Abstract
Halogenated organic compounds are naturally occurring in subsurface environments; however, accumulation of the degradative intermediate cis-1,2-dichloroethene (cDCE) at soil and groundwater sites contaminated with xenobiotic chlorinated ethenes is a global environmental and public health issue. Identifying microorganisms capable of cDCE degradation in these environments is of interest because of their potential application to bioremediation techniques. In this study, we sequenced, assembled, and analyzed the complete genome of Acinetobacter pittii CEP14, a strain isolated from chloroethene-contaminated groundwater, that has demonstrated the ability for aerobic cometabolic degradation of cDCE in the presence of n-hexane, phenol, and toluene. The A. pittii CEP14 genome consists of a 3.93 Mbp-long chromosome (GenBank accession no. CP084921) with a GC content of 38.9% and three plasmids (GenBank accession no. CP084922, CP084923, and CP084924). Gene function was assigned to 83.4% of the 3,930 coding DNA sequences. Functional annotation of the genome revealed that the CEP14 strain possessed all genetic elements to mediate the degradation of a range of aliphatic and aromatic compounds, including n-hexane and phenol. In addition, it harbors gene clusters involved in cytosol detoxification and oxidative stress resistance, which could play a role in the mitigation of toxic chemical intermediates that can arise during the degradation of cDCE. Gene clusters for heavy metal and antibiotic resistance were also identified in the genome of CEP14. These results suggest that CEP14 may be a versatile degrader of xenobiotic compounds and well-adapted to polluted environments, where a combination of heavy metal and organic compound pollution is often found.
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References
Abbasian F, Lockington R, Mallavarapu M, Naidu R (2015) A comprehensive review of aliphatic hydrocarbon biodegradation by bacteria. Appl Biochem Biotechnol 176(3):670–699. https://doi.org/10.1007/s12010-015-1603-5
Allocati N, Federici L, Masulli M, Di Ilio C (2009) Glutathione transferases in bacteria. FEBS J 276(1):58–75. https://doi.org/10.1111/j.1742-4658.2008.06743.x
Aramaki T, Blanc-Mathieu R, Endo H, Ohkubo K, Kanehisa M, Goto S, Ogata H (2020) KofamKOALA: KEGG Ortholog assignment based on profile HMM and adaptive score threshold. Bioinformatics 36(7):2251–2252. https://doi.org/10.1093/bioinformatics/btz859
Ben Fekih I, Zhang C, Li YP, Zhao Y, Alwathnani HA, Saquib Q, Rensing C, Cervantes C (2018) Distribution of arsenic resistance genes in prokaryotes. Front Microbiol 9:2473. https://doi.org/10.3389/fmicb.2018.02473
Bertelli C, Laird MR, Williams KP, Simon Fraser University Research Computing Group, Lau BY, Hoad G, Winsor GL, Brinkman FSL (2017) IslandViewer 4: expanded prediction of genomic islands for larger-scale datasets. Nucleic Acids Res 45(W1):W30–W35. https://doi.org/10.1093/nar/gkx343
Bolger AM, Lohse M, Usadel B (2014) Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30(15):2114–2120. https://doi.org/10.1093/bioinformatics/btu170
Broholm K, Ludvigsen L, Jensen TF, Østergaard H (2005) Aerobic biodegradation of vinyl chloride and cis-1,2-dichloroethylene in aquifer sediments. Chemosphere 60(11):1555–1564. https://doi.org/10.1016/j.chemosphere.2005.02.056
Bundy BM, Campbell AL, Neidle EL (1998) Similarities between the antABC-encoded anthranilate dioxygenase and the benABC-encoded benzoate dioxygenase of Acinetobacter sp. strain ADP1. J Bacteriol 180(17):4466–4474. https://doi.org/10.1128/JB.180.17.4466-4474.1998
Chun J, Oren A, Ventosa A, Christensen H, Arahal DR, da Costa MS, Rooney AP, Yi H, Xu XW, De Meyer S, Trujillo ME (2018) Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. Int J Syst Evol 68(1):461–466. https://doi.org/10.1099/ijsem.0.002516
Clark TJ, Momany C, Neidle EL (2002) The benPK operon, proposed to play a role in transport, is part of a regulon for benzoate catabolism in Acinetobacter sp. strain ADP1. Microbiology 148(Pt 4):1213–1223. https://doi.org/10.1099/00221287-148-4-1213
Coleman N, Mattes T, Gossett J, Spain J (2002) Biodegradation of cis-dichloroethene as the sole carbon source by a beta-proteobacterium. Appl Environ Microbiol 68(6):2726–2730. https://doi.org/10.1128/aem.68.6.2726-2730.2002
Collier LS, Gaines GL 3rd, Neidle EL (1998) Regulation of benzoate degradation in Acinetobacter sp. strain ADP1 by BenM, a LysR-type transcriptional activator. J Bacteriol 180(9):2493–2501. https://doi.org/10.1128/JB.180.9.2493-2501.1998
Czinnerová M, Vološčuková O, Marková K, Ševců A, Černík M, Nosek J (2020) Combining nanoscale zero-valent iron with electrokinetic treatment for remediation of chlorinated ethenes and promoting biodegradation: a long-term field study. Water Res 175:115692. https://doi.org/10.1016/j.watres.2020.115692
Dal S, Steiner I, Gerischer U (2002) Multiple operons connected with catabolism of aromatic compounds in Acinetobacter sp. strain ADP1 are under carbon catabolite repression. J Mol Microbiol Biotechnol 4(4):389–404
Denby KJ, Iwig J, Bisson C, Westwood J, Rolfe MD, Sedelnikova SE, Higgins K, Maroney MJ, Baker PJ, Chivers PT et al (2016) The mechanism of a formaldehyde-sensing transcriptional regulator. Sci Rep 6(1):38879. https://doi.org/10.1038/srep38879
DiMarco AA, Averhoff B, Ornston LN (1993) Identification of the transcriptional activator pobR and characterization of its role in the expression of pobA, the structural gene for p-hydroxybenzoate hydroxylase in Acinetobacter calcoaceticus. J Bacteriol 175(14):4499–4506. https://doi.org/10.1128/jb.175.14.4499-4506.1993
Doherty RE (2000) A history of the production and use of carbon tetrachloride, tetrachloroethylene, trichloroethylene and 1,1,1-trichloroethane in the United States: part 1—historical background; carbon tetrachloride and tetrachloroethylene. Environ Forensics 1(2):69–81. https://doi.org/10.1006/enfo.2000.0010
Dolinová I, Štrojsová M, Černík M, Němeček J, Macháčková J, Ševců A (2017) Microbial degradation of chloroethenes: a review. Environ Sci Pollut Res 24(15):13262–13283. https://doi.org/10.1007/s11356-017-8867-y
Doughty DM, Sayavedra-Soto LA, Arp DJ, Bottomley PJ (2005) Effects of dichloroethene isomers on the induction and activity of butane monooxygenase in the alkane-oxidizing bacterium “Pseudomonas butanovora.” Appl Environ Microbiol 71(10):6054–6059. https://doi.org/10.1128/AEM.71.10.6054-6059.2005
Ensign SA, Hyman MR, Arp DJ (1992) Cometabolic degradation of chlorinated alkenes by alkene monooxygenase in a propylene-grown Xanthobacter strain. Appl Environ Microbiol 58(9):3038–3046. https://doi.org/10.1128/aem.58.9.3038-3046.1992
Feng L, Wang W, Cheng J, Ren Y, Zhao G, Gao C, Tang Y, Liu X, Han W, Peng X et al (2007) Genome and proteome of long-chain alkane degrading Geobacillus thermodenitrificans NG80-2 isolated from a deep-subsurface oil reservoir. Proc Natl Acad Sci 104(13):5602–5607. https://doi.org/10.1073/pnas.0609650104
Fernández C, Díaz E, García JL (2014) Insights on the regulation of the phenylacetate degradation pathway from Escherichia coli. Environ Microbiol Rep 6(3):239–250. https://doi.org/10.1111/1758-2229.12117
Fraraccio S, Strejcek M, Dolinova I, Macek T, Uhlik O (2017) Secondary compound hypothesis revisited: selected plant secondary metabolites promote bacterial degradation of cis-1,2-dichloroethylene (cDCE). Sci Rep 7(1):8406. https://doi.org/10.1038/s41598-017-07760-1
Ge Y, Eltis LD (2003) Characterization of hybrid toluate and benzoate dioxygenases. J Bacteriol 185(18):5333–5341. https://doi.org/10.1128/JB.185.18.5333-5341.2003
Geißdörfer W, Kok RG, Ratajczak A, Hellingwerf KJ, Hillen W (1999) The genes rubA and rubB for alkane degradation in Acinetobacter sp. strain ADP1 are in an operon with estB, encoding an esterase, andoxyR. J Bacteriol 181(14):4292–4298. https://doi.org/10.1128/JB.181.14.4292-4298.1999
Grant JR, Stothard P (2008) The CGView Server: a comparative genomics tool for circular genomes. Nucleic Acids Res 36(suppl_2):W181–W184. https://doi.org/10.1093/nar/gkn179
Haritash AK, Kaushik CP (2009) Biodegradation aspects of polycyclic aromatic hydrocarbons (PAHs): a review. J Hazard Mater 169(1):1–15. https://doi.org/10.1016/j.jhazmat.2009.03.137
Hayes F (2003) Toxins-antitoxins: plasmid maintenance, programmed cell death, and cell cycle arrest. Science 301(5639):1496–1499. https://doi.org/10.1126/science.1088157
Huerta-Cepas J, Forslund K, Coelho LP, Szklarczyk D, Jensen LJ, von Mering C, Bork P (2017) Fast genome-wide functional annotation through orthology assignment by eggNOG-Mapper. Mol Biol Evol 34(8):2115–2122. https://doi.org/10.1093/molbev/msx148
Inoue Y, Fukunaga Y, Katsumata H, Ohji S, Hosoyama A, Mori K, Ando K (2020) Aerobic degradation of cis-dichloroethene by the marine bacterium Marinobacter salsuginis strain 5N–3. J Gen Appl Microbiol 66(4):215–219. https://doi.org/10.2323/jgam.2019.10.001
Ismail W, El-Sayed W (2013) Degradation of phenylacetate by Acinetobacter spp.: evidence for the phenylacetyl-coenzyme A pathway. Ann Microbiol 63:1451–1458. https://doi.org/10.1007/s13213-013-0608-y
Jennings LK, Chartrand MMG, Lacrampe-Couloume G, Lollar BS, Spain JC, Gossett JM (2009) Proteomic and transcriptomic analyses reveal genes upregulated by cis-dichloroethene in Polaromonas sp. strain JS666. Appl Environ Microbiol 75(11):3733–3744. https://doi.org/10.1128/AEM.00031-09
Jerg B, Gerischer U (2008) Relevance of nucleotides of the PcaU binding site from Acinetobacter baylyi. Microbiology 154:756–766. https://doi.org/10.1099/mic.0.2007/013508-0
Ji Y, Mao G, Wang Y, Bartlam M (2013) Structural insights into diversity and n-alkane biodegradation mechanisms of alkane hydroxylases. Front Microbiol. https://doi.org/10.3389/fmicb.2013.00058
Jugder B-E, Ertan H, Lee M, Manefield M, Marquis CP (2015) Reductive dehalogenases come of age in biological destruction of organohalides. Trends Biotechnol 33(10):595–610. https://doi.org/10.1016/j.tibtech.2015.07.004
Kanehisa M, Furumichi M, Sato Y, Ishiguro-Watanabe M, Tanabe M (2021) KEGG: integrating viruses and cellular organisms. Nucleic Acids Res 49(D1):D545–D551. https://doi.org/10.1093/nar/gkaa970
Kolmogorov M (2019) Fast and accurate de novo assembler for single molecule sequencing reads: fenderglass/Flye
Letunic I, Bork P (2019) Interactive tree of life (iTOL) v4: recent updates and new developments. Nucleic Acids Res 47(W1):W256–W259. https://doi.org/10.1093/nar/gkz239
Li L, Liu X, Yang W, Xu F, Wang W, Feng L, Bartlam M, Wang L, Rao Z (2008) Crystal structure of long-chain alkane monooxygenase (LadA) in complex with coenzyme FMN: unveiling the long-chain alkane hydroxylase. J Mol Biol 376(2):453–465. https://doi.org/10.1016/j.jmb.2007.11.069
Li H (2013) Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. http://arxiv.org/abs/1303.3997
Matsumura E, Sakai M, Hayashi K, Murakami S, Takenaka S, Aoki K (2006) Constitutive expression of catABC genes in the aniline-assimilating bacterium Rhodococcus species AN-22: production, purification, characterization and gene analysis of CatA. CatB and CatC Biochem J 393(Pt 1):219–226. https://doi.org/10.1042/BJ20050740
Meier-Kolthoff JP, Göker M (2019) TYGS is an automated high-throughput platform for state-of-the-art genome-based taxonomy. Nat Commun 10(1):2182. https://doi.org/10.1038/s41467-019-10210-3
Moran MJ, Zogorski JS, Squillace PJ (2007) Chlorinated solvents in groundwater of the United States. Environ Sci Technol 41(1):74–81. https://doi.org/10.1021/es061553y
Morawski B, Segura A, Ornston LN (2000) Substrate range and genetic analysis of Acinetobacter vanillate demethylase. J Bacteriol 182(5):1383–1389. https://doi.org/10.1128/JB.182.5.1383-1389.2000
National Center for Biotechnology Information (NCBI) (1988) [accessed 2021 Jul 18]. https://www.ncbi.nlm.nih.gov/
Navarro CA, Orellana LH, Mauriaca C, Jerez CA (2009) Transcriptional and functional studies of Acidithiobacillus ferrooxidans genes related to survival in the presence of copper. Appl Environ Microbiol 75(19):6102–6109. https://doi.org/10.1128/AEM.00308-09
Nies DH (1992) Resistance to cadmium, cobalt, zinc, and nickel in microbes. Plasmid 27(1):17–28. https://doi.org/10.1016/0147-619X(92)90003-S
Nishino SF, Shin KA, Gossett JM, Spain JC (2013) Cytochrome P450 Initiates the degradation of cis-dichloroethene by Polaromonas sp strain JS666. Appl Environ Microbiol 79(7):2263–2272. https://doi.org/10.1128/AEM.03445-12
O’Connell J, Schulz-Trieglaff O, Carlson E, Hims MM, Gormley NA, Cox AJ (2015) NxTrim: optimized trimming of Illumina mate pair reads. Bioinformatics 31(12):2035–2037. https://doi.org/10.1093/bioinformatics/btv057
Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW (2015) CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res 25(7):1043–1055
Qin J, Feng Y, Lü X, Zong Z, Lal R (2021) Precise species identification for acinetobacter: a genome-based study with description of two novel acinetobacter species. mSystems 6(3):e00237-e321. https://doi.org/10.1128/mSystems.00237-21
Ratajczak A, Geißdörfer W, Hillen W (1998) Expression of alkane hydroxylase from Acinetobacter sp. strain ADP1 is induced by a broad range of n-alkanes and requires the transcriptional activator AlkR. J Bacteriol 180(22):5822–5827. https://doi.org/10.1128/JB.180.22.5822-5827.1998
Ridl J, Suman J, Fraraccio S, Hradilova M, Strejcek M, Cajthaml T, Zubrova A, Macek T, Strnad H, Uhlik O (2018) Complete genome sequence of Pseudomonas alcaliphila JAB1 (=DSM 26533), a versatile degrader of organic pollutants. Stand Genomic Sci 13:3. https://doi.org/10.1186/s40793-017-0306-7
Roane TM, Josephson KL, Pepper IL (2001) Dual-bioaugmentation strategy to enhance remediation of cocontaminated soil. Appl Environ Microbiol 67(7):3208–3215. https://doi.org/10.1128/AEM.67.7.3208-3215.2001
Sestok AE, Linkous RO, Smith AT (2018) Toward a mechanistic understanding of Feo-mediated ferrous iron uptake. Metallomics 10(7):887–898. https://doi.org/10.1039/c8mt00097b
Shim H, Ryoo D, Barbieri P, Wood TK (2001) Aerobic degradation of mixtures of tetrachloroethylene, trichloroethylene, dichloroethylenes, and vinyl chloride by toluene-o-xylene monooxygenase of Pseudomonas stutzeri OX1. Appl Microbiol Biotechnol 56(1–2):265–269. https://doi.org/10.1007/s002530100650
Small FJ, Ensign SA (1997) Alkene monooxygenase from Xanthobacter strain Py2. J Biol Chem 272(40):24913–24920. https://doi.org/10.1128/AEM.65.4.1589-1595.1999
Strejcek M, Smrhova T, Junkova P, Uhlik O (2018) Whole-cell MALDI-TOF MS versus 16S rRNA gene analysis for identification and dereplication of recurrent bacterial isolates. Front Microbiol 9:1294. https://doi.org/10.3389/fmicb.2018.01294
Tani A, Ishige T, Sakai Y, Kato N (2001) Gene structures and regulation of the alkane hydroxylase complex in Acinetobacter sp. strain M-1. J Bacteriol 183(5):1819–1823. https://doi.org/10.1128/JB.183.5.1819-1823.2001
Tatusov RL, Galperin MY, Natale DA, Koonin EV (2000) The COG database: a tool for genome-scale analysis of protein functions and evolution. Nucleic Acids Res 28(1):33–36. https://doi.org/10.1093/nar/28.1.33
Tatusova T, DiCuccio M, Badretdin A, Chetvernin V, Nawrocki EP, Zaslavsky L, Lomsadze A, Pruitt KD, Borodovsky M, Ostell J (2016) NCBI prokaryotic genome annotation pipeline. Nucleic Acids Res 44(14):6614–6624. https://doi.org/10.1093/nar/gkw569
Tsien HC, Brusseau GA, Hanson RS, Waclett LP (1989) Biodegradation of trichloroethylene by Methylosinus trichosporium OB3b. Appl Environ Microbiol 55(12):3155–3161. https://doi.org/10.1128/aem.55.12.3155-3161.1989
Walker BJ, Abeel T, Shea T, Priest M, Abouelliel A, Sakthikumar S, Cuomo CA, Zeng Q, Wortman J, Young SK (2014) Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement. PLoS ONE 9(11):e112963. https://doi.org/10.1371/journal.pone.0112963
World Health Organization (1996) 1,2-Dichloroethene in drinking water. In: Guidelines for drinking-water quality. 2nd ed. Geneva. p 4
Xu Y, Chen M, Zhang W, Lin M (2003) Genetic organization of genes encoding phenol hydroxylase, benzoate 1,2-dioxygenase alpha subunit and its regulatory proteins in Acinetobacter calcoaceticus PHEA-2. Curr Microbiol 46(4):235–240. https://doi.org/10.1007/s00284-002-3840-4
Xu C, Bilya SR, Xu W (2019) adeABC efflux gene in Acinetobacter baumannii. New Microbes New Infect 30:100549. https://doi.org/10.1016/j.nmni.2019.100549
Yoon SH, Ha SM, Lim JM, Kwon SJ, Chun J (2017) A large-scale evaluation of algorithms to calculate average nucleotide identity. Antonie Van Leeuwenhoek 110:1281–1286. https://doi.org/10.1007/s10482-017-0844-4
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The research reported herein was supported by the INTER-EXCELLENCE program of the Ministry of Education, Youth and Sports of the Czech Republic (MEYS CZ) under grant no. LTAUSA19013 and the Czech Science Foundation under grant no. 22-00150S. Further support is acknowledged of the ELIXIR CZ research infrastructure project (MEYS CZ grant no. LM2018131), specifically for access to computing and storage facilities.
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Conceptualization: OU, JS, MS; Methodology: MD, SF, JS, MS, OU; Formal analysis and investigation: MD, SF, JR, HK; Writing—original draft preparation: MD; Writing—review and editing: SF, JS, MS, OU; Resources: ID, AS, JR, HS, HK; Funding acquisition: OU, AS; Supervision: OU.
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The genome sequence assembly can be found under GenBank accession numbers CP084921 (chromosome), CP084922 (plasmid01), CP084923 (plasmid02), CP084924 (plasmid03).
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Desmarais, M., Fraraccio, S., Dolinova, I. et al. Genomic analysis of Acinetobacter pittii CEP14 reveals its extensive biodegradation capabilities, including cometabolic degradation of cis-1,2-dichloroethene. Antonie van Leeuwenhoek 115, 1041–1057 (2022). https://doi.org/10.1007/s10482-022-01752-6
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DOI: https://doi.org/10.1007/s10482-022-01752-6