Stenotrophomonas rhizophila strain:BIGb262
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ABSTRACT:
PROVIDER: PRJNA986126 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
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| SRR24981871.fastq.gz | Fastqsanger.gz |
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Project description:Microbiome remodeling through bacterial competition and host behavior enables rapid adaptation to environmental toxins
| PRJNA1036219 | ENA
Project description:Human activity is altering the environment at a rapid pace, challenging the adaptive capacities of genetic variation within animal populations. Animals also harbor extensive gut microbiomes, which play diverse roles in host health and fitness and may help expanding host capabilities. The unprecedented scale of human usage of xenobiotics and contamination with environmental toxins describes one challenge against which bacteria with their immense biochemical diversity are particularly suited to offer solutions. To explore the paths leading to bacteria-assisted rapid adaptation, we used Caenorhabditis elegans harboring a defined microbiome, and the antibiotic neomycin as a model toxin, harmful for the worm host and neutralized to different extents by microbiome members. Worms exposed to neomycin showed delayed development and decreased survival but were protected when colonized by neomycin-resistant members of the microbiome. Through a combination of 16S gene sequencing, counting of live bacteria and behavioral assays we identified two distinct mechanisms that facilitated adaptation: gut enrichment for a neomycin-modifying strain driven by altered bacterial competition; and host avoidance behavior, which depended on the stress-activated KGB-1/JNK and enabled preference of neomycin-protective bacteria. The straightforwardness of these mechanisms suggests that bacteria-assisted host adaptation may be more common than currently appreciated, protecting animals from novel stressors. However, gut remodeling may also cause dysbiosis, and additional experiments identified fitness trade-offs including increased susceptibility to infection as well as metabolic remodeling. Extending these results to other toxins suggests yet unaccounted-for microbiome-dependent long-term consequences of toxin exposure.
2023-11-09 | GSE246966 | GEO
Project description:Although Stenotrophomonas maltophilia strains are efficient biocontrol agents, their field applications have raised concerns due to their possible threat to human health. The non-pathogenic Stenotrophomonas rhizophila species, which is closely related to S. maltophilia, has been proposed as an alternative. However, knowledge regarding the genetics of S. rhizophila is limited. Thus, the aim of the study was to define any genetic differences between the species and to characterise their ability to promote the growth of plant hosts as well as to enhance phytoremediation efficiency. We compared 37 strains that belong to both species using the tools of comparative genomics and identified 96 genetic features that are unique to S. maltophilia (e.g., chitin-binding protein, mechanosensitive channels of small conductance and KGG repeat-containing stress-induced protein) and 59 that are unique to S. rhizophila (e.g., glucosylglycerol-phosphate synthase, cold shock protein with the DUF1294 domain, and pteridine-dependent dioxygenase-like protein). The strains from both species have a high potential for biocontrol, which is mainly related to the production of keratinases (KerSMD and KerSMF), proteinases and chitinases. Plant growth promotion traits are attributed to the biosynthesis of siderophores, spermidine, osmoprotectants such as trehalose and glucosylglycerol, which is unique to S. rhizophila. In eight out of 37 analysed strains, the genes that are required to degrade protocatechuate were present. While our results show genetic differences between the two species, they had a similar growth promotion potential. Considering the information above, S. rhizophila constitutes a promising alternative for S. maltophilia for use in agricultural biotechnology.
| S-EPMC7404187 | biostudies-literature
Project description:In the presented research the extracellular chitinase of Stenotrophomonas rhizophila G22 was biochemically and molecularly characterized. The studied enzyme was purified from a 72-h bacterial culture about 14 times, with a recovery of 63%. The molecular weight of the purified protein was estimated at 50 kDa by SDS-PAGE. The enzyme showed high activity against colloidal chitin. Significantly lower activities were observed with native chitin powder and chitosan. Adsorption of the enzyme to colloidal chitin and to powdered chitin at the level of 75% and 37%, respectively, was observed after 30 min of reaction. Optimum temperature and pH were 37 °C and 5.9, respectively. The enzyme demonstrated higher activity against nitrophenyl-? d N, N', N?-triacetylchitotriose and approx. 5 times lower activity for 4-nitrophenyl-N, N'-diacetyl-?-d-chitobiose. The enzyme is an endochitinase, which is confirmed by the K m and V max values determined in the studies. S. rhizophila G22 endochitinase was inhibited in the presence of cysteine-specific inhibitors, which indicates the role of cysteine moieties in the mechanism of catalysis or in stabilisation of the enzyme molecule. Also Ca2+ and Mn2+ ions may stabilise the protein's spatial structure. SDS and ions: Fe2+, Cu2+, Co2+, Zn2+ inhibited the activity of enzyme. A full-length (2109 bp) gene coding chitinase from S. rhizophila G22 was obtained. Four domains typical for glycoside hydrolase family 18 (GH 18) chitinases were identified: catalytic Gly_18, chitin-binding-ChtBD3, type-III fibronectin-FN3 and polycystic kidney disease domain-PKD domain.
| S-EPMC6904715 | biostudies-literature
Project description:Stenotrophomonas rhizophila Genome sequencing and assembly
| PRJNA662620 | ENA
Project description:Stenotrophomonas rhizophila overview
| PRJNA184640 | ENA
Project description:Stenotrophomonas rhizophila PCA13 genome sequence
| PRJEB334 | ENA
Project description:Stenotrophomonas rhizophila has great potential for applications in biotechnology and biological control due to its ability to both promote plant growth and protect roots against biotic and a-biotic stresses, yet little is known about the mode of interactions in the root-environment system. We studied mechanisms associated with osmotic stress using transcriptomic and microscopic approaches. In response to salt or root extracts, the transcriptome of S. rhizophila DSM14405(T) changed drastically. We found a notably similar response for several functional gene groups responsible for general stress protection, energy production, and cell motility. However, unique changes in the transcriptome were also observed: the negative regulation of flagella-coding genes together with the up-regulation of the genes responsible for biofilm formation and alginate biosynthesis were identified as a single mechanism of S. rhizophila DSM14405(T) against salt shock. However, production and excretion of glucosylglycerol (GG) were found as a remarkable mechanism for the stress protection of this Stenotrophomonas strain. For S. rhizophila treated with root exudates, the shift from the planktonic lifestyle to a sessile one was measured as expressed in the down-regulation of flagellar-driven motility. These findings fit well with the observed positive regulation of host colonization genes and microscopic images that show different colonization patterns of oilseed rape roots. Spermidine, described as a plant growth regulator, was also newly identified as a protector against stress. Overall, we identified mechanisms of Stenotrophomonas to protect roots against osmotic stress in the environment. In addition to both the changes in life style and energy metabolism, phytohormons, and osmoprotectants were also found to play a key role in stress protection.
| S-EPMC3653106 | biostudies-literature
Project description:The rhizobacterium Stenotrophomonas rhizophila accumulates the compatible solutes glucosylglycerol (GG) and trehalose under salt stress conditions. The complete gene for the GG synthesis enzyme was cloned and sequenced. This enzyme from S. rhizophila represented a novel fusion protein composed of a putative C-terminal GG-phosphate synthase domain and an N-terminal putative GG-phosphate phosphatase domain, which was named GgpPS. A similar gene was cloned from Pseudomonas sp. strain OA146. The ggpPS gene was induced after a salt shock in S. rhizophila cells. After the salt-loaded cells reached stationary phase, the ggpPS mRNA content returned to the low level characteristic of the control cells, and GG was released into the medium. The complete ggpPS gene and a truncated version devoid of the phosphatase part were obtained as recombinant proteins. Enzyme activity tests revealed the expected abilities of the full-length protein to synthesize GG and the truncated GgpPS to synthesize GG-phosphate. However, dephosphorylation of GG-phosphate was detected only with the complete GgpPS protein. These enzyme activities were confirmed by complementation experiments using defined GG-defective mutants of the cyanobacterium Synechocystis sp. strain PCC 6803. Genes coding for proteins very similar to the newly identified fusion protein GgpPS for GG synthesis in S. rhizophila were found in genome sequences of related bacteria, where these genes are often linked to a gene coding for a transporter of the Mfs superfamily.
| S-EPMC2519522 | biostudies-literature