Metagenomic analysis of soil microbial communities
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 ap...
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| Format: | Article |
| Language: | English |
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University of Belgrade, University of Novi Sad
2010-01-01
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| Series: | Archives of Biological Sciences |
| Subjects: | |
| Online Access: | http://www.doiserbia.nb.rs/img/doi/0354-4664/2010/0354-46641003559D.pdf |
| _version_ | 1811281490788483072 |
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| author | Đokić Lidija Savić M. Narančić Tanja Vasiljević Branka |
| author_facet | Đokić Lidija Savić M. Narančić Tanja Vasiljević Branka |
| author_sort | Đokić Lidija |
| collection | DOAJ |
| description | 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. . |
| first_indexed | 2024-04-13T01:34:40Z |
| format | Article |
| id | doaj.art-c15c968eaf2b46e2bed79f2bf121a1e0 |
| institution | Directory Open Access Journal |
| issn | 0354-4664 |
| language | English |
| last_indexed | 2024-04-13T01:34:40Z |
| publishDate | 2010-01-01 |
| publisher | University of Belgrade, University of Novi Sad |
| record_format | Article |
| series | Archives of Biological Sciences |
| spelling | doaj.art-c15c968eaf2b46e2bed79f2bf121a1e02022-12-22T03:08:26ZengUniversity of Belgrade, University of Novi SadArchives of Biological Sciences0354-46642010-01-0162355956410.2298/ABS1003559DMetagenomic analysis of soil microbial communitiesĐokić LidijaSavić M.Narančić TanjaVasiljević BrankaRamonda 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. .http://www.doiserbia.nb.rs/img/doi/0354-4664/2010/0354-46641003559D.pdfmetagenomeRFLPOTUFISH |
| spellingShingle | Đokić Lidija Savić M. Narančić Tanja Vasiljević Branka Metagenomic analysis of soil microbial communities Archives of Biological Sciences metagenome RFLP OTU FISH |
| title | Metagenomic analysis of soil microbial communities |
| title_full | Metagenomic analysis of soil microbial communities |
| title_fullStr | Metagenomic analysis of soil microbial communities |
| title_full_unstemmed | Metagenomic analysis of soil microbial communities |
| title_short | Metagenomic analysis of soil microbial communities |
| title_sort | metagenomic analysis of soil microbial communities |
| topic | metagenome RFLP OTU FISH |
| url | http://www.doiserbia.nb.rs/img/doi/0354-4664/2010/0354-46641003559D.pdf |
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