Analysis of genetic diversity and phylogeny of partial coat protein domain in Czech and Italian GFLV isolates

Eichmeier, Aleš; Baránek, Miroslav; Pidra, M.

doi:10.17221/10/2010-pps

Cited by 21 publications

(16 citation statements)

References 13 publications

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“…After RNA quantification, four samples taken randomly were pooled resulting in a total of five replicates every batch of 20 plants. Subsequently, RNA was transcribed to cDNA as described by Eichmeier et al (2010).…”

Section: Rna Extractionmentioning

confidence: 99%

High-throughput amplicon sequencing-based analysis of active fungal communities inhabiting grapevine after hot-water treatments reveals unexpectedly high fungal diversity

et al. 2018

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The ecology of total fungal communities in grapevine is so far largely derived from the studies on culture-dependent methods or cultivation-independent rDNA approaches. Sequencing the ribosomal RNA transcripts (rRNA) would rather reveal the functionally and metabolically active important taxa of the fungal community and provide insights into its activity in the wood. The present study investigated changes in the potentially active fungal communities of internal grapevine wood after Hot-Water Treatment (HWT) in planting material from Czech Republic and Spain at two different moments of the propagation process and from two plant zones. We examined fungal communities using both traditional microbiological approach and highthroughput amplicon sequencing (HTAS) of internal transcribed spacer 2 (ITS2) region in extracted total RNA. HTAS from metatranscriptomic RNA increased the resolution of the fungal community analysis and revealed a highly diverse mycoflora of grapevine wood compared to the traditional method. Fungal diversity differed between grapevine genotypes and showed a temporal variation over the vegetative period. Grapevine planting materials exhibited high fungal diversity after HWT, which demonstrates that the HWT process does not sterilize the internal wood of grapevine. HWT reduced the infection caused by fungal trunk disease pathogens but was not completely effective in eliminating their growth. This study provides important and practically useful insights into dynamics of active fungal communities in hotwater treated plants and represents the first approach to study active fungal communities on grapevine grafted plants by comparing traditional and next-generation sequencing methods.

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Section: Rna Extractionmentioning

confidence: 99%

High-throughput amplicon sequencing-based analysis of active fungal communities inhabiting grapevine after hot-water treatments reveals unexpectedly high fungal diversity

et al. 2018

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“…Target amplicon, the part of the 16S rRNA, V3 and V4 region (Klindworth et al 2013) was amplifi ed with GoTaq® G2 Flexi kit (Promega, Madison, USA). Th e PCR products corresponding to the expected size were gel-purifi ed using NucleoSpin Gel and PCR Clean-up (Macherey-Nagel, Düren, Germany) and subjected to nucleotide sequencing as described by Eichmeier et al (2010). Th e obtained nucleotide sequences were analysed using CLC Genomics Workbench 6.0 (CLC Bio, Aarhus, Denmark).…”

Section: Pcr Reaction and Sequencingmentioning

confidence: 99%

Rapid Communication. Monitoring the occurrence of bacteria in stored cabbage heads

Eichmeier¹,

Peňázová²,

Pecenka³

et al. 2016

Journal of Plant Protection Research

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Twenty-six cabbage heads stored under typical conditions in a storage hall in Moravia, Czech Republic, were tested for the presence of bacteria by the method of isolation from three diff erent parts of the cabbage heads. Isolations were carried out from stalks, inner and superfi cial leaves. Two samplings were done; in November 2015 and February 2016. Bacterial cultures were sequenced in the part of 16S rRNA region; bacteria were identifi ed according to the sequences obtained. Th e most prevalent bacteria were of the genus Pseudomonas. Genera: Klebsiella, Erwinia, Pantoea, Bacillus were also identifi ed. Th e results provided an interesting insight into the bacterial spectrum in stored cabbage heads and their dynamics during storage. Th e nucleotide sequences which were found were saved in GenBank/NCBI under accession numbers KX160104-KX160145.

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“…The presence of bacteria was evaluated in three different head parts: cabbage stalk, inner leaves and superficial leaves ( Figure S1). From each part, three pieces of plant tissue (4 × 4 mm) were disinfected in 2% sodium hypochlorite solution and washed twice in sterile distilled water according to Eichmeier et al [31]. Tissue samples were placed on two different media, both supplemented with 0.05 g/L cycloheximide (Biosynth, Staad, Switzerland) to avoid fungal contamination.…”

Section: Isolation Of Bacteria From Cabbage Headsmentioning

confidence: 99%

“…In cases where none of the four targeted species was detected, DNA was extracted using 5 mg of bacterial culture according to Roothie and Umesha [37]. The identity of isolates was determined by Sanger sequencing of the V3-V4 region of 16S rRNA [38], as described by Eichmeier et al [31]. CLC Genomics Workbench 6.0 (CLC Bio, Aarhus, Denmark) was used to analyze the obtained sequences.…”

Section: Detection Of the Bacterial Group Pcr And Sequencingmentioning

confidence: 99%

The Change of Bacterial Spectrum after Storage of X. campestris pv. campestris Inoculated Cabbage Heads (Brassica oleracea var. capitata L.)

et al. 2020

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Changes in the bacterial spectrum of cabbage heads after storage under commonly used storage conditions were examined in this study. Cabbage seeds (Brassica oleracea var. capitata L.) were artificially inoculated with X. campestris pv. campestris (Xcc), a serious pathogen of cruciferous plants causing black rot. Isolation of bacterial cultures from Xcc-inoculated and non-inoculated cabbage heads were carried out in two time points—at the day of harvest and after four months of storage. According to our previous research and literature reports, the most frequent genera of bacteria were chosen for PCR testing, i.e., Bacillus cereus group, Bacillus subtilis group, Pseudomonas sp., and X. campestris pv. campestris. A few of the obtained bacterial cultures were negative for the four above-mentioned species. In those, other bacteria were identified by 16S rRNA sequencing. In both Xcc-inoculated and non-inoculated cabbage heads, changes of the bacterial spectrum over time were observed. The severity of Xcc infection of heads increased after four months of storage. Bacillus species represented the most frequently occurring bacterial genus. The presence of the Bacillus subtilis group increased significantly after storage in non-inoculated cabbage heads. The minor part of the other genera identified by sequencing in the first sampling were not detected in the stored cabbage heads. This was associated with a possible antagonistic behavior of Pseudomonas sp. and Bacillus sp.

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Analysis of genetic diversity and phylogeny of partial coat protein domain in Czech and Italian GFLV isolates

Cited by 21 publications

References 13 publications

High-throughput amplicon sequencing-based analysis of active fungal communities inhabiting grapevine after hot-water treatments reveals unexpectedly high fungal diversity

High-throughput amplicon sequencing-based analysis of active fungal communities inhabiting grapevine after hot-water treatments reveals unexpectedly high fungal diversity

Rapid Communication. Monitoring the occurrence of bacteria in stored cabbage heads

The Change of Bacterial Spectrum after Storage of X. campestris pv. campestris Inoculated Cabbage Heads (Brassica oleracea var. capitata L.)

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