The structure of the culturable root bacterial endophyte community of Nicotiana attenuata is organized by soil composition and host plant ethylene production and perception

Abstract Background Tobacco rattle virus (TRV) based virus-induced gene silencing (VIGS), a widely used functional genomics tool, requires growth temperatures typically lower than those of the plant’s native environment. Enabling VIGS under native conditions in the field according to applicable safety regulations could be a revolutionary advance for ecological research. Results Here, we report the development of an enhanced thermal tolerant VIGS vector system based on a TRV California isolate. cDNA clones representing the whole viral genome were sequenced and used to construct separate binary plant transformation vectors for functional elements of RNA1 (6765 nt) and RNA2 (3682 nt). VIGS of target genes was induced by transient transformation of the host plant with both vectors or by treating the host plant with sap from already VIGS induced plants. In Nicotiana attenuata the silencing efficiency of the PDS (phytoene desaturase) gene was 90% at 28 °C and 78% at 30 °C. Silencing at these temperatures was more prominent and durable than silencing induced by the widely used TRV PpK20-based pBINTRA6/pTV00 system, but was associated with a viral phenotype. Differences in the suppressor protein and RNA dependent RNA polymerase sequences between the TRV California isolate and PpK20 may be the reason for their different thermal tolerance. Conclusions The new TRV California-based VIGS vectors induce gene silencing in Nicotiana attenuata at higher temperatures than the existing pBINTRA6/pTV00 vector system, but cause greater growth defects. The new vector system opens up an avenue to study genes functions in planta under field conditions.

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The characterization and diversity of bacterial endophytes of grapevine

Canadian Journal of Microbiology ◽

10.1139/w10-004 ◽

2010 ◽

Vol 56 (3) ◽

pp. 209-216 ◽

Cited By ~ 64

Author(s):

E. R. West ◽

E. J. Cother ◽

C. C. Steel ◽

G. J. Ash

Keyword(s):

Gas Chromatography ◽

Denaturing Gradient Gel Electrophoresis ◽

Methyl Esters ◽

Similarity Index ◽

Vitis Vinifera L ◽

Bacterial Endophytes ◽

Bacterial Endophyte ◽

Streptomyces Spp ◽

Gradient Gel Electrophoresis ◽

Endophyte Community

The diversity of culturable and nonculturable bacterial endophytes of grapevine ( Vitis vinifera L.) was examined using a combination of cultivation and molecular methods. Entire grapevines were sampled to characterize bacterial diversity from different locations throughout the vine. Gas chromatography of fatty acid methyl esters (FAMEs) was used to identify culturable isolates prior to subsequent further microbiological characterization, whilst denaturing gradient gel electrophoresis (DGGE) was used to profile the ribosomal DNA of the bacterial endophyte community extracted from grapevines. Gas chromatography of FAMEs identified 75% of culturable bacterial endophytes to genus level (similarity index >0.3). Many isolates were identified as Bacillus spp., Pseudomonas spp., and Curtobacterium spp. Additionally, actinomycetes are reported for the first time as endophytes of grapevines, with a number of isolates identified as Streptomyces spp. DGGE was successfully used to identify major bands present in samples and indicated a degree of homogeneity of bacterial endophyte community profiles within the grapevines sampled. The major bacterial bands were sequenced and used in identification. Comparison with bacterial markers produced from cultured bacterial endophytes suggested that bacteria in the DGGE profiles were not the species most commonly cultured. Additional research demonstrated similarities between epiphytic and endophytic populations and examined potential entry vectors. Endophyte entry was demonstrated in both field-grown and potted grapevines (‘Chardonnay’) using a rifampicin-resistant Bacillus cereus mutant. The possibility of grapevine epiphytes becoming endophytes, if the opportunity arises, was supported by comparison of gas chromatography of FAMEs from epiphytic and endophytic populations. This research adds grapevine bacterial endophyte communities to those that have been characterized by a multifaceted approach.

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Identification of culturable bacterial endophyte community isolated from tissues ofVitisvinifera“Glera”

Plant Biosystems - An International Journal Dealing with all Aspects of Plant Biology ◽

10.1080/11263504.2014.916364 ◽

2014 ◽

Vol 148 (3) ◽

pp. 508-516 ◽

Cited By ~ 30

Author(s):

E. Baldan ◽

S. Nigris ◽

F. Populin ◽

M. Zottini ◽

A. Squartini ◽

...

Keyword(s):

Bacterial Endophyte ◽

Endophyte Community

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Bacterial Endophyte Community Dynamics in Apple (Malus domestica Borkh.) Germplasm and Their Evaluation for Scab Management Strategies

Journal of Fungi ◽

10.3390/jof7110923 ◽

2021 ◽

Vol 7 (11) ◽

pp. 923

Author(s):

Shahid A. Padder ◽

Sheikh Mansoor ◽

Sajad A. Bhat ◽

Tawseef Rehman Baba ◽

Rauoof Ahmad Rather ◽

...

Keyword(s):

Community Dynamics ◽

Venturia Inaequalis ◽

Disease Incidence ◽

Management Strategies ◽

Apple Scab ◽

Alpha Diversity ◽

Diversity Indices ◽

Apple Varieties ◽

Bacterial Endophyte ◽

Endophyte Community

The large genetic evolution due to the sexual reproduction-mediated gene assortments and propensities has made Venturia inaequalis (causing apple scab) unique with respect to its management strategies. The resistance in apple germplasm against the scab, being controlled for by more than fifteen genes, has limited gene alteration-based investigations. Therefore, a biological approach of bacterial endophyte community dynamics was envisioned across the apple germplasm in context to the fungistatic behavior against V. inaequalis. A total of 155 colonies of bacterial endophytes were isolated from various plant parts of the apple, comprising 19 varieties, and after screening for antifungal behavior followed by morphological, ARDRA, and sequence analysis, a total of 71 isolates were selected for this study. The alpha diversity indices were seen to fluctuate greatly among the isolation samples in context to microflora with antifungal behavior. As all the isolates were screened for the presence of various metabolites and some relevant genes that directly or indirectly influence the fungistatic behavior of the isolated microflora, a huge variation among the isolated microflora was observed. The outstanding isolates showing highest percentage growth inhibition of V. inaequalis were exploited to raise a bio-formulation, which was tested against the scab prevalence in eight apple varieties under controlled growth conditions. The formulation at all the concentrations caused considerable reductions in both the disease severity and disease incidence in all the tested apple varieties. Red Delicious being most important cultivar of the northwestern Himalayas was further investigated for its biochemical behavior in formulation and the investigation revealed different levels of enzyme production, chlorophyll, and sugars against the non-inoculated control.

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