SEARCH WITHIN CONTENT
Citation Information : Polish Journal of Microbiology. Volume 66, Issue 3, Pages 345-352, DOI: https://doi.org/10.5604/01.3001.0010.4865
License : (CC BY-NC-ND 4.0)
Received Date : 02-May-2016 / Accepted: 04-April-2017 / Published Online: 27-September-2017
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.
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.
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.
Brady N.C. and R.R. Weil. 1999. The nature and properties of soils, 12th ed. Prentice-Hall Inc., Upper Saddle River, NJ, USA.
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.
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.
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.
de Kimpe C.R. and J.L. Morel. 2000. Urban soil management:A growing concern. Soil Sci. 165: 31–40.
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.
Kozdrój J. 2013. Metagenome – a new source of information about soil microorganisms. Post. Microbiol. 52: 185–200.
Lal R. 2004. Soil carbon sequestration impacts on global climate change and food security. Science 304: 1623–1627.
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.
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.
Ławniczak Ł., A. Syguda, A. Borkowski, P. Cyplik, K. Marcinkowska, 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.
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.
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.
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.
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.
Panagos P., P. Borrelli, J. Poesen, C. Ballabio, E. Lugato, K. Meusburger, L. Montanarella and C. Alewell. 2015. The new assessment of soil loss by water erosion in Europe. Environ. Sci. Policy 54: 438–447.
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.
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.
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.
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.
Sydow M., Z. Szczepaniak, G. Framski, J. Staninska, M. Owsianiak,A. Szulc, A. Piotrowsk-Cyplik, A. Zgoła-Grześkowiak, A. Wyrwasand Ł. Chrzanowski. 2015. Persistence of selected ammonium- and phosphonium-based ionic liquids in urban park soil microcosms. Int. Biodeter. Biodegr. 103: 91–96.
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.
Szczepaniak Z., P. Cyplik, W. Juzwa, J. Czarny, J. Staninska andA. Piotrowska-Cyplik. 2015. Antibacterial effect of the Trichoderma viride fungi on soil microbiome during PAH’s biodegradation. Int. Biodeter. Biodegr. 104: 170–177.
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.
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.
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.
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.
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.