Spolupracovali sme na publikáciach
2020
4.
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.
3.
Böhmer, M; Smoľak, D; Ženišová, K; Čaplová, Z; Pangallo, D; Puškárová, A; Bučková, M; Cabicarová, T; Budiš, J; Šoltýs, K; Rusňáková, D; Kuchta, T; Szemes, T
Comparison of microbial diversity during two different wine fermentation processes Journal Article
V: FEMS microbiology letters, 367 (18), 2020, ISSN: 15746968.
Abstrakt | Linky | BibTeX | Značky: Bacteria, Food microbiome, Fungi, Metagenomics, Plants
@article{Böhmer2020b,
title = {Comparison of microbial diversity during two different wine fermentation processes},
author = {M Böhmer and D Smoľak and K Ženišová and Z Čaplová and D Pangallo and A Puškárová and M Bučková and T Cabicarová and J Budiš and K Šoltýs and D Rusňáková and T Kuchta and T Szemes},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85091808679&doi=10.1093%2ffemsle%2ffnaa150&partnerID=40&md5=bc04ad6a27036f5f7562c73abecb183f},
doi = {10.1093/femsle/fnaa150},
issn = {15746968},
year = {2020},
date = {2020-01-01},
journal = {FEMS microbiology letters},
volume = {367},
number = {18},
publisher = {NLM (Medline)},
abstract = {Wine production is a complex procedure in which an important role is played by many microorganisms, particularly yeasts and bacteria. In modern wineries, alcoholic fermentation is usually carried out by adding microbial starter cultures of Saccharomyces cerevisiae strains for precisely controlled production. Nowadays, in the Slovak Republic, autochthonous vinification is getting more popular. The present article deals with the comparison of two vinification approaches, namely spontaneous fermentation and fermentation controlled by a standard commercial S. cerevisiae starter, from the point of view of microbiota dynamics and the chemical characteristics of the wines produced. The dynamics of microbial populations were determined during the fermentation process by a 16S and 28S rRNA next-generation sequencing approach. A profile of the volatile compounds during these fermentation processes was identified by solid-phase microextraction (SPME) coupled to gas chromatography-mass spectrometry (GC-MS). In summary, the microbial diversity in the m1 phase (initial must) was higher, despite the presence of the starter culture. In the m3 phase (young wine), the microbiome profiles of both batches were very similar. It seems that the crucial phase in order to study the relationship of the microbiome and the resulting product should be based on the m2 phase (fermented must), where the differences between the autochthonous and inoculated batches were more evident. © The Author(s) 2020. Published by Oxford University Press on behalf of FEMS.},
keywords = {Bacteria, Food microbiome, Fungi, Metagenomics, Plants},
pubstate = {published},
tppubtype = {article}
}
Wine production is a complex procedure in which an important role is played by many microorganisms, particularly yeasts and bacteria. In modern wineries, alcoholic fermentation is usually carried out by adding microbial starter cultures of Saccharomyces cerevisiae strains for precisely controlled production. Nowadays, in the Slovak Republic, autochthonous vinification is getting more popular. The present article deals with the comparison of two vinification approaches, namely spontaneous fermentation and fermentation controlled by a standard commercial S. cerevisiae starter, from the point of view of microbiota dynamics and the chemical characteristics of the wines produced. The dynamics of microbial populations were determined during the fermentation process by a 16S and 28S rRNA next-generation sequencing approach. A profile of the volatile compounds during these fermentation processes was identified by solid-phase microextraction (SPME) coupled to gas chromatography-mass spectrometry (GC-MS). In summary, the microbial diversity in the m1 phase (initial must) was higher, despite the presence of the starter culture. In the m3 phase (young wine), the microbiome profiles of both batches were very similar. It seems that the crucial phase in order to study the relationship of the microbiome and the resulting product should be based on the m2 phase (fermented must), where the differences between the autochthonous and inoculated batches were more evident. © The Author(s) 2020. Published by Oxford University Press on behalf of FEMS.
2.
Šubr, Z; Predajňa, L; Šoltys, K; Bokor, B; Budiš, J; Glasa, M
Comparative transcriptome analysis of two cucumber cultivars with different sensitivity to cucumber mosaic virus infection Journal Article
V: Pathogens, 9 (2), 2020, ISSN: 20760817.
Abstrakt | Linky | BibTeX | Značky: Plants, Transcriptomics, Viruses
@article{Šubr2020,
title = {Comparative transcriptome analysis of two cucumber cultivars with different sensitivity to cucumber mosaic virus infection},
author = {Z Šubr and L Predajňa and K Šoltys and B Bokor and J Budiš and M Glasa},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85079843504&doi=10.3390%2fpathogens9020145&partnerID=40&md5=c92697bfc9481af2a87da1aae35966e1},
doi = {10.3390/pathogens9020145},
issn = {20760817},
year = {2020},
date = {2020-01-01},
journal = {Pathogens},
volume = {9},
number = {2},
publisher = {MDPI AG},
abstract = {Cucumber mosaic virus (CMV), with extremely broad host range including both monocots and dicots around the world, belongs to most important viral crop threats. Either natural or genetically constructed sources of resistance are being intensively investigated; for this purpose, exhaustive knowledge of molecular virus-host interaction during compatible and incompatible infection is required. New technologies and computer-based “omics” on various levels contribute markedly to this topic. In this work, two cucumber cultivars with different response to CMV challenge were tested, i.e., sensitive cv. Vanda and resistant cv. Heliana. The transcriptomes were prepared from both cultivars at 18 days after CMV or mock inoculation. Subsequently, four independent comparative analyses of obtained data were performed, viz. mock-and CMV-inoculated samples within each cultivar, samples from mock-inoculated cultivars to each other and samples from virus-inoculated cultivars to each other. A detailed picture of CMV-influenced genes, as well as constitutive differences in cultivar-specific gene expression was obtained. The compatible CMV infection of cv. Vanda caused downregulation of genes involved in photosynthesis, and induction of genes connected with protein production and modification, as well as components of signaling pathways. CMV challenge caused practically no change in the transcription profile of the cv. Heliana. The main differences between constitutive transcription activity of the two cultivars relied in the expression of genes responsible for methylation, phosphorylation, cell wall organization and carbohydrate metabolism (prevailing in cv. Heliana), or chromosome condensation and glucan biosynthesis (prevailing in cv. Vanda). Involvement of several genes in the resistant cucumber phenotype was predicted; this can be after biological confirmation potentially applied in breeding programs for virus-resistant crops. © 2020 by the authors. Licensee MDPI, Basel, Switzerland.},
keywords = {Plants, Transcriptomics, Viruses},
pubstate = {published},
tppubtype = {article}
}
Cucumber mosaic virus (CMV), with extremely broad host range including both monocots and dicots around the world, belongs to most important viral crop threats. Either natural or genetically constructed sources of resistance are being intensively investigated; for this purpose, exhaustive knowledge of molecular virus-host interaction during compatible and incompatible infection is required. New technologies and computer-based “omics” on various levels contribute markedly to this topic. In this work, two cucumber cultivars with different response to CMV challenge were tested, i.e., sensitive cv. Vanda and resistant cv. Heliana. The transcriptomes were prepared from both cultivars at 18 days after CMV or mock inoculation. Subsequently, four independent comparative analyses of obtained data were performed, viz. mock-and CMV-inoculated samples within each cultivar, samples from mock-inoculated cultivars to each other and samples from virus-inoculated cultivars to each other. A detailed picture of CMV-influenced genes, as well as constitutive differences in cultivar-specific gene expression was obtained. The compatible CMV infection of cv. Vanda caused downregulation of genes involved in photosynthesis, and induction of genes connected with protein production and modification, as well as components of signaling pathways. CMV challenge caused practically no change in the transcription profile of the cv. Heliana. The main differences between constitutive transcription activity of the two cultivars relied in the expression of genes responsible for methylation, phosphorylation, cell wall organization and carbohydrate metabolism (prevailing in cv. Heliana), or chromosome condensation and glucan biosynthesis (prevailing in cv. Vanda). Involvement of several genes in the resistant cucumber phenotype was predicted; this can be after biological confirmation potentially applied in breeding programs for virus-resistant crops. © 2020 by the authors. Licensee MDPI, Basel, Switzerland.
2019
1.
Planý, M; Czolderová, M; Kraková, L; Puškárová, A; Bučková, M; Šoltys, K; Budiš, J; Szemes, T; Mackulak, T; Wu, J -H; Pangallo, D
Biogas production: evaluation of the influence of K2FeO4 pretreatment of maple leaves (Acer platanoides) on microbial consortia composition Journal Article
V: Bioprocess and Biosystems Engineering, 42 (7), pp. 1151-1163, 2019, ISSN: 16157591.
Abstrakt | Linky | BibTeX | Značky: Bacteria, Biogas production, Fungi, Metagenomics, Plants
@article{Planý20191151,
title = {Biogas production: evaluation of the influence of K2FeO4 pretreatment of maple leaves (Acer platanoides) on microbial consortia composition},
author = {M Planý and M Czolderová and L Kraková and A Puškárová and M Bučková and K Šoltys and J Budiš and T Szemes and T Mackulak and J -H Wu and D Pangallo},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85064487903&doi=10.1007%2fs00449-019-02112-x&partnerID=40&md5=49c72565995160169ee6d43ac9524510},
doi = {10.1007/s00449-019-02112-x},
issn = {16157591},
year = {2019},
date = {2019-01-01},
journal = {Bioprocess and Biosystems Engineering},
volume = {42},
number = {7},
pages = {1151-1163},
publisher = {Springer Verlag},
abstract = {The potential of K2FeO4 as a pretreatment agent of a lignocellulosic material was examined on leaves of Acer platanodides as the sole substrate for biogas production by anaerobic digestion carried out through modelling laboratory-scaled semi-continuous reactors differing in loading rates and substrate (pretreated and untreated leaves). The quality of bioagas produced by K2FeO4-pretreated leaves was significantly better in terms of higher methane content and lower content of H2S. K2FeO4 had no crucial influence on growth inhibition of biogas-producing bacteria, which were analysed by comprehensive culture-independent methods utilising high-throughput sequencing of specific genes [bacterial and archaeal 16S rRNA, formyltetrahydrofolate synthetase gene (fhs), methyl-coenzyme M reductase α subunit gene (mcrA) and fungal internal transcribed spacers (ITS)]. The higher amount of CH4 in biogas utilising pretreated leaves as substrate could be caused by a shift to acetoclastic methanogenesis pathway, which was indicated by the higher amount of homoacetogenic bacteria and acetotrophic methanogens detected in those reactors. © 2019, Springer-Verlag GmbH Germany, part of Springer Nature.},
keywords = {Bacteria, Biogas production, Fungi, Metagenomics, Plants},
pubstate = {published},
tppubtype = {article}
}
The potential of K2FeO4 as a pretreatment agent of a lignocellulosic material was examined on leaves of Acer platanodides as the sole substrate for biogas production by anaerobic digestion carried out through modelling laboratory-scaled semi-continuous reactors differing in loading rates and substrate (pretreated and untreated leaves). The quality of bioagas produced by K2FeO4-pretreated leaves was significantly better in terms of higher methane content and lower content of H2S. K2FeO4 had no crucial influence on growth inhibition of biogas-producing bacteria, which were analysed by comprehensive culture-independent methods utilising high-throughput sequencing of specific genes [bacterial and archaeal 16S rRNA, formyltetrahydrofolate synthetase gene (fhs), methyl-coenzyme M reductase α subunit gene (mcrA) and fungal internal transcribed spacers (ITS)]. The higher amount of CH4 in biogas utilising pretreated leaves as substrate could be caused by a shift to acetoclastic methanogenesis pathway, which was indicated by the higher amount of homoacetogenic bacteria and acetotrophic methanogens detected in those reactors. © 2019, Springer-Verlag GmbH Germany, part of Springer Nature.