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Comparative analysis of rhizosphere soil between three plantation types in Karst Rocky Desertification area by widely targeted metabolomics

ABSTRACT:

Understanding the differences in rhizosphere soil microbial metabolites between severely and mildly rocky desertified areas is crucial for developing ecological restoration strategies and land management measures in rocky desertification regions. This study systematically analyzed the differences in rhizosphere soil microbial metabolites of Toona sinensis, Vernicia fordii, and Cornus wilsoniana in severely and mildly rocky desertified areas of Western Hunan using untargeted metabolomics. The results showed that the types and quantities of primary and secondary metabolites in the rhizosphere soil of severely rocky desertified areas were significantly lower than those in mildly rocky desertified areas. Additionally, under severe rocky desertification conditions, 15 common compounds (e.g., 17a-Estradiol, Adenine, all-trans-Retinoic acid) were significantly increased in the rhizosphere soil microbial metabolites of the three tree species. These compounds may provide defense mechanisms for plants to adapt to harsh environments. KEGG metabolic pathway analysis revealed that under severe rocky desertification conditions, Toona sinensis, Vernicia fordii, and Cornus wilsoniana shared six enriched pathways, which play an important role in the biosynthesis of compounds such as phenylpropanoids and unsaturated fatty acids. By revealing the differences in rhizosphere soil microbial metabolites, this study not only deepens the understanding of rocky desertification ecosystems but also provides valuable scientific evidence for ecological restoration and sustainable land management.

INSTRUMENT(S): Liquid Chromatography MS - negative - reverse phase, Liquid Chromatography MS - positive - reverse phase

PROVIDER: MTBLS11482 | MetaboLights | 2025-02-24

REPOSITORIES: MetaboLights

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Project description:Relentless mining operations have destroyed our environment significantly. Soil inhabiting microbes play a significant role in ecological restoration of these areas. Microbial weathering processes like chemical dissolution of rocks significantly promotes the soil properties and enhances the rock to soil ratio respectively. Earlier studies have reported that bacteria exhibit efficient rock-dissolution abilities by releasing organic acids and other chemical elements from the silicate rocks. However, rock-dissolving mechanisms of the bacterium remain to be unclear till date. Thus, we have performed rock-dissolution experiments followed by genome and transcriptome sequencing of novel Pseudomonas sp.NLX-4 strain to explore the efficiency of microbe-mediated habitat restoration and its molecular mechanisms underlying this biological process. Results obtained from initial rock dissolution experiments revealed that Pseudomonas sp. NLX-4 strain efficiently accelerates the dissolution of silicate rocks by secreting amino acids, exopolysaccharides, and organic acids with elevated concentrations of potassium, silicon and aluminium elements. The rock dissolution experiments of NLX-4 strain exhibited an initial increase in particle diameter variation values between 0-15 days and decline after 15 days-time respectively. The 6,771,445-base pair NLX-4 genome exhibited 63.21 GC percentage respectively with a total of 6041 protein coding genes. Genome wide annotations of NLX-4 strain exhibits 5045-COG, 3996-GO, 5342-InterPro, 4386-KEGG proteins respectively Transcriptome analysis of NLX-4 cultured with/without silicate rocks resulted in 539 (288-up and 251-down) differentially expressed genes (DEGs). Fifteen DEGs encoding for siderophore transport, EPS and amino acids synthesis, organic acids metabolism, and bacterial resistance to adverse environmental conditions were highly up-regulated by cultured with silicate rocks. This study has not only provided a new strategy for the ecological restoration of rock mining areas, but also enriched the applicable bacterial and genetic resources.

Project description:It has long been recognized that species occupy a specific ecological niche within their ecosystem. The ecological niche is defined as the number of conditions and resources that limit species distribution. Within their ecological niche, species do not exist in a single physiological state but in a number of states we call the Natural Operating Range. In this paper we link ecological niche theory to physiological ecology by measuring gene expression levels of collembolans exposed to various natural conditions. The soil-dwelling collembolan Folsomia candida was exposed to 26 natural soils with different soil characteristics (soil type, land use, practice, etc). The animals were exposed for two days and gene expression levels were measured. The main factor found to regulate gene expression was the soil type (sand or clay), in which 18.5% of the measured genes were differentially expressed. Gene Ontology analysis showed animals exposed to sandy soils experience general stress, affecting cell homeostasis and replication. Multivariate analysis linking soil chemical data to gene expression data revealed that soil fertility influences gene expression. Land-use and practice had less influence on gene expression; only forest soils showed a different expression pattern. A variation in gene expression variation analysis showed overall low variance in gene expression. The large difference in response to soil type was caused by the soil physicochemical properties where F. candida experiences clay soils and sandy soils as very different from each other. This collembolan prefers fertile soils with high organic matter content, as soil fertility was found to correlate with gene expression and animals exposed to sandy soils (which, in general, have lower organic matter content) experience more general stress. Finally, we conclude that there is no such thing as a fixed physiological state for animals in their ecological niche and the boundary between the ecological niche and a stressed state depends on the genes/pathways investigated.

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Comparative analysis of rhizosphere soil between three plantation types in Karst Rocky Desertification area by widely targeted metabolomics

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