Influence of host genotype in establishing root associated microbiome of indica rice cultivars for plant growth promotion

Singh, Arjun; Kumar, Murugan; Chakdar, Hillol; Pandiyan, Kurinji; Kumar, Shiv Charan; Zeyad, Mohammad Tarique; Singh, Bansh Narayan; Ravikiran, K. T.; Mahto, Arunima; Srivastava, Alok Kumar; Saxena, Anil Kumar

doi:10.3389/fmicb.2022.1033158

Cited by 14 publications

(7 citation statements)

References 125 publications

(133 reference statements)

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“…The growth and development of different blueberry cultivars were enhanced by recruiting specific rhizosphere microflora based on genotype ( Jacoby et al, 2017 ). Our results showed that the different genotypes of cotton recruited specific rhizosphere microbiomes, suggesting that the rhizosphere microbial community was regulated by host genotypes, consistent with the results in soybean, rice, and barley ( Bulgarelli et al, 2015 ; Singh et al, 2022 ; Qu et al, 2023 ). In addition, resistant cultivars may resist pathogen invasion by enriching specific bacterial or fungal groups in the rhizosphere ( Mendes et al, 2017 ; Kwak et al, 2018 ).…”

Section: Discussionsupporting

confidence: 89%

Different responses of the rhizosphere microbiome to Verticillium dahliae infection in two cotton cultivars

Tie,

Wang,

Chen

et al. 2023

Front. Microbiol.

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Verticillium wilt is a disastrous disease caused by Verticillium dahliae that severely damages the production of cotton in China. Even under homogeneous conditions, the same cotton cultivar facing V. dahliae tends to either stay healthy or become seriously ill and die. This binary outcome may be related to the interactions between microbiome assembly and plant health. Understanding how the rhizosphere microbiome responds to V. dahliae infection is vital to controlling Verticillium wilt through the manipulation of the microbiome. In this study, we evaluated the healthy and diseased rhizosphere microbiome of two upland cotton cultivars that are resistant to V. dahliae, Zhong 2 (resistant) and Xin 36 (susceptible), using 16S rRNA and ITS high-throughput sequencing. The results showed that the healthy rhizosphere of both resistant cultivar and susceptible cultivar had more unique bacterial ASVs than the diseased rhizosphere, whereas fewer unique fungal ASVs were found in the healthy rhizosphere of resistant cultivar. There were no significant differences in alpha diversity and beta diversity between the resistant cultivar and susceptible cultivar. In both resistant cultivar and susceptible cultivar, bacterial genera such as Pseudomonas and Acidobacteria bacterium LP6, and fungal genera such as Cephalotrichum and Mortierella were both highly enriched in the diseased rhizosphere, and Pseudomonas abundance in diseased rhizospheres was significantly higher than that in the healthy rhizosphere regardless of the cultivar type. However, cultivar and V. dahliae infection can cause composition changes in the rhizosphere bacterial and fungal communities, especially in the relative abundances of core microbiome members, which varied significantly, with different responses in the two cotton cultivars. Analysis of co-occurrence networks showed that resistant cultivar has a more complex network relationship than susceptible cultivar in the bacterial communities, and V. dahliae has a significant impact on the bacterial community structure. These findings will further broaden the understanding of plant-rhizosphere microbiome interactions and provide an integrative perspective on the cotton rhizosphere microbiome, which is beneficial to cotton health and production.

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Section: Discussionsupporting

confidence: 89%

Different responses of the rhizosphere microbiome to Verticillium dahliae infection in two cotton cultivars

Tie,

Wang,

Chen

et al. 2023

Front. Microbiol.

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“…Other studies have noted mixed results on the association between host plant diversity and overall diversity of microbes in their rhizospheres. For example, Zverev et al ( 2021 ) did not find a correlation between alpha diversity of plants and rhizosphere bacteria in farmed and fallow fields, but Singh et al ( 2022 ) reported that alpha diversity varied among rice cultivars. These studies suggest a complex interplay of factors likely determine the level of microbial diversity associated with plants, as well as the specific types of microbes present.…”

Section: Discussionmentioning

confidence: 99%

Fine‐scale genetic structure in rhizosphere microbial communities associated with Chamaecrista fasciculata (Fabaceae)

Nobarinezhad,

Wallace

2023

Ecology and Evolution

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Soil microbiota of the rhizosphere are an important extension of the plant phenotype because they impact the health and fitness of host plants. The composition of these communities is expected to differ among host plants due to influence by host genotype. Given that many plant populations exhibit fine‐scale genetic structure (SGS), associated microbial communities may also exhibit SGS. In this study, we tested this hypothesis using Chamaecrista fasciculata, a legume species that has previously been determined to have significant SGS. We collected genetic data from prokaryotic and fungal rhizosphere communities in association with 70 plants in an area of ~400 square meters to investigate the presence of SGS in microbial communities. Bacteria of Acidobacteria, Protobacteria, and Bacteroidetes and fungi of Basidiomycota, Ascomycota, and Mortierellomycota were dominant members of the rhizosphere. Although microbial alpha diversity did not differ significantly among plants hosts, we detected significant compositional differences among the microbial communities as well as isolation by distance. The strongest factor associated with microbial distance was genetic distance of the other microbial community, followed by geographic distance, but there was not a significant association with plant genetic distance for either microbial community. This study further demonstrates the strong potential for spatial structuring of soil microbial communities at the smallest spatial scales and provides further insight into the complexity of factors that influence microbial composition in soils and in association with host plants.

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“…Geography and host genotype could have major influences on the microbiome the fungus encounters as different rice genotypes have been found to have different microbiomes ( Xiong et al . 2021 ; Singh et al . 2022 ; Zhang et al .…”

Section: Discussionmentioning

confidence: 99%

Distinct genomic contexts predict gene presence–absence variation in different pathotypes of Magnaporthe oryzae

Joubert,

Krasileva

2024

Genetics

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Fungi use the accessory gene content of their pangenomes to adapt to their environments. While gene presence-absence variation (PAV) contributes to shaping accessory gene reservoirs, the genomic contexts that shape these events remain unclear. Since pangenome studies are typically species-wide and do not analyze different populations separately, it is yet to be uncovered whether PAV patterns and mechanisms are consistent across populations. Fungal plant pathogens are useful models for studying PAV because they rely on it to adapt to their hosts, and members of a species often infect distinct hosts. We analyzed gene PAV in the blast fungus, Magnaporthe oryzae (syn. Pyricularia oryzae), and found that PAV genes involved in host-pathogen and microbe-microbe interactions may drive the adaptation of the fungus to its environment. We then analyzed genomic and epigenomic features of PAV and observed that proximity to transposable elements, gene GC content, gene length, expression level in the host, and histone H3K27me3 marks were different between PAV genes and conserved genes. We used these features to construct a model that was able to predict whether a gene is likely to experience PAV with high precision (86.06%) and recall (92.88%) in M. oryzae. Finally, we found that PAV genes in the rice and wheat pathotypes of M. oryzae differed in their number and their genomic context. Our results suggest that genomic and epigenomic features of gene PAV can be used to better understand and predict fungal pangenome evolution. We also show that substantial intra-species variation can exist in these features.

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Influence of host genotype in establishing root associated microbiome of indica rice cultivars for plant growth promotion

Cited by 14 publications

References 125 publications

Different responses of the rhizosphere microbiome to Verticillium dahliae infection in two cotton cultivars

Different responses of the rhizosphere microbiome to Verticillium dahliae infection in two cotton cultivars

Fine‐scale genetic structure in rhizosphere microbial communities associated with Chamaecrista fasciculata (Fabaceae)

Distinct genomic contexts predict gene presence–absence variation in different pathotypes of Magnaporthe oryzae

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