Dataset Information

A drought resistance-promoting microbiome is selected by root system under desert farming.

ABSTRACT:

Background

Traditional agro-systems in arid areas are a bulwark for preserving soil stability and fertility, in the sight of "reverse desertification". Nevertheless, the impact of desert farming practices on the diversity and abundance of the plant associated microbiome is poorly characterized, including its functional role in supporting plant development under drought stress.

Methodology/principal findings

We assessed the structure of the microbiome associated to the drought-sensitive pepper plant (Capsicum annuum L.) cultivated in a traditional Egyptian farm, focusing on microbe contribution to a crucial ecosystem service, i.e. plant growth under water deficit. The root system was dissected by sampling root/soil with a different degree of association to the plant: the endosphere, the rhizosphere and the root surrounding soil that were compared to the uncultivated soil. Bacterial community structure and diversity, determined by using Denaturing Gradient Gel Electrophoresis, differed according to the microhabitat, indicating a selective pressure determined by the plant activity. Similarly, culturable bacteria genera showed different distribution in the three root system fractions. Bacillus spp. (68% of the isolates) were mainly recovered from the endosphere, while rhizosphere and the root surrounding soil fractions were dominated by Klebsiella spp. (61% and 44% respectively). Most of the isolates (95%) presented in vitro multiple plant growth promoting (PGP) activities and stress resistance capabilities, but their distribution was different among the root system fractions analyzed, with enhanced abilities for Bacillus and the rhizobacteria strains. We show that the C. annuum rhizosphere under desert farming enriched populations of PGP bacteria capable of enhancing plant photosynthetic activity and biomass synthesis (up to 40%) under drought stress.

Conclusions/significance

Crop cultivation provides critical ecosystem services in arid lands with the plant root system acting as a "resource island" able to attract and select microbial communities endowed with multiple PGP traits that sustain plant development under water limiting conditions.

SUBMITTER: Marasco R

PROVIDER: S-EPMC3485337 | biostudies-literature | 2012

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

A drought resistance-promoting microbiome is selected by root system under desert farming.

Marasco Ramona R Rolli Eleonora E Ettoumi Besma B Vigani Gianpiero G Mapelli Francesca F Borin Sara S Abou-Hadid Ayman F AF El-Behairy Usama A UA Sorlini Claudia C Cherif Ameur A Zocchi Graziano G Daffonchio Daniele D

PloS one 20121031 10

<h4>Background</h4>Traditional agro-systems in arid areas are a bulwark for preserving soil stability and fertility, in the sight of "reverse desertification". Nevertheless, the impact of desert farming practices on the diversity and abundance of the plant associated microbiome is poorly characterized, including its functional role in supporting plant development under drought stress.<h4>Methodology/principal findings</h4>We assessed the structure of the microbiome associated to the drought-sens ...[more]

PMID: 23119032

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Project description:In order to clarify the molecular mechanisms of drought tolerance between different maize (Zea mays L.) varieties at the protein level, iTRAQ (the isobaric tags for relative and absolute quantitation) quantitative proteomics were used for the comparative analysis of protein expression in the seedling roots of the drought-tolerant Chang 7-2 and drought-sensitive TS141 maize varieties under 20% PEG 6000 (polyethylene glycol 6000)-simulated drought stress. A total of 7723 proteins were identified using iTRAQ in the maize seedling roots. We detected 39371 peptides and 30148 unique peptides. The identified protein molecular mass was mainly distributed between 10–60 kDa. COG analysis divided these proteins into 24 categories, among which general function prediction contained the largest number of proteins (19.1%), followed by posttranslational modification, protein turnover, and chaperones (10.52%). In the identified differentially expressed proteins, 1552 of which were significantly differentially expressed. Of these, 1249 were differentially expressed in Chang 7-2 following drought stress, 577 of which were up-regulated and 672 were down-regulated. Four hundred and twenty five differentially expressed proteins were identified in TS141, 249 of which were up-regulated and 176 were down-regulated. Of these proteins, 32 demonstrated opposite expression levels in the two varieties, and there were 56 up-regulated proteins that were common between the two varieties. Comparing the Chang 7-2 treatment group and control group, the DEPS in the cellular component category were mainly enriched in cytoplasmic membrane-bounded vesicles, cytoplasmic vesicles, membrane-bound vesicles and vesicles; in the molecular function category, the DEPs were mainly enriched in cation binding and metal ion binding; and in the biological process category, the major enriched categories included phosphate-containing compound metabolic process, single-organism transport cellular component organization or biogenesis, carbohydrate metabolic process, and cellular component organization. Comparing the TS141 treatment group and control group, the DEPS in the cellular component category were primarily enriched in cytoplasmic membrane-bounded vesicles, cytoplasmic vesicles, membrane-bound vesicles, and vesicle; in the molecular function category, the DEPs were mainly enriched in cation binding and metal ion binding; and in the biological process category, the major enrichment categories included oxidation-reduction process and carbohydrate metabolic process. In Chang 7-2, the differentially expressed proteins were associated with ribosome pathway, glycolysis/gluconeogenesis pathway, and amino sugar and nucleotide sugar metabolism. In TS141, the differentially expressed proteins were associated with metabolic pathway, phenylpropanoid biosynthesis pathway, and starch and sucrose metabolism.

Project description:Nature farming is a farming system that entails cultivating crops without using chemical fertilizers and pesticides. The present study investigated the bacterial and fungal communities in the rhizosphere of soybean grown in conventional and nature farming soils using wild-type and non-nodulating mutant soybean. The effect of soil fumigant was also analyzed to reveal its perturbation of microbial communities and subsequent effects on the growth of soybean. Overall, the wild-type soybean exhibited a better growth index compared to mutant soybean and especially in nature farming. Nodulation and arbuscular mycorrhiza (AM) fungi colonization were higher in plants under nature farming than in conventionally managed soil; however, fumigation drastically affected these symbioses with greater impacts on plants in nature farming soil. The rhizosphere microbiome diversity in nature farming was higher than that in conventional farming for both cultivars. However, the diversity was significantly decreased after fumigation treatment with a greater impact on nature farming. Principal coordinate analysis revealed that nature farming and conventional farming soil harbored distinct microbial communities and that soil fumigation significantly altered the communities in nature farming soils but not in conventional farming soils. Intriguingly, some beneficial microbial taxa related to plant growth and health, including Rhizobium, Streptomyces, and Burkholderia, were found as distinct microbes in the nature farming soil but were selectively bleached by fumigant treatment. Network analysis revealed a highly complex microbial network with high taxa connectivity observed under nature farming soil than in conventional soil; however, fumigation strongly broke it. Overall, the results highlighted that nature farming embraced higher microbial diversity and the abundance of beneficial soil microbes with a complex and interconnected network structure, and also demonstrated the underlying resilience of the microbial community to environmental perturbations, which is critical under nature farming where chemical fertilizers and pesticides are not applied.

Dataset Information

A drought resistance-promoting microbiome is selected by root system under desert farming.

Background

Methodology/principal findings

Conclusions/significance

Publications

A drought resistance-promoting microbiome is selected by root system under desert farming.

Similar Datasets

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