Genomics as a potential tool to unravel the rhizosphere microbiome interactions on plant health

Priya, Piyush; Aneesh, Balakrishna Pillai; Harikrishnan, K.

doi:10.1016/j.mimet.2021.106215

Cited by 17 publications

(6 citation statements)

References 322 publications

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“…This approach has led to a better understanding of the structure, abundance, spatial distribution diversity, and important members of the rhizosphere community [66]. A challenge in the analyses of omics data is the choice of bioinformatics tools to deal with large sequenced datasets with minimal errors, in a fast and accurate way and with huge data storage [67]. Nowadays, the increasing omics, bioinformatics, and statistical tools would allow to produce robust predictions and models based on crop-soil-climate data about plant adaptation under climate change [68,69].…”

Section: Diversity and Complementarity Of Omics Approaches In Studying Plant-microbe Interactionsmentioning

confidence: 99%

Abiotic Stress and Belowground Microbiome: The Potential of Omics Approaches

Sandrini

Nerva

Sillo

et al. 2022

IJMS

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Nowadays, the worldwide agriculture is experiencing a transition process toward more sustainable production, which requires the reduction of chemical inputs and the preservation of microbiomes’ richness and biodiversity. Plants are no longer considered as standalone entities, and the future of agriculture should be grounded on the study of plant-associated microorganisms and all their potentiality. Moreover, due to the climate change scenario and the resulting rising incidence of abiotic stresses, an innovative and environmentally friendly technique in agroecosystem management is required to support plants in facing hostile environments. Plant-associated microorganisms have shown a great attitude as a promising tool to improve agriculture sustainability and to deal with harsh environments. Several studies were carried out in recent years looking for some beneficial plant-associated microbes and, on the basis of them, it is evident that Actinomycetes and arbuscular mycorrhizal fungi (AMF) have shown a considerable number of positive effects on plants’ fitness and health. Given the potential of these microorganisms and the effects of climate change, this review will be focused on their ability to support the plant during the interaction with abiotic stresses and on multi-omics techniques which can support researchers in unearthing the hidden world of plant–microbiome interactions. These associated microorganisms can increase plants’ endurance of abiotic stresses through several mechanisms, such as growth-promoting traits or priming-mediated stress tolerance. Using a multi-omics approach, it will be possible to deepen these mechanisms and the dynamic of belowground microbiomes, gaining fundamental information to exploit them as staunch allies and innovative weapons against crop abiotic enemies threatening crops in the ongoing global climate change context.

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Section: Diversity and Complementarity Of Omics Approaches In Studying Plant-microbe Interactionsmentioning

confidence: 99%

Abiotic Stress and Belowground Microbiome: The Potential of Omics Approaches

Sandrini

Nerva

Sillo

et al. 2022

IJMS

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“…Hence, the impact of soil microbial communities must be addressed to evaluate the plant response in diverse environmental conditions. Metagenomic sequencing emerged as a comprehensive genomic tool to evaluate the microbiome and its complex interactions in the rhizospheric zone of the plant (Priya et al, 2021). Furthermore, metabolomic profiling has been extensively used to simultaneously detect several endogenous metabolites produced by the rhizosphere microbiome (van Dam and Bouwmeester, 2016).…”

Section: Introductionmentioning

confidence: 99%

Fosthiazate inhibits root-knot disease and alters rhizosphere microbiome of Cucumis melo var. saccharinus

et al. 2023

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Root-knot nematodes especially Meloidogyne spp. are considered as most destructive obligate parasites that substantially reduce crop yield and quality. Fosthiazate is an efficient organothiophosphate chemical with nematicidal activity against Meloidogyne spp. The present study aimed to analyze the efficacy of fosthiazate against root-knot disease in Cucumis melo var. saccharinus and its potential effects on rhizosphere microbiome and metabolites. The fosthiazate (40%) was applied two times by spraying on the day of transplanting and during the pollination period (after 31 days). Samples from treatment (fosthiazate 40%: MF) and control groups (untreated plants; MCK) were analysed through metagenomic and metabolomic profiling of rhizospheres. Results revealed that root-knot index of the MF group (9.26 ± 1.28) was significantly (p < 0.05) lower than the MCK group (22.06 ± 0.71) with a control effect of 57.85% after 31 days of the first spray, whereas fosthiazate efficacy reduced to 31.87% after 38 days of second application with significantly (p < 0.05) different root-knot index values (MF: 56 ± 1.43 and; MCK: 82.26 ± 3.87). However, Cucumis melo var. saccharinus fruit yield in both groups (MCK: 21.1 ± 0.9 and MF: 21.53 ± 0.85) showed no differences (p > 0.05). Metagenomic profiling revealed Proteobacteria, Acidobacteriota, and Firmicutes as predominant phyla and Bacillus, Sphingomonas, and Acidibacter as predominant genera in rhizosphere soil samples of both MF and MCK groups. Further, a t-test revealed higher differential enrichment of Firmicutes at phylum level and Bacillus at genus level in MF than MCK. Metabolomic profiling of rhizospheric soil revealed a total of six differential metabolites (p < 0.05), four of them (Sucrose, Hexaonic acid 1, (Z)-9-Octadecenamide 1, and Hexadecanamide) were up-regulated in MF group, whereas two of them (2,3,4-Trihydroxy-3-(Hydroxymethyl) Butanol and Sulfurous acid, 2, ethylhexylundecyl ester) were down-regulated in CK group. Our study concluded that fosthiazate exhibits a better control over the rook-knot disease in the short term and resulted in trackable changes in rhizosphere microbiome and metabolome.

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“…Metagenomics is a static catalog of the genes present across the species of a sample, while metaproteomics provides a dynamic catalog of species and expressed proteins in terms of which genes are expressed and which species possess which function. Metaproteomics of a wide variety of complex microbial and ecological systems, including gut bacteria [2] , [3] , [4] , [5] , [6] , saliva [7] , oral environment [8] , ocean water [9] , hydrothermal vents [10] , plant lignin degradation [11] , soil rhizosphere [12] , and brewing vinegar [13] , have been studied to obtain inter/intra communication/networks via cataloging of proteins and species. The collected information is invaluable for understanding the mechanisms of biological systems, including homeostasis, disease, and differentiation [14] .…”

Section: Introductionmentioning

confidence: 99%