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ABSTRACT: Sugarcane soil bacteria

PROVIDER: PRJNA1191409 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR31534678_1.fastq.gz	Fastqsanger.gz
	SRR31534678_2.fastq.gz	Fastqsanger.gz
	SRR31534679_1.fastq.gz	Fastqsanger.gz
	SRR31534679_2.fastq.gz	Fastqsanger.gz
	SRR31534680_1.fastq.gz	Fastqsanger.gz

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Circadian rhythms of sense and antisense transcription in a highly polyploid crop.

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Transcriptome and proteome profiles of the diazotroph Nitrospirillum amazonense strain CBAmC in response to the sugarcane apoplast fluid

Project description:Background and aims The endophytic diazotrophic strain CBAmC of Nitrospirillum amazonense has been reported as a plant growth promoter of sugarcane variety RB867515 when grown under field conditions. The present work aimed to assess the influence of apoplast fluid from RB867515 on the transcriptomic and proteomic profiles of CBAmC cultured in vitro. Methods RNA-Seq in Ion Proton™ and ESI-LC-MS/MS peptide analysis were used to evaluate the transcriptomic and proteomic profiles, respectively, of CBAmC exposed for 2 h to the sugarcane apoplast fluid. Results The bacterial transcriptomic and proteomic profiles were well correlated. The overall response of CBAmC to the apoplast fluid included overexpression of defense systems against reactive oxygen species (ROS) and osmotic stress, RND efflux pumps for toxic compounds, Sec and Tat secretory systems, and assimilative metabolism of iron. In contrast, active transporters of organic compounds, chemotaxis system and flagellum structure were underexpressed. Conclusions The bacterial metabolic pathways / functions activated in response to the sugarcane apoplast fluid are most likely related to its adaptation to the peculiar characteristics of the fluid. The activation of some of those functions could be determinant for its adaptation to the sugarcane apoplastic niche, and perhaps be involved in the previously observed effect of promoting plant growth. SUBMITTER_CITATION: Terra, L.A., de Soares, C.P., Meneses, C.H.S.G. et al. Plant Soil (2019). Transcriptome and proteome profiles of the diazotroph Nitrospirillum amazonense strain CBAmC in response to the sugarcane apoplast fluid.

2019-04-26 | GSE130321 | GEO

TMT Quantitative Proteomics Analyzed of E .roggenkampii ED5 and Sugarcane Interaction

Project description:Using TMT quantitative proteomics to analyze the differentially expressed proteins (DEPs) of the interaction between plant growth-promoting bacteria Enterobacter roggenkampii ED5 and sugarcane. The results found that a total of 27508 proteins from 73823 peptides, matching 301280 spectrograms were identified. Among them, 378 DEPs were found in sugarcane B8 and 177 DEPs were identified in sugarcane GT11.

2021-05-31 | PXD026390 |

Project description:Bacteria in sugarcane endophytic bacteria

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Dual transcriptomic analysis of the interaction between the ectomycorrhizal fungus Laccaria bicolor S238N and soil bacteria Pseudomonas fluorescens BB6cR8 and Pf29Arp

Project description:In order to get insights into the ability of ectomycorrhizal fungi to perceive their biotic environment as well as into the mechanisms of the interactions between ectomycorrhizal fungi and soil bacteria, we analysed the transcriptomic response of the ectomycorrhizal fungus L. bicolor and of two beneficial, and neutral soil bacteria during their interactions in vitro.

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Project description:Custom made functional gene micoarray (E-FGA) consisting of 13,056 mRNA-enriched anonymus microbial clones from dirverse microbial communities to profile microbial gene transcript in agricultural soils with low and high flux of N2O. A total of 96 genes displayed expression that differed significantly between low and high N2O emitting soils. Creation and validation of an cDNA microarray from environmental microbial mRNA, to use as a monitoring tool for microbial gene expression Microbial expression profiles comparing two high N2O-emitting sites (3 soil replicates and microarrays each) and two low N2O-emitting sites (3 soil replicates and microarray each) from sugarcane site in Mackay, Australia

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Methanotrophic community microarray

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Identification of microRNA responsive to pathogen infection in sugarcane

Project description:Sugarcane is a very efficient crop to produce ethanol. In recent years, extensive efforts have been made in order to increase sugarcane yields. To reach this goal, molecular biology tools have been used comprehensively, identifying genes, pathways and genetic polymorphisms. However, some important molecular components, like microRNAs, have not been deeply investigated. MicroRNAs are an important class of endogenous small, noncoding RNAs that regulate gene expression at the post-transcription level and play fundamental roles in diverse aspects of animal and plant biology. Plant genomes harbor numerous miRNA genes that regulate many protein-coding genes to influence key processes ranging from development, metabolism, and responses to abiotic and biotic stresses. There is wide range of pests and diseases that affect sugarcane, yet the mechanisms that regulate pathogen interactions with sugarcane have not been thoroughly investigated. To gain knowledge on the physiological responses to pathogens mediated by microRNAs in sugarcane, we screened the transcriptoma of sugarcane plants infected with Acidovorax avenae subsp avenae, the causal agent of red stripe disease in sugarcane, and detected several microRNAs modulated in the presence of the pathogen. Furthermore, we validated with qPCR a number of microRNA expression patterns observed by bioinformatics analysis. In addition, we observed high expression levels of several star microRNAs, in numbers larger than the mature microRNAs in some cases. Interestingly, sof-miR408 was consistently down-regulated in the presence of several pathogens, but not in the presence beneficial microbes. This result indicates that the sugarcane senses pathogenic or beneficial microorganisms differentially and triggers specific epigenetic regulatory mechanisms accordingly

2012-11-30 | GSE42628 | GEO

Circadian rhythms of sense and antisense transcription in a highly polyploid crop.

Project description:Sugarcane plants were grown in soil in a 12h light/ 12h dark photoperiod and 26oC for 3 months. Then, the plants were transferred to constant light conditions and 24 h later, leaves were harvested every 4 h for 48 h. Samples were collected from 24 h in constant light to 68 h in constant light and were labelled accordingly. Two biological replicates of each time point were made, with a dye swap with the reference. The reference used was a equimolar solution of all samples.

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