Dataset Information

Genomic Landscape Highlights Molecular Mechanisms Involved in Silicate Solubilization, Stress Tolerance, and Potential Growth-Promoting Activity of Bacterium Enterobacter sp. LR6.

ABSTRACT: Silicon (Si) is gaining widespread attention due to its prophylactic activity to protect plants under stress conditions. Despite Si's abundance in the earth's crust, most soils do not have enough soluble Si for plants to absorb. In the present study, a silicate-solubilizing bacterium, Enterobacter sp. LR6, was isolated from the rhizospheric soil of rice and subsequently characterized through whole-genome sequencing. The size of the LR6 genome is 5.2 Mb with a GC content of 54.9% and 5182 protein-coding genes. In taxogenomic terms, it is similar to E. hormaechei subsp. xiangfangensis based on average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH). LR6 genomic data provided insight into potential genes involved in stress response, secondary metabolite production, and growth promotion. The LR6 genome contains two aquaporins, of which the aquaglyceroporin (GlpF) is responsible for the uptake of metalloids including arsenic (As) and antimony (Sb). The yeast survivability assay confirmed the metalloid transport activity of GlpF. As a biofertilizer, LR6 isolate has a great deal of tolerance to high temperatures (45 °C), salinity (7%), and acidic environments (pH 9). Most importantly, the present study provides an understanding of plant-growth-promoting activity of the silicate-solubilizing bacterium, its adaptation to various stresses, and its uptake of different metalloids including As, Ge, and Si.

SUBMITTER: Raturi G

PROVIDER: S-EPMC9688052 | biostudies-literature | 2022 Nov

REPOSITORIES: biostudies-literature

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Genomic Landscape Highlights Molecular Mechanisms Involved in Silicate Solubilization, Stress Tolerance, and Potential Growth-Promoting Activity of Bacterium <i>Enterobacter</i> sp. LR6.

Raturi Gaurav G Sharma Yogesh Y Mandlik Rushil R Kumawat Surbhi S Rana Nitika N Dhar Hena H Tripathi Durgesh Kumar DK Sonah Humira H Sharma Tilak Raj TR Deshmukh Rupesh R

Cells 20221115 22

Silicon (Si) is gaining widespread attention due to its prophylactic activity to protect plants under stress conditions. Despite Si's abundance in the earth's crust, most soils do not have enough soluble Si for plants to absorb. In the present study, a silicate-solubilizing bacterium, <i>Enterobacter</i> sp. LR6, was isolated from the rhizospheric soil of rice and subsequently characterized through whole-genome sequencing. The size of the LR6 genome is 5.2 Mb with a GC content of 54.9% and 5182 ...[more]

PMID: 36429050

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Project description:Enterobacter sp. 638 is an endophytic plant growth promoting gamma-proteobacterium that was isolated from the stem of poplar (Populus trichocarpaxdeltoides cv. H11-11), a potentially important biofuel feed stock plant. The Enterobacter sp. 638 genome sequence reveals the presence of a 4,518,712 bp chromosome and a 157,749 bp plasmid (pENT638-1). Genome annotation and comparative genomics allowed the identification of an extended set of genes specific to the plant niche adaptation of this bacterium. This includes genes that code for putative proteins involved in survival in the rhizosphere (to cope with oxidative stress or uptake of nutrients released by plant roots), root adhesion (pili, adhesion, hemagglutinin, cellulose biosynthesis), colonization/establishment inside the plant (chemiotaxis, flagella, cellobiose phosphorylase), plant protection against fungal and bacterial infections (siderophore production and synthesis of the antimicrobial compounds 4-hydroxybenzoate and 2-phenylethanol), and improved poplar growth and development through the production of the phytohormones indole acetic acid, acetoin, and 2,3-butanediol. Metabolite analysis confirmed by quantitative RT-PCR showed that, the production of acetoin and 2,3-butanediol is induced by the presence of sucrose in the growth medium. Interestingly, both the genetic determinants required for sucrose metabolism and the synthesis of acetoin and 2,3-butanediol are clustered on a genomic island. These findings point to a close interaction between Enterobacter sp. 638 and its poplar host, where the availability of sucrose, a major plant sugar, affects the synthesis of plant growth promoting phytohormones by the endophytic bacterium. The availability of the genome sequence, combined with metabolome and transcriptome analysis, will provide a better understanding of the synergistic interactions between poplar and its growth promoting endophyte Enterobacter sp. 638. This information can be further exploited to improve establishment and sustainable production of poplar as an energy feedstock on marginal, non-agricultural soils using endophytic bacteria as growth promoting agents.

Project description:AimThis study aims to reveal the passenger endophytic bacterium Enterobacter cloacae S23 isolated from groundnut nodules and to underpin the molecular mechanism and genes responsible for abiotic stress tolerance.BackgroundA variety of microorganisms that contribute to nodulation and encourage plant development activity in addition to the nodulating Rhizobium. Passenger endophytes (PE) are endophytes that accidentally penetrate the plant without any selective pressure keeping them in the interior tissue of the plant. PE possesses characteristics that encourage plant development and boost output while reducing pathogen infection and improving biotic and abiotic stress tolerance. However, there is a lack of molecular evidence on the passenger endophyte-mediated alleviation of abiotic stresses.ObjectiveThis study was formulated to reveal the draft genome sequence of Enterobacter cloacae S23, as well as genes and characteristics involved in plant growth promotion and stress tolerance.MethodThe data were submitted to PATRIC and the TORMES-1.0 Unicyclker tools were used to conduct a complete genome study of Enterobacter cloacae S23. The TORMES-1.0 platform was used to process the reads. RAST tool kit (RASTtk) was used to annotate the S23 sequence. The plant growth-promoting traits such as indole acetic acid production, siderophore secretion, production of extracellular polysaccharides, biofilm formation, phosphate solubilization, and accumulation of osmolytes were examined under normal, 7% NaCl and 30% polyethylene glycol amended conditions to determine their ability to withstand salt and moisture stressed conditions, respectively.ResultWe report the size of Enterobacter cloacae S23 is 4.82Mb which contains 4511 protein-coding sequences, 71 transfer RNA genes, and 3 ribosomal RNA with a G+C content of DNA is 55.10%. Functional analysis revealed that most of the genes are involved in the metabolism of amino acids, cofactors, vitamins, stress response, nutrient solubilization (kdp, pho, pst), biofilm formation (pga) IAA production (trp), siderophore production (luc, fhu, fep, ent, ybd), defense, and virulence. The result revealed that E. cloacae S23 exhibited multiple plant growth-promoting traits under abiotic stress conditions.ConclusionOur research suggested that the discovery of anticipated genes and metabolic pathways might characterise this bacterium as an environmentally friendly bioresource to support groundnut growth through several mechanisms of action under multi-stresses.

Dataset Information

Genomic Landscape Highlights Molecular Mechanisms Involved in Silicate Solubilization, Stress Tolerance, and Potential Growth-Promoting Activity of Bacterium Enterobacter sp. LR6.

Publications

Genomic Landscape Highlights Molecular Mechanisms Involved in Silicate Solubilization, Stress Tolerance, and Potential Growth-Promoting Activity of Bacterium <i>Enterobacter</i> sp. LR6.

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