Bacterial community composition and biogeochemical heterogeneity in PAH-contaminated riverbank sediments
Tóm tắt
Predicting response of microbial communities to pollution requires an underlying understanding of the linkage between microbial community structure and geochemical conditions. Yet, there is scarce information about microbial communities in polycyclic aromatic hydrocarbons (PAH)-contaminated riverbank sediments. The aim of this study was to characterize bacterial communities in highly PAH-contaminated sediments and establish correlations between bacterial communities and environmental geochemistry of the sediments. Sediment core samples were collected from a highly PAH-contaminated site for (1) analysis of geochemical parameters including total nitrogen, total organic matter, moisture, total carbon, sulfate, pH, and PAH concentrations and (2) bacterial enumeration, 16S rDNA-based terminal restriction fragment length polymorphism analysis and sequencing. Non-metric dimensional scaling analyses revealed that bacterial community composition was strongly influenced by PAH concentration. Sulfate, organic matter, pH, and moisture were also related to community composition. A diverse microbial community was identified by the large number of operational taxonomic units recovered and by phylogenetic analyses. δ-Proteobacteria, firmicutes, and bacteriodetes were the dominant groups recovered. We also observed a high number of phylotypes associated with sulfate-reducing bacteria, some of which have been previously described as important in PAH degradation. Our study suggests that, despite intense pollution, bacterial community composition did exhibit temporal and spatial variations and were influenced by sediment geochemistry. Significant relationships between bacterial community composition and PAHs suggest that, potentially, extant microbial communities may contribute to natural attenuation and/or bioremediation of PAHs.
Tài liệu tham khảo
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