Insights into aerobic microbial community in the Kamniška Bistrica river sediment with culture-dependent and molecular biology approach

Authors

  • Lijana FANEDL Univ. of Ljubljana, Biotechnical Fac., Dept. of Animal Science, Groblje 3, SI-1230 Domžale, Slovenia

DOI:

https://doi.org/10.14720/aas.2014.104.2.6

Keywords:

microbiology, aerobic bacteria, river sediment, culture-dependent methods, molecular methods, environment protection, Slovenia

Abstract

River systems are exposed to anthropogenic disturbances, including chemical pollution and eutrophication. They may affect a structure and diversity of microbial communities in river sediment. The aim of the study was to describe diversity and structure of a bacterial community in the Kamniška Bistrica river sediment using culture-dependent and molecular methods. Sediment samples were collected from three sampling stations along the Kamniška Bistrica river: upstream (Kamniška Bistrica), midstream (Vir) and downstream (Bišče), and physico-chemical analysis was conducted on-site. Isolates were recovered from three different agar plate media (LB, NB in R2A) and micro- as well as macromorphologically described. DNA was extracted from pure cultures and directly from sediment samples, and 16S rRNA gene segments were PCR amplified using universal bacterial primers. The PCR products were subjected to denaturing gradient gel electrophoresis (DGGE). The results showed that the DGGE was an appropriate method for monitoring the changes in the community structure of the river sediment and allows to determine the impact of environmental factors on bacterial diversity. The comparative analysis of the DGGE profiles from isolates and sediment samples showed that the DGGE banding patterns revealed different bacterial community structures for all three sampling stations, while the DGGE profiles of isolates did not represent dominant bacterial populations of the sediment. On the bases of the DGGE profiles, 25 isolates were chosen and their 16S rRNA genes were amplified and sequenced. All partial nucleotide sequences of 16S rRNA genes were preleminary taxonomically identified by using BLAST. The majority of sequenced isolates belonged to bacteria normally present in aquatic environments.

References

Atlas R.M., Bartha R. 1998. Microbial ecology: fundamentals and applications. 4th ed. Menlo Park, California; Benjamin/Cummings Publishing Company, Inc.: 694 str.

Bogataj J. 2009. Problematika nizkih pretokov Kamniške Bistrice med Kamnikom in Domžalami. Diplomsko delo. Ljubljana, Univerza v Ljubljani, FGG: 123 str.

Brečko Grubar V. 2007. Vloga naravnogeografskih značilnosti porečja pri sonaravnem upravljanju z vodnimi viri v porečju Kamniške Bistrice. Dela 28: 305–321, doi:10.4312/dela.28.21.305-321

Direktiva 2008/105/ES Evropskega parlamenta in Sveta z dne z dne 16. decembra 2008 o okoljskih standardih kakovosti na področju vodne politike, spremembi in poznejši razveljaviti direktiv 82/176/EGS, 83/513/EGS, 84/156/EGS, 84/491/EGS, 86/280/EGS ter spremembi Direktive 2000/60/ES Evropskega parlamenta in Sveta. http://vlex.com/source/uradni-list-evropske-unije-2193/issue/2008/12/24/01 (10. sep. 2010)

Edwards I.P., Bürgmann H., Miniaci C., Zeyer J. 2006. Variation in Microbial Community Composition and Culturability in the Rhizosphere of Leucanthemopsis alpina (L.) Heywood and Adjacent Bare Soil along an Alpine Chronosequence. Microbial Ecology, 52: 679–692, doi:10.1007/s00248-006-9097-x

Findlay S. 2010. Stream microbial ecology. Journal of the North American Benthological Society, 29, 1: 170–181, doi:10.1899/09-023.1

Globevnik L. 2002. Vodnogospodarska osnova povodja Kamniške Bistrice. Ljubljana, Vodnogospodarski inštitut: 92 str.

Hodnik A. 1988. Tekstura tal. V: Kemične analize talnih vzorcev, rastlinskih vzorcev in odcednih vod., BF, Katedra za pedologijo, prehrano rastlin in ekologijo: 59–62. http://www.arso.gov.si/vode/podatki/arhiv/Podatki%20reke%202010%20LOQ_za%20splet.pdf (13. nov. 2014)

http://www.arso.gov.si/vode/podatki/arhiv/Sava_zgornji_del_2008.pdf (10. sep. 2010)

http://www.ccn-domzale.si/ (20. sep. 2014)

Hullar M.A.J., Kplan L.A., Stahl D. 2006. Racurring seasonal dynamics of microbial communities in stream habitats. Applied and Environmental Microbiology, 72: 713–722, doi:10.1128/AEM.72.1.713-722.2006

Lane D.J. 1991. 16S/23S rRNA sequencing. V: Nucleic Acid Techniques in Bacterial Systematics. Stackebrandt E., Goodfellow M. (eds.). New York, John Wiley & Sons, Inc.: 115–148

Letno poročilo o kvaliteti pitne vode v letu 2006 iz vodovodov v upravljanju Javnega komunalnega podjetja Prodnik d.o.o. Domžale. Zavod za zdravstveno varstvo Kranj. 20 str. http://www.prodnik.si/images/editor_pic/Microsoft%20Word%20-%20ZZV%20Prodnik07b.pdf (13. sep. 2010)

Letno poročilo o kvaliteti pitne vode v letu 2007 iz vodovodov v upravljanju Javnega komunalnega podjetja Prodnik d.o.o. Domžale. Zavod za zdravstveno varstvo Kranj. 22 str. http://www.prodnik.si/images/editor_pic/Microsoft%20Word%20-%20Prodnik07.pdf (13. sep. 2010)

Litchfield C.D., Floodgate G.D. 1975. Biochemistry and microbiology of some Irish Sea sediments: II. Bacteriological analyses. Marine Biology, 30: 97–103, doi:10.1007/BF00391584

Marsh T.L., Saxman P., Cole J., Tiedje J. 2000. Terminal restriction fragment length polymorpism analysis program, a web-based research tool for microbial community analysis. Applied and Environmental Microbiology, 66, 8: 3616–3620, doi:10.1128/AEM.66.8.3616-3620.2000

Monitoring kakovosti površinskih vodotokov v Sloveniji v letu 2006. 2008. Ljubljana, Ministrstvo za okolje in prostor, ARSO: 127 str.

Muyzer G, de Waal EC, Uitterlinden AG. 1993. Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA. Appl Environ Microbiol., 59, 3: 695–700

Nealson K.H. 1997. Sediment bacteria: Who's there, what are they doing, and what's new? Annual Review of Earth and Planetary Sciences, 25: 403–434, doi:10.1146/annurev.earth.25.1.403

Nübel U., Engelen B., Felske A., Snaidr J., Weishuber A., Amann R.I., Ludwig W., Backhaus, H. 1996. Sequence heterogeneities of genes encoding 16S rRNAs in Paenibacillus polymyxa detected by TGGE. Journal of Bacteriology, 178: 5636–5643

Ocena ekološkega in kemijskega stanja rek v Sloveniji v letih 2007 in 2008. 2010. Ljubljana, Ministrstvo za okolje in prostor, ARSO: 116 str.

Ocena stanja rek v Sloveniji v letih 2009 in 2010. 2012. Agencija Republike Slovenije za okolje: 35 str. www.arso.gov.si/vode/reke/.../REKE%20porocilo%202009-2010.pdf (10. nov. 2014)

Odlok o območjih vodonosnikov in njihovih hidrografskih zaledij, ogroženih zaradi fitofarmacevtskih sredstev. 2002. Ur. l. RS, št. 97/02: 10627

Pantanella F., Berlutti F., Passariello C., Sarli S., Morea C., Schippa S. 2007. Violacein and biofilm production in Janthinobacterium lividum. Journal of Applied Microbiology, 102: 992–999

Polz M.F., Cavanaugh C.M. 1998. Bias in template-to-product ratios in multitemplate PCR. Applied and Environmental Microbiology, 64, 10: 3724–30

Poročilo o delu CČN Domžale-Kamnik d.o.o. za leto 2007. Domžale: 80 str. http://www.ccn-domzale.si/images/stories/o-podjetju/porocila/porocilo_o_delu_2007.pdf (15. sep. 2010)

Poročilo o delu CČN Domžale-Kamnik d.o.o. za leto 2008. Domžale: 82 str. http://www.ccn-domzale.si/images/stories/o-podjetju/porocila/porocilo_o_delu_2008.pdf (15. sep. 2014)

Poročilo o delu CČN Domžale-Kamnik d.o.o. za leto 2009. Domžale: 76 str. http://www.ccn-domzale.si/images/stories/porocilo2009.pdf (15. sep. 2010)

Poročilo o kakovosti pitne vode iz vodooskrbnih sistemov v upravljanju Javnega komunalnega podjetja Prodnik d.o.o. za leto 2008. Zavod za zdravstveno varstvo Kranj: 26 str. http://www.prodnik.si/images/editor_pic/LetPro_08.pdf (13. sep. 2010)

Poročilo o kakovosti pitne vode iz vodooskrbnih sistemov v upravljanju Javnega komunalnega podjetja Prodnik d.o.o. za leto 2009. Zavod za zdravstveno varstvo Kranj: 23 str. http://www.prodnik.si/images/editor_pic/LProd09.pdf (13. sep. 2010)

Poročilo o pitni vodi iz vodooskrbnih sistemov v upravljanju Javnega komunalnega podjetja Prodnik d.o.o. za leto 2010. Zavod za zdravstveno varstvo Kranj: 22 str. http://www.prodnik.si/e_files/content/zzvk2010.pdf (15. okt. 2014)

Speksnijder A.G.C.L., Kowalchuk G.A., De Jong S., Kline E., Stephen J.R., Laanbroek H.J. 2001. Microvariation Artifacts Introduced by PCR and Cloning of Closely Related 16S rRNA Gene Sequences. Applied and Environmental Microbiology, 67, 1: 469–472, doi:10.1128/AEM.67.1.469-472.2001

Spring S., Schulze R., Overmann J., Schleifer K.-H. 2000. Identification and characterization of ecologically significant prokaryotes in the sediment of freshwater lakes: molecular and cultivation studies. FEMS Microbiology Reviews, 24: 573–590, doi:10.1111/j.1574-6976.2000.tb00559.x

Staley J.T., Konopka A. 1985. Measurement of in situ activities of nonphotosynthetic microorganisms in aquatic and terrestrial habitats. Annual Review of Microbiology, 39: 321–46, doi:10.1146/annurev.mi.39.100185.001541

Strokovne podlage za razglasitev ogroženosti podzemne vode v Republiki Sloveniji. 2002. Ministrstvo za okolje, prostor in energijo, Agencija Republike Slovenije za okolje: 98 str.

Thiyagarajan V., Lau S., Tsoi M., Zhang W., Qian P.Y. 2010. Monitoring bacterial biodiversity in surface sediment using terminal restriction fragment lenght polymorphism analysis (T-RFLP): application to coastal environment. Coastal Environmental and Ecosystem Issues of the East China Sea, 151–163

Uredba o stanju površinskih voda. Ur.l. RS, št. 14/09, št.98/10 http://zakonodaja.gov.si/rpsi/r00/predpis_URED5010.html (10. sep. 2014)

von Wintzigerode F., Gobel U.B., Stackebrandt E. 1997. Detrmination of microbial diversity in environmental samples: pitfalls of PCR-based rRNA analysis. FEMS Microbiology Reviews, 21: 213–229, doi:10.1111/j.1574-6976.1997.tb00351.x

Weisburg W.G., Barns S.M., Pelletier D.A., Lane D. 1991. 16S ribosomal DNA amplification for phylogenetic study. Journal of Bacteriology, 173, 2: 697–703

Published

25. 11. 2015

Issue

Section

Animal Science section

How to Cite

FANEDL, L. (2015). Insights into aerobic microbial community in the Kamniška Bistrica river sediment with culture-dependent and molecular biology approach. Acta Agriculturae Slovenica, 104(2), 109–118. https://doi.org/10.14720/aas.2014.104.2.6

Similar Articles

1-10 of 854

You may also start an advanced similarity search for this article.