Metagenomska analiza zemljišnih mikrobioloških zajednica
Metagenomic analysis of soil microbial communities
Apstrakt
Ramonda serbica i Ramonda nathaliae, retke biljke 'vaskrsnice' koje rastu na Balkanskom poluostrvu, u odgovoru na stres produkuju velike količine fenola. Bakterijske zajednice poreklom iz rizosfere ovih biljaka analizirane su metagenomskim pristupom. Fluorescentna 'in situ' hibridizacija (FISH) i DAPI bojenje pokazali su da u analiziranim zemljištima ima svega 5% metabolički aktivnih bakterija. Upotrebom prajmera specifičnih za bakterijsku DNK umnoženi su geni za 16S rDNK i konstruisane su dve genske biblioteke. Biblioteke su pretraživane uz pomoć RFLP metode. Od ukupno 192 klona dobijena iz uzorka rizosfere R. nathaliae identifikovano je 35 operativnih taksonomskih jedinica (OTJ), dok je iz uzorka rizosfere R. serbica dobijeno 13 OTJ od ukupno 80 klonova. Predstavnici svake OTJ su sekvencirani. Analizirane zajednice odlikuje veoma mali diverzitet i većina dobijenih sekvenci je pokazala malu sličnost sa DNK sekvencama do sada kultivisanih bakterija.
Ramonda serbica and Ramonda nathaliae, rare resurrection plants growing in the Balkan Peninsula, produce a high amount of phenolic compounds as a response to stress. The composition and size of bacterial communities in two rhizosphere soil samples of these plants were analyzed using a metagenomic approach. Fluorescent in situ hybridization (FISH) experiments together with DAPI staining showed that the metabolically active bacteria represent only a small fraction, approximately 5%, of total soil bacteria. Using universal bacteria - specific primers 16S rDNA genes were amplified directly from metagenomic DNAs and two libraries were constructed. The Restriction Fragment Length Polymorphism (RLFP) method was used in library screening. Amongst 192 clones, 35 unique operational taxonomic units (OTUs) were determined from the rhizosphere of R. nathaliae, and 13 OTUs out of 80 clones in total from the library of R. serbica. Representative clones from each OTU were sequenced. The majority of se...quences from metagenomes showed very little similarity to any cultured bacteria. In conclusion, the bacterial communities in the studied soil samples showed quite poor diversity.
Ključne reči:
RFLP / OTU / metagenome / FISHIzvor:
Archives of Biological Sciences, 2010, 62, 3, 559-564Izdavač:
- Srpsko biološko društvo, Beograd, i dr.
Finansiranje / projekti:
- Ekspresija i regulacija farmaceutski značajnih gena u mikroorganizmima (RS-MESTD-MPN2006-2010-143056)
DOI: 10.2298/ABS1003559D
ISSN: 0354-4664
WoS: 000281482000007
Scopus: 2-s2.0-77955224412
Institucija/grupa
Institut za molekularnu genetiku i genetičko inženjerstvoTY - JOUR AU - Đokić, Lidija AU - Savić, M. AU - Narančić, Tanja AU - Vasiljević, Branka PY - 2010 UR - https://imagine.imgge.bg.ac.rs/handle/123456789/447 AB - Ramonda serbica i Ramonda nathaliae, retke biljke 'vaskrsnice' koje rastu na Balkanskom poluostrvu, u odgovoru na stres produkuju velike količine fenola. Bakterijske zajednice poreklom iz rizosfere ovih biljaka analizirane su metagenomskim pristupom. Fluorescentna 'in situ' hibridizacija (FISH) i DAPI bojenje pokazali su da u analiziranim zemljištima ima svega 5% metabolički aktivnih bakterija. Upotrebom prajmera specifičnih za bakterijsku DNK umnoženi su geni za 16S rDNK i konstruisane su dve genske biblioteke. Biblioteke su pretraživane uz pomoć RFLP metode. Od ukupno 192 klona dobijena iz uzorka rizosfere R. nathaliae identifikovano je 35 operativnih taksonomskih jedinica (OTJ), dok je iz uzorka rizosfere R. serbica dobijeno 13 OTJ od ukupno 80 klonova. Predstavnici svake OTJ su sekvencirani. Analizirane zajednice odlikuje veoma mali diverzitet i većina dobijenih sekvenci je pokazala malu sličnost sa DNK sekvencama do sada kultivisanih bakterija. AB - Ramonda serbica and Ramonda nathaliae, rare resurrection plants growing in the Balkan Peninsula, produce a high amount of phenolic compounds as a response to stress. The composition and size of bacterial communities in two rhizosphere soil samples of these plants were analyzed using a metagenomic approach. Fluorescent in situ hybridization (FISH) experiments together with DAPI staining showed that the metabolically active bacteria represent only a small fraction, approximately 5%, of total soil bacteria. Using universal bacteria - specific primers 16S rDNA genes were amplified directly from metagenomic DNAs and two libraries were constructed. The Restriction Fragment Length Polymorphism (RLFP) method was used in library screening. Amongst 192 clones, 35 unique operational taxonomic units (OTUs) were determined from the rhizosphere of R. nathaliae, and 13 OTUs out of 80 clones in total from the library of R. serbica. Representative clones from each OTU were sequenced. The majority of sequences from metagenomes showed very little similarity to any cultured bacteria. In conclusion, the bacterial communities in the studied soil samples showed quite poor diversity. PB - Srpsko biološko društvo, Beograd, i dr. T2 - Archives of Biological Sciences T1 - Metagenomska analiza zemljišnih mikrobioloških zajednica T1 - Metagenomic analysis of soil microbial communities EP - 564 IS - 3 SP - 559 VL - 62 DO - 10.2298/ABS1003559D ER -
@article{ author = "Đokić, Lidija and Savić, M. and Narančić, Tanja and Vasiljević, Branka", year = "2010", abstract = "Ramonda serbica i Ramonda nathaliae, retke biljke 'vaskrsnice' koje rastu na Balkanskom poluostrvu, u odgovoru na stres produkuju velike količine fenola. Bakterijske zajednice poreklom iz rizosfere ovih biljaka analizirane su metagenomskim pristupom. Fluorescentna 'in situ' hibridizacija (FISH) i DAPI bojenje pokazali su da u analiziranim zemljištima ima svega 5% metabolički aktivnih bakterija. Upotrebom prajmera specifičnih za bakterijsku DNK umnoženi su geni za 16S rDNK i konstruisane su dve genske biblioteke. Biblioteke su pretraživane uz pomoć RFLP metode. Od ukupno 192 klona dobijena iz uzorka rizosfere R. nathaliae identifikovano je 35 operativnih taksonomskih jedinica (OTJ), dok je iz uzorka rizosfere R. serbica dobijeno 13 OTJ od ukupno 80 klonova. Predstavnici svake OTJ su sekvencirani. Analizirane zajednice odlikuje veoma mali diverzitet i većina dobijenih sekvenci je pokazala malu sličnost sa DNK sekvencama do sada kultivisanih bakterija., Ramonda serbica and Ramonda nathaliae, rare resurrection plants growing in the Balkan Peninsula, produce a high amount of phenolic compounds as a response to stress. The composition and size of bacterial communities in two rhizosphere soil samples of these plants were analyzed using a metagenomic approach. Fluorescent in situ hybridization (FISH) experiments together with DAPI staining showed that the metabolically active bacteria represent only a small fraction, approximately 5%, of total soil bacteria. Using universal bacteria - specific primers 16S rDNA genes were amplified directly from metagenomic DNAs and two libraries were constructed. The Restriction Fragment Length Polymorphism (RLFP) method was used in library screening. Amongst 192 clones, 35 unique operational taxonomic units (OTUs) were determined from the rhizosphere of R. nathaliae, and 13 OTUs out of 80 clones in total from the library of R. serbica. Representative clones from each OTU were sequenced. The majority of sequences from metagenomes showed very little similarity to any cultured bacteria. In conclusion, the bacterial communities in the studied soil samples showed quite poor diversity.", publisher = "Srpsko biološko društvo, Beograd, i dr.", journal = "Archives of Biological Sciences", title = "Metagenomska analiza zemljišnih mikrobioloških zajednica, Metagenomic analysis of soil microbial communities", pages = "564-559", number = "3", volume = "62", doi = "10.2298/ABS1003559D" }
Đokić, L., Savić, M., Narančić, T.,& Vasiljević, B.. (2010). Metagenomska analiza zemljišnih mikrobioloških zajednica. in Archives of Biological Sciences Srpsko biološko društvo, Beograd, i dr.., 62(3), 559-564. https://doi.org/10.2298/ABS1003559D
Đokić L, Savić M, Narančić T, Vasiljević B. Metagenomska analiza zemljišnih mikrobioloških zajednica. in Archives of Biological Sciences. 2010;62(3):559-564. doi:10.2298/ABS1003559D .
Đokić, Lidija, Savić, M., Narančić, Tanja, Vasiljević, Branka, "Metagenomska analiza zemljišnih mikrobioloških zajednica" in Archives of Biological Sciences, 62, no. 3 (2010):559-564, https://doi.org/10.2298/ABS1003559D . .