1. bookVolume 66 (2017): Issue 3 (September 2017)
Journal Details
License
Format
Journal
eISSN
2544-4646
First Published
04 Mar 1952
Publication timeframe
4 times per year
Languages
English
access type Open Access

Metagenomic Analysis of Soil Bacterial Community and Level of Genes Responsible for Biodegradation of Aromatic Hydrocarbons

Published Online: 27 Sep 2017
Volume & Issue: Volume 66 (2017) - Issue 3 (September 2017)
Page range: 345 - 352
Received: 02 May 2016
Accepted: 04 Apr 2017
Journal Details
License
Format
Journal
eISSN
2544-4646
First Published
04 Mar 1952
Publication timeframe
4 times per year
Languages
English
Abstract

The aim of the studies was to compare the composition of soil bacterial metabiomes originating from urbanized areas and areas contaminated with hydrocarbons with those from agricultural soil and forest soil obtained from a protected wild-life park area. It should be noted that hydrocarbons are everywhere therefore bacteria capable of their utilization are present in every soil type. In the hydrocarbon- contaminated soil and in the soil of anthropogenic origin, the bacteria belonging to Gammaproteobacteria were dominant (28.4–36.6%), whereas in the case of agricultural soil and protected wild-life park soil their ratios decreased (22.8–23.0%) and were similar to that of Alphaproteobacteria. No statistically significant changes were observed in terms of the Operational Taxonomic Unit identified in the studies soils, however, based on the determined alpha-diversity it can be established that contaminated soils were characterized by lower biodiversity indices compared to agricultural and forest soils. Furthermore, the dioxygenase level was also evaluated in the studied soils, which are genes encoding crucial enzymes for the decomposition of mono- and polycyclic aromatic hydrocarbons during the biodegradation of diesel oil (PAHRHDαGN, PAHRHDαGP, xylE, Cat 2,3, ndoB). It was concluded that both the population structure of the soil metabiome and the number of genes crucial for biodegradation processes differed significantly between the soils. The level of analysed genes showed a similar trend, as their highest number in relations to genes encoding 16S RNA was determined in urban and hydrocarbon-contaminated soil.

Keywords

Afzal M., S. Yousaf, T.G. Reichenauer, M. Kuffner and A. Sessitsch. 2011. Soil type affects plant colonization, activity and catabolic gene expression of inoculated bacterial strains during phytoremediation of diesel 2011. J. Hazard. Mater. 186: 1568–1575. Search in Google Scholar

Bosco C., D. de Rigo, O. Dewitte, J. Poesen and P. Panagos. 2015. Modelling soil erosion at European scale: towards harmonization and reproducibility. Nat. Hazards Earth Syst. Sci. 15: 225–245.10.5194/nhess-15-225-2015 Search in Google Scholar

Brady N.C. and R.R. Weil. 1999. The nature and properties of soils, 12th ed. Prentice-Hall Inc., Upper Saddle River, NJ, USA. Search in Google Scholar

Caporaso J.G., C.L. Lauber, W.A. Walters, D. Berg-Lyons, J. Huntley, N. Fierer, S.M. Owens, J. Betley, L. Fraser, M. Bauer and others. 2012. Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms. ISME J. 6: 1621–1624.10.1038/ismej.2012.8340041322402401Search in Google Scholar

Cébron A., M.-P. Norini, T. Beguiristain and C. Leyval. 2008. Real-Time PCR quantification of PAH-ring hydroxylating dioxygenase (PAH-RHDα) genes from Gram positive and Gram negative. J. Microbiol. Methods 73: 148–159.10.1016/j.mimet.2008.01.00918329116 Search in Google Scholar

Cerqueira V.S., E.B. Hollenbach, F. Maboni, M.H. Vainstein, F.A.O. Camargo, A.O. Flavio, M.D.R. Peralba and F.M. Bento. 2011. Biodegradation potential of oily sludge by pure and mixed bacterial cultures. Bioresour. Technol. 102: 11003–11010.10.1016/j.biortech.2011.09.07421993328 Search in Google Scholar

de Kimpe C.R. and J.L. Morel. 2000. Urban soil management: A growing concern. Soil Sci. 165: 31–40.10.1097/00010694-200001000-00005 Search in Google Scholar

Fuentes S., V. Méndez, P. Aguila and M. Seeger. 2014. Bioremediation of petroleum hydrocarbons: catabolic genes, microbial communities, and applications. Appl. Microbiol. Biotechnol. 98: 4781–4794.10.1007/s00253-014-5684-924691868Search in Google Scholar

Kozdrój J. 2013. Metagenome – a new source of information about soil microorganisms. Post. Microbiol. 52: 185–200. Search in Google Scholar

Lal R. 2004. Soil carbon sequestration impacts on global climate change and food security. Science 304: 1623–1627.10.1126/science.109739615192216 Search in Google Scholar

Laramee L., J.R. Lawrence and C.W. Greer. 2000. Molecular analysis and development of 16S rRNA oligonucleotide probes to characterize a diclofop-methyl-degrading biofilm consortium. Can. J. Microbiol. 46: 133–142.10.1139/w99-12910721481 Search in Google Scholar

Lisiecki P., Ł. Chrzanowski, A. Szulc, Ł. Ławniczak, W. Białas, M. Dziadas, M. Owsianiak, J. Staniewski, P. Cyplik, R. Marecik and others. 2014. Biodegradation of diesel/biodiesel blends in saturated sand microcosms. Fuel 116: 321–327.10.1016/j.fuel.2013.08.009 Search in Google Scholar

Ławniczak Ł., A. Syguda, A. Borkowski, P. Cyplik, K. Mar- cinkowska, Ł. Wolko, T. Praczyk, Ł. Chrzanowski and J. Pernak. 2016. Influence of oligomeric herbicidal ionic liquids with MCPA and Dicamba anions on the community structure of autochthonic bacteria present in agricultural soil. Sci. Total Environ. 563–564: 247–255.10.1016/j.scitotenv.2016.04.10927135587 Search in Google Scholar

Marecik R., J. Wojtera-Kwiczor, L. Lawniczak, P. Cyplik, A. Szulc, A. Piotrowska-Cyplik and L. Chrzanowski. 2012. Rhamnolipids increase the phytotoxicity of diesel oil towards four common plant species in a terrestrial environment. Water Air Soil Pollut. 223(7): 4275–4282. Search in Google Scholar

Marquez-Rocha F.J., V. Hernandez-Rodri and M.T. Lamela. 2001. Biodegradation of diesel oil in soil by a microbial consortium. Water Air Soil Pollut. 128: 313–320.10.1023/A:1010392821353 Search in Google Scholar

Mrozik A. and Z. Piotrowska-Seget. 2010. Bioaugmentation as a strategy for cleaning up of soils contaminated with aromatic compounds. Microbiol. Res. 165(5): 363-375. Search in Google Scholar

Newman M.M., N. Hoilett, N. Lorenz, R.P. Dick, M.R. Liles, C. Ramsier and J.W. Kloepper. 2016. Glyphosate effects on soil rhizosphere-associated bacterial communities. Sci. Total Environ. 543(2016): 155–160. Search in Google Scholar

Panagos P., P. Borrelli, J. Poesen, C. Ballabio, E. Lugato, K. Meus- burger, L. Montanarella and C. Alewell. 2015. The new assessment of soil loss by water erosion in Europe. Environ. Sci. Policy 54: 438–447.10.1016/j.envsci.2015.08.012Search in Google Scholar

Panicker G., N. Mojib, J. Aislabie and A.K. Bej. 2010. Detection, expression and quantitation of the biodegradative genes in Antarctic microorganisms using PCR. Antonie van Leeuwenhoek 97: 275–287.Search in Google Scholar

Piotrowska-Cyplik A. and Z. Czarnecki. 2003. Phytoextraction of heavy metals by hemp during anaerobic sewage sludge management in the non-industrial sites. Pol. J. Environ. Stud.12(6): 779–784.Search in Google Scholar

Quast C., E. Pruesse, P. Yilmaz, J. Gerken, T. Schweer, P. Yarza, J. Peplies and F.O. Glöckner. 2013. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucl. Acids Res. 41: 590–596.10.1093/nar/gks1219353111223193283 Search in Google Scholar

Seneviratne S.I., T. Corti, E.L. Davin, M. Hirschi, E.B. Jaeger, I. Lehner, B. Orlowsky and A. Teuling. 2010. Investigating soil moisture–climate interactions in a changing climate: A review. Earth-Sci. Rev. 99: 125–161.10.1016/j.earscirev.2010.02.004 Search in Google Scholar

Sydow M., Z. Szczepaniak, G. Framski, J. Staninska, M. Owsianiak, A. Szulc, A. Piotrowsk-Cyplik, A. Zgoła-Grześkowiak, A. Wyrwas and Ł. Chrzanowski. 2015. Persistence of selected ammonium- and phosphonium-based ionic liquids in urban park soil microcosms. Int. Biodeter. Biodegr. 103: 91–96.10.1016/j.ibiod.2015.04.019 Search in Google Scholar

Sydow M., M. Owsianiak, Z. Szczepaniak, G. Framski, B.F. Smets, Ł. Ławniczak, P. Lisiecki, A. Szulc, P. Cyplik and Ł. Chrzanowski. 2016. Evaluating robustness of a dieseldegrading bacterial consortium isolated from contaminated soil. New Biotechnol. 33(6): 852–859.10.1016/j.nbt.2016.08.00327568238Search in Google Scholar

Szczepaniak Z., P. Cyplik, W. Juzwa, J. Czarny, J. Staninska and A. Piotrowska-Cyplik. 2015. Antibacterial effect of the Trichoderma viride fungi on soil microbiome during PAH’s biodegradation. Int. Biodeter. Biodegr. 104: 170–177.10.1016/j.ibiod.2015.06.002 Search in Google Scholar

Szczepaniak Z., J. Czarny, J. Staninska-Pięta, P. Lisiecki, A. Zgoła- Grześkowiak, P. Cyplik, Ł. Chrzanowski, Ł. Wolko, R. Marecik, Juzwa and others. 2016. Influence of soil contamination with PAH on microbial community dynamics and expression level of genes responsible for biodegradation of PAH and production of rhamnolipids. Environ. Sci. Pollut. Res. 23: 23043–23056.10.1007/s11356-016-7500-9510128927585583 Search in Google Scholar

Szulc A., D. Ambrozewicz, M. Sydow, L. Lawniczak, A. Piotrowska- -Cyplik, R. Marecik and Ł. Chrzanowski. 2014. The influence of bioaugmentation and biosurfactant addition on bioremediation efficiency of diesel-oil contaminated soil: Feasibility during field studies. J. Environ. Manage. 132: 121–128.10.1016/j.jenvman.2013.11.00624291585 Search in Google Scholar

Verheijen F.G.A., R.J.A. Jones, R.J. Rickson and C.J. Smith. 2009. Tolerable versus actual soil erosion rates in Europe. Earth-Sci. Rev. 94: 23–38.10.1016/j.earscirev.2009.02.003 Search in Google Scholar

Wyrwas B., Z. Dymaczewski, A. Zgola-Grzeskowiak, A. Szymanski, M. Franska, I. Kruszelnicka, D. Ginter-Kramarczyk, P. Cyplik, L. Lawniczak and Ł. Chrzanowski. 2013. Biodegradation of Triton X-100 and its primary metabolites by a bacterial community isolated from activated sludge. J. Environ. Manage. 128: 292–299.10.1016/j.jenvman.2013.05.02823770380 Search in Google Scholar

Zhou J., D. Guan, B. Zhou, B. Zhao, M. Ma, J. Qin, X. Jiang, S. Chen, F. Cao, D. Shen and J. Li. 2015. Influence of 34-years of fertilization on bacterial communities in an intensively cultivated black soil in northeast China. Soil Biol. Biochem. 90: 42–51. 10.1016/j.soilbio.2015.07.005 Search in Google Scholar

Recommended articles from Trend MD

Plan your remote conference with Sciendo