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.

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. Test animals were exposed to 26 natural soils + 2 control soils. 4 biological replicates per soil containing 25 grams of soil and 30 23-day-old animals per replicate, RNA was isolated after two days of exposure. for the micro-array hybridization design we made use of an interwoven loop design. from the four replicates per soil two were labeled with Cy3 and 2 with Cy5. It was made sure that now two replicates of the same soil were ever hybridized against the same soil.

Project description:BACKGROUND: The coevolution and interaction between plants and microorganisms have long been a subject of significant research interest. Dark septate endophytes (DSE) have garnered great attention in contemporary research due to their functional diversity, in vitro cultivation ability, and ability to establish symbiotic associations with host plants. In the present study, three DSE strains, namely Acrocalymma vagum, Zopfiella marina, and Phoma herbarum, which were obtained from the roots of Astragalus membranaceus, were introduced into maize plants through inoculation. We evaluated the effects of DSE inoculation on maize growth and root secretion activity through a multi omics methods, and proposed mechanisms for 'internal pathways' and 'external pathways'.RESULTS: The findings indicated that A. vagum exhibited superior growth-promoting ability on maize compared to Z. marina and P. herbarum.GO and KEGG enrichment analysis found that A. vagum inoculation resulted in significant enrichment of differentially expressed genes in annotation functions related to hormone regulation and lipid metabolism. A. vagum inoculation revealed that the gene pathways involved in plant hormone signaling and plant pathogen interactions play a crucial role in promoting host growth, and A. vagum inoculation group exhibited the highest number of differentially expressed genes, the most intricate protein-protein interaction (PPI) model, and the most pronounced relationship between differentially expressed genes. After the inoculation of A.vagum, the levels of salicylic acid, zeatin, and IAA in maize plants significantly increased. Additionally, the diversity and abundance of endophytic fungi, as well as the proportion of harmful bacteria and beneficial fungi, had significantly increased. Compared with Z. marina and P. herbarum, the net photosynthetic rate (Pn) and stomatal conductance (Gs) of A.vagum inoculated plants significantly increased. Inoculation with A.vagum could enhance the ability of corn roots to secrete lipids, sugars, and amino acids, resulted in a notable augmentation of beneficial bacteria and fungi, accompanied by a significant reduction in the proportion of harmful bacteria in the rhizosphere soil, such as Fusarium solani and Fusarium lacertarum, exhibited significant inhibition, whereas Bacillus niabensis and Bacillus nealsonii demonstrated enrichment trends. Soil pH, organic matter, available potassium content, acid phosphatase, alkaline phosphatase and urease activity exhibited significant increases following the inoculation of A. vagum. Variance decomposition and structural equation modeling (SEM) analysis indicated that the 'internal pathway', maize growth is mainly influenced by the interaction of endogenous hormones, endophytic microorganisms, and photosynthetic parameters, whereas within the 'external pathway', the interaction between soil microorganisms and soil physicochemical properties exerted a dominant influence. Compared with the Z. marina and P. herbarum inoculation, A. vagum inoculation showed a more significant impact on maize growth, both in terms of 'internal pathway' and 'external pathway', in terms of pathway level and quantity.CONCLUSIONS: These findings provide a new perspective for understanding the potential mechanisms of 'microbe-plant' interactions and also contribute to the exploration of targeted functional microorganisms that promote growth and stress resistance.

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