Apple endophytic microbiota of different rootstock/scion combinations suggests a genotype-specific influence

Liu, Jia; Abdelfattah, Ahmed; Norelli, John L.; Burchard, Erik; Schena, Leonardo; Droby, Samir; Wisniewski, Michael

doi:10.1186/s40168-018-0403-x

Cited by 154 publications

(122 citation statements)

References 42 publications

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“…2b; Additional file 1: Figure S2). This was consistent with microbiome study in Brassicaceae [24], sunflower [45] and Apple [46], where host genotypes have a stronger effect on fungal microbiota than bacteria. Unexpectedly, the microbial community of gramineous seeds of Avena sativa clustered far from Elymus sibiricus and Elymus dahuricus, and the bacterial community even clustered together with the Trifolium repens and Medicago sativa.…”

Section: Differences In Fungal Communities Across Grass Speciessupporting

confidence: 91%

Seed-resident microbiomes of leguminous and gramineous grasses are related to host stress tolerance

Dai¹,

Li²,

Wang³

et al. 2019

Preprint

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Background: The grasses in adverse environment such as Qinghai-Tibet Plateau are hypothesized to survive the harsh climate in part upon their seed-borne microorganisms, and yet the characteristics of the grass seed microbial communities remain undetermined. Here, we assessed the seed microbial communities of three native gramineous grass species (Avena sativa, Elymus sibiricus and Elymus dahuricus) and four candidate legumes (Vicia villosa, Trifolium repens, Trifolium pretense and Medicago sativa) on the Qinghai-Tibet Plateau by high-throughput sequencing. Results: A total of 1,013 bacterial operational taxonomic units (OTUs) and 922 fungal OTUs were observed. The OTUs that shared in all the samples were in high abundance but with different relative abundances. The majority of bacterial sequences were assigned to Proteobacteria (54~90%) and Firmicutes (5~41%), and the fungal communities were mainly composed of Ascomycota (23~96%) and Basidiomycota (2~11%). The fungal communities were more affected by host genetic distance than bacteria. The three gramineous grasses were speculated to survive the adversity partly due to their high abundance of beneficial bacteria like Pantoea or Bacillus, and non-pathogenic fungi like Candida or unclassified Helotiaceae. Also enriched with these potential beneficial taxa, the four leguminous grasses may be competent to adapt the Qinghai-Tibet Plateau stress. Furthermore, the higher tolerance grasses (Elymus sibiricus and Elymus dahuricus) possessed a greater number of growth-promoting and tolerance bacterial and non-pathogenic fungi. Conversely, the less tolerance grass Medicago sativa contained lower levels of such microorganisms, and showed higher abundance of pathogenic taxa. Furthermore, the isolated Bacillus subtilis or Pantoea agglomerans could more probably promote seeding growth of hosts with lower abundance of them, while inhibit if the endo-abundance of was high. Conclusions: Seed-resident microbiome structure of the four cold-tolerance legumes and three Qinghai-Tibet Plateau gramineae is host dependent and related to stress resistance. It also has a strong influence on the response of seedlings to biological seed treatments. This study provides valuable data for studying plant resilience, identifying more biocontrol strains, maximizing microbial functions in ‘smart farming’ practices.

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Section: Differences In Fungal Communities Across Grass Speciessupporting

confidence: 91%

Seed-resident microbiomes of leguminous and gramineous grasses are related to host stress tolerance

Dai¹,

Li²,

Wang³

et al. 2019

Preprint

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“…The endophyte community in woody stems was less affected by cultivars when ‘Scifresh’ was included, with only total fungal and γ‐proteobacterial taxa shown to be different. Liu et al () found that cultivars with closer pedigree had more similar microbial communities than those with distantly‐related pedigrees. ‘Scifresh’ is a cross of ‘Braeburn’ and ‘Royal Gala’, and thus is intermediate between the two cultivars.…”

Section: Discussionmentioning

confidence: 99%

“…Also using DGGE, Patel and Archana () demonstrated culturable endophytic diazotrophic communities were similar in different plant tissues (leaf, stem and root) of cereal plants ( Poaceae ), which revealed their diverse but nonspecific colonization in cereal plants. Apple endophyte community was found to be associated with cultivar and cultivar‐rootstock combinations by Illumina‐based next‐generation sequencing, and cultivars with closer pedigree had more similar microbial communities than those with distantly related pedigrees (Liu et al ). Using terminal restriction fragment length polymorphism, Hirakue and Sugiyama () showed that resistance of apple cultivars to Alternaria leaf spot (caused by Alternaria mali ) was related to the fungal endophyte diversity in leaves.…”

Section: Introductionmentioning

confidence: 99%

Apple endophyte community is shaped by tissue type, cultivar and site and has members with biocontrol potential againstNeonectria ditissima

2020

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Aims This research aimed to identify factors influencing endophyte community structure in apple shoots and the bioactivity of cultured representatives against the fungal pathogen Neonectria ditissima. Methods and Results The endophyte community in leaves and stems of the apple cultivars ‘Royal Gala’ and ‘Braeburn’ were analysed by a cultivation‐independent method (PCR‐DGGE) which showed that tissue type, cultivar and site were determinant factors, with the endophyte taxa in ‘Royal Gala’ more variable than that in ‘Braeburn’, with leaf endophyte communities typically differing from stems in both cultivars. Seasonal (spring vs autumn) and regional (Nelson vs Hawke’s Bay) variations were not obvious in woody stems. A collection of 783 bacterial and 87 fungal endophytes were recovered from leaves and stems of ‘Royal Gala’, ‘Braeburn’, ‘Scilate’ and/or ‘Scifresh’ from Nelson (nine sites) and Hawke’s Bay (five sites) in spring and from Nelson (three sites) in autumn. A dual culture plating assay was used to test their ability to inhibit the mycelial growth of N. ditissima. Thirteen bacterial (mean of percent inhibition ≥20%) and 17 fungal isolates were antagonistic towards N. ditissima. These isolates belonged to the bacterial genera Bacillus and Pseudomonas, and fungal genera Chaetomium, Epicoccum, Biscogniauxia, Penicillium, Diaporthe, Phlyctema and two unidentified fungal isolates. Conclusions Endophyte communities in apple shoots were determined by tissue type, cultivar and site. Endophytic bacterial and fungal isolates inhibiting N. ditissima growth in vitro were found. Significance and Impact of the Study These results provided new evidence of factors influencing apple endophyte community in New Zealand. Endophytes with potential to reduce N. ditissima infection were identified, with the potential to be developed into a biocontrol strategy for European canker.

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“…The composition of endophytic mycobiota of fruit trees can be diverse depending on the tree species [23]. Liu et al [31] suggested a genotype-specific influence of different rootstock/scion combinations on apple endophytic microbiota. Another study revealed limited geographic differentiation of fungal communities in apples trees, while a high diversity of fungal community structures was found in blackcurrant from different regions [32].…”

Section: Introductionmentioning

confidence: 99%

Endophytic Mycobiota of Jingbai Pear Trees in North China

Ren

Dong

Sun

et al. 2019

Forests

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Endophytic fungi exist in all known plants and play an important role for plant growth and health. As an important forest tree the Jingbai pear (the best quality cultivar of Pyrus ussuriensi Maxim. ex Rupr.) has great ecological as well as economic value in north China. However, the mycobiota of the pear tree is still unknown. In this study, the fungal communities in different organs of the tree and in rhizosphere soils were investigated by Illumina Miseq sequencing of ITS rDNA. For organs, the roots had the highest fungal richness and diversity, while the flowers had the lowest richness and diversity. The results demonstrated that each of the organs investigated harbored a distinctive fungal assemblage. Overall, Ascomycota was the most abundant phyla, followed by Basidiomycota and Zygomycota. Fungal communities from the different soils also differed from each other. The redundancy analysis (RDA) showed that fungal community structure correlated significantly with soil temperature, soil pH, soil nitrogen and soil carbon contents. The results indicate that plant organs, site conditions and soil properties may have important influences on the endophytic fungal community structure associated with Jingbai pear trees.

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Apple endophytic microbiota of different rootstock/scion combinations suggests a genotype-specific influence

Cited by 154 publications

References 42 publications

Seed-resident microbiomes of leguminous and gramineous grasses are related to host stress tolerance

Seed-resident microbiomes of leguminous and gramineous grasses are related to host stress tolerance

Apple endophyte community is shaped by tissue type, cultivar and site and has members with biocontrol potential againstNeonectria ditissima

Endophytic Mycobiota of Jingbai Pear Trees in North China

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