
Chaudhary DK, Kim J (2019) Insights into bioremediation strategies for oil-contaminated soil in cold environments. Int Biodeter Biodegr IODEGR 142:58–72. https://doi.org/10.1016/j.ibiod.2019.05.001
Chen C, Shen JM, Yang L et al (2021) Identification of structural properties influencing the metabolism of polycyclic aromatic hydrocarbons by cytochrome P450 1A1. Sci Total Environ 758:143997. https://doi.org/10.1016/j.scitotenv.2020.143997
Cho HJ, Kim K, Sohn SY et al (2010) Substrate binding mechanism of a type I extradiol dioxygenase. J Biol Chem 285:34643–34652. https://doi.org/10.1074/jbc.M110.130310
De-Carvalho CCCR, Fischer MA, Kirsten S et al (2016) Adaptive response of Rhodococcus opacus PWD4 to salt and phenolic stress on the level of mycolic acids. AMB Express 6:66. https://doi.org/10.1186/s13568-016-0241-9
De-Carvalho CCCR, Marques MPC, Hachicho N et al (2014) Rapid adaptation of Rhodococcus erythropolis cells to salt stress by synthesizing polyunsaturated fatty acids. Appl Microbiol Biotechnol 98:5599–5606. https://doi.org/10.1007/s00253-014-5549-2
Ding J, Guotao LI, Huang Z (2018) Research progress in microbial cytochrome P450 and xenobiotic metabolism. Chin J Appl Environ Biol 24:657–662. https://doi.org/10.19675/j.cnki.1006-687x.2017.06026
Egorova DO, Gorbunova TI, Kir’Yanova TD et al (2021) Modeling of the biphenyl dioxygenase α-subunit structure of Rhodococcus strains and features of the destruction of chlorinated and hydroxylated biphenyls at different temperatures. Appl Biochem Micro+ 57:732–742. https://doi.org/10.1134/S0003683821060028
Eltis LD, Karlson U, Timmis KN (1993) Purification and characterization of cytochrome P450RR1 from Rhodococcus rhodochrous. Eur J Biochem 213:211–216. https://doi.org/10.1111/j.1432-1033.1993.tb17750.x
Ely CS, Smets BF (2019) Guild composition of root-associated bacteria changes with increased soil contamination. Microb Ecol 78:416–427. https://doi.org/10.1007/s00248-019-01326-6
Garrido-Sanz D, Sansegundo-Lobato P, Redondo-Nieto M et al (2020) Analysis of the biodegradative and adaptive potential of the novel polychlorinated biphenyl degrader Rhodococcus sp. WAY2 revealed by its complete genome sequence. Microb Genom 6:000363. https://doi.org/10.1099/mgen.0.000363
Gennaro P, Terreni P, Masi G (2010) Identification and characterization of genes involved in naphthalene degradation in Rhodococcus opacus R7. Appl Microbiol Biot 87:297–308. https://doi.org/10.1007/s00253-010-2497-3
Gennaro PD, Zampolli J, Presti I et al (2014) Genome sequence of Rhodococcus opacus Strain R7, a biodegrader of mono- and polycyclic aromatic hydrocarbons. Genome Announcements 2:e00827–e00814. https://doi.org/10.1128/genomeA.00827-14
G-Sanz M (2023) Rhodococcus Equi—what is new this decade? Vet Clin North Am Equine Pract 39:1–14. https://doi.org/10.1016/j.cveq.2022.11.002
Gu H, Yan J, Liu Y et al (2023) Autochthonous bioaugmentation accelerates phenanthrene degradation in acclimated soil. Environ Res 224:115543. https://doi.org/10.1016/j.envres.2023.115543
Han Q, Qin YL, Li DF (2021) Advances in bacterial Rieske non-heme iron ring-hydroxylating dioxygenases that initiate polycyclic aromatic hydrocarbons degradation. Sheng Wu Gong Cheng Xue Bao 37:3439–3458. https://doi.org/10.13345/j.cjb.210402
Hu X, Qiao Y, Chen LQ et al (2019) Enhancement of solubilization and biodegradation of petroleum by biosurfactant from Rhodococcus erythropolis HX-2. Geomicrobiology 37:159–169. https://doi.org/10.1080/01490451.2019.1678702
Ilker U, Duan YP, Ogram A (2000) Characterization of the naphthalene-degrading bacterium, Rhodococcus opacus M213. Fems Microbiol Lett 185:231–238. https://doi.org/10.1016/S0378-1097(00)00095-1
Ivshina IB, Krivoruchko AV, Kuyukina MS et al (2022) Adhesion of Rhodococcus bacteria to solid hydrocarbons and enhanced biodegradation of these compounds. Sci Rep 12:21559. https://doi.org/10.1038/s41598-022-26173-3
Jia X, He Y, Huang L (2018) n-Hexadecane and pyrene biodegradation and metabolization by Rhodococcus sp. T1 isolated from oil contaminated soil. Chin J Chem Eng 27:184–190. https://doi.org/10.1016/j.cjche.2018.03.034
Jiang R, Li Y, Wang H et al (2020) A study on the degradation efficiency of fluoranthene and the transmembrane protein mechanism of Rhodococcus sp. BAP-1 based on iTRAQ. Sci Total Environ 737:140208. https://doi.org/10.1016/j.scitotenv.2020.140208
Jin JN, Yao J, Zhang QY et al (2015) An integrated approach of bioassay and molecular docking to study the dihydroxylation mechanism of pyrene by naphthalene dioxygenase in Rhodococcus sp. ustb-1. Chemosphere 128:307–313. https://doi.org/10.1016/j.chemosphere.2015.02.012
Kan J, Peng T, Huang TW et al (2020) NarL, a novel repressor for CYP108j1 expression during PAHs degradation in Rhodococcus sp. P14. Int J Mol Sci 21:983. https://doi.org/10.3390/ijms21030983
Khairy H, Wubbeler JH, Steinbuchel A (2016) The NADH:flavin oxidoreductase Nox from Rhodococcus erythropolis MI2 is the key enzyme of 4,4′-dithiodibutyric acid degradation. Lett Appl Microbiol 63:434–441. https://doi.org/10.1111/lam.12662
Kim CH, Lee DW, Heo YM et al (2019) Desorption and solubilization of anthracene by a rhamnolipid biosurfactant from Rhodococcus fascians. Water Environ Res 91:739–747. https://doi.org/10.1002/wer.1103
Kim D, Lee JS, Choi KY et al (2007) Effect of functional groups on the regioselectivity of a novel o-xylene dioxygenase from Rhodococcus sp. strain DK17. Enzyme Microb Tech 41:221–225. https://doi.org/10.1016/j.enzmictec.2007.01.021
Kim D, Park MJ, Koh SC et al (2002) Three separate pathways for the initial oxidation of limonene, biphenyl, and phenol by Rhodococcus sp. strain T104. J Microbiol 40:86–89. https://doi.org/10.1016/S0167-7012(01)00364-5
Kim D, Yoo M, Choi KY et al (2011) Differential degradation of bicyclics with aromatic and alicyclic rings by Rhodococcus sp. strain DK17. Appl Environ Microb 77:8280–8287. https://doi.org/10.1128/AEM.06359-11
Kimura N, Kitagawa W, Mori T et al (2006) Genetic and biochemical characterization of the dioxygenase involved in lateral dioxygenation of dibenzofuran from Rhodococcus opacus strain SAO101. Appl Microbiol Biotechnol 73:474–484. https://doi.org/10.1007/s00253-006-0481-8
Kitagawa W, Hata M, Sekizuka T et al (2014) Draft genome sequence of Rhodococcus erythropolis JCM 6824, an aurachin RE antibiotic producer. Genome Announc 2:e01026–e01014. https://doi.org/10.1128/genomeA.01026-14
Kong FX, Sun GD, Liu ZP (2018) Degradation of polycyclic aromatic hydrocarbons in soil mesocosms by microbial/plant bioaugmentation: performance and mechanism. Chemosphere 198:83–91. https://doi.org/10.1016/j.chemosphere.2018.01.097
Kotake T, Matsuzawa J, Suzuki-Minakuchi C (2016) Purification and partial characterization of the extradiol dioxygenase, 2′-carboxy-2,3-dihydroxybiphenyl 1,2-dioxygenase, in the fluorene degradation pathway from Rhodococcus sp. strain DFA3. Biosci Biotech Bioch 80:719–725. https://doi.org/10.1080/09168451.2015.1123605
Kulakov LA, Chen S, Allen CCR et al (2005) Web-type evolution of Rhodococcus gene clusters associated with utilization of naphthalene. Appl Environ Microb 71:1754–1764. https://doi.org/10.1128/AEM.71.4.1754-1764.2005
Kwasiborski A, Mondy S, Chong TM et al (2015) Transcriptome of the quorum-sensing signal-degrading Rhodococcus erythropolis responds differentially to virulent and avirulent Pectobacterium atrosepticum. Heredity 114:476–484. https://doi.org/10.1038/hdy.2014.121
Lang FS, Destain J, Delvigne F et al (2016) Biodegradation of polycyclic aromatic hydrocarbons in mangrove sediments under different strategies: natural attenuation, biostimulation, and bioaugmentation with Rhodococcus erythropolis T902.1. Water Air Soil Poll 227:297. https://doi.org/10.1007/s11270-016-2999-4
Larkin MJ, Allen C, Kulakov LA et al (1999) Purification and characterization of a novel naphthalene dioxygenase from Rhodococcus sp. strain NCIMB12038. J Bacteriol 181:6200–6204. https://doi.org/10.1128/JB.181.19.6200-6204.1999
Lavrov KV, Novikov AD, Ryabchenko LE et al (2014) Expression of acylamidase gene in Rhodococcus erythropolis strains. Russ J Genet+ 50:1003–1007. https://doi.org/10.1134/S1022795414090087
Lee EH, Kim J, Cho KS (2010) Degradation of hexane and other recalcitrant hydrocarbons by a novel isolate, Rhodococcus sp. EH831. Environ Sci Pollut R 17:64–77. https://doi.org/10.1007/s11356-009-0238-x
Li JB, Zhang DY, Song MK (2017) Novel bacteria capable of degrading phenanthrene in activated sludge revealed by stable-isotope probing coupled with high-throughput sequencing. Biodegradation 28:423–436. https://doi.org/10.1007/s10532-017-9806-9
Liang CY, Huang Y, Wang Y et al (2019) Distribution of bacterial polycyclic aromatic hydrocarbon (PAH) ring-hydroxylating dioxygenases genes in oilfield soils and mangrove sediments explored by gene-targeted metagenomics. Appl Microbiol Biot 103:2427–2440. https://doi.org/10.1007/s00253-018-09613-x
Liu J, Zhang AN, Liu YJ et al (2021) Analysis of the mechanism for enhanced pyrene biodegradation based on the interactions between iron-ions and Rhodococcus ruber strain L9. Ecotox Environ Safe 225:112789. https://doi.org/10.1016/j.ecoenv.2021.112789
Liu TT, Xu Y, Liu H et al (2011) Functional characterization of a gene cluster involved in gentisate catabolism in Rhodococcus sp. strain NCIMB 12038. Appl Microbiol Biot 90:671–678. https://doi.org/10.1007/s00253-010-3033-1
Lu Y, Tang F, Wang Y et al (2009) Biodegradation of dimethyl phthalate, diethyl phthalate and di-n-butyl phthalate by Rhodococcus sp. L4 isolated from activated sludge. J Hazard Mater 168:938–943. https://doi.org/10.1016/j.jhazmat.2009.02.126
Madankar CS, Meshram A (2022) Review on classification, physicochemical properties and applications of microbial surfactants. Tenside Surfact Det 59:1–16. https://doi.org/10.1515/tsd-2021-2353
Mansouri A, Abbes C, Ben-Mouhoub R et al (2019) Enhancement of mixture pollutant biodegradation efficiency using a bacterial consortium under static magnetic field. PLOS ONE 14:e0208431. https://doi.org/10.1371/journal.pone.0208431
Margesin R, Moertelmaier C, Mair J (2013) Low-temperature biodegradation of petroleum hydrocarbons (n-alkanes, phenol, anthracene, pyrene) by four actinobacterial strains. Int Biodeter Biodegr 84:185–191. https://doi.org/10.1016/j.ibiod.2012.05.004
Masy T, Caterina D, Tromme O et al (2016) Electrical resistivity tomography to monitor enhanced biodegradation of hydrocarbons with Rhodococcus erythropolis T902.1 at a pilot scale. J Contam Hydrol 184:1–13. https://doi.org/10.1016/j.jconhyd.2015.11.001
Miao LL, Qu J, Liu ZP (2020) Hydroxylation at multiple positions initiated the biodegradation of indeno[1,2,3-cd]pyrene in Rhodococcus aetherivorans IcdP1. Front Microbiol 11:568381. https://doi.org/10.3389/fmicb.2020.568381
Mikolasch A, Reinhard A, Alimbetova A et al (2016) From oil spills to barley growth—oil-degrading soil bacteria and their promoting effects. J Basic Microb 56:1252–1273. https://doi.org/10.1002/jobm.201600300
Mishra S, Singh SN, Pande V (2014) Bacteria induced degradation of fluoranthene in minimal salt medium mediated by catabolic enzymes in vitro condition. Bioresour Technol 164:299–308. https://doi.org/10.1016/j.biortech.2014.04.076
Mohapatra B, Phale PS (2021) Microbial degradation of naphthalene and substituted naphthalenes: metabolic diversity and genomic insight for bioremediation. Front Bioeng Biotech 9:602445. https://doi.org/10.3389/fbioe.2021.602445
Morales P, Caceres M, Scott F et al (2017) Biodegradation of benzo[α]pyrene, toluene, and formaldehyde from the gas phase by a consortium of Rhodococcus erythropolis and Fusarium solani. Appl Microbiol Biot 101:6765–6777. https://doi.org/10.1007/s00253-017-8400-8
Muangchinda C, Yamazoe A, Polrit D et al (2017) Biodegradation of high concentrations of mixed polycyclic aromatic hydrocarbons by indigenous bacteria from a river sediment: a microcosm study and bacterial community analysis. Environ Sci Pollut Res 24:4591–4602. https://doi.org/10.1007/s11356-016-8185-9
Nazari MT, Simon V, Machado BS et al (2022) Rhodococcus: a promising genus of actinomycetes for the bioremediation of organic and inorganic contaminants. J Environ Manage 323:116220. https://doi.org/10.1016/j.jenvman.2022.116220
Orro A, Cappelletti M, D’Ursi P et al (2015) Genome and phenotype microarray analyses of Rhodococcus sp. BCP1 and Rhodococcus opacus R7: genetic determinants and metabolic abilities with environmental relevance. PLOS ONE 10:e0139467. https://doi.org/10.1371/journal.pone.0139467
Pacchioni RG, Carvalho FM, Thompson CE et al (2014) Taxonomic and functional profiles of soil samples from Atlantic forest and Caatinga biomes in northeastern Brazil. Microbiologyopen 3:299–315. https://doi.org/10.1002/mbo3.169
Patek M, Grulich M, Nesvera J (2021) Stress response in Rhodococcus strains. Biotechnol Adv 53:107698. https://doi.org/10.1016/j.biotechadv.2021.107698
Pathak A, Chauhan A, Blom J et al (2016) comparative genomics and metabolic analysis reveals peculiar characteristics of Rhodococcus opacus strain M213 particularly for naphthalene degradation. PLOS ONE 11:e0161032. https://doi.org/10.1371/journal.pone.0161032
Peng F, Liu Z, Wang L et al (2007) An oil-degrading bacterium: Rhodococcus erythropolis strain 3C-9 and its biosurfactants. J Appl Microbiol 102:1603–1611. https://doi.org/10.1111/j.1365-2672.2006.03267.x
Peng L, Yang C, Zeng G et al (2014) Characterization and application of bioflocculant prepared by Rhodococcus erythropolis using sludge and livestock wastewater as cheap culture media. Appl Microbiol Biotechnol 98:6847–6858. https://doi.org/10.1007/s00253-014-5725-4
Peng T, Kan J, Hu J et al (2020) Genes and novel sRNAs involved in PAHs degradation in marine bacteria Rhodococcus sp. P14 revealed by the genome and transcriptome analysis. 3 Biotech 10:140. https://doi.org/10.1007/s13205-020-2133-6
Peng T, Luo A, Kan J et al (2018) Identification of a ring-hydroxylating dioxygenases capable of anthracene and benz[a]anthracene oxidization from Rhodococcus sp. P14. J Mol Microb Biotech 28:183–189. https://doi.org/10.1159/000494384
Pirog T, Shulyakova M, Sofilkanych A et al (2015) Biosurfactant synthesis by Rhodococcus erythropolis IMV Ac-5017, Acinetobacter calcoaceticus IMV B-7241 and Nocardia vaccinii IMV B-7405 on byproduct of biodiesel production. Food Bioprod Process 93:11–18. https://doi.org/10.1016/j.fbp.2013.09.003
Priefert H, O’Brien XM, Lessard PA et al (2004) Indene bioconversion by a toluene inducible dioxygenase of Rhodococcus sp. I24. Appl Microbiol Biot 65:168–176. https://doi.org/10.1007/s00253-004-1589-3
Ringelberg DB, Talley JW, Perkins EJ et al (2001) Succession of phenotypic, genotypic, and metabolic community characteristics during in vitro bioslurry treatment of polycyclic aromatic hydrocarbon-contaminated sediments. Appl Environ Microb 67:1542–1550. https://doi.org/10.1128/AEM.67.4.1542-1550.2001
Rodriguez A, Zarate SG, Bastida A (2022) Identification of new dioxygenases able to recognize polycyclic aromatic hydrocarbons with high aromaticity. Catalysts 12:279. https://doi.org/10.3390/catal12030279
Sakshi SSK, Haritash AK (2021) Catabolic enzyme activities during biodegradation of three-ring PAHs by novel DTU-1Y and DTU-7P strains isolated from petroleum-contaminated soil. Arch Microbiol 203:3101–3110. https://doi.org/10.1007/s00203-021-02297-4
Sazykin I, Makarenko M, Khmelevtsova L et al (2019) Cyclohexane, naphthalene, and diesel fuel increase oxidative stress, CYP153, sodA, and recA gene expression in Rhodococcus erythropolis. Microbiology 8:e00855. https://doi.org/10.1002/mbo3.855
Silva RA, Grossi V, Olivera NL et al (2010) Characterization of indigenous Rhodococcus sp. 602, a strain able to accumulate triacylglycerides from naphthyl compounds under nitrogen-starved conditions. Res Microbiol 161:198–207. https://doi.org/10.1016/j.resmic.2010.01.007
Singhi D, Jain A, Srivastava P (2016) Localization of low copy number plasmid pRC4 in replicating rod and non-replicating cocci cells of Rhodococcus erythropolis PR4. PLOS ONE 11:e0166491. https://doi.org/10.1371/journal.pone.0166491
Stancu MM (2015) Response of Rhodococcus erythropolis strain IBBPo1 to toxic organic solvents. Braz J Microbiol 46:1009–1018. https://doi.org/10.1590/S1517-838246420140462
Stes E, Francis I, Pertry I et al (2013) The leafy gall syndrome induced by Rhodococcus fascians. FEMS Microbiol Lett 342:187–194. https://doi.org/10.1111/1574-6968.12119
Subashchandrabose SR, Venkateswarlu K, Naidu R et al (2019a) Biodegradation of high-molecular weight PAHs by Rhodococcus wratislaviensis strain 9: overexpression of amidohydrolase induced by pyrene and BaP. Sci Total Environ 651:813–821. https://doi.org/10.1016/j.scitotenv.2018.09.192
Subashchandrabose SR, Venkateswarlu K, Venkidusamy K et al (2019b) Bioremediation of soil long-term contaminated with PAHs by algal–bacterial synergy of Chlorella sp. MM3 and Rhodococcus wratislaviensis strain 9 in slurry phase. Sci Total Environ 659:724–731. https://doi.org/10.1016/j.scitotenv.2018.12.453
Subbotina NM, Chernykh AM, Taranov AI et al (2020) Gentisate 1,2-dioxygenase from the gram-positive bacteria Rhodococcus opacus 1CP: identical active sites vs. different substrate selectivities. Biochimie 180:90–103. https://doi.org/10.1016/j.biochi.2020.10.016
Sun GD, Xu Y, Liu Y et al (2014) Microbial community dynamics of soil mesocosms using Orychophragmus violaceus combined with Rhodococcus ruber Em1 for bioremediation of highly PAH-contaminated soil. Appl Microbiol Biot 98:10243–10253. https://doi.org/10.1007/s00253-014-5971-5
Sun SS, Wang HZ, Fu BX et al (2020) Non-bioavailability of extracellular 1-hydroxy-2-naphthoic acid restricts the mineralization of phenanthrene by Rhodococcus sp. WB9. Sci Total Environ 704:135331. https://doi.org/10.1016/j.scitotenv.2019.135331
Svec P, Cernohlavkova J, Busse HJ et al (2015) Classification of strain CCM 4446T as Rhodococcus degradans sp. nov. Int J Syst Evol Microbiol 65:4381–4387. https://doi.org/10.1099/ijsem.0.000584
Taguchi K, Motoyama M, Iida T et al (2007) Polychlorinated biphenyl/biphenyl degrading gene clusters in Rhodococcus sp. K37, HA99, and TA431 are different from well-known bph gene clusters of Rhodococci. Biosci Biotech Bioch 71:1136–1144. https://doi.org/10.1271/bbb.60551
Takeda H, Masai E, Yamada A et al (2004) Characterization of transcriptional regulatory genes for biphenyl degradation in Rhodococcus sp. strain RHA1. J Bacteriol 186:2134–2146. https://doi.org/10.1128/JB.186.7.2134-2146.2004
Tamura A, Fukutani Y, Takami T et al (2015) Packaging guest proteins into the encapsulin nanocompartment from Rhodococcus erythropolis N771. Biotechnol Bioeng 112:13–20. https://doi.org/10.1002/bit.25322
Tao S, Gao Y, Li K et al (2020) Engineering substrate recognition sites of cytochrome P450 monooxygenase CYP116B3 from Rhodococcus ruber for enhanced regiospecific naphthalene hydroxylation. Mol Catal 493:111089. https://doi.org/10.1016/j.mcat.2020.111089
Tartaglia M, Zuzolo D, Postiglione A et al (2022) Biotechnological combination for co-contaminated soil remediation: focus on tripartite “meta-enzymatic” activity. Front Plant Sci 13:852513. https://doi.org/10.3389/fpls.2022.852513
Teng TT, Liang JD, Zhu JW et al (2022) Altered active pyrene degraders in biosurfactant-assisted bioaugmentation as revealed by RNA stable isotope probing. Environ Pollut 313:120192. https://doi.org/10.1016/j.envpol.2022.120192
Tomás-Gallardo L, Gómez-Alvarez H, Santero E et al (2014) Combination of degradation pathways for naphthalene utilization in Rhodococcus sp. strain TF. Microb Biotechnol 7:100–113. https://doi.org/10.1111/1751-7915.12096
Undabarrena A, Salva-Serra F, Jaen-Luchoro D et al (2018) Complete genome sequence of the marine Rhodococcus sp. H-CA8f isolated from Comau fjord in Northern Patagonia. Chile Mar Genom 40:13–17. https://doi.org/10.1016/j.margen.2018.01.004
Urano N, Kataoka M, Ishige T et al (2011) Genetic analysis around aminoalcohol dehydrogenase gene of Rhodococcus erythropolis MAK154: a putative GntR transcription factor in transcriptional regulation. Appl Microbiol Biotechnol 89:739–746. https://doi.org/10.1007/s00253-010-2924-5
Vaidya S, Jain K, Madamwar D (2017) Metabolism of pyrene through phthalic acid pathway by enriched bacterial consortium composed of Pseudomonas, Burkholderia, and Rhodococcus (PBR). 3 Biotech 7:29. https://doi.org/10.1007/s13205-017-0598-8
Van-Hamme JD, Singh A, Ward OP (2003) Recent advances in petroleum microbiology. Microbiol Mol Biol Rev 67:503. https://doi.org/10.1128/MMBR.67.4.503-549.2003
Viesser JA, Sugai-Guerios MH, Malucelli LC (2020) Petroleum-tolerant rhizospheric bacteria: isolation, characterization and bioremediation potential. Sci Rep 10:2060. https://doi.org/10.1038/s41598-020-59029-9
Wang H, Hu J, Xu K et al (2018) Biodegradation and chemotaxis of polychlorinated biphenyls, biphenyls, and their metabolites by Rhodococcus spp. Biodegradation 29:1–10. https://doi.org/10.1007/s10532-017-9809-6
Wang HQ, Yang Y, Xu J et al (2019a) iTRAQ-based comparative proteomic analysis of differentially expressed proteins in Rhodococcus sp. BAP-1 induced by fluoranthene. Ecotoxicol Environ Saf 169:282–291. https://doi.org/10.1016/j.ecoenv.2018.11.022
Wang WP, Zhong RQ, Shan DP et al (2014) Indigenous oil-degrading bacteria in crude oil-contaminated seawater of the Yellow sea, China. Appl Microbiol Biot 98:7253–7269. https://doi.org/10.1007/s00253-014-5817-1
Wang XN, Chen JX, Wang YG et al (2022) Promoting resuscitation of the VBNC bacteria and enrichment of naphthalene-degrading bacteria from oil-contaminated soils with the Rpf4 from Rhodococcus erythropolis KB1. Geomicrobiol J 39:916–924. https://doi.org/10.1080/01490451.2022.2097339
Wang Y, Nie MQ, Diwu ZJ et al (2019b) Characterization of trehalose lipids produced by a unique environmental isolate bacterium Rhodococcus qingshengii strain FF. J Appl Microbiol 127:1442–1453. https://doi.org/10.1111/jam.14390
Wang Y, Nie MQ, Diwu ZJ et al (2021) Toxicity evaluation of the metabolites derived from the degradation of phenanthrene by one of a soil ubiquitous PAHs-degrading strain Rhodococcus qingshengii FF. J Hazard Mater 415:125657. https://doi.org/10.1016/j.jhazmat.2021.125657
Wang ZL, Sun Y, Li XD et al (2017) A novel acetaldehyde dehydrogenase with salicylaldehyde dehydrogenase activity from Rhodococcus ruber strain OA1. Curr Microbiol 74:1404–1410. https://doi.org/10.1007/s00284-017-1333-8
Warren R, Hsiao WWL, Kudo H et al (2003) Functional characterization of a catabolic plasmid from polychlorinated biphenyl-degrading Rhodococcus sp. strain RHA1. J Bacteriol 186:7783–7795. https://doi.org/10.1128/JB.186.22.7783-7795.2004
Wu P, Wang YS (2021) Fluorene degradation by Rhodococcus sp. A2-3 isolated from hydrocarbon contaminated sediment of the Pearl River estuary. China. Ecotoxicol 30:929–935. https://doi.org/10.1007/s10646-021-02379-5
Xu J, Wang H, Kong D (2018) 2-DE Compared with iTRAQ-based proteomic analysis of the functional regulation of proteins in Rhodococcus sp. BAP-1 response to fluoranthene. IOP Conference Series-Earth and Environmental. Science 111:012032. https://doi.org/10.1088/1755-1315/111/1/012032
Yam KC, van der Geize R, Eltis LD (2010) Catabolism of aromatic compounds and steroids by Rhodococcus. Microbiol Monogr 16:133–169. https://doi.org/10.1007/978-3-642-12937-7_6
Yang HY, Jia RB, Chen C (2014) Degradation of recalcitrant aliphatic and aromatic hydrocarbons by a dioxin-degrader Rhodococcus sp. strain p52. Environ Sci Pollit R 21:11086–11093. https://doi.org/10.1007/s11356-014-3027-0
Yang X, Liu X, Song L et al (2010) Characterization and functional analysis of a novel gene cluster involved in biphenyl degradation in Rhodococcus sp. strain R04. J Appl Microbiol 103:2214–2224. https://doi.org/10.1111/j.1365-2672.2007.03461.x
Yoo M, Kim D, Zylstra GJ et al (2011) Biphenyl hydroxylation enhanced by an engineered o-xylene dioxygenase from Rhodococcus sp. strain DK17. Res Microbiol 162:724–728. https://doi.org/10.1016/j.resmic.2011.04.013
Yu C, Wang H, Blaustein RA et al (2022) Pangenomic and functional investigations for dormancy and biodegradation features of an organic pollutant-degrading bacterium Rhodococcus biphenylivorans TG9. Sci Total Environ 809:151141. https://doi.org/10.1016/j.scitotenv.2021.151141
Yu C, Yao J, Cai M et al (2014) Polycyclic aromatic hydrocarbons degrading microflora in a tropical oil-production well. Bull Environ Contam Toxicol 93:632–636. https://doi.org/10.1007/s00128-014-1371-x
Zainal PNS, Alang-Ahmad SA, Abdul-Aziz SFN et al (2022) Polycyclic aromatic hydrocarbons: occurrence, electroanalysis, challenges, and future outlooks. Crit Rev Anal Chem 52:878–896. https://doi.org/10.1080/10408347.2020.1839736
Zampolli J, De-Giani A, Di-Canito A et al (2022) Identification of a novel biosurfactant with antimicrobial activity produced by Rhodococcus opacus R7. Microorganisms 10:475. https://doi.org/10.3390/microorganisms10020475
Zhang Y, Qin FJ, Qiao J et al (2012) Draft genome sequence of Rhodococcus sp. strain P14, a biodegrader of high-molecular-weight polycyclic aromatic hydrocarbons. J Bacteriol 194:3546. https://doi.org/10.1128/JB.00555-12
Zhu SN, Liu DQ, Fan L et al (2008) Isolation, identification and degradation characteristics of a quinoline-degrading bacterium Rhodococcus sp. QL2. Huanjing Kexue 29:488–493. https://doi.org/10.3321/j.issn:0250-3301.2008.02.035
Zopf W (1891) Ueber Ausscheidung von Fettfarbstoffen (Lipochromen) seitens gewisser Spaltpilze. Ber Dtsch Bot Ges 9:22–28. https://doi.org/10.1111/j.1438-8677.1891.tb05764.x
Funding
This work was financially supported by the National Natural Science Foundation of China (Grant No. 31760028 and No. 4226070032), the Natural Science Foundation of Gansu Province, China (Grant No. 21JR11RA108), the University Innovation Fund Project of Gansu Provincial Department of Education (2021B-049), the Cuiying Scientific and Technological Innovation Program of Lanzhou University Second Hospital (Grant No.2020QN-02), and the Cuiying Student Research and Cultivation Project of Lanzhou University Second Hospital (CYXZ2021-20 and CYXZ2021-21).
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JM: writing—original draft, figures. YZ: writing—original draft, figures. YW: conceptualization, supervision, funding acquisition. NZ: formal analysis. TW: review, editing. HX: review, editing. JC: validation, funding acquisition.
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Ma, ., Zhuang, Y., Wang, Y. et al. Update on new trend and progress of the mechanism of polycyclic aromatic hydrocarbon biodegradation by Rhodococcus, based on the new understanding of relevant theories: a review. Environ Sci Pollut Res 30, 93345–93362 (2023). https://doi.org/10.1007/s11356-023-28894-y
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DOI: https://doi.org/10.1007/s11356-023-28894-y