Vertical response of microbial community and degrading genes to petroleum hydrocarbon contamination in saline alkaline soil
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摘要
A column microcosm was conducted by amending crude oil into Dagang Oilfield soil to simulate the bioremediation process. The dynamic change of microbial communities and metabolic genes in vertical depth soil from 0 to 80 cm were characterized to evaluate the petroleum degradation potential of indigenous microorganism. The influence of environmental variables on the microbial responds to petroleum contamination were analyzed. Degradation extent of 42.45% of n-alkanes(C8–C40) and 34.61% of 16ΣPAH were reached after 22 weeks. Relative abundance of alkB, nah, and phe gene showed about 10-fold increment in different depth of soil layers. Result of HTS profiles demonstrated that Pseudomonas, Marinobacter and Lactococcus were the major petroleum-degrading bacteria in0–30 and 30–60 cm depth of soils. Fusarium and Aspergillus were the dominant oil-degrading fungi in the 0–60 cm depth of soils. In 60–80 cm deep soil, anaerobic bacteria such as Bacteroidetes, Lactococcus, and Alcanivorax played important roles in petroleum degradation.Redundancy analysis(RDA) and correlation analysis demonstrated that petroleum hydrocarbons(PHs) as well as soil salinity, clay content, and anaerobic conditions were the dominant effect factors on microbial community compositions in 0–30, 30–60, and 60–80 cm depth of soils, respectively.
A column microcosm was conducted by amending crude oil into Dagang Oilfield soil to simulate the bioremediation process. The dynamic change of microbial communities and metabolic genes in vertical depth soil from 0 to 80 cm were characterized to evaluate the petroleum degradation potential of indigenous microorganism. The influence of environmental variables on the microbial responds to petroleum contamination were analyzed. Degradation extent of 42.45% of n-alkanes(C8–C40) and 34.61% of 16ΣPAH were reached after 22 weeks. Relative abundance of alkB, nah, and phe gene showed about 10-fold increment in different depth of soil layers. Result of HTS profiles demonstrated that Pseudomonas, Marinobacter and Lactococcus were the major petroleum-degrading bacteria in0–30 and 30–60 cm depth of soils. Fusarium and Aspergillus were the dominant oil-degrading fungi in the 0–60 cm depth of soils. In 60–80 cm deep soil, anaerobic bacteria such as Bacteroidetes, Lactococcus, and Alcanivorax played important roles in petroleum degradation.Redundancy analysis(RDA) and correlation analysis demonstrated that petroleum hydrocarbons(PHs) as well as soil salinity, clay content, and anaerobic conditions were the dominant effect factors on microbial community compositions in 0–30, 30–60, and 60–80 cm depth of soils, respectively.
A column microcosm was conducted by amending crude oil into Dagang Oilfield soil to simulate the bioremediation process. The dynamic change of microbial communities and metabolic genes in vertical depth soil from 0 to 80 cm were characterized to evaluate the petroleum degradation potential of indigenous microorganism. The influence of environmental variables on the microbial responds to petroleum contamination were analyzed. Degradation extent of 42.45% of n-alkanes(C8–C40) and 34.61% of 16ΣPAH were reached after 22 weeks. Relative abundance of alkB, nah, and phe gene showed about 10-fold increment in different depth of soil layers. Result of HTS profiles demonstrated that Pseudomonas, Marinobacter and Lactococcus were the major petroleum-degrading bacteria in0–30 and 30–60 cm depth of soils. Fusarium and Aspergillus were the dominant oil-degrading fungi in the 0–60 cm depth of soils. In 60–80 cm deep soil, anaerobic bacteria such as Bacteroidetes, Lactococcus, and Alcanivorax played important roles in petroleum degradation.Redundancy analysis(RDA) and correlation analysis demonstrated that petroleum hydrocarbons(PHs) as well as soil salinity, clay content, and anaerobic conditions were the dominant effect factors on microbial community compositions in 0–30, 30–60, and 60–80 cm depth of soils, respectively.
引文
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Liang,Y.,Zhao,H.,Deng,Y.,Zhou,J.,Li,G.,Sun,B.,2016.Longterm oil contamination alters the molecular ecological networks of soil microbial functional genes.Front.Microbiol.7,60.
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Mukherjee,P.K.,Chandra,J.,Retuerto,M.,Sikaroodi,M.,Brown,R.E.,Jurevic,R.,et al.,2014.Oral mycobiome analysis of HIV-infected patients:identification of pichia as an antagonist of opportunistic fungi.PLoS Pathog.10,e1003996.
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Patowary,K.,Patowary,R.,Kalita,M.C.,Deka,S.,2017.Characterization of biosurfactant produced during degradation of hydrocarbons using crude oil as sole source of carbon.Front.Microbiol.8,279.
Peng,S.,Zhou,Q.,Cai,Z.,Zhang,Z.,2009.Phytoremediation of petroleum contaminated soils by Mirabilis Jalapa L.in a greenhouse plot experiment.J.Hazard.Mater.168,1490-1496.
Ponsin,V.,Maier,J.,Guelorget,Y.,Hunkeler,D.,Bouchard,D.,Villavicencio,H.,et al.,2015.Documentation of time-scales for onset of natural attenuation in an aquifer treated by a crudeoil recovery system.Sci.Total Environ.512-513,62-73.
Pronk,G.J.,Heister,K.,K?gel-Knabner,I.,2013.Is turnover and development of organic matter controlled by mineral composition?Soil Biol.Biochem.67,235-244.
Rajakovic,V.,Aleksic,G.,Radetic,M.,Rajakovic,L.,2007.Efficiency of oil removal from real wastewater with different sorbent materials.J.Hazard.Mater.143,494-499.
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Schloss,P.D.,2013.Secondary structure improves OTU assignments of 16S rRNA gene sequences.Isme.J.7,457-460.
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Bouhajja,E.,McGuire,M.,Liles,M.R.,Bataille,G.,Agathos,S.N.,George,I.F.,2017.Identification of novel toluene monooxygenase genes in a hydrocarbon-polluted sediment using sequence-and function-based screening of metagenomic libraries.Appl.Microbiol.Biotechnol.101,797-808.
Cabral,L.,Pereira de Sousa,S.T.,Júnior,G.V.L.,Hawley,E.,Andreote,F.D.,Hess,M.,et al.,2018.Microbial functional responses to long-term anthropogenic impact in mangrove soils.Ecotox.Environ.Safe.160,231-239.
Callaghan,A.V.,Davidova,I.A.,Savage-Ashlock,K.,Parisi,V.A.,Gieg,L.M.,Suflita,J.M.,et al.,2010.Diversity of benzyl-and alkylsuccinate synthase genes in hydrocarbon-impacted environments and enrichment cultures.Environ.Sci.Technol.44,7287-7294.
Caporaso,J.G.,Kuczynski,J.,Stombaugh,J.,Bittinger,K.,Bushman,F.D.,Costello,E.K.,et al.,2010.QIIME allows analysis of highthroughput community sequencing data.Nat.Methods 7,335-336.
Caporaso,J.G.,Lauber,C.L.,Walters,W.A.,Berg-Lyons,D.,Lozupone,C.A.,Turnbaugh,P.J.,et al.,2011.Global patterns of16S rRNA diversity at a depth of millions of sequences per sample.Proc.Natl.Acad.Sci.U.S.A.108,4516-4522.
Cébron,A.,Norini,M.-P.,Beguiristain,T.,Leyval,C.,2008.Realtime PCR quantification of PAH-ring hydroxylating dioxygenase(PAH-RHDα)genes from Gram positive and Gram negative bacteria in soil and sediment samples.J.Microbiol.Meth.73,148-159.
Cheng,Z.,Chen,Y.,Zhang,F.,2018.Effect of reclamation of abandoned salinized farmland on soil bacterial communities in arid northwest China.Sci.Total Environ.630,799-808.
Crisafi,F.,Genovese,M.,Smedile,F.,Russo,D.,Catalfamo,M.,Yakimov,M.,et al.,2016.Bioremediation technologies for polluted seawater sampled after an oil-spill in Taranto Gulf(Italy):a comparison of biostimulation,bioaugmentation and use of a washing agent in microcosm studies.Mar.Pollut.Bull.106,119-126.
Edgar,R.C.,2013.UPARSE:highly accurate OTU sequences from microbial amplicon reads.Nat.Methods 10,996-998.
Espada,J.J.,Fernańdez,S.,Velasco,L.,Coto,B.,2013.Evaluation of different methodologies to determine the n-paraffin distribution of petroleum fractions.Fuel 109,470-475.
Feng,X.,Gustafsson,?.,Holmes,R.M.,Vonk,J.E.,Van Dongen,B.E.,Semiletov,I.P.,et al.,2015.Multimolecular tracers of terrestrial carbon transfer across the pan-Arctic:14Ccharacteristics of sedimentary carbon components and their environmental controls.Global Biogeochem.Cycles 29,1855-1873.
Hamamura,N.,Fukui,M.,Ward,D.M.,Inskeep,W.P.,2008.Assessing soil microbial populations responding to crude-oil amendment at different temperatures using phylogenetic,functional gene(alkB)and physiological analyses.Environ.Sci.Technol.42,7580-7586.
Harayama,S.,Kishira,H.,Kasai,Y.,Shutsubo,K.,1999.Petroleum biodegradation in marine environments.J.Mol.Microb.Biotechnol.1,63-70.
Jaraula,C.M.B.,Kenig,F.,Doran,P.T.,Priscu,J.C.,Welch,K.A.,2008.SPME-GCMS study of the natural attenuation of aviation diesel spilled on the perennial ice cover of Lake Fryxell,Antarctica.Sci.Total Environ.407,250-262.
Jiménez,N.,Vi?as,M.,Guiu-Aragonés,C.,Bayona,J.M.,Albaigés,J.,Solanas,A.M.,2011.Polyphasic approach for assessing changes in an autochthonous marine bacterial community in the presence of prestige fuel oil and its biodegradation potential.Appl.Microbiol.Biotechnol.91,823-834.
Jin,H.M.,Kim,J.M.,Lee,H.J.,Madsen,E.L.,Jeon,C.O.,2012.Alteromonas as a key agent of polycyclic aromatic hydrocarbon biodegradation in crude oil-contaminated coastal sediment.Environ.Sci.Technol.46,7731-7740.
Labbé,D.,Margesin,R.,Schinner,F.,Whyte,L.G.,Greer,C.W.,2007.Comparative phylogenetic analysis of microbial communities in pristine and hydrocarbon-contaminated Alpine soils.FEMSMicrobiol.Ecol.59,466-475.
Lee,D.W.,Lee,H.,Lee,A.H.,Kwon,B.O.,Khim,J.S.,Yim,U.H.,et al.,2018.Microbial community composition and PAHs removal potential of indigenous bacteria in oil contaminated sediment of Taean coast,Korea.Environ.Pollut.234,503-512.
Liang,Y.,Zhao,H.,Deng,Y.,Zhou,J.,Li,G.,Sun,B.,2016.Longterm oil contamination alters the molecular ecological networks of soil microbial functional genes.Front.Microbiol.7,60.
Liu,H.,Xu,J.,Liang,R.,Liu,J.,2014.Characterization of the medium-and long-chain n-alkanes degrading Pseudomonas aeruginosa strain SJTD-1 and its alkane hydroxylase genes.PLoS One 9,e105506.
Liu,Q.,Tang,J.,Bai,Z.,Hecker,M.,Giesy,J.P.,2015.Distribution of petroleum degrading genes and factor analysis of petroleum contaminated soil from the Dagang Oilfield,China.Sci.Rep.5,11068.
Liu,Q.,Tang,J.,Liu,X.,Song,B.,Zhen,M.,Ashbolt,N.J.,2017.Response of microbial community and catabolic genes to simulated petroleum hydrocarbon spills in soils/sediments from different geographic locations.J.Appl.Microbiol.123,875-885.
Lladó,S.,Covino,S.,Solanas,A.M.,Vi?as,M.,Petruccioli,M.,D'Annibale,A.,2013.Comparative assessment of bioremediation approaches to highly recalcitrant PAH degradation in a real industrial polluted soil.J.Hazard.Mater.248-249,407-414.
Looper,J.K.,Cotto,A.,Kim,B.Y.,Lee,M.K.,Liles,M.R.,NíChadhain,S.M.,et al.,2013.Microbial community analysis of deepwater horizon oil-spill impacted sites along the Gulf coast using functional and phylogenetic markers.Environ.Sci.Proc.Impacts.15,2068-2079.
Mukherjee,P.K.,Chandra,J.,Retuerto,M.,Sikaroodi,M.,Brown,R.E.,Jurevic,R.,et al.,2014.Oral mycobiome analysis of HIV-infected patients:identification of pichia as an antagonist of opportunistic fungi.PLoS Pathog.10,e1003996.
Muyzer,G.,De Waal,E.C.,Uitterlinden,A.G.,1993.Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reactionamplified genes coding for 16S rRNA.Appl.Environ.Microb.59,695-700.
Omrani,R.,Spini,G.,Puglisi,E.,Saidane,D.,2018.Modulation of microbial consortia enriched from different polluted environments during petroleum biodegradation.Biodegradation 29,187-209.
Patowary,K.,Patowary,R.,Kalita,M.C.,Deka,S.,2017.Characterization of biosurfactant produced during degradation of hydrocarbons using crude oil as sole source of carbon.Front.Microbiol.8,279.
Peng,S.,Zhou,Q.,Cai,Z.,Zhang,Z.,2009.Phytoremediation of petroleum contaminated soils by Mirabilis Jalapa L.in a greenhouse plot experiment.J.Hazard.Mater.168,1490-1496.
Ponsin,V.,Maier,J.,Guelorget,Y.,Hunkeler,D.,Bouchard,D.,Villavicencio,H.,et al.,2015.Documentation of time-scales for onset of natural attenuation in an aquifer treated by a crudeoil recovery system.Sci.Total Environ.512-513,62-73.
Pronk,G.J.,Heister,K.,K?gel-Knabner,I.,2013.Is turnover and development of organic matter controlled by mineral composition?Soil Biol.Biochem.67,235-244.
Rajakovic,V.,Aleksic,G.,Radetic,M.,Rajakovic,L.,2007.Efficiency of oil removal from real wastewater with different sorbent materials.J.Hazard.Mater.143,494-499.
Salminen,J.M.,Tuomi,P.M.,J?rgensen,K.S.,2008.Functional gene abundances(nahAc,alkB,xylE)in the assessment of the efficacy of bioremediation.Appl.Biochem.Biotechnol.151,638-652.
Schloss,P.D.,2013.Secondary structure improves OTU assignments of 16S rRNA gene sequences.Isme.J.7,457-460.
Schloss,P.D.,Gevers,D.,Westcott,S.L.,2011.Reducing the effects of PCR amplification and sequencing artifacts on 16S rRNA-based studies.PLoS One 6,e27310.
Shahi,A.,Aydin,S.,Ince,B.,Ince,O.,2016.Reconstruction of bacterial community structure and variation for enhanced petroleum hydrocarbons degradation through biostimulation of oil contaminated soil.Chem.Eng.J.306,60-66.
Sherry,A.,Gray,N.D.,Ditchfield,A.K.,Aitken,C.M.,Jones,D.M.,R?ling,W.F.M.,et al.,2013.Anaerobic biodegradation of crude oil under sulphate-reducing conditions leads to only modest enrichment of recognized sulphate-reducing taxa.Int.Biodeter.Biodegr.81,105-113.
Shin,K.H.,Lim,Y.,Ahn,J.H.,Khil,J.,Cha,C.J.,Hur,H.G.,2005.Anaerobic biotransformation of dinitrotoluene isomers by Lactococcus lactis subsp.lactis strain 27 isolated from earthworm intestine.Chemosphere 61,30-39.
Smits,T.H.M.,Balada,S.B.,Witholt,B.,van Beilen,J.B.,2002.Functional analysis of alkane hydroxylases from Gram-negative and Gram-positive bacteria.J.Bacteriol.184,1733-1742.
Stagars,M.H.,Mishra,S.,Treude,T.,Amann,R.,Knittel,K.,2017.Microbial community response to simulated petroleum seepage in Caspian Sea sediments.Front.Microbiol.8,764.
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