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Bacteria

ABSTRACT: Genome sequencing of duckweed-based synthetic bacterial community

PROVIDER: PRJDB17029 | ENA |

REPOSITORIES: ENA

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			Action	DRS
		Other
	DRR514962_subreads.fastq.gz	Fastqsanger.gz
	DRR514963_subreads.fastq.gz	Fastqsanger.gz
	DRR514964_subreads.fastq.gz	Fastqsanger.gz
	DRR514965_subreads.fastq.gz	Fastqsanger.gz

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Project description:Duckweed-associated plant growth-promoting bacteria (PGPB) have attracted considerable attention for enhancing duckweed biomass production; however, the mechanisms underlying strain-specific plant growth promotion remain largely unknown. Here, we compared the effects of two duckweed-associated bacterial strains, Terrimicrobium sp. PS02 and Aeromicrobium sp. PS05, on the growth, biomass composition, colonization behavior, and transcriptomic responses of Spirodela polyrhiza. While both strains enhanced duckweed biomass, PS02 yielded a 1.2-fold increase, whereas PS05 induced a statistically significant increase (1.4-fold) compared with the uninoculated control. Markedly, PS05 established approximately one order of magnitude higher bacterial populations than PS02 and formed dense extracellular polymeric substance (EPS)-mediated microcolonies on duckweed surfaces. Transcriptome analysis revealed that PS05 induced 1,108 differentially expressed genes, compared with 454 genes for PS02, indicating substantially greater host transcriptomic reprogramming. Functional enrichment analyses demonstrated that PS05 preferentially regulated carbohydrate biosynthesis and central carbon metabolism. Consistently, both transcriptomic and RT-qPCR analyses showed up-regulation of key genes involved in starch biosynthesis and carbon allocation, resulting in significantly enhanced starch accumulation and turion formation without reducing protein or photosynthetic pigment content. This study provides the first integrated evidence linking bacterial colonization strategy, host transcriptomic regulation, carbon allocation, and biomass production in duckweed, thereby establishing a mechanistic basis for engineering high-performance duckweed–microbiome systems for sustainable biomass production.

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Project description:Origanum oil (ORO), garlic oil (GAO), and peppermint oil (PEO) were shown to effectively lower methane production, decrease abundance of methanogens, and change abundances of several bacterial populations important to feed digestion in vitro. In this study, the impact of these essential oils (EOs, at 0.50 g/L), on the rumen bacterial community composition was further examined using the recently developed RumenBactArray.

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Project description:Chemical signaling in the plant microbiome can have drastic effects on microbial community structure, and on host growth and development. Previously, we demonstrated that the auxin metabolic signal interference performed by the bacterial genus Variovorax via a novel auxin degradation locus was essential for maintaining stereotypic root development in an ecologically-relevant bacterial synthetic community. Here, we dissect the Variovorax auxin degradation locus to define the genes necessary and sufficient for indole-3-acetic acid (IAA) degradation and signal interference. We determine the crystal structures and binding properties of the operon’s MarR-family repressor with IAA and other auxins. We identify auxin-degradation operons across the bacterial tree of life and define two distinct types based on gene content and metabolic products: iac-like and iad-like. We solve the structures of MarRs from representatives of each auxin degradation operon type, establishing that each have distinct IAA binding pockets. Comparison of representative IAA degrading strains from diverse bacterial genera show that while all degrade IAA, only strains containing iad-like auxin degrading operons interfere with auxin signaling in a complex synthetic community context. This suggests that iad-like operon containing strains, including Variovorax species, play a key ecological role in modulating auxins in the plant microbiome.

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