Soil Microbiomes—a Promising Strategy for Contaminated Soil Remediation: A Review
|
摘要
Bioremediation is a process mediated by microorganisms and represents a sustainable and eco-friendly way to degrade and detoxify environmental contaminants. Soil microbiomes clearly become a key component of bioremediation as they are more stable and effcient than pure cultures, being recognized as one of the scientific frontiers of the soil environmental science and technology fields. Recently,many advancements have been made regarding the investigation of remediation mechanisms by soil microbiomes and the interactions inside them. This has greatly expanded our ability to characterize the remediating function of soil microbiomes and identify the factors that influence their effciency for remediation. Here, we suggest that soil microbiomes are a promising strategy for soil remediation.Research is now needed to identify how we can manipulate and manage soil microbiomes to improve remediation effciency and increase soil fertility at the same time. Therefore, this review aims to emphasize the importance of soil microbiomes in bioremediation and promote further development of this strategy into a widely accepted technique.
Bioremediation is a process mediated by microorganisms and represents a sustainable and eco-friendly way to degrade and detoxify environmental contaminants. Soil microbiomes clearly become a key component of bioremediation as they are more stable and effcient than pure cultures, being recognized as one of the scientific frontiers of the soil environmental science and technology fields. Recently,many advancements have been made regarding the investigation of remediation mechanisms by soil microbiomes and the interactions inside them. This has greatly expanded our ability to characterize the remediating function of soil microbiomes and identify the factors that influence their effciency for remediation. Here, we suggest that soil microbiomes are a promising strategy for soil remediation.Research is now needed to identify how we can manipulate and manage soil microbiomes to improve remediation effciency and increase soil fertility at the same time. Therefore, this review aims to emphasize the importance of soil microbiomes in bioremediation and promote further development of this strategy into a widely accepted technique.
Bioremediation is a process mediated by microorganisms and represents a sustainable and eco-friendly way to degrade and detoxify environmental contaminants. Soil microbiomes clearly become a key component of bioremediation as they are more stable and effcient than pure cultures, being recognized as one of the scientific frontiers of the soil environmental science and technology fields. Recently,many advancements have been made regarding the investigation of remediation mechanisms by soil microbiomes and the interactions inside them. This has greatly expanded our ability to characterize the remediating function of soil microbiomes and identify the factors that influence their effciency for remediation. Here, we suggest that soil microbiomes are a promising strategy for soil remediation.Research is now needed to identify how we can manipulate and manage soil microbiomes to improve remediation effciency and increase soil fertility at the same time. Therefore, this review aims to emphasize the importance of soil microbiomes in bioremediation and promote further development of this strategy into a widely accepted technique.
引文
Alivisatos A P,Blaser M J,Brodie E L,Chun M,Dangl J L,Donohue T J,Dorrestein P C,Gilbert J A,Green J L,Jansson J K,Knight R,Maxon M E,McFall-Ngai M J,Miller JF,Pollard K S,Ruby E G,Taha S A,Unified Microbiome Initiative Consortium.2015.A unified initiative to harness earth’s microbiomes.Science.350:507-508.
Arora P K,Kumar M,Chauhan A,Raghava G P S,Jain RK.2009.OxDBase:A database of oxygenases involved in biodegradation.BMC Res Notes.2:67.
Arora P K,Srivastava A,Singh V P.2010.Application of monooxygenases in dehalogenation,desulphurization,denitrification and hydroxylation of aromatic compounds.J Bioremed Biodegrad.1:1000112.
Brenner K,You L C,Arnold F H.2008.Engineering microbial consortia:A new frontier in synthetic biology.Trends Biotechnol.26:483-489.
Cerqueira V S,Hollenbach E B,Maboni F,Vainstein M H,Camargo F A O,Peralba M D C R,Bento F M.2011.Biodegradation potential of oily sludge by pure and mixed bacterial cultures.Bioresour Technol.102:11003-11010.
Chakraborty J,Das S.2016.Molecular perspectives and recent advances in microbial remediation of persistent organic pollutants.Environ Sci Pollut Res.23:16883-16903.
Chakraborty R,Wu C H,Hazen T C.2012.Systems biology approach to bioremediation.Curr Opin Biotechnol.23:483-490.
Chandra S,Sharma R,Singh K,Sharma A.2013.Application of bioremediation technology in the environment contaminated with petroleum hydrocarbon.Ann Microbiol.63:417-431.
Chibuike G U,Obiora S C.2014.Heavy metal polluted soils:Effect on plants and bioremediation methods.Appl Environ Soil Sci.2014:752708
Chowdhury A,Pradhan S,Saha M,Sanyal N.2008.Impact of pesticides on soil microbiological parameters and possible bioremediation strategies.Indian J Microbiol.48:114-127.
Coyte K Z,Schluter J,Foster K R.2015.The ecology of the microbiome:Networks,competition,and stability.Science.350:663-666.
D’Costa V M,McGrann K M,Hughes D W,Wright G D.2006.Sampling the antibiotic resistome.Science.311:374-377.
De Roy K,Marzorati M,Van den Abbeele P,Van de Wiele T,Boon N.2014.Synthetic microbial ecosystems:An exciting tool to understand and apply microbial communities.Environ Microbiol.16:1472-1481.
de-Bashan L E,Hernandez J P,Bashan Y.2012.The potential contribution of plant growth-promoting bacteria to reduce environmental degradation-a comprehensive evaluation.Appl Soil Ecol.61:171-189.
DeBruyn J M,Mead T J,Sayler G S.2012.Horizontal transfer of PAH catabolism genes in Mycobacterium:Evidence from comparative genomics and isolated pyrene-degrading bacteria.Environ Sci Technol.46:99-106.
Delgado-Baquerizo M,Grinyer J,Reich P B,Singh B K.2016.Relative importance of soil properties and microbial community for soil functionality:Insights from a microbial swap experiment.Funct Ecol.30:1862-1873.
Dias R L,Ruberto L,Hernández E,Vázquez S C,Lo Balbo A,Del Panno M T,Mac Cormack W P.2012.Bioremediation of an aged diesel oil-contaminated Antarctic soil:Evaluation of the“on site”biostimulation strategy using different nutrient sources.Int Biodeterior Biodegrad.75:96-103.
Dubilier N,McFall-Ngai M,Zhao L P.2015.Microbiology:Create a global microbiome effort.Nature.526:631-634.
Edwards S J,Kjellerup B V.2013.Applications of biofilms in bioremediation and biotransformation of persistent organic pollutants,pharmaceuticals/personal care products,and heavy metals.Appl Microbiol Biotechnol.97:9909-9921.
Escalante A E,Rebolleda-Gómez M,Benítez M,Travisano M.2015.Ecological perspectives on synthetic biology:Insights from microbial population biology.Front Microbiol.6:143.
Fernando Bautista L,Sanz R,Carmen Molina M,González N,Sánchez D.2009.Effect of different non-ionic surfactants on the biodegradation of PAHs by diverse aerobic bacteria.Int Biodeterior Biodegrad.63:913-922.
Festa S,Coppotelli B M,Morelli I S.2016.Comparative bioaugmentation with a consortium and a single strain in a phenanthrene-contaminated soil:Impact on the bacterial community and biodegradation.Appl Soil Ecol.98:8-19.
Fierer N.2017.Embracing the unknown:Disentangling the complexities of the soil microbiome.Nat Rev Microbiol.15:579-590.
Fredrickson J K.2015.Ecological communities by design.Science.348:1425-1427.
Gambino M,Cappitelli F.2016.Mini-review:Biofilm responses to oxidative stress.Biofouling.32:167-178.
Gillespie I M M,Philp J C.2013.Bioremediation,an environmental remediation technology for the bioeconomy.Trends Biotechnol.31:329-332.
Girvan M S,Campbell C D,Killham K,Prosser J I,Glover L A.2005.Bacterial diversity promotes community stability and functional resilience after perturbation.Environ Microbiol.7:301-313.
González N,Simarro R,Molina M C,Bautista L F,Delgado L,Villa J A.2011.Effect of surfactants on PAH biodegradation by a bacterial consortium and on the dynamics of the bacterial community during the process.Bioresour Technol.102:9438-9446.
Gounou C,Bousserrhine N,Varrault G,Mouchel J M.2010.In-fluence of the iron-reducing bacteria on the release of heavy metals in anaerobic river sediment.Water Air Soil Pollut.212:123-139.
Gro?kopf T,Soyer O S.2014.Synthetic microbial communities.Curr Opin Microbiol.18:72-77.
Gupta A,Joia J,Sood A,Sood R,Sidhu C,Kaur G.2016.Microbes as potential tool for remediation of heavy metals:Areview.J Microb Biochem Technol.8:364-372.
Gupta G,Kumar V,Pal A K.2016.Biodegradation of polycyclic aromatic hydrocarbons by microbial consortium:Adistinctive approach for decontamination of soil.Soil Sediment ContamInt J.25:597-623.
Gurav R,Lyu H,Ma J L,Tang J C,Liu Q L,Zhang H R.2017.Degradation of n-alkanes and PAHs from the heavy crude oil using salt-tolerant bacterial consortia and analysis of their catabolic genes.Environ Sci Pollut Res.24:11392-11403.
Hao X,Taghavi S,Xie P,Orbach M J,Alwathnani H A,Rensing C,Wei G.2014.Phytoremediation of heavy and transition metals aided by legume-rhizobia symbiosis.Int J Phytoremed.16:179-202.
Haritash A K,Kaushik C P.2009.Biodegradation aspects of polycyclic aromatic hydrocarbons(PAHs):A review.J Hazard Mater.169:1-15.
Hayase N,Taira K,Furukawa K.1990.Pseudomonas putida KF-715 bphABCD operon encoding biphenyl and polychlorinated biphenyl degradation:Cloning,analysis,and expression in soil bacteria.J Bacteriol.172:1160-1164.
Hendrickx B,Junca H,Vosahlova J,Lindner A,Rüegg I,BucheliWitschel M,Faber F,Egli T,Mau M,Schl?mann M,Brennerova M,Brenner V,Pieper D H,Top E M,Dejonghe W,Bastiaens L,Springael D.2006.Alternative primer sets for PCR detection of genotypes involved in bacterial aerobic B-TEX degradation:Distribution of the genes in BTEX degrading isolates and in subsurface soils of a BTEX contaminated industrial site.J Microbiol Methods.64:250-265.
Hibbing M E,Fuqua C,Parsek M R,Peterson S B.2010.Bacterial competition:Surviving and thriving in the microbial jungle.Nat Rev Microbiol.8:15-25.
Hiraishi T.2016.Poly(aspartic acid)(PAA)hydrolases and PAAbiodegradation:Current knowledge and impact on applications.Appl Microbiol Biotechnol.100:1623-1630.
Horne I,Sutherland T D,Harcourt R L,Russell R J,Oakeshott J G.2002.Identification of an opd(organophosphate degradation)gene in an Agrobacterium isolate.Appl Environ Microbiol.68:3371-3376.
Imadi S R,Ali Z,Hasan H,Gul A.2016.Soil pollution and remediation.In Hakeem K R,Akhtar M S(eds.)Plant,Soil and Microbes.Volume 2.Mechanisms and Molecular Interactions.Springer International Publishing,Cham.pp.423-438.
Iwai S,Johnson T A,Chai B L,Hashsham S A,Tiedje J M.2011.Comparison of the specificities and effcacies of primers for aromatic dioxygenase gene analysis of environmental samples.Appl Environ Microbiol.77:3551-3557.
Jan A T,Azam M,Ali A,Haq Q M R.2014.Prospects for exploiting bacteria for bioremediation of metal pollution.Crit Rev Environ Sci Technol.44:519-560.
Jiang L L,Zhou J J,Quan C S,Xiu Z L.2017.Advances in industrial microbiome based on microbial consortium for biore-finery.Bioresour Bioprocess.4:11.
Johnsen A R,Karlson U.2004.Evaluation of bacterial strategies to promote the bioavailability of polycyclic aromatic hydrocarbons.Appl Microbiol Biotechnol.63:452-459.
Juhas M,van der Meer J R,Gaillard M,Harding R M,Hood D W,Crook D W.2009.Genomic islands:Tools of bacterial horizontal gene transfer and evolution.FEMS Microbiol Rev.33:376-393.
Kahng H Y,Malinverni J C,Majko M M,Kukor J J.2001.Genetic and functional analysis of the tbc operons for catabolism of alkyl-and chloroaromatic compounds in Burkholderia sp.strain JS150.Appl Environ Microbiol.67:4805-4816.
Kang C H,Kwon Y J,So J S.2016.Bioremediation of heavy metals by using bacterial mixtures.Ecol Eng.89:64-69.
Karigar C S,Rao S S.2011.Role of microbial enzymes in the bioremediation of pollutants:A review.Enzyme Res.2011:805187.
Kau A L,Ahern P P,Griffn N W,Goodman A L,Gordon J I.2011.Human nutrition,the gut microbiome and the immune system.Nature.474:327-336.
Kim S J,Song J,Kweon O,Holland R D,Kim D W,Kim J,Yu L R,Cerniglia C E.2012.Functional robustness of a polycyclic aromatic hydrocarbon metabolic network examined in a nidA aromatic ring-hydroxylating oxygenase mutant of Mycobacterium vanbaalenii PYR-1.Appl Environ Microbiol.78:3715-3723.
Kotas′J,Stasicka Z.2000.Chromium occurrence in the environment and methods of its speciation.Environ Pollut.107:263-283.
Kowalska J B,Mazurek R,G?asiorek M,Zaleski T.2018.Pollution indices as useful tools for the comprehensive evaluation of the degree of soil contamination-a review.Environ Geochem Health.40:2395-2420.
Kuppusamy S,Thavamani P,Venkateswarlu K,Lee Y B,Naidu R,Megharaj M.2017.Remediation approaches for polycyclic aromatic hydrocarbons(PAHs)contaminated soils:Technological constraints,emerging trends and future directions.Chemosphere.168:944-968.
Kuzyakov Y,Blagodatskaya E.2015.Microbial hotspots and hot moments in soil:Concept&review.Soil Biol Biochem.83:184-199.
Kweon O,Kim S J,Holland R D,Chen H Y,Kim D W,Gao Y,Yu L R,Baek S,Baek D H,Ahn H,Cerniglia C E.2011.Polycyclic aromatic hydrocarbon metabolic network in Mycobacterium vanbaalenii PYR-1.J Bacteriol.193:4326-4337.
Kylilis N,Tuza Z A,Stan G B,Polizzi K M.2018.Tools for engineering coordinated system behaviour in synthetic microbial consortia.Nat Commun.9:2677.
Lakshmanan V,Selvaraj G,Bais H P.2014.Functional soil microbiome:Belowground solutions to an aboveground problem.Plant Physiol.166:689-700.
Lamichhane S,Bal Krishna K C,Sarukkalige R.2016.Polycyclic aromatic hydrocarbons(PAHs)removal by sorption:A review.Chemosphere.148:336-353.
Lenoir I,Lounes-Hadj Sahraoui A,Fontaine J.2016.Arbuscular mycorrhizal fungal-assisted phytoremediation of soil contaminated with persistent organic pollutants:A review.Eur J Soil Sci.67:624-640.
Li X N,Jiao W T,Xiao R B,Chen W P,Chang A C.2015.Soil pollution and site remediation policies in China:A review.Environ Rev.23:263-274.
Lohmann R,Breivik K,Dachs J,Muir D.2007.Global fate of POPs:Current and future research directions.Environ Pollut.150:150-165.
Mackova M,Uhlik O,Lovecka P,Viktorova J,Novakova M,Demnerova K,Sylvestre M,Macek T.2010.Bacterial degradation of polychlorinated biphenyls.In Barton L L,Mandl M,Loy A(eds.)Geomicrobiology:Molecular and Environmental Perspective.Springer,Dordrecht.pp.347-366.
Madhaiyan M,Poonguzhali S,Sa T M.2007.Metal tolerating methylotrophic bacteria reduces nickel and cadmium toxicity and promotes plant growth of tomato(Lycopersicon esculentum L.).Chemosphere.69:220-228.
Mah T F C,O’Toole G A.2001.Mechanisms of biofilm resistance to antimicrobial agents.Trends Microbiol.9:34-39.
Mariano A P,Bonotto D M,de Angelis D D F,Pir?ollo M P S,Contiero J.2008.Biodegradability of commercial and weathered diesel oils.Braz J Microbiol.39:133-142.
Martiny J B H,Jones S E,Lennon J T,Martiny A C.2015.Microbiomes in light of traits:A phylogenetic perspective.Science.350:aac9323.
Mee M T,Collins J J,Church G M,Wang H H.2014.Syntrophic exchange in synthetic microbial communities.Proc Natl Acad Sci USA.111:E2149-E2156.
Mendes L W,Tsai S M,Navarrete A A,de Hollander M,van Veen J A,Kuramae E E.2015.Soil-borne microbiome:Linking diversity to function.Microb Ecol.70:255-265.
Mikeskova′H,NovotnyˇC,Svobodová K.2012.Interspecific interactions in mixed microbial cultures in a biodegradation perspective.Appl Microbiol Biotechnol.95:861-870.
Mineki S,Suzuki K,Iwata K,Nakajima D,Goto S.2015.Degradation of polyaromatic hydrocarbons by fungi isolated from soil in Japan.Polycyclic Aromat Compd.35:120-128.
Mrozik A,Piotrowska-Seget Z,Labuzek S.2003.Bacterial degradation and bioremediation of polycyclic aromatic hydrocarbons.Pol J Environ Stud.12:15-25.
NíChadhain S M,Norman R S,Pesce K V,Kukor J J,Zylstra G J.2006.Microbial dioxygenase gene population shifts during polycyclic aromatic hydrocarbon biodegradation.Appl Environ Microbiol.72:4078-4087.
Nzila A.2013.Update on the cometabolism of organic pollutants by bacteria.Environ Pollut.178:474-482.
Ojuederie O B,Babalola O O.2017.Microbial and plant-assisted bioremediation of heavy metal polluted environments:A review.Int J Environ Res Public Health.14:1504.
Okai M,Kubota K,Fukuda M,Nagata Y,Nagata K,Tanokura M.2010.Crystal structure ofγ-hexachlorocyclohexane dehydrochlorinase LinA from Sphingobium japonicum UT26.JMol Biol.403:260-269.
Owsianiak M,Szulc A,Chrzanowski L,Cyplik P,Bogacki M,Olejnik-Schmidt A K,Heipieper H J.2009.Biodegradation and surfactant-mediated biodegradation of diesel fuel by 218microbial consortia are not correlated to cell surface hydrophobicity.Appl Microbiol Biotechnol.84:545-553.
Pal A,Paul A K.2008.Microbial extracellular polymeric substances:Central elements in heavy metal bioremediation.Indian J Microbiol.48:49-64.
Papenfort K,Bassler B L.2016.Quorum sensing signal-response systems in Gram-negative bacteria.Nat Rev Microbiol.14:576-588.
Parsek M R,Greenberg E P.2000.Acyl-homoserine lactone quorum sensing in Gram-negative bacteria:A signaling mechanism involved in associations with higher organisms.Proc Natl Acad Sci USA.97:8789-8793.
Passatore L,Rossetti S,Juwarkar A A,Massacci A.2014.Phytoremediation and bioremediation of polychlorinated biphenyls(PCBs):State of knowledge and research perspectives.J Hazard Mater.278:189-202.
Peralta A L,Stuart D,Kent A D,Lennon J T.2014.A socialecological framework for“micromanaging”microbial services.Front Ecol Environ.12:524-531.
Perez-Garcia O,Lear G,Singhal N.2016.Metabolic network modeling of microbial interactions in natural and engineered environmental systems.Front Microbiol.7:673.
Peters C A,Bratton S P.2016.Urbanization is a major influence on microplastic ingestion by sunfish in the Brazos River Basin,Central Texas,USA.Environ Pollut.210:380-387.
Pieper D H,Seeger M.2008.Bacterial metabolism of polychlorinated biphenyls.J Mol Microbiol Biotechnol.15:121-138.
Pushpanathan M,Jayashree S,Gunasekaran P,Rajendhran J.2014.Microbial bioremediation:A metagenomic approach.In Das S(ed.)Microbial Biodegradation and Bioremediation.Elsevier,Oxford.pp.525-546.
Ren G D,Ren W J,Teng Y,Li Z G.2015.Evident bacterial community changes but only slight degradation when polluted with pyrene in a red soil.Front Microbiol.6:22.
Ren G D,Teng Y,Ren W J,Dai S X,Li Z G.2016.Pyrene dissipation potential varies with soil type and associated bacterial community changes.Soil Biol Biochem.103:71-85.
Rodriguez S,Bishop P L.2008.Enhancing the biodegradation of polycyclic aromatic hydrocarbons:Effects of nonionic surfactant addition on biofilm function and structure.J Environ Eng.134:505-512.
Sathishkumar M,Binupriya A R,Baik S H,Yun S E.2008.Biodegradation of crude oil by individual bacterial strains and a mixed bacterial consortium isolated from hydrocarbon contaminated areas.Clean Soil Air Water.36:92-96.
Schalk I J,Hannauer M,Braud A.2011.New roles for bacterial siderophores in metal transport and tolerance.Environ Microbiol.13:2844-2854.
Schmidt T M.2006.The maturing of microbial ecology.Int Microbiol.9:217-223.
Sedlmayer F,Hell D,Müller M,Ausl?nder D,Fussenegger M.2018.Designer cells programming quorum-sensing interference with microbes.Nat Commun.9:1822.
Serna-Chavez H M,Fierer N,van Bodegom P M.2013.Global drivers and patterns of microbial abundance in soil.Global Ecol Biogeogr.22:1162-1172.
Shah A A,Hasan F,Hameed A,Ahmed S.2008.Biological degradation of plastics:A comprehensive review.Biotechnol Adv.26:246-265.
Shankar S,Kansrajh C,Dinesh M G,Satyan R S,Kiruthika S,Tharanipriya A.2014.Application of indigenous microbial consortia in bioremediation of oil-contaminated soils.Int JEnviron Sci Technol.11:367-376.
Shields M S,Reagin M J,Gerger R R,Campbell R,Somerville C.1995.TOM,a new aromatic degradative plasmid from Burkholderia(Pseudomonas)cepacia G4.Appl Environ Microbiol.61:1352-1356.
Singleton D R,Guzmán Ramirez L,Aitken M D.2009.Characterization of a polycyclic aromatic hydrocarbon degradation gene cluster in a phenanthrene-degrading Acidovorax strain.Appl Environ Microbiol.75:2613-2620.
Skariyachan S,Shamsundar Setlur A,Naik S,Amaresh Naik A,Usharani M,S Vasist K.2017.Enhanced biodegradation of low and high-density polyethylene by novel bacterial consortia formulated from plastic-contaminated cow dung under thermophilic conditions.Environ Sci Pollut Res.24:8443-8457.
Song H,Ding M Z,Jia X Q,Ma Q,Yuan Y J.2014.Synthetic microbial consortia:From systematic analysis to construction and applications.Chem Soc Rev.43:6954-6981.
Souza E C,Vessoni-Penna T C,de Souza Oliveira R P.2014.Biosurfactant-enhanced hydrocarbon bioremediation:An overview.Int Biodeterior Biodegrad.89:88-94.
Sprocati A R,Alisi C,Tasso F,Marconi P,Sciullo A,Pinto V,Chiavarini S,Ubaldi C,Cremisini C.2012.Effectiveness of a microbial formula,as a bioaugmentation agent,tailored for bioremediation of diesel oil and heavy metal co-contaminated soil.Process Biochem.47:1649-1655.
Tardy V,Mathieu O,Le′v?eque J,Terrat S,Chabbi A,Lemanceau P,Ranjard L,Maron P A.2014.Stability of soil microbial structure and activity depends on microbial diversity.Environ Microbiol Rep.6:173-183.
Tauler M,Vila J,Nieto J M,Grifoll M.2016.Key high molecular weight PAH-degrading bacteria in a soil consortium enriched using a sand-in-liquid microcosm system.Appl Microbiol Biotechnol.100:3321-3336.
Teng Y,Wang X M,Li L N,Li Z G,Luo Y M.2015.Rhizobia and their bio-partners as novel drivers for functional remediation in contaminated soils.Front Plant Sci.6:32.
Thamer M,Rahman Al-Kubaisi A,Zahraw Z,Aldin Abdullah H,Hindy I,Abd Khadium A.2013.Biodegradation of Kirkuk light crude oil by Bacillus thuringiensis,northern of Iraq.Nat Sci.5:865-873.
Thavamani P,Megharaj M,Naidu R.2012.Bioremediation of high molecular weight polyaromatic hydrocarbons co-contaminated with metals in liquid and soil slurries by metal tolerant PAHs degrading bacterial consortium.Biodegradation.23:823-835.
Thomas C M,Nielsen K M.2005.Mechanisms of,and barriers to,horizontal gene transfer between bacteria.Nat Rev Microbiol.3:711-721.
Torsvik V,?vre?as L.2002.Microbial diversity and function in soil:From genes to ecosystems.Curr Opin Microbiol.5:240-245.
Varjani S J,Thaker M B,Upasani V N.2014.Optimization of growth conditions of native hydrocarbon utilizing bacterial consortium“HUBC”obtained from petroleum pollutant contaminated sites.Microbiology.4:474-476.
Varjani S J,Upasani V N.2016.Coreflood study for enhanced oil recovery through ex-situ bioaugmentation with thermo-and halo-tolerant rhamnolipid produced by Pseudomonas aeruginosa NCIM 5514.Bioresour Technol.220:175-182.
Varjani S J.2017.Microbial degradation of petroleum hydrocarbons.Bioresour Technol.223:277-286.
Varjani S J,Upasani V N.2017.A new look on factors affecting microbial degradation of petroleum hydrocarbon pollutants.Int Biodeterior Biodegrad.120:71-83.
Wang B B,Teng Y,Xu Y F,Chen W,Ren W J,Li Y,Christie P,Luo Y M.2018.Effect of mixed soil microbiomes on pyrene removal and the response of the soil microorganisms.Sci Total Environ.640-641:9-17.
Wang B Z,Guo P,Hang B J,Li L,He J,Li S P.2009.Cloning of a novel pyrethroid-hydrolyzing carboxylesterase gene from Sphingobium sp.strain JZ-1 and characterization of the gene product.Appl Environ Microbiol.75:5496-5500.
Wang F K,Li C,Wang H J,Chen W L,Huang Q Y.2016.Characterization of a phenanthrene-degrading microbial consortium enriched from petrochemical contaminated environment.Int Biodeterior Biodegrad.115:286-292.
Wang S Q,Chng K R,Wilm A,Zhao S Y,Yang K L,Nagarajan N,He J Z.2014.Genomic characterization of three unique Dehalococcoides that respire on persistent polychlorinated biphenyls.Proc Natl Acad Sci USA.111:12103-12108.
Wang W P,Shao Z Z.2012.Genes involved in alkane degradation in the Alcanivorax hongdengensis strain A-11-3.Appl Microbiol Biotechnol.94:437-448.
Wang X M,Teng Y,Tu C,Luo Y M,Greening C,Zhang N,Dai S X,Ren W J,Zhao L,Li Z G.2018.Coupling between nitrogenfixation and tetrachlorobiphenyl dechlorination in a rhizobium-legume symbiosis.Environ Sci Technol.52:2217-2224.
Wang Y X,Oyaizu H.2011.Enhanced remediation of dioxinsspiked soil by a plant-microbe system using a dibenzofurandegrading Comamonas sp.and Trifolium repens L.Chemosphere.85:1109-1114.
Waters C M,Bassler B L.2005.Quorum sensing:Cell-to-cell communication in bacteria.Annu Rev Cell Dev Biol.21:319-346.
Wi lkomirski B,Sudnik-Wójcikowska B,Galera H,Wierzbicka M,Malawska M.2011.Railway transportation as a serious source of organic and inorganic pollution.Water Air Soil Pollut.218:333-345.
Williams P.2007.Quorum sensing,communication and crosskingdom signalling in the bacterial world.Microbiology.153:3923-3938.
Xu X H,Zarecki R,Medina S,Ofaim S,Liu X W,Chen C,Hu S L,Brom D,Gat D,Porob S,Eizenberg H,Ronen Z,Jiang J D,Freilich S.2019.Modeling microbial communities from atrazine contaminated soils promotes the development of biostimulation solutions.ISME J.13:494-508.
Yim G,Wang H H,Davies J.2007.Antibiotics as signalling molecules.Philos Trans B Biol Sci.362:1195-1200.
Yoshida S,Ogawa N,Fujii T,Tsushima S.2009.Enhanced biofilm formation and 3-chlorobenzoate degrading activity by the bacterial consortium of Burkholderia sp.NK8 and Pseudomonas aeruginosa PAO1.J Appl Microbiol.106:790-800.
Yoshida S,Hiraga K,Takehana T,Taniguchi I,Yamaji H,Maeda Y,Toyohara K,Miyamoto K,Kimura Y,Oda K.2016.A bacterium that degrades and assimilates poly(ethylene terephthalate).Science.351:1196-1199.
Zeng J,Zhu Q H,Wu Y C,Lin X G.2016.Oxidation of polycyclic aromatic hydrocarbons using Bacillus subtilis CotAwith high laccase activity and copper independence.Chemosphere.148:1-7.
Zhang W W,Chen L X,Liu D Y.2012.Characterization of a marine-isolated mercury-resistant Pseudomonas putida strain SP1 and its potential application in marine mercury reduction.Appl Microbiol Biotechnol.93:1305-1314.
Zhao D F,Liu C S,Liu L H,Zhang Y B,Liu Q Y,Wu WM.2011.Selection of functional consortium for crude oilcontaminated soil remediation.Int Biodeterior Biodegrad.65:1244-1248.
Arora P K,Kumar M,Chauhan A,Raghava G P S,Jain RK.2009.OxDBase:A database of oxygenases involved in biodegradation.BMC Res Notes.2:67.
Arora P K,Srivastava A,Singh V P.2010.Application of monooxygenases in dehalogenation,desulphurization,denitrification and hydroxylation of aromatic compounds.J Bioremed Biodegrad.1:1000112.
Brenner K,You L C,Arnold F H.2008.Engineering microbial consortia:A new frontier in synthetic biology.Trends Biotechnol.26:483-489.
Cerqueira V S,Hollenbach E B,Maboni F,Vainstein M H,Camargo F A O,Peralba M D C R,Bento F M.2011.Biodegradation potential of oily sludge by pure and mixed bacterial cultures.Bioresour Technol.102:11003-11010.
Chakraborty J,Das S.2016.Molecular perspectives and recent advances in microbial remediation of persistent organic pollutants.Environ Sci Pollut Res.23:16883-16903.
Chakraborty R,Wu C H,Hazen T C.2012.Systems biology approach to bioremediation.Curr Opin Biotechnol.23:483-490.
Chandra S,Sharma R,Singh K,Sharma A.2013.Application of bioremediation technology in the environment contaminated with petroleum hydrocarbon.Ann Microbiol.63:417-431.
Chibuike G U,Obiora S C.2014.Heavy metal polluted soils:Effect on plants and bioremediation methods.Appl Environ Soil Sci.2014:752708
Chowdhury A,Pradhan S,Saha M,Sanyal N.2008.Impact of pesticides on soil microbiological parameters and possible bioremediation strategies.Indian J Microbiol.48:114-127.
Coyte K Z,Schluter J,Foster K R.2015.The ecology of the microbiome:Networks,competition,and stability.Science.350:663-666.
D’Costa V M,McGrann K M,Hughes D W,Wright G D.2006.Sampling the antibiotic resistome.Science.311:374-377.
De Roy K,Marzorati M,Van den Abbeele P,Van de Wiele T,Boon N.2014.Synthetic microbial ecosystems:An exciting tool to understand and apply microbial communities.Environ Microbiol.16:1472-1481.
de-Bashan L E,Hernandez J P,Bashan Y.2012.The potential contribution of plant growth-promoting bacteria to reduce environmental degradation-a comprehensive evaluation.Appl Soil Ecol.61:171-189.
DeBruyn J M,Mead T J,Sayler G S.2012.Horizontal transfer of PAH catabolism genes in Mycobacterium:Evidence from comparative genomics and isolated pyrene-degrading bacteria.Environ Sci Technol.46:99-106.
Delgado-Baquerizo M,Grinyer J,Reich P B,Singh B K.2016.Relative importance of soil properties and microbial community for soil functionality:Insights from a microbial swap experiment.Funct Ecol.30:1862-1873.
Dias R L,Ruberto L,Hernández E,Vázquez S C,Lo Balbo A,Del Panno M T,Mac Cormack W P.2012.Bioremediation of an aged diesel oil-contaminated Antarctic soil:Evaluation of the“on site”biostimulation strategy using different nutrient sources.Int Biodeterior Biodegrad.75:96-103.
Dubilier N,McFall-Ngai M,Zhao L P.2015.Microbiology:Create a global microbiome effort.Nature.526:631-634.
Edwards S J,Kjellerup B V.2013.Applications of biofilms in bioremediation and biotransformation of persistent organic pollutants,pharmaceuticals/personal care products,and heavy metals.Appl Microbiol Biotechnol.97:9909-9921.
Escalante A E,Rebolleda-Gómez M,Benítez M,Travisano M.2015.Ecological perspectives on synthetic biology:Insights from microbial population biology.Front Microbiol.6:143.
Fernando Bautista L,Sanz R,Carmen Molina M,González N,Sánchez D.2009.Effect of different non-ionic surfactants on the biodegradation of PAHs by diverse aerobic bacteria.Int Biodeterior Biodegrad.63:913-922.
Festa S,Coppotelli B M,Morelli I S.2016.Comparative bioaugmentation with a consortium and a single strain in a phenanthrene-contaminated soil:Impact on the bacterial community and biodegradation.Appl Soil Ecol.98:8-19.
Fierer N.2017.Embracing the unknown:Disentangling the complexities of the soil microbiome.Nat Rev Microbiol.15:579-590.
Fredrickson J K.2015.Ecological communities by design.Science.348:1425-1427.
Gambino M,Cappitelli F.2016.Mini-review:Biofilm responses to oxidative stress.Biofouling.32:167-178.
Gillespie I M M,Philp J C.2013.Bioremediation,an environmental remediation technology for the bioeconomy.Trends Biotechnol.31:329-332.
Girvan M S,Campbell C D,Killham K,Prosser J I,Glover L A.2005.Bacterial diversity promotes community stability and functional resilience after perturbation.Environ Microbiol.7:301-313.
González N,Simarro R,Molina M C,Bautista L F,Delgado L,Villa J A.2011.Effect of surfactants on PAH biodegradation by a bacterial consortium and on the dynamics of the bacterial community during the process.Bioresour Technol.102:9438-9446.
Gounou C,Bousserrhine N,Varrault G,Mouchel J M.2010.In-fluence of the iron-reducing bacteria on the release of heavy metals in anaerobic river sediment.Water Air Soil Pollut.212:123-139.
Gro?kopf T,Soyer O S.2014.Synthetic microbial communities.Curr Opin Microbiol.18:72-77.
Gupta A,Joia J,Sood A,Sood R,Sidhu C,Kaur G.2016.Microbes as potential tool for remediation of heavy metals:Areview.J Microb Biochem Technol.8:364-372.
Gupta G,Kumar V,Pal A K.2016.Biodegradation of polycyclic aromatic hydrocarbons by microbial consortium:Adistinctive approach for decontamination of soil.Soil Sediment ContamInt J.25:597-623.
Gurav R,Lyu H,Ma J L,Tang J C,Liu Q L,Zhang H R.2017.Degradation of n-alkanes and PAHs from the heavy crude oil using salt-tolerant bacterial consortia and analysis of their catabolic genes.Environ Sci Pollut Res.24:11392-11403.
Hao X,Taghavi S,Xie P,Orbach M J,Alwathnani H A,Rensing C,Wei G.2014.Phytoremediation of heavy and transition metals aided by legume-rhizobia symbiosis.Int J Phytoremed.16:179-202.
Haritash A K,Kaushik C P.2009.Biodegradation aspects of polycyclic aromatic hydrocarbons(PAHs):A review.J Hazard Mater.169:1-15.
Hayase N,Taira K,Furukawa K.1990.Pseudomonas putida KF-715 bphABCD operon encoding biphenyl and polychlorinated biphenyl degradation:Cloning,analysis,and expression in soil bacteria.J Bacteriol.172:1160-1164.
Hendrickx B,Junca H,Vosahlova J,Lindner A,Rüegg I,BucheliWitschel M,Faber F,Egli T,Mau M,Schl?mann M,Brennerova M,Brenner V,Pieper D H,Top E M,Dejonghe W,Bastiaens L,Springael D.2006.Alternative primer sets for PCR detection of genotypes involved in bacterial aerobic B-TEX degradation:Distribution of the genes in BTEX degrading isolates and in subsurface soils of a BTEX contaminated industrial site.J Microbiol Methods.64:250-265.
Hibbing M E,Fuqua C,Parsek M R,Peterson S B.2010.Bacterial competition:Surviving and thriving in the microbial jungle.Nat Rev Microbiol.8:15-25.
Hiraishi T.2016.Poly(aspartic acid)(PAA)hydrolases and PAAbiodegradation:Current knowledge and impact on applications.Appl Microbiol Biotechnol.100:1623-1630.
Horne I,Sutherland T D,Harcourt R L,Russell R J,Oakeshott J G.2002.Identification of an opd(organophosphate degradation)gene in an Agrobacterium isolate.Appl Environ Microbiol.68:3371-3376.
Imadi S R,Ali Z,Hasan H,Gul A.2016.Soil pollution and remediation.In Hakeem K R,Akhtar M S(eds.)Plant,Soil and Microbes.Volume 2.Mechanisms and Molecular Interactions.Springer International Publishing,Cham.pp.423-438.
Iwai S,Johnson T A,Chai B L,Hashsham S A,Tiedje J M.2011.Comparison of the specificities and effcacies of primers for aromatic dioxygenase gene analysis of environmental samples.Appl Environ Microbiol.77:3551-3557.
Jan A T,Azam M,Ali A,Haq Q M R.2014.Prospects for exploiting bacteria for bioremediation of metal pollution.Crit Rev Environ Sci Technol.44:519-560.
Jiang L L,Zhou J J,Quan C S,Xiu Z L.2017.Advances in industrial microbiome based on microbial consortium for biore-finery.Bioresour Bioprocess.4:11.
Johnsen A R,Karlson U.2004.Evaluation of bacterial strategies to promote the bioavailability of polycyclic aromatic hydrocarbons.Appl Microbiol Biotechnol.63:452-459.
Juhas M,van der Meer J R,Gaillard M,Harding R M,Hood D W,Crook D W.2009.Genomic islands:Tools of bacterial horizontal gene transfer and evolution.FEMS Microbiol Rev.33:376-393.
Kahng H Y,Malinverni J C,Majko M M,Kukor J J.2001.Genetic and functional analysis of the tbc operons for catabolism of alkyl-and chloroaromatic compounds in Burkholderia sp.strain JS150.Appl Environ Microbiol.67:4805-4816.
Kang C H,Kwon Y J,So J S.2016.Bioremediation of heavy metals by using bacterial mixtures.Ecol Eng.89:64-69.
Karigar C S,Rao S S.2011.Role of microbial enzymes in the bioremediation of pollutants:A review.Enzyme Res.2011:805187.
Kau A L,Ahern P P,Griffn N W,Goodman A L,Gordon J I.2011.Human nutrition,the gut microbiome and the immune system.Nature.474:327-336.
Kim S J,Song J,Kweon O,Holland R D,Kim D W,Kim J,Yu L R,Cerniglia C E.2012.Functional robustness of a polycyclic aromatic hydrocarbon metabolic network examined in a nidA aromatic ring-hydroxylating oxygenase mutant of Mycobacterium vanbaalenii PYR-1.Appl Environ Microbiol.78:3715-3723.
Kotas′J,Stasicka Z.2000.Chromium occurrence in the environment and methods of its speciation.Environ Pollut.107:263-283.
Kowalska J B,Mazurek R,G?asiorek M,Zaleski T.2018.Pollution indices as useful tools for the comprehensive evaluation of the degree of soil contamination-a review.Environ Geochem Health.40:2395-2420.
Kuppusamy S,Thavamani P,Venkateswarlu K,Lee Y B,Naidu R,Megharaj M.2017.Remediation approaches for polycyclic aromatic hydrocarbons(PAHs)contaminated soils:Technological constraints,emerging trends and future directions.Chemosphere.168:944-968.
Kuzyakov Y,Blagodatskaya E.2015.Microbial hotspots and hot moments in soil:Concept&review.Soil Biol Biochem.83:184-199.
Kweon O,Kim S J,Holland R D,Chen H Y,Kim D W,Gao Y,Yu L R,Baek S,Baek D H,Ahn H,Cerniglia C E.2011.Polycyclic aromatic hydrocarbon metabolic network in Mycobacterium vanbaalenii PYR-1.J Bacteriol.193:4326-4337.
Kylilis N,Tuza Z A,Stan G B,Polizzi K M.2018.Tools for engineering coordinated system behaviour in synthetic microbial consortia.Nat Commun.9:2677.
Lakshmanan V,Selvaraj G,Bais H P.2014.Functional soil microbiome:Belowground solutions to an aboveground problem.Plant Physiol.166:689-700.
Lamichhane S,Bal Krishna K C,Sarukkalige R.2016.Polycyclic aromatic hydrocarbons(PAHs)removal by sorption:A review.Chemosphere.148:336-353.
Lenoir I,Lounes-Hadj Sahraoui A,Fontaine J.2016.Arbuscular mycorrhizal fungal-assisted phytoremediation of soil contaminated with persistent organic pollutants:A review.Eur J Soil Sci.67:624-640.
Li X N,Jiao W T,Xiao R B,Chen W P,Chang A C.2015.Soil pollution and site remediation policies in China:A review.Environ Rev.23:263-274.
Lohmann R,Breivik K,Dachs J,Muir D.2007.Global fate of POPs:Current and future research directions.Environ Pollut.150:150-165.
Mackova M,Uhlik O,Lovecka P,Viktorova J,Novakova M,Demnerova K,Sylvestre M,Macek T.2010.Bacterial degradation of polychlorinated biphenyls.In Barton L L,Mandl M,Loy A(eds.)Geomicrobiology:Molecular and Environmental Perspective.Springer,Dordrecht.pp.347-366.
Madhaiyan M,Poonguzhali S,Sa T M.2007.Metal tolerating methylotrophic bacteria reduces nickel and cadmium toxicity and promotes plant growth of tomato(Lycopersicon esculentum L.).Chemosphere.69:220-228.
Mah T F C,O’Toole G A.2001.Mechanisms of biofilm resistance to antimicrobial agents.Trends Microbiol.9:34-39.
Mariano A P,Bonotto D M,de Angelis D D F,Pir?ollo M P S,Contiero J.2008.Biodegradability of commercial and weathered diesel oils.Braz J Microbiol.39:133-142.
Martiny J B H,Jones S E,Lennon J T,Martiny A C.2015.Microbiomes in light of traits:A phylogenetic perspective.Science.350:aac9323.
Mee M T,Collins J J,Church G M,Wang H H.2014.Syntrophic exchange in synthetic microbial communities.Proc Natl Acad Sci USA.111:E2149-E2156.
Mendes L W,Tsai S M,Navarrete A A,de Hollander M,van Veen J A,Kuramae E E.2015.Soil-borne microbiome:Linking diversity to function.Microb Ecol.70:255-265.
Mikeskova′H,NovotnyˇC,Svobodová K.2012.Interspecific interactions in mixed microbial cultures in a biodegradation perspective.Appl Microbiol Biotechnol.95:861-870.
Mineki S,Suzuki K,Iwata K,Nakajima D,Goto S.2015.Degradation of polyaromatic hydrocarbons by fungi isolated from soil in Japan.Polycyclic Aromat Compd.35:120-128.
Mrozik A,Piotrowska-Seget Z,Labuzek S.2003.Bacterial degradation and bioremediation of polycyclic aromatic hydrocarbons.Pol J Environ Stud.12:15-25.
NíChadhain S M,Norman R S,Pesce K V,Kukor J J,Zylstra G J.2006.Microbial dioxygenase gene population shifts during polycyclic aromatic hydrocarbon biodegradation.Appl Environ Microbiol.72:4078-4087.
Nzila A.2013.Update on the cometabolism of organic pollutants by bacteria.Environ Pollut.178:474-482.
Ojuederie O B,Babalola O O.2017.Microbial and plant-assisted bioremediation of heavy metal polluted environments:A review.Int J Environ Res Public Health.14:1504.
Okai M,Kubota K,Fukuda M,Nagata Y,Nagata K,Tanokura M.2010.Crystal structure ofγ-hexachlorocyclohexane dehydrochlorinase LinA from Sphingobium japonicum UT26.JMol Biol.403:260-269.
Owsianiak M,Szulc A,Chrzanowski L,Cyplik P,Bogacki M,Olejnik-Schmidt A K,Heipieper H J.2009.Biodegradation and surfactant-mediated biodegradation of diesel fuel by 218microbial consortia are not correlated to cell surface hydrophobicity.Appl Microbiol Biotechnol.84:545-553.
Pal A,Paul A K.2008.Microbial extracellular polymeric substances:Central elements in heavy metal bioremediation.Indian J Microbiol.48:49-64.
Papenfort K,Bassler B L.2016.Quorum sensing signal-response systems in Gram-negative bacteria.Nat Rev Microbiol.14:576-588.
Parsek M R,Greenberg E P.2000.Acyl-homoserine lactone quorum sensing in Gram-negative bacteria:A signaling mechanism involved in associations with higher organisms.Proc Natl Acad Sci USA.97:8789-8793.
Passatore L,Rossetti S,Juwarkar A A,Massacci A.2014.Phytoremediation and bioremediation of polychlorinated biphenyls(PCBs):State of knowledge and research perspectives.J Hazard Mater.278:189-202.
Peralta A L,Stuart D,Kent A D,Lennon J T.2014.A socialecological framework for“micromanaging”microbial services.Front Ecol Environ.12:524-531.
Perez-Garcia O,Lear G,Singhal N.2016.Metabolic network modeling of microbial interactions in natural and engineered environmental systems.Front Microbiol.7:673.
Peters C A,Bratton S P.2016.Urbanization is a major influence on microplastic ingestion by sunfish in the Brazos River Basin,Central Texas,USA.Environ Pollut.210:380-387.
Pieper D H,Seeger M.2008.Bacterial metabolism of polychlorinated biphenyls.J Mol Microbiol Biotechnol.15:121-138.
Pushpanathan M,Jayashree S,Gunasekaran P,Rajendhran J.2014.Microbial bioremediation:A metagenomic approach.In Das S(ed.)Microbial Biodegradation and Bioremediation.Elsevier,Oxford.pp.525-546.
Ren G D,Ren W J,Teng Y,Li Z G.2015.Evident bacterial community changes but only slight degradation when polluted with pyrene in a red soil.Front Microbiol.6:22.
Ren G D,Teng Y,Ren W J,Dai S X,Li Z G.2016.Pyrene dissipation potential varies with soil type and associated bacterial community changes.Soil Biol Biochem.103:71-85.
Rodriguez S,Bishop P L.2008.Enhancing the biodegradation of polycyclic aromatic hydrocarbons:Effects of nonionic surfactant addition on biofilm function and structure.J Environ Eng.134:505-512.
Sathishkumar M,Binupriya A R,Baik S H,Yun S E.2008.Biodegradation of crude oil by individual bacterial strains and a mixed bacterial consortium isolated from hydrocarbon contaminated areas.Clean Soil Air Water.36:92-96.
Schalk I J,Hannauer M,Braud A.2011.New roles for bacterial siderophores in metal transport and tolerance.Environ Microbiol.13:2844-2854.
Schmidt T M.2006.The maturing of microbial ecology.Int Microbiol.9:217-223.
Sedlmayer F,Hell D,Müller M,Ausl?nder D,Fussenegger M.2018.Designer cells programming quorum-sensing interference with microbes.Nat Commun.9:1822.
Serna-Chavez H M,Fierer N,van Bodegom P M.2013.Global drivers and patterns of microbial abundance in soil.Global Ecol Biogeogr.22:1162-1172.
Shah A A,Hasan F,Hameed A,Ahmed S.2008.Biological degradation of plastics:A comprehensive review.Biotechnol Adv.26:246-265.
Shankar S,Kansrajh C,Dinesh M G,Satyan R S,Kiruthika S,Tharanipriya A.2014.Application of indigenous microbial consortia in bioremediation of oil-contaminated soils.Int JEnviron Sci Technol.11:367-376.
Shields M S,Reagin M J,Gerger R R,Campbell R,Somerville C.1995.TOM,a new aromatic degradative plasmid from Burkholderia(Pseudomonas)cepacia G4.Appl Environ Microbiol.61:1352-1356.
Singleton D R,Guzmán Ramirez L,Aitken M D.2009.Characterization of a polycyclic aromatic hydrocarbon degradation gene cluster in a phenanthrene-degrading Acidovorax strain.Appl Environ Microbiol.75:2613-2620.
Skariyachan S,Shamsundar Setlur A,Naik S,Amaresh Naik A,Usharani M,S Vasist K.2017.Enhanced biodegradation of low and high-density polyethylene by novel bacterial consortia formulated from plastic-contaminated cow dung under thermophilic conditions.Environ Sci Pollut Res.24:8443-8457.
Song H,Ding M Z,Jia X Q,Ma Q,Yuan Y J.2014.Synthetic microbial consortia:From systematic analysis to construction and applications.Chem Soc Rev.43:6954-6981.
Souza E C,Vessoni-Penna T C,de Souza Oliveira R P.2014.Biosurfactant-enhanced hydrocarbon bioremediation:An overview.Int Biodeterior Biodegrad.89:88-94.
Sprocati A R,Alisi C,Tasso F,Marconi P,Sciullo A,Pinto V,Chiavarini S,Ubaldi C,Cremisini C.2012.Effectiveness of a microbial formula,as a bioaugmentation agent,tailored for bioremediation of diesel oil and heavy metal co-contaminated soil.Process Biochem.47:1649-1655.
Tardy V,Mathieu O,Le′v?eque J,Terrat S,Chabbi A,Lemanceau P,Ranjard L,Maron P A.2014.Stability of soil microbial structure and activity depends on microbial diversity.Environ Microbiol Rep.6:173-183.
Tauler M,Vila J,Nieto J M,Grifoll M.2016.Key high molecular weight PAH-degrading bacteria in a soil consortium enriched using a sand-in-liquid microcosm system.Appl Microbiol Biotechnol.100:3321-3336.
Teng Y,Wang X M,Li L N,Li Z G,Luo Y M.2015.Rhizobia and their bio-partners as novel drivers for functional remediation in contaminated soils.Front Plant Sci.6:32.
Thamer M,Rahman Al-Kubaisi A,Zahraw Z,Aldin Abdullah H,Hindy I,Abd Khadium A.2013.Biodegradation of Kirkuk light crude oil by Bacillus thuringiensis,northern of Iraq.Nat Sci.5:865-873.
Thavamani P,Megharaj M,Naidu R.2012.Bioremediation of high molecular weight polyaromatic hydrocarbons co-contaminated with metals in liquid and soil slurries by metal tolerant PAHs degrading bacterial consortium.Biodegradation.23:823-835.
Thomas C M,Nielsen K M.2005.Mechanisms of,and barriers to,horizontal gene transfer between bacteria.Nat Rev Microbiol.3:711-721.
Torsvik V,?vre?as L.2002.Microbial diversity and function in soil:From genes to ecosystems.Curr Opin Microbiol.5:240-245.
Varjani S J,Thaker M B,Upasani V N.2014.Optimization of growth conditions of native hydrocarbon utilizing bacterial consortium“HUBC”obtained from petroleum pollutant contaminated sites.Microbiology.4:474-476.
Varjani S J,Upasani V N.2016.Coreflood study for enhanced oil recovery through ex-situ bioaugmentation with thermo-and halo-tolerant rhamnolipid produced by Pseudomonas aeruginosa NCIM 5514.Bioresour Technol.220:175-182.
Varjani S J.2017.Microbial degradation of petroleum hydrocarbons.Bioresour Technol.223:277-286.
Varjani S J,Upasani V N.2017.A new look on factors affecting microbial degradation of petroleum hydrocarbon pollutants.Int Biodeterior Biodegrad.120:71-83.
Wang B B,Teng Y,Xu Y F,Chen W,Ren W J,Li Y,Christie P,Luo Y M.2018.Effect of mixed soil microbiomes on pyrene removal and the response of the soil microorganisms.Sci Total Environ.640-641:9-17.
Wang B Z,Guo P,Hang B J,Li L,He J,Li S P.2009.Cloning of a novel pyrethroid-hydrolyzing carboxylesterase gene from Sphingobium sp.strain JZ-1 and characterization of the gene product.Appl Environ Microbiol.75:5496-5500.
Wang F K,Li C,Wang H J,Chen W L,Huang Q Y.2016.Characterization of a phenanthrene-degrading microbial consortium enriched from petrochemical contaminated environment.Int Biodeterior Biodegrad.115:286-292.
Wang S Q,Chng K R,Wilm A,Zhao S Y,Yang K L,Nagarajan N,He J Z.2014.Genomic characterization of three unique Dehalococcoides that respire on persistent polychlorinated biphenyls.Proc Natl Acad Sci USA.111:12103-12108.
Wang W P,Shao Z Z.2012.Genes involved in alkane degradation in the Alcanivorax hongdengensis strain A-11-3.Appl Microbiol Biotechnol.94:437-448.
Wang X M,Teng Y,Tu C,Luo Y M,Greening C,Zhang N,Dai S X,Ren W J,Zhao L,Li Z G.2018.Coupling between nitrogenfixation and tetrachlorobiphenyl dechlorination in a rhizobium-legume symbiosis.Environ Sci Technol.52:2217-2224.
Wang Y X,Oyaizu H.2011.Enhanced remediation of dioxinsspiked soil by a plant-microbe system using a dibenzofurandegrading Comamonas sp.and Trifolium repens L.Chemosphere.85:1109-1114.
Waters C M,Bassler B L.2005.Quorum sensing:Cell-to-cell communication in bacteria.Annu Rev Cell Dev Biol.21:319-346.
Wi lkomirski B,Sudnik-Wójcikowska B,Galera H,Wierzbicka M,Malawska M.2011.Railway transportation as a serious source of organic and inorganic pollution.Water Air Soil Pollut.218:333-345.
Williams P.2007.Quorum sensing,communication and crosskingdom signalling in the bacterial world.Microbiology.153:3923-3938.
Xu X H,Zarecki R,Medina S,Ofaim S,Liu X W,Chen C,Hu S L,Brom D,Gat D,Porob S,Eizenberg H,Ronen Z,Jiang J D,Freilich S.2019.Modeling microbial communities from atrazine contaminated soils promotes the development of biostimulation solutions.ISME J.13:494-508.
Yim G,Wang H H,Davies J.2007.Antibiotics as signalling molecules.Philos Trans B Biol Sci.362:1195-1200.
Yoshida S,Ogawa N,Fujii T,Tsushima S.2009.Enhanced biofilm formation and 3-chlorobenzoate degrading activity by the bacterial consortium of Burkholderia sp.NK8 and Pseudomonas aeruginosa PAO1.J Appl Microbiol.106:790-800.
Yoshida S,Hiraga K,Takehana T,Taniguchi I,Yamaji H,Maeda Y,Toyohara K,Miyamoto K,Kimura Y,Oda K.2016.A bacterium that degrades and assimilates poly(ethylene terephthalate).Science.351:1196-1199.
Zeng J,Zhu Q H,Wu Y C,Lin X G.2016.Oxidation of polycyclic aromatic hydrocarbons using Bacillus subtilis CotAwith high laccase activity and copper independence.Chemosphere.148:1-7.
Zhang W W,Chen L X,Liu D Y.2012.Characterization of a marine-isolated mercury-resistant Pseudomonas putida strain SP1 and its potential application in marine mercury reduction.Appl Microbiol Biotechnol.93:1305-1314.
Zhao D F,Liu C S,Liu L H,Zhang Y B,Liu Q Y,Wu WM.2011.Selection of functional consortium for crude oilcontaminated soil remediation.Int Biodeterior Biodegrad.65:1244-1248.