Methanogenesis coupled hydrocarbon biodegradation enhanced by ferric and sulphate ions.
Aliphatics
Aromatics
Bioremediation
Electron acceptors
Methane
Oil
Journal
Applied microbiology and biotechnology
ISSN: 1432-0614
Titre abrégé: Appl Microbiol Biotechnol
Pays: Germany
ID NLM: 8406612
Informations de publication
Date de publication:
29 Aug 2024
29 Aug 2024
Historique:
received:
23
05
2024
accepted:
08
08
2024
revised:
05
08
2024
medline:
31
8
2024
pubmed:
31
8
2024
entrez:
29
8
2024
Statut:
epublish
Résumé
Bioremediation provides an environmentally sound solution for hydrocarbon removal. Although bioremediation under anoxic conditions is slow, it can be coupled with methanogenesis and is suitable for energy recovery. By altering conditions and supplementing alternative terminal electron acceptors to the system to induce syntrophic partners of the methanogens, this process can be enhanced. In this study, we investigated a hydrocarbon-degrading microbial community derived from chronically contaminated soil. Various hydrocarbon mixtures were used during our experiments in the presence of different electron acceptors. In addition, we performed whole metagenome sequencing to identify the main actors of hydrocarbon biodegradation in the samples. Our results showed that the addition of ferric ions or sulphate increased the methane yield. Furthermore, the addition of CO
Identifiants
pubmed: 39207532
doi: 10.1007/s00253-024-13278-0
pii: 10.1007/s00253-024-13278-0
doi:
Substances chimiques
Sulfates
0
Methane
OP0UW79H66
Hydrocarbons
0
Ferric Compounds
0
Soil Pollutants
0
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
449Subventions
Organisme : The European Union and the State of Hungary
ID : EFOP-3.6.2-16-2017-00010
Organisme : Hungarian Prime Minister's Office
ID : NTP-NFTÖ-20-B-0027
Organisme : University of Szeged Open Access Found
ID : 7036
Informations de copyright
© 2024. The Author(s).
Références
Abbasian F, Lockington R, Mallavarapu M, Naidu R (2015) A comprehensive review of aliphatic hydrocarbon biodegradation by bacteria. Appl Biochem Biotechnol 176:670–699. https://doi.org/10.1007/S12010-015-1603-5
doi: 10.1007/S12010-015-1603-5
pubmed: 25935219
Abbasian F, Palanisami T, Megharaj M, Naidu R, Lockington R, Ramadass K (2016) Microbial diversity and hydrocarbon degrading gene capacity of a crude oil field soil as determined by metagenomics analysis. Biotechnol Prog 32(3):638–648. https://doi.org/10.1002/btpr.2249
doi: 10.1002/btpr.2249
pubmed: 26914145
Achong GR, Rodriguez AM, Spormann AM (2001) Benzylsuccinate synthase of Azoarcus sp. strain T: cloning, sequencing, transcriptional organization, and its role in anaerobic toluene and m-xylene mineralization. J Bacteriol 183:6763–6770. https://doi.org/10.1128/JB.183.23.6763-6770.2001
doi: 10.1128/JB.183.23.6763-6770.2001
pubmed: 11698363
pmcid: 95515
Alneberg J, Bjarnason BS, De Bruijn I, Schirmer M, Quick J, Ijaz UZ, Lahti L, Loman NJ, Andersson AF, Quince C (2014) Binning metagenomic contigs by coverage and composition. Nat Methods 11:1144–1146. https://doi.org/10.1038/nmeth.3103
doi: 10.1038/nmeth.3103
pubmed: 25218180
Andrews S (2010) FastQC : a quality control tool for high throughput sequence data. https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ . Accessed 3 Apr 2020
Anselmann SEL, Löffler C, Stärk HJ, Jehmlich N, von Bergen M, Brüls T, Boll M (2019) The class II benzoyl-coenzyme A reductase complex from the sulfate-reducing Desulfosarcina cetonica. Environ Microbiol 21:4241–4252. https://doi.org/10.1111/1462-2920.14784
doi: 10.1111/1462-2920.14784
pubmed: 31430028
Arslan M, Gamal El-Din M (2021) Bacterial diversity in petroleum coke based biofilters treating oil sands process water. Sci Total Environ 782:146742. https://doi.org/10.1016/J.SCITOTENV.2021.146742
doi: 10.1016/J.SCITOTENV.2021.146742
pubmed: 33839672
Astuti DI, Purwasena IA, Priharto N, Ariadji T, Afifah LN, Saputro RB, Aditiawati P, Persada GP, Ananggadipa AA, Abqory MH, Amaniyah M, Dewi UR (2022) Bacterial community dynamics during MEOR biostimulation of an oil reservoir in Sumatera Indonesia. J Pet Sci Eng 208:109558. https://doi.org/10.1016/J.PETROL.2021.109558
doi: 10.1016/J.PETROL.2021.109558
Aulenta F, Tucci M, Cruz Viggi C, Dolfing J, Head IM, Rotaru A (2020) An underappreciated DIET for anaerobic petroleum hydrocarbon‐degrading microbial communities. Microb Biotechnol 1751-7915.13654. https://doi.org/10.1111/1751-7915.13654
Backman LRF, Funk MA, Dawson CD, Drennan CL (2017) New tricks for the glycyl radical enzyme family. Crit Rev Biochem Mol Biol 52:674. https://doi.org/10.1080/10409238.2017.1373741
doi: 10.1080/10409238.2017.1373741
pubmed: 28901199
pmcid: 5911432
Baoune H, Aparicio JD, Pucci G, Ould El Hadj-Khelil A, Polti MA (2019) Bioremediation of petroleum-contaminated soils using Streptomyces sp. Hlh1. J Soils Sediments 19:2222–2230. https://doi.org/10.1007/S11368-019-02259-W
doi: 10.1007/S11368-019-02259-W
Batool I, Gulfraz M, Asad MJ, Kabir F, Khadam S, Ahmed A (2018) Cellulomonas sp. Isolated from termite gut for saccharification and fermentation of agricultural biomass. BioResources 13:752–763. https://doi.org/10.15376/BIORES.13.1.752-763
doi: 10.15376/BIORES.13.1.752-763
Begmatov S, Beletsky AV, Dedysh SN, Mardanov AV, Ravin NV (2022) Genome analysis of the candidate phylum MBNT15 bacterium from a boreal peatland predicted its respiratory versatility and dissimilatory iron metabolism. Front Microbiol 13:951761. https://doi.org/10.3389/FMICB.2022.951761
doi: 10.3389/FMICB.2022.951761
pubmed: 35992725
pmcid: 9386147
Bolger AM, Lohse M, Usadel B (2014) Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30:2114–2120. https://doi.org/10.1093/bioinformatics/btu170
doi: 10.1093/bioinformatics/btu170
pubmed: 24695404
pmcid: 4103590
Boll M, Löffler C, Morris BEL, Kung JW (2014) Anaerobic degradation of homocyclic aromatic compounds via arylcarboxyl-coenzyme A esters: organisms, strategies and key enzymes. Environ Microbiol 16:612–627. https://doi.org/10.1111/1462-2920.12328
doi: 10.1111/1462-2920.12328
pubmed: 24238333
Bowers RM, Kyrpides NC, Stepanauskas R, Harmon-Smith M, Doud D, Reddy TBK, Schulz F, Jarett J, Rivers AR, Eloe-Fadrosh EA, Tringe SG, Ivanova NN, Copeland A, Clum A, Becraft ED, Malmstrom RR, Birren B, Podar M, Bork P, Weinstock GM, Garrity GM, Dodsworth JA, Yooseph S, Sutton G, Glöckner FO, Gilbert JA, Nelson WC, Hallam SJ, Jungbluth SP, Ettema TJG, Tighe S, Konstantinidis KT, Liu WT, Baker BJ, Rattei T, Eisen JA, Hedlund B, McMahon KD, Fierer N, Knight R, Finn R, Cochrane G, Karsch-Mizrachi I, Tyson GW, Rinke C, Lapidus A, Meyer F, Yilmaz P, Parks DH, Eren AM, Schriml L, Banfield JF, Hugenholtz P, Woyke T (2017) Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea. Nat Biotechnol 35:725–731
doi: 10.1038/nbt.3893
pubmed: 28787424
pmcid: 6436528
Buckel W, Kung JW, Boll M (2014) The benzoyl-coenzyme A reductase and 2-hydroxyacyl-coenzyme A dehydratase radical enzyme family. ChemBioChem 15:2188–2194. https://doi.org/10.1002/CBIC.201402270
doi: 10.1002/CBIC.201402270
pubmed: 25204868
Buckingham-Howes S, Holmes K, Glenn Morris J, Grattan LM (2019) Prolonged financial distress after the deepwater horizon oil spill predicts behavioral health. J Behav Heal Serv Res 46:294–305. https://doi.org/10.1007/S11414-018-9602-2
doi: 10.1007/S11414-018-9602-2
Callaghan AV (2013) Enzymes involved in the anaerobic oxidation of n-alkanes: from methane to long-chain paraffins. Front Microbiol 4:42641. https://doi.org/10.3389/FMICB.2013.00089
doi: 10.3389/FMICB.2013.00089
Cébron A, Borreca A, Beguiristain T, Biache C (2022) Faure P (2022) Taxonomic and functional trait-based approaches suggest that aerobic and anaerobic soil microorganisms allow the natural attenuation of oil from natural seeps. Sci Reports 121(12):1–16. https://doi.org/10.1038/s41598-022-10850-4
doi: 10.1038/s41598-022-10850-4
Chaumeil P-A, Mussig AJ, Hugenholtz P, Parks DH (2020) GTDB-Tk: a toolkit to classify genomes with the genome taxonomy database. Bioinformatics 36:1925–1927. https://doi.org/10.1093/bioinformatics/btz848
doi: 10.1093/bioinformatics/btz848
Chunyan X, Qaria MA, Qi X, Daochen Z (2023) The role of microorganisms in petroleum degradation: current development and prospects. Sci Total Environ 865:161112. https://doi.org/10.1016/J.SCITOTENV.2022.161112
doi: 10.1016/J.SCITOTENV.2022.161112
pubmed: 36586680
Coates JD, Ellis DJ, Gaw CV, Lovley DR (1999) Geothrix fermentans gen. nov., sp. nov., a novel Fe(III)-reducing bacterium from a hydrocarbon-contaminated aquifer. Int J Syst Bacteriol 49:1615–1622. https://doi.org/10.1099/00207713-49-4-1615
doi: 10.1099/00207713-49-4-1615
pubmed: 10555343
Conners EM, Rengasamy K, Bose A (2022) Electroactive biofilms: how microbial electron transfer enables bioelectrochemical applications. J Ind Microbiol Biotechnol 49(4):kuac012. https://doi.org/10.1093/JIMB/KUAC012
doi: 10.1093/JIMB/KUAC012
pubmed: 35381088
pmcid: 9338886
Davidson CJ, Hannigan JH, Bowen SE (2021) Effects of inhaled combined benzene, toluene, ethylbenzene, and xylenes (BTEX): toward an environmental exposure model. Environ Toxicol Pharmacol 81:103518. https://doi.org/10.1016/J.ETAP.2020.103518
doi: 10.1016/J.ETAP.2020.103518
pubmed: 33132182
Dhar K, Subashchandrabose SR, Venkateswarlu K, Krishnan K, Megharaj M (2020) Anaerobic microbial degradation of polycyclic aromatic hydrocarbons: a comprehensive review. Rev Environ Contam Toxicol 251:25–108. https://doi.org/10.1007/398_2019_29
doi: 10.1007/398_2019_29
pubmed: 31011832
Dojka MA, Hugenholtz P, Haack SK, Pace NR (1998) Microbial diversity in a hydrocarbon- and chlorinated-solvent- contaminated aquifer undergoing intrinsic bioremediation. Appl Environ Microbiol 64:3869–3877. https://doi.org/10.1128/AEM.64.10.3869-3877.1998
doi: 10.1128/AEM.64.10.3869-3877.1998
pubmed: 9758812
pmcid: 106571
Erb TJ (2011) Carboxylases in natural and synthetic microbial pathways. Appl Environ Microbiol 77:8466. https://doi.org/10.1128/AEM.05702-11
doi: 10.1128/AEM.05702-11
pubmed: 22003013
pmcid: 3233076
Ewels P, Magnusson M, Lundin S, Käller M (2016) MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics 32:3047–3048. https://doi.org/10.1093/bioinformatics/btw354
doi: 10.1093/bioinformatics/btw354
pubmed: 27312411
pmcid: 5039924
Fuchs G, Boll M, Heider J (2011) Microbial degradation of aromatic compounds — from one strategy to four. Nat Rev Microbiol 9:803–816. https://doi.org/10.1038/nrmicro2652
doi: 10.1038/nrmicro2652
pubmed: 21963803
Gurevich A, Saveliev V, Vyahhi N, Tesler G (2013) QUAST: quality assessment tool for genome assemblies. Bioinformatics 29:1072–1075. https://doi.org/10.1093/bioinformatics/btt086
doi: 10.1093/bioinformatics/btt086
pubmed: 23422339
pmcid: 3624806
Halios CH, Landeg-Cox C, Lowther SD, Middleton A, Marczylo T, Dimitroulopoulou S (2022) Chemicals in European residences – part i: a review of emissions, concentrations and health effects of volatile organic compounds (VOCs). Sci Total Environ 839:156201. https://doi.org/10.1016/J.SCITOTENV.2022.156201
doi: 10.1016/J.SCITOTENV.2022.156201
pubmed: 35623519
Hansson G, Molin N (1981) End product inhibition in methane fermentations: effects of carbon dioxide and methane on methanogenic bacteria utilizing acetate. Eur J Appl Microbiol Biotechnol 13:236–241. https://doi.org/10.1007/BF00500105
doi: 10.1007/BF00500105
Holmes DE, Shrestha PM, Walker DJF, Dang Y, Nevin KP, Woodard TL, Lovley DR (2017) Metatranscriptomic evidence for direct interspecies electron transfer between Geobacter and Methanothrix species in methanogenic rice paddy soils. Appl Environ Microbiol 83:223–240. https://doi.org/10.1128/AEM.00223-17
doi: 10.1128/AEM.00223-17
Hsia KF, Chen CC, Ou JH, Lo KH, Sheu YT, Kao CM (2021) Treatment of petroleum hydrocarbon-polluted groundwater with innovative in situ sulfate-releasing biobarrier. J Clean Prod 295:126424. https://doi.org/10.1016/J.JCLEPRO.2021.126424
doi: 10.1016/J.JCLEPRO.2021.126424
Huang D, Du Y, Xu Q, Ko JH (2022) Quantification and control of gaseous emissions from solid waste landfill surfaces. J Environ Manage 302:114001. https://doi.org/10.1016/J.JENVMAN.2021.114001
doi: 10.1016/J.JENVMAN.2021.114001
pubmed: 34731706
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 34:2115–2122. https://doi.org/10.1093/molbev/msx148
doi: 10.1093/molbev/msx148
pubmed: 28460117
pmcid: 5850834
Hunter JD (2007) Matplotlib: a 2D graphics environment. Comput Sci Eng 9:90–95. https://doi.org/10.1109/MCSE.2007.55
doi: 10.1109/MCSE.2007.55
Kang DD, Froula J, Egan R, Wang Z (2015) MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities. PeerJ 3:e1165. https://doi.org/10.7717/peerj.1165
doi: 10.7717/peerj.1165
pubmed: 26336640
pmcid: 4556158
Keating KS, Becker S, Davis IF, Chandler T, Slack T, Beedasy J (2020) Families coping with financial loss following the deepwater horizon oil spill. Fam Relat 69:887–906. https://doi.org/10.1111/FARE.12510
doi: 10.1111/FARE.12510
Khanal A, Hur HG, Fredrickson JK, Lee JH (2021) Direct and indirect reduction of Cr(VI) by fermentative Fe(III)-reducing Cellulomonas sp. strain Cellu-2a. J Microbiol Biotechnol 31:1519–1525. https://doi.org/10.4014/JMB.2107.07038
doi: 10.4014/JMB.2107.07038
pubmed: 34489371
pmcid: 9706010
Khanh Nguyen V, Kumar Chaudhary D, Hari Dahal R, Hoang Trinh N, Kim J, Chang SW, Hong Y, La Duc D, Nguyen XC, Hao Ngo H, Chung WJ, Nguyen DD (2021) Review on pretreatment techniques to improve anaerobic digestion of sewage sludge. Fuel 285:119105. https://doi.org/10.1016/J.FUEL.2020.119105
doi: 10.1016/J.FUEL.2020.119105
Laczi K, Erdeiné Kis Á, Szilágyi Á, Bounedjoum N, Bodor A, Vincze GE, Kovács T, Rákhely G, Perei K (2020) New frontiers of anaerobic hydrocarbon biodegradation in the multi-omics era. Front Microbiol 11:2886
doi: 10.3389/fmicb.2020.590049
Leahy SC, Janssen PH, Attwood GT, Mackie RI, McAllister TA, Kelly WJ (2022) Electron flow: key to mitigating ruminant methanogenesis. Trends Microbiol 30:209–212. https://doi.org/10.1016/J.TIM.2021.12.005
doi: 10.1016/J.TIM.2021.12.005
pubmed: 35027237
Lee J, Kwon S, Joung W, Kim D (2017) Measurement of the calorific value of methane by calorimetry using metal burner. Int J Thermophys 38:1–16. https://doi.org/10.1007/S10765-017-2306-7
doi: 10.1007/S10765-017-2306-7
Leuthner B, Heider J (2000) Anaerobic toluene catabolism of Thauera aromatica: the bbs operon codes for enzymes of β oxidation of the intermediate benzylsuccinate. J Bacteriol 182:272–277. https://doi.org/10.1128/JB.182.2.272-277.2000
doi: 10.1128/JB.182.2.272-277.2000
pubmed: 10629170
pmcid: 94273
Li CH, Zhou HW, Wong YS, Tam NFY (2009) Vertical distribution and anaerobic biodegradation of polycyclic aromatic hydrocarbons in mangrove sediments in Hong Kong, South China. Sci Total Environ 407:5772–5779. https://doi.org/10.1016/J.SCITOTENV.2009.07.034
doi: 10.1016/J.SCITOTENV.2009.07.034
pubmed: 19683792
Li D, Liu C-M, Luo R, Sadakane K, Lam T-W (2015) MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph. Bioinformatics 31:1674–1676. https://doi.org/10.1093/bioinformatics/btv033
doi: 10.1093/bioinformatics/btv033
pubmed: 25609793
Li X, Li Y, Zhang X, Zhao X, Sun Y, Weng L, Li Y (2019) Long-term effect of biochar amendment on the biodegradation of petroleum hydrocarbons in soil microbial fuel cells. Sci Total Environ 651:796–806. https://doi.org/10.1016/J.SCITOTENV.2018.09.098
doi: 10.1016/J.SCITOTENV.2018.09.098
pubmed: 30253361
Liu H, Yin H, Tang S, Wei K, Peng H, Lu G, Dang Z (2019) Effects of benzo [a] pyrene (BaP) on the composting and microbial community of sewage sludge. Chemosphere 222:517–526. https://doi.org/10.1016/j.chemosphere.2019.01.180
doi: 10.1016/j.chemosphere.2019.01.180
pubmed: 30721810
Liu Y-F, Chen J, Liu Z-L, Hou Z-W, Liang B, Wang L-Y, Zhou L, Shou L-B, Lin D-D, Yang S-Z, Liu J-F, Wu X-L, Gu J-D, Mu B-Z (2022) Long-term cultivation and meta-omics reveal methylotrophic methanogenesis in hydrocarbon-impacted habitats. Engineering 24:264–275. https://doi.org/10.1016/J.ENG.2021.08.027
doi: 10.1016/J.ENG.2021.08.027
Luo J, Chen Y, Feng L (2016) Polycyclic aromatic hydrocarbon affects acetic acid production during anaerobic fermentation of waste activated sludge by altering activity and viability of acetogen. Environ Sci Technol 50:6921–6929. https://doi.org/10.1021/ACS.EST.6B00003
doi: 10.1021/ACS.EST.6B00003
pubmed: 27267805
Lv L, Sun L, Yuan C, Han Y, Huang Z (2022) The combined enhancement of RL, nZVI and AQDS on the microbial anaerobic-aerobic degradation of PAHs in soil. Chemosphere 307:135609. https://doi.org/10.1016/J.CHEMOSPHERE.2022.135609
doi: 10.1016/J.CHEMOSPHERE.2022.135609
pubmed: 35809750
Majdinasab A, Zhang Z, Yuan Q (2017) Modelling of landfill gas generation: a review. Rev Environ Sci Biotechnol 16:361–380. https://doi.org/10.1007/S11157-017-9425-2
doi: 10.1007/S11157-017-9425-2
Mayumi D, Dolfing J, Sakata S, Maeda H, Miyagawa Y, Ikarashi M, Tamaki H, Takeuchi M, Nakatsu CH (2013) Kamagata Y (2013) Carbon dioxide concentration dictates alternative methanogenic pathways in oil reservoirs. Nat Commun 41(4):1–6. https://doi.org/10.1038/ncomms2998
doi: 10.1038/ncomms2998
McKinney W (2010) Data structuresfor statistical computingin Python. In: van der Walt S, Millman J (eds) Proceedings of the 9th Pythonin Science Conference. Austin, Texas, pp 56–61
Menzel P, Ng KL, Krogh A (2016) Fast and sensitive taxonomic classification for metagenomics with Kaiju. Nat Commun 7:1–9. https://doi.org/10.1038/ncomms11257
doi: 10.1038/ncomms11257
Molnár J, Magyar B, Schneider G, Laczi K, Valappil SK, Kovács ÁL, Nagy IK, Rákhely G, Kovács T (2020) Identification of a novel archaea virus, detected in hydrocarbon polluted Hungarian and Canadian samples. PLoS ONE 15:e0231864. https://doi.org/10.1371/journal.pone.0231864
doi: 10.1371/journal.pone.0231864
pubmed: 32302368
pmcid: 7164591
Morris BEL, Henneberger R, Huber H, Moissl-Eichinger C (2013) Microbial syntrophy: interaction for the common good. FEMS Microbiol Rev 37(3):384–406. https://doi.org/10.1111/1574-6976.12019
Müller H, Marozava S, Probst AJ (2019) Meckenstock RU (2019) Groundwater cable bacteria conserve energy by sulfur disproportionation. ISME J 142(14):623–634. https://doi.org/10.1038/s41396-019-0554-1
doi: 10.1038/s41396-019-0554-1
Ning Z, Zhang M, Zhang N, Guo C, Hao C, Zhang S, Shi C, Sheng Y, Chen Z (2022) Metagenomic characterization of a novel enrichment culture responsible for dehalogenation of 1,2,3-trichloropropane to allyl chloride. J Environ Chem Eng 10:108907. https://doi.org/10.1016/J.JECE.2022.108907
doi: 10.1016/J.JECE.2022.108907
Oonk H (2012) Efficiency of landfill gas collection for methane emission reduction. Greenh Gas Meas Manag 2:129–145. https://doi.org/10.1080/20430779.2012.730798
doi: 10.1080/20430779.2012.730798
Palanisamy V, Gajendiran V, Mani K (2021) Meta-analysis to identify the core microbiome in diverse wastewater. Int J Environ Sci Technol 19:5079–5096. https://doi.org/10.1007/S13762-021-03349-4
doi: 10.1007/S13762-021-03349-4
Parameswaran TG, Sivakumar Babu GL (2022) Design of gas collection systems: issues and challenges. Waste Manag Res 40:1608–1617. https://doi.org/10.1177/0734242X221086949
doi: 10.1177/0734242X221086949
pubmed: 35373627
Parkes J (1999) (1999) Cracking anaerobic bacteria. Nat 4016750(401):217–218. https://doi.org/10.1038/45686
doi: 10.1038/45686
Parks DH, Rinke C, Chuvochina M, Chaumeil PA, Woodcroft BJ, Evans PN, Hugenholtz P, Tyson GW (2017) Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life. Nat Microbiol 2:1533–1542. https://doi.org/10.1038/s41564-017-0012-7
doi: 10.1038/s41564-017-0012-7
pubmed: 28894102
Qin W, Zhu Y, Fan F, Wang Y, Liu X, Ding A, Dou J (2017) Biodegradation of benzo(a)pyrene by Microbacterium sp. strain under denitrification: degradation pathway and effects of limiting electron acceptors or carbon source. Biochem Eng J 121:131–138. https://doi.org/10.1016/J.BEJ.2017.02.001
doi: 10.1016/J.BEJ.2017.02.001
Rabus R, Boll M, Golding B, Wilkes H (2016) Anaerobic degradation of p-alkylated benzoates and toluenes. J Mol Microbiol Biotechnol 26:63–75. https://doi.org/10.1159/000441144
doi: 10.1159/000441144
pubmed: 26960059
Rinke C, Chuvochina M, Mussig AJ, Chaumeil PA, Davín AA, Waite DW, Whitman WB, Parks DH (2021) Hugenholtz P (2021) A standardized archaeal taxonomy for the Genome Taxonomy Database. Nat Microbiol 67(6):946–959. https://doi.org/10.1038/s41564-021-00918-8
doi: 10.1038/s41564-021-00918-8
Rizoulis A, Al LWM, Pancost RD, Polya DA, van Dongen BE, Lloyd JR, Rizoulis A, Al LWM, Pancost RD, Polya DA, van Dongen BE, Lloyd JR (2014) Microbially mediated reduction of FeIII and AsV in Cambodian sediments amended with 13C-labelled hexadecane and kerogen. Environ Chem 11:538–546. https://doi.org/10.1071/EN13238
doi: 10.1071/EN13238
Sales da Silva IG, Gomes de Almeida FC, Padilha da Rocha e Silva NM, Casazza AA, Converti A, Asfora Sarubbo L (2020) Soil bioremediation: Overview of technologies and trends. Energies 13(18):4664. https://doi.org/10.3390/EN13184664
Sangeetha M, Sivarajan A, Radhakrishnan M, Siddharthan N, Balagurunathan R (2022) Biosequestration of carbon dioxide using carbonic anhydrase from novel Streptomyces kunmingensis. Arch Microbiol 204:1–11. https://doi.org/10.1007/S00203-022-02887-W
doi: 10.1007/S00203-022-02887-W
Sani R, Peyton B, Smith W, Apel W, Petersen J (2002) Dissimilatory reduction of Cr(VI), Fe(III), and U(VI) by Cellulomonas isolates. Appl Microbiol Biotechnol 60:192–199. https://doi.org/10.1007/S00253-002-1069-6
doi: 10.1007/S00253-002-1069-6
pubmed: 12382063
Seemann T (2014) Prokka: rapid prokaryotic genome annotation. Bioinformatics 30:2068–2069. https://doi.org/10.1093/bioinformatics/btu153
doi: 10.1093/bioinformatics/btu153
pubmed: 24642063
Sela-Adler M, Ronen Z, Herut B, Antler G, Vigderovich H, Eckert W, Sivan O (2017) Co-existence of methanogenesis and sulfate reduction with common substrates in sulfate-rich estuarine sediments. Front Microbiol 8:766
doi: 10.3389/fmicb.2017.00766
pubmed: 28529500
pmcid: 5418336
Selesi D, Jehmlich N, Von Bergen M, Schmidt F, Rattei T, Tischler P, Lueders T, Meckenstock RU (2010) Combined genomic and proteomic approaches identify gene clusters involved in anaerobic 2-methylnaphthalene degradation in the sulfate-reducing enrichment culture N47. J Bacteriol 192:295–306. https://doi.org/10.1128/JB.00874-09
doi: 10.1128/JB.00874-09
pubmed: 19854898
Semenova EM, Grouzdev DS, Sokolova DS, Tourova TP, Poltaraus AB, Potekhina NV, Shishina PN, Bolshakova MA, Avtukh AN, Ianutsevich EA, Tereshina VM, Nazina TN (2022) Physiological and genomic characterization of Actinotalea subterranea sp. nov. from oil-degrading methanogenic enrichment and reclassification of the family Actinotaleaceae. Microorganisms 10:378. https://doi.org/10.3390/MICROORGANISMS10020378/S1
doi: 10.3390/MICROORGANISMS10020378/S1
pubmed: 35208832
pmcid: 8878594
Siddique T, Fedorak PM, MacKinnon MD, Foght JM (2007) Metabolism of BTEX and naphtha compounds to methane in oil sands tailings. Environ Sci Technol 41:2350–2356. https://doi.org/10.1021/es062852q
doi: 10.1021/es062852q
pubmed: 17438786
Siegert M, Cichocka D, Herrmann S, Gründger F, Feisthauer S, Richnow H-H, Springael D, Krüger M (2011) Accelerated methanogenesis from aliphatic and aromatic hydrocarbons under iron- and sulfate-reducing conditions. FEMS Microbiol Lett 315:6–16. https://doi.org/10.1111/j.1574-6968.2010.02165.x
doi: 10.1111/j.1574-6968.2010.02165.x
pubmed: 21133990
So CM, Phelps CD, Young LY (2003) Anaerobic transformation of alkanes to fatty acids by a sulfate-reducing bacterium, strain Hxd3. Appl Environ Microbiol 69:3892–3900. https://doi.org/10.1128/AEM.69.7.3892-3900.2003
doi: 10.1128/AEM.69.7.3892-3900.2003
pubmed: 12839758
pmcid: 165127
Suda K, Ikarashi M, Tamaki H, Tamazawa S, Sakata S, Haruo M, Kamagata Y, Kaneko M, Ujiie T, Shinotsuka Y, Wakayama T, Iwama H, Osaka N, Mayumi D, Yonebayashi H (2021) Methanogenic crude oil degradation induced by an exogenous microbial community and nutrient injections. J Pet Sci Eng 201:108458. https://doi.org/10.1016/J.PETROL.2021.108458
doi: 10.1016/J.PETROL.2021.108458
Sun K, Song Y, He F, Jing M, Tang J, Liu R (2021) A review of human and animals exposure to polycyclic aromatic hydrocarbons: health risk and adverse effects, photo-induced toxicity and regulating effect of microplastics. Sci Total Environ 773:145403. https://doi.org/10.1016/J.SCITOTENV.2021.145403
doi: 10.1016/J.SCITOTENV.2021.145403
pubmed: 33582342
Tan B, Nesbø C, Foght J (2014) Re-analysis of omics data indicates Smithella may degrade alkanes by addition to fumarate under methanogenic conditions. ISME J 8:2353–2356. https://doi.org/10.1038/ismej.2014.87
doi: 10.1038/ismej.2014.87
pubmed: 24865771
pmcid: 4260707
Tan BF, Semple K, Foght J (2015) Anaerobic alkane biodegradation by cultures enriched from oil sands tailings ponds involves multiple species capable of fumarate addition. FEMS Microbiol Ecol 91:1–42. https://doi.org/10.1093/femsec/fiv042
doi: 10.1093/femsec/fiv042
Tang TT, Li J, Yang Z, Luo XY, Chen Y (2019) Effect of straw on microbial community composition and degradation efficiency of polycyclic aromatic hydrocarbons in sludge digester. Int J Environ Sci Technol 16:7973–7986. https://doi.org/10.1007/S13762-019-02261-2
doi: 10.1007/S13762-019-02261-2
Tange O (2011) Gnu parallel-the command-line power tool. Usenix Mag 36(1):42
Tiedt O, Fuchs J, Eisenreich W, Boll M (2018) A catalytically versatile benzoyl-CoA reductase, key enzyme in the degradation of methyl- and halobenzoates in denitrifying bacteria. J Biol Chem 293:10264–10274. https://doi.org/10.1074/jbc.RA118.003329
doi: 10.1074/jbc.RA118.003329
pubmed: 29769313
pmcid: 6028946
Uritskiy GV, Diruggiero J, Taylor J (2018) MetaWRAP - a flexible pipeline for genome-resolved metagenomic data analysis 08 Information and Computing Sciences 0803 Computer Software 08 Information and Computing Sciences 0806 Information Systems. Microbiome 6:158. https://doi.org/10.1186/s40168-018-0541-1
doi: 10.1186/s40168-018-0541-1
pubmed: 30219103
pmcid: 6138922
Vick SHW, Greenfield P, Tetu SG, Midgley DJ (2019) Paulsen IT (2019) Genomic and phenotypic insights point to diverse ecological strategies by facultative anaerobes obtained from subsurface coal seams. Sci Reports 91(9):1–13. https://doi.org/10.1038/s41598-019-52846-7
doi: 10.1038/s41598-019-52846-7
Waite DW, Chuvochina M, Pelikan C, Parks DH, Yilmaz P, Wagner M, Loy A, Naganuma T, Nakai R, Whitman WB, Hahn MW, Kuever J, Hugenholtz P (2020) Proposal to reclassify the proteobacterial classes Deltaproteobacteria and Oligoflexia, and the phylum Thermodesulfobacteria into four phyla reflecting major functional capabilities. Int J Syst Evol Microbiol 70:5972–6016. https://doi.org/10.1099/IJSEM.0.004213
doi: 10.1099/IJSEM.0.004213
pubmed: 33151140
Walter JM, Bagi A, Pampanin DM (2019) Insights into the potential of the Atlantic cod gut microbiome as biomarker of oil contamination in the marine environment. Microorganisms 7(7):209. https://doi.org/10.3390/MICROORGANISMS7070209
doi: 10.3390/MICROORGANISMS7070209
pubmed: 31336609
pmcid: 6680985
Wartell B, Boufadel M, Rodriguez-Freire L (2021) An effort to understand and improve the anaerobic biodegradation of petroleum hydrocarbons: a literature review. Int Biodeterior Biodegradation 157:105156. https://doi.org/10.1016/J.IBIOD.2020.105156
doi: 10.1016/J.IBIOD.2020.105156
Waskom M (2021) Seaborn: statistical data visualization. J Open Source Softw 6(60):3021. https://doi.org/10.21105/joss.03021
doi: 10.21105/joss.03021
Wrighton KC, Castelle CJ, Varaljay VA, Satagopan S, Brown CT, Wilkins MJ, Thomas BC, Sharon I, Williams KH, Tabita FR (2016) Banfield JF (2016) RubisCO of a nucleoside pathway known from Archaea is found in diverse uncultivated phyla in bacteria. ISME J 1011(10):2702–2714. https://doi.org/10.1038/ismej.2016.53
doi: 10.1038/ismej.2016.53
Wu Y-W, Simmons BA, Singer SW (2016) MaxBin 2.0: an automated binning algorithm to recover genomes from multiple metagenomic datasets. Bioinformatics 32:605–607. https://doi.org/10.1093/bioinformatics/btv638
doi: 10.1093/bioinformatics/btv638
pubmed: 26515820
Xia W, Shen W, Yu L, Zheng C, Yu W, Tang Y (2016) Conversion of petroleum to methane by the indigenous methanogenic consortia for oil recovery in heavy oil reservoir. Appl Energy 171:646–655. https://doi.org/10.1016/J.APENERGY.2016.03.059
doi: 10.1016/J.APENERGY.2016.03.059
Zedelius J, Rabus R, Grundmann O, Werner I, Brodkorb D, Schreiber F, Ehrenreich P, Behrends A, Wilkes H, Kube M, Reinhardt R, Widdel F (2011) Alkane degradation under anoxic conditions by a nitrate-reducing bacterium with possible involvement of the electron acceptor in substrate activation. Environ Microbiol Rep 3:125–135. https://doi.org/10.1111/j.1758-2229.2010.00198.x
doi: 10.1111/j.1758-2229.2010.00198.x
pubmed: 21837252
Zeng G (2020) Study on landfill gas migration in landfilled municipal solid waste based on gas–solid coupling model. Environ Prog Sustain Energy 39:e13352. https://doi.org/10.1002/EP.13352
doi: 10.1002/EP.13352
Zhan W, Tian Y, Zhang J, Zuo W, Li L, Jin Y, Lei Y, Xie A, Zhang X (2021) Mechanistic insights into the roles of ferric chloride on methane production in anaerobic digestion of waste activated sludge. J Clean Prod 296:126527. https://doi.org/10.1016/j.jclepro.2021.126527
doi: 10.1016/j.jclepro.2021.126527
Zhang JW, Dong HP, Hou LJ, Liu Y, Ou YF, Zheng YL, Han P, Liang X, Yin GY, Wu DM, Liu M (2021) Li M (2021) Newly discovered Asgard archaea Hermodarchaeota potentially degrade alkanes and aromatics via alkyl/benzyl-succinate synthase and benzoyl-CoA pathway. ISME J 156(15):1826–1843. https://doi.org/10.1038/s41396-020-00890-x
doi: 10.1038/s41396-020-00890-x
Zhang L, Zhou X, Hu C, Yao S, Shi L, Niu T, Li X, Tong L, Zhang J, Ma T, Xia W (2023) CO
doi: 10.1016/J.ENVRES.2023.115541
pubmed: 36828250
Zhou Y, Zou Q, Fan M, Xu Y, Chen Y (2020) Highly efficient anaerobic co-degradation of complex persistent polycyclic aromatic hydrocarbons by a bioelectrochemical system. J Hazard Mater 381:120945. https://doi.org/10.1016/J.JHAZMAT.2019.120945
doi: 10.1016/J.JHAZMAT.2019.120945
pubmed: 31421548
Zhou J, Smith JA, Li M, Holmes DE (2023) Methane production by Methanothrix thermoacetophila via direct interspecies electron transfer with Geobacter metallireducens. Mbio 14:e0036023. https://doi.org/10.1128/MBIO.00360-23
doi: 10.1128/MBIO.00360-23
pubmed: 37306514