Thành phần cộng đồng vi khuẩn và tính không đồng nhất sinh địa hóa trong trầm tích bờ sông bị ô nhiễm PAH

Acosta-Gonzalez R-M, Marques S (2013) Characterization of the anaerobic microbial community in oil-polluted subtidal sediments: aromatic biodegradation potential after the Prestige oil spill. Environ Microbiol 15:77–92 Almeida R, Mucha A, Teixeira C, Bordalo A, Almeida M (2013) Biodegradation of petroleum hydrocarbons in estuarine sediments: metal influence. Biodegradation 24:111–123 Amin I, Jacobs A (2013) A study of the contaminated banks of the Mahoning River, Northeastern Ohio, USA: characterization of the contaminated bank sediments and river water-groundwater interactions. Env Earth Sci 70:3237–3244 Bamforth S, Singleton I (2005) Bioremediation of polycyclic aromatic hydrocarbons: current knowledge and future directions. J Chem Technol Biotech 80:723–736 Baniulyte D, Favila E, Kelly J (2009) Shifts in microbial community composition following surface application of dredged river sediments. Microb Ecol 57:160–169 Barns S, Cain E, Sommerville L, Kuske C (2007) Acidobacteria phylum sequences in uranium-contaminated subsurface sediments greatly expand the known diversity within the phylum. Appl Environ Microbiol 73:3113–3116 Bastiaens L, Springael D, Wattiau P, Harms H, deWatcher R, Verachert H, Diels L (2000) Isolation of adherent polycyclic aromatic hydrocarbon (PAH)-degrading bacteria using PAH-sorbing carriers. Appl Environ Microbiol 66:1834–1843 Bernhard A, Colbert D, McManus J, Field K (2005) Microbial community dynamics based on 16S rRNA gene profiles in a Pacific Northwest estuary and its tributaries. FEMS Microb Ecol 52:115–128 Buckley C, Hynes S, Mechan S (2012) Supply of an ecosystem service—farmers’ willingness to adopt riparian buffer zones in agricultural catchments. Environ Sci Pol 24:101–109 Cao Z, Liu J, Luan Y, Li Y, Ma M, Xu J, Han S (2010) Distribution and ecosystem risk assessment of polycyclic aromatic hydrocarbons in the Luan River, China. Ecotoxicology 19:827–837 Cardenas E, Wu W, Leigh M, Carley J, Carroll S, Gentry T, Luo J, Watson D, Gu B, Ginder-Vogel M, Kitanidis P, Jardine P, Zhou J, Criddle C, Marsh T, Tiedje J (2008) Microbial communities in contaminated sediments, associated with bioremediation of uranium to submicromolar levels. Appl Environ Microbiol 74:3718–3729 Carter M (2000) Soil sampling and methods of analysis. Carter M, Gregorich E (eds). Florida, Canadian Society of Soil Science Christen B, Dalgaard T (2013) Buffers for biomass production in temperature European agriculture: a review and synthesis on function, ecosystem services and implementation. Biomass Bioenergy 55:53–67 Cleary DFR, Oliveira V, Lillebø AI, Gomes NCM, Pereira A, Henriques I, Marques B, Almeida A, Cunha A, Correia A, Lillebo A (2012) Impact of plant species on local environmental conditions, microbiological parameters and microbial composition in a historically Hg-contaminated salt marsh. Mar Pollut Bull 64:263–271 Dell’Anno A, Beolchini F, Gabellini M, Rocchetti L, Pusceddu A, Danovaro R (2009) Bioremediation of petroleum hydrocarbons in anoxic marine sediments: consequences on the speciation of heavy metals. Mar Pollut Bull 58:1808–1814 Edlund A, Jansson JK (2006) Changes in active bacterial communities before and after dredging of highly polluted Baltic Sea sediments. Appl Environ Microbiol 72:6800–6807 Eggleton J, Thomas K (2004) A review of factors affecting the release and bioavailability of contaminants during sediment disturbance events. Environ Inter 30:973–980 Feris K, Frazar P, Rillig C, Moore M, Gannon J, Holben WE (2004) Seasonal dynamics of shallow-hyporheic-zone microbial community structure along a heavy-metal contamination gradient. Appl Environ Microbiol 70:2323–2331 Gieg L, Fowler SJ, Berdugo-Clavijo C (2014) Syntrophic biodegradation of hydrocarbon contaminants. Curr Opin Biotech 26:21–29 Gomes N, Flocco C, Costa R, Junca H, Vilchez R, Piepe D, Krögerrecklenfort E, Pranhos R, Mendoça-Hagler L, Smalla K (2013) Mangrove microniches determine the structural and functional diversity of enriched petroleum hydrocarbon-degrading consortia. FEMS Ecol 74:276–290 Gudasz C, Bastiviken D, Prenme K, Steger K, Tranvik L (2012) Constrained microbial processing of allochthonous organic carbon in boreal lake sediments. Limnol Oceanogr 57:163–175 Guo W, He M, Yang Z, Lin C, Quan X, Wang H (2007) Distribution of polycyclic aromatic hydrocarbons in water, suspended particular matter and sediment from Daliao River watershed, China. Chemosphere 68:93–104 Haller L, Onolla M, Zopfi J, Peduzzi R, Wildi W, Pote J (2011) Composition of bacterial and archaeal communities in freshwater sediments with different contamination levels (Lake Geneva, Switzerland). Water Res 45:1213–1228 Ho Y, Jackson M, Yang Y, Mueller J, Pritchard P (2000) Characterization of fluoranthene and pyrene degrading bacteria isolated from PAH-contaminated soils and sediments. J Ind Microbiol Biotechnol 24:100–112 Holland M (2008) Non metric multidimensional scaling (MDS) University of Georgia, Department of Geology. http://strata.uga.edu/software/pdf/mdsTutorial.pdf Hullar M, Kaplan L, Stahl D (2006) Recurring seasonal dynamics of microbial communities in stream habitats. Appl Environ Microbiol 72:713–722 Jiang L, Zheng Y, Peng X, Zhou H, Zhang C, Xiao X, Wang F (2009) Vertical distribution and diversity of sulfate-reducing prokaryotes in the Pearl River estuarine sediments, Southern China. FEMS Microbiol Ecol 70:249–262 Johnsen A, Karlson U (2004) Evaluation of bacterial strategies to promote the bioavailability of polycyclic aromatic hydrocarbons. Appl Microbiol Biotechnol 63:452–459 Johnsen A, Wick L, Harms H (2005) Principles of microbial PAH degradation in soil. Environ Pollut 133:71–84 Johnston C, Johnston G (2012) Bioremediation of polycyclic aromatic hydrocarbons. In: Arora R (ed) Microbial biotechnology. Energy and Environment, UK, pp 279–296 Kadnikov V, Loakina A, Likhoshvai A, Gorshkov A, Pogodaeva T, Beletsky A, Mardanov A, Zemskaya T, Ravin N (2013) Composition of the microbial communities of bituminous constructions at natural oil seeps at the bottom of Lake Baikal. Microbiology 82:373–382 Kumar S, Tamura K, Nei M (2004) MEGA3: integrated software for molecular evolutionary genetics analysis and sequence alignment. Brief Bioinform 5:150–163 Lemke M, Leff L (2006) Culturability of stream bacteria assessed at the assemblage and population levels. Microb Ecol 51:365–374 Li W, Godzik A (2006) Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics 22:1658–1659 Li C, Zhou H, Wong S, Tam N (2009) Vertical distribution and anaerobic biodegradation of polycyclic aromatic hydrocarbons in mangrove sediments in Hong Kong, South China. Sci Total Environ 407:5772–5779 Liu W, Marsh T, Cheng H, Forney L (1997) Characterization of microbial diversity by determining terminal restriction fragment length polymorphisms of genes encoding 16S rRNA. Appl Environ Microbiol 63:4516–4522 Lors C, Ryngaert A, Périé F, Diels L, Damidot D (2010) Evolution of bacterial community during bioremediation of PAHs in a coal tar contaminated soil. Chemosphere 81:1263–1271 Machado A, Magalhaes C, Mucha A, Almeida C, Bordalo A (2012) Microbial communities within saltmarsh sediments: composition, abundance and pollution constraints. Est Coast Shelf Sci 99:145–152 Miletto M, Loy A, Antheunisse M, Loeb R, Bodelier P, Laanbroek H (2008) Biogeography of sulfate-reducing prokaryotes in river floodplains. FEMS Microbiol Ecol 64:395–406 Mosher J, Findlay R, Johnston C (2006) Physical and chemical factors affecting microbial biomass and activity in contaminated subsurface sediment. Can J Microbiol 52:397–403 Pies C, Hoffmann P, Petrowsky J, Yang Y, Ternes T, Hofmann T (2008) Characterization and source identification of polycyclic aromatic hydrocarbons (PAHs) in river bank soils. Chemosphere 72:1594–1601 Porat I, Vishnivetskaya T, Mosher J, Brandt C, Yang S, Brooks S, Liang L, Drake M, Podar M, Brown S, Palumbo A (2010) Characterization of the archaeal community in contaminated and uncontaminated surface stream sediments. Microb Ecol 60:784–795 Pratt B, Riesen R, Johnston CG (2012) PLFA analyses of microbial communities associated with PAH-contaminated riverbank sediment. Microb Ecol 64:680–691 Rogers S, Ong S, Moorman T (2007) Mineralization of PAHs in coal–tar impacted aquifer sediments and associated microbial community structure investigated with FISH. Chemosphere 69:1563–1573 Shen J, Shao X (2005) A comparison of accelerated solvent extraction, Soxhlet extraction, and ultrasonic-assisted extraction for analysis of terpenoids and sterols in tobacco. Anal Bioanal Chem 6:1003–1008 Shi W, Bischoff M, Turco R, Konopka A (2005) Microbial catabolic diversity in soils contaminated with hydrocarbons and heavy metals. Environ Sci Technol 39:1974–1979 Smoot J, Findlay R (2001) Spatial and seasonal variation in a reservoir sedimentary microbial community as determined by phospholipid analysis. Microb Ecol 42:350–358 Sponseller R, Heffernan J, Fisher S (2013) On the multiple ecological roles of water in river networks. Ecosphere 4(art17):1–17. doi:10.1890/ES12-00225.1 Suárez-Suárez A, Lopez-Lopez A, Tovar-Sanchez A, Yarza P, Orfila A, Terrados J, Arnds J, Marques S, Niehmann H, Schmitt-Kopplin P, Amann R, Rossello-Mora R (2011) Response of sulfate-reducing bacteria to an artificial oil-spill in a coastal marine sediment. Environ Microbiol 13:1488–1499 Sun M, Dafforn K, Johnston E, Brown M (2013) Core sediment bacteria drive community response to anthropogenic contamination over multiple environmental gradients. Environ Microbiol 15:2517–2531 United States Army Corps of Engineers (USACE) (1999) Mahoning River Environmental Dredging Reconnaissance Study, USACE Publications United States Army Corps of Engineers (USACE) (2001) Lower Mahoning River, Pennsylvania Environmental Dredging Reconnaissance Study. U.S. Army Corps of Engineers Pittsburgh District Final Report United States Environmental Protection Agency (USEPA) (1996) Test methods for evaluation of solid waste, SW-846, Method 3540C, Soxhlet Extraction Revision 3. USEPA, http://www.epa.gov/osw/hazard/testmethods/sw846/pdfs/3540c.pdf United States Environmental Protection Agency (USEPA) (2007) Test methods for evaluation of solid waste, SW-846, method 8270D, semivolatile organic compounds by gas chromatography/mass spectrometry (GCMS) Revision 4. USEPA, http://www.epa.gov/osw/hazard/testmethods/sw846/pdfs/8270d.pdf United States Environmental Protection Agency (USEPA) (2012) Selected analytical methods for environmental remediation and recovery (SAM)-2012. Office of Research and Development National Homeland Security Research Center http://cfpub.epa.gov/…/si_public_file_download Vishnivetskaya T, Mosher J, Castro H, Palumbo A, Podar M, Brown S, Elias D, Drake M, Gilmour C, Wall J, Brandt C (2011) Mercury and other heavy metals influence bacterial community structure in contaminated Tennessee streams. Appl Environ Microbiol 77:302–311 Wang Y, Tam N (2012) Natural attenuation of contaminated marine sediments from an old floating dock part II: changes of sediment microbial community structure and its relationship with environmental variables. Sci Total Environ 324:95–103 Wentzel A, Ellingsen T, Kotlar H, Zotchev S, Throne-Holst M (2007) Bacterial metabolism of long-chain n-alkanes. Appl Microb Biotechnol 76:1209–1221 Zeinali M, Vossoughi M, Ardestani S (2007) Characterization of a moderate thermophilic Nocardia species able to grow on polycyclic aromatic hydrocarbons. Lett Appl Microbiol 45:622–628 Zhang W, Ki J, Qian P (2008) Microbial diversity in polluted harbor sediments I: bacterial community assessment based on four clone libraries of 16S rDNA. Est Coast Shelf Sci 76:668–681