Spolupracovali sme na publikáciach
2020
2.
Böhmer, M; Ozdín, D; Račko, M; Lichvár, M; Budiš, J; Szemes, T
Identification of bacterial and fungal communities in the roots of orchids and surrounding soil in heavy metal contaminated area of mining heaps Journal Article
V: Applied Sciences (Switzerland), 10 (20), pp. 1-18, 2020, ISSN: 20763417.
Abstrakt | Linky | BibTeX | Značky: Bacteria, Environmental microbiome, Metagenomics, Plants
@article{Böhmer20201,
title = {Identification of bacterial and fungal communities in the roots of orchids and surrounding soil in heavy metal contaminated area of mining heaps},
author = {M Böhmer and D Ozdín and M Račko and M Lichvár and J Budiš and T Szemes},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85093967272&doi=10.3390%2fapp10207367&partnerID=40&md5=a65386928d7c2f6f118d18ce7a0e4bb3},
doi = {10.3390/app10207367},
issn = {20763417},
year = {2020},
date = {2020-01-01},
journal = {Applied Sciences (Switzerland)},
volume = {10},
number = {20},
pages = {1-18},
publisher = {MDPI AG},
abstract = {Orchids represent a unique group of plants that are well adapted to extreme conditions. In our study, we aimed to determine if different soil contamination and pH significantly change fungal and bacterial composition. We identified bacterial and fungal communities from the roots and the surrounding soil of the family Orchidaceae growing on different mining sites in Slovakia. These communities were detected from the samples of Cephalanthera longifolia and Epipactis pontica from Fe deposit Sirk, E. atrorubens from Ni-Co deposit Dobšiná and Pb-Zn deposit Jasenie and Platanthera bifolia by 16S rRNA gene and ITS next-generation sequencing method. A total of 171 species of fungi and 30 species of bacteria were detected from five samples of orchids. In summary, slight differences in pH of the initial soils do not significantly affect the presence of fungi and bacteria and thus the presence of the studied orchids in these localities. Similarly, the toxic elements in the studied localities, do not affect the occurrence of fungi, bacteria, and orchids. Moreover, Cortinarius saturatus, as a dominant fungus, and Candidatus Udaeobacter as a dominant bacterium were present in all soil samples and some root samples. Finally, many of these fungal and bacterial communities have the potential to be used in the bioremediation of the mining areas. © 2020 by the authors. Licensee MDPI, Basel, Switzerland.},
keywords = {Bacteria, Environmental microbiome, Metagenomics, Plants},
pubstate = {published},
tppubtype = {article}
}
Orchids represent a unique group of plants that are well adapted to extreme conditions. In our study, we aimed to determine if different soil contamination and pH significantly change fungal and bacterial composition. We identified bacterial and fungal communities from the roots and the surrounding soil of the family Orchidaceae growing on different mining sites in Slovakia. These communities were detected from the samples of Cephalanthera longifolia and Epipactis pontica from Fe deposit Sirk, E. atrorubens from Ni-Co deposit Dobšiná and Pb-Zn deposit Jasenie and Platanthera bifolia by 16S rRNA gene and ITS next-generation sequencing method. A total of 171 species of fungi and 30 species of bacteria were detected from five samples of orchids. In summary, slight differences in pH of the initial soils do not significantly affect the presence of fungi and bacteria and thus the presence of the studied orchids in these localities. Similarly, the toxic elements in the studied localities, do not affect the occurrence of fungi, bacteria, and orchids. Moreover, Cortinarius saturatus, as a dominant fungus, and Candidatus Udaeobacter as a dominant bacterium were present in all soil samples and some root samples. Finally, many of these fungal and bacterial communities have the potential to be used in the bioremediation of the mining areas. © 2020 by the authors. Licensee MDPI, Basel, Switzerland.
2016
1.
Kraková, L; Šoltys, K; Budiš, J; Grivalský, T; Ďuriš, F; Pangallo, D; Szemes, T
Investigation of bacterial and archaeal communities: novel protocols using modern sequencing by Illumina MiSeq and traditional DGGE-cloning Journal Article
V: Extremophiles, 20 (5), pp. 795-808, 2016, ISSN: 14310651.
Abstrakt | Linky | BibTeX | Značky: Bacteria, Environmental microbiome, Metagenomics
@article{Kraková2016795,
title = {Investigation of bacterial and archaeal communities: novel protocols using modern sequencing by Illumina MiSeq and traditional DGGE-cloning},
author = {L Kraková and K Šoltys and J Budiš and T Grivalský and F Ďuriš and D Pangallo and T Szemes},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84976272674&doi=10.1007%2fs00792-016-0855-5&partnerID=40&md5=a73c4e305f7b0f97139840b4328bff01},
doi = {10.1007/s00792-016-0855-5},
issn = {14310651},
year = {2016},
date = {2016-01-01},
journal = {Extremophiles},
volume = {20},
number = {5},
pages = {795-808},
publisher = {Springer Tokyo},
abstract = {Different protocols based on Illumina high-throughput DNA sequencing and denaturing gradient gel electrophoresis (DGGE)-cloning were developed and applied for investigating hot spring related samples. The study was focused on three target genes: archaeal and bacterial 16S rRNA and mcrA of methanogenic microflora. Shorter read lengths of the currently most popular technology of sequencing by Illumina do not allow analysis of the complete 16S rRNA region, or of longer gene fragments, as was the case of Sanger sequencing. Here, we demonstrate that there is no need for special indexed or tailed primer sets dedicated to short variable regions of 16S rRNA since the presented approach allows the analysis of complete bacterial 16S rRNA amplicons (V1–V9) and longer archaeal 16S rRNA and mcrA sequences. Sample augmented with transposon is represented by a set of approximately 300 bp long fragments that can be easily sequenced by Illumina MiSeq. Furthermore, a low proportion of chimeric sequences was observed. DGGE-cloning based strategies were performed combining semi-nested PCR, DGGE and clone library construction. Comparing both investigation methods, a certain degree of complementarity was observed confirming that the DGGE-cloning approach is not obsolete. Novel protocols were created for several types of laboratories, utilizing the traditional DGGE technique or using the most modern Illumina sequencing. © 2016, Springer Japan.},
keywords = {Bacteria, Environmental microbiome, Metagenomics},
pubstate = {published},
tppubtype = {article}
}
Different protocols based on Illumina high-throughput DNA sequencing and denaturing gradient gel electrophoresis (DGGE)-cloning were developed and applied for investigating hot spring related samples. The study was focused on three target genes: archaeal and bacterial 16S rRNA and mcrA of methanogenic microflora. Shorter read lengths of the currently most popular technology of sequencing by Illumina do not allow analysis of the complete 16S rRNA region, or of longer gene fragments, as was the case of Sanger sequencing. Here, we demonstrate that there is no need for special indexed or tailed primer sets dedicated to short variable regions of 16S rRNA since the presented approach allows the analysis of complete bacterial 16S rRNA amplicons (V1–V9) and longer archaeal 16S rRNA and mcrA sequences. Sample augmented with transposon is represented by a set of approximately 300 bp long fragments that can be easily sequenced by Illumina MiSeq. Furthermore, a low proportion of chimeric sequences was observed. DGGE-cloning based strategies were performed combining semi-nested PCR, DGGE and clone library construction. Comparing both investigation methods, a certain degree of complementarity was observed confirming that the DGGE-cloning approach is not obsolete. Novel protocols were created for several types of laboratories, utilizing the traditional DGGE technique or using the most modern Illumina sequencing. © 2016, Springer Japan.