Dataset Information

Bacterial Microbiota of Rice Roots: 16S-Based Taxonomic Profiling of Endophytic and Rhizospheric Diversity, Endophytes Isolation and Simplified Endophytic Community.

ABSTRACT: Rice is currently the most important food crop in the world and we are only just beginning to study the bacterial associated microbiome. It is of importance to perform screenings of the core rice microbiota and also to develop new plant-microbe models and simplified communities for increasing our understanding about the formation and function of its microbiome. In order to begin to address this aspect, we have performed a 16S rDNA taxonomic bacterial profiling of the rhizosphere and endorhizosphere of two high-yield rice cultivars-Pionero 2010 FL and DANAC SD20A-extensively grown in Venezuela in 2014. Fifteen putative bacterial endophytes were then isolated from surface-sterilized roots and further studied in vitro and in planta. We have then performed inoculation of rice seedlings with a simplified community composed by 10 of the isolates and we have tracked them in the course of 30 days in greenhouse cultivation. The results obtained suggest that a set was able to significantly colonize together the rice endorhizospheres, indicating possible cooperation and the ability to form a stable multispecies community. This approach can be useful in the development of microbial solutions for a more sustainable rice production.

SUBMITTER: Moronta-Barrios F

PROVIDER: S-EPMC5874628 | biostudies-literature | 2018 Feb

REPOSITORIES: biostudies-literature

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Bacterial Microbiota of Rice Roots: 16S-Based Taxonomic Profiling of Endophytic and Rhizospheric Diversity, Endophytes Isolation and Simplified Endophytic Community.

Moronta-Barrios Felix F Gionechetti Fabrizia F Pallavicini Alberto A Marys Edgloris E Venturi Vittorio V

Microorganisms 20180211 1

Rice is currently the most important food crop in the world and we are only just beginning to study the bacterial associated microbiome. It is of importance to perform screenings of the core rice microbiota and also to develop new plant-microbe models and simplified communities for increasing our understanding about the formation and function of its microbiome. In order to begin to address this aspect, we have performed a 16S rDNA taxonomic bacterial profiling of the rhizosphere and endorhizosph ...[more]

PMID: 29439478

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Project description:Increased soil salinity poses serious limitations in crop yield and quality; thus, an attempt was made to explore microbial agents to mitigate the ill effects of salinity in rice. The hypothesis was mapping of microbial induction of stress tolerance in rice. Since the rhizosphere and endosphere are two different functional niches directly affected by salinity, it could be very crucial to evaluate them for salinity alleviation. In this experiment, endophytic and rhizospheric microbes were tested for differences in salinity stress alleviation traits in two rice cultivars, CO51 and PB1. Two endophytic bacteria, Bacillus haynesii 2P2 and Bacillus safensis BTL5, were tested with two rhizospheric bacteria, Brevibacterium frigoritolerans W19 and Pseudomonas fluorescens 1001, under elevated salinity (200 mM NaCl) along with Trichoderma viride as an inoculated check. The pot study indicated towards the presence of variable salinity mitigation mechanisms among these strains. Improvement in the photosynthetic machinery was also recorded. These inoculants were evaluated for the induction of antioxidant enzymes viz. CAT, SOD, PO, PPO, APX, and PAL activity along with the effect on proline levels. Modulation of the expression of salt stress responsive genes OsPIP1, MnSOD1, cAPXa, CATa, SERF, and DHN was assessed. Root architecture parameters viz. cumulative length of total root, projection area, average diameter, surface area, root volume, fractal dimension, number of tips, and forks were studied. Confocal scanning laser microscopy indicated accumulation of Na+ in leaves using cell impermeant Sodium Green™, Tetra (Tetramethylammonium) Salt. It was found that each of these parameters were induced differentially by endophytic bacteria, rhizospheric bacteria, and fungus, indicating different paths to complement one ultimate plant function. The biomass accumulation and number of effective tillers were highest in T4 (Bacillus haynesii 2P2) plants in both cultivars and showed the possibility of cultivar specific consortium. These strains and their mechanisms could form the basis for further evaluating microbial strains for climate-resilient agriculture.

Project description:BackgroundRice (Oryza sativa L. ssp. indica) seeds as plant microbiome present both an opportunity and a challenge to colonizing bacterial community living in close association with plants. Nevertheless, the roles and activities of bacterial endophytes remain largely unexplored and insights into plant-microbe interaction are compounded by its complexity. In this study, putative functions or physiological properties associated with bacterial endophytic nature were assessed. Also, endophytic roles in plant growth and germination that may allow them to be selectively chosen by plants were also studied.ResultsThe cultivable seed endophytes were dominated by Proteobacteria particularly class Gammaproteobacteria. Highly identical type strains were isolated from the seed endosphere regardless of the rice host's physiological tolerance to salinity. Among the type strains, Flavobacterium sp., Microbacterium sp. and Xanthomonas sp. were isolated from the salt-sensitive and salt-tolerant cultivars. PCA-Biplot ordination also showed that specific type strains isolated from different rice cultivars have distinguishing similar characteristics. Flavobacterium sp. strains are phosphate solubilizers and indole-3-acetic acid producers with high tolerance to salinity and osmotic stress. Pseudomonas strains are characterized as high siderophore producers while Microbacterium sp. and Xanthomonas sp. strains have very high pectinase and cellulase activity. Among the physiological traits of the seed endophytes, bacterial pectinase and cellulase activity are positively correlated as well as salt and osmotic tolerance. Overall characterization shows that majority of the isolates could survive in 4-8% salt concentration as well as in 0.6 M and 1.2 M sucrose solution. The activities of catalase, pectinase and cellulase were also observed in almost all of the isolates indicating the importance of these characteristics for survival and colonization into the seed endosphere. Seed bacterial endophytes also showed promising plant growth promoting activities including hormone modulation, nitrogen fixation, siderophore production and phosphate solubilization.ConclusionThough many of the isolates possess similar PGP and endophytic physiological traits, this study shows some prominent and distinguishing traits among bacterial groups indicating key determinants for their success as endophytes in the rice seed endosphere. Rice seeds are also inhabited by bacterial endophytes that promote growth during early seedling development.

Project description:The plant microbiome plays a critical role in plant growth, development, and health, with endophytes being recognized as essential members due to their close interactions with host plants. However, knowledge gaps remain in understanding the mechanisms driving the colonization and establishment of endophytic communities. To address this issue, we investigated the microbiota of tobacco roots and leaves, including both epiphytic and endophytic microorganisms. We found that Actinobacteria and Alphaproteobacteria were significantly enriched in the root endosphere. Additionally, we identified higher abundances of functional traits involved in antibiotic synthesis, plant cell wall degradation, iron metabolism, secretion systems, and nicotine degradation enzymes in the endosphere. We further studied metagenome-assembled genomes from the rhizosphere and root endosphere, revealing a greater diversity of secondary metabolites in bacteria within the root endosphere. Together, this study provides insights into the taxonomic and functional assembly cues that may contribute to shaping the endophytic plant microbiota.IMPORTANCEThe presence of diverse microorganisms within plant tissues under natural conditions is a well-established fact. However, due to the plant immune system's barrier and the unique microhabitat of the plant interior, it remains unclear what specific characteristics bacteria require to successfully colonize and thrive in the plant endosphere. Recognizing the significance of unraveling these functional features, our study focused on investigating the enriched traits in the endophytic microbiota compared to the epiphytes. Through our research, we have successfully identified the taxonomic and functional assembly cues that drive the enrichment of the endophytic microbiota across the epiphytic compartments. These findings shed new light on the intricate mechanisms of endophyte colonization, thereby deepening our understanding of plant-microbe interactions and paving the way for further advancements in microbiome manipulation.

Project description:BackgroundThe natural interactions between plant roots and their rhizospheric microbiome are vital to plant fitness, modulating both growth promotion and disease suppression. In rice (Oryza sativa), a globally important food crop, as much as 30% of yields are lost due to blast disease caused by fungal pathogen Magnaporthe oryzae. Capitalizing on the abilities of naturally occurring rice soil bacteria to reduce M. oryzae infections could provide a sustainable solution to reduce the amount of crops lost to blast disease.ResultsNaturally occurring root-associated rhizospheric bacteria were isolated from California field grown rice plants (M-104), eleven of which were taxonomically identified by 16S rRNA gene sequencing and fatty acid methyl ester (FAME) analysis. Bacterial isolates were tested for biocontrol activity against the devastating foliar rice fungal pathogen, M. oryzae pathovar 70-15. In vitro, a Pseudomonas isolate, EA105, displayed antibiosis through reducing appressoria formation by nearly 90% as well as directly inhibiting fungal growth by 76%. Although hydrogen cyanide (HCN) is a volatile commonly produced by biocontrol pseudomonads, the activity of EA105 seems to be independent of its HCN production. During in planta experiments, EA105 reduced the number of blast lesions formed by 33% and Pantoea agglomerans isolate, EA106 by 46%. Our data also show both EA105 and EA106 trigger jasmonic acid (JA) and ethylene (ET) dependent induced systemic resistance (ISR) response in rice.ConclusionsOut of 11 bacteria isolated from rice soil, pseudomonad EA105 most effectively inhibited the growth and appressoria formation of M. oryzae through a mechanism that is independent of cyanide production. In addition to direct antagonism, EA105 also appears to trigger ISR in rice plants through a mechanism that is dependent on JA and ET signaling, ultimately resulting in fewer blast lesions. The application of native bacteria as biocontrol agents in combination with current disease protection strategies could aid in global food security.

Dataset Information

Bacterial Microbiota of Rice Roots: 16S-Based Taxonomic Profiling of Endophytic and Rhizospheric Diversity, Endophytes Isolation and Simplified Endophytic Community.

Publications

Bacterial Microbiota of Rice Roots: 16S-Based Taxonomic Profiling of Endophytic and Rhizospheric Diversity, Endophytes Isolation and Simplified Endophytic Community.

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