Project description:Transcriptome profiling of whole proboscis and body wall of the marine Polychaeta Eulalia sp. (Eulalia viridis), adults, wild population (sex undiscriminated), collected from the rocky intertidal at W Portugal (2018).
Project description:Boreal toads (Anaxyrus boreas boreas) of the Southern Rocky Mountain population are declining due to the introduction of the chytrid fungus Batrachochytrium dendrobatidis (Bd). Boreal toads in Colorado are generally susceptible to Bd infection, but some Bd-tolerant populations persist in parts of the Southern Rocky Mountain and broader Eastern boreal toad population. We conducted a Bd challenge with lab-reared sibling toads from Bd-susceptible Colorado and purportedly Bd-tolerant Utah populations and report on transcriptomic responses to Bd during late infection in skin and liver tissue. Fewer immune genes were expressed in response to Bd in Colorado toads, but with greater upregulation compared to Utah toads, indicating a dysregulated immune response. Signatures of Bd-tolerance in Utah toads included more moderate upregulation in immune gene expression and a significantly enriched suite of gene functions related to innate and adaptive immune responses. Our transcriptomic results support the notion that Utah toads are tolerant to Bd, rather than resistant, carrying Bd loads similar to Colorado yet having a unique transcriptomic profile and presenting minimal clinical signs of chytridiomycosis. We conclude that closely related populations have divergent transcriptomic responses to Bd with a dysregulated immune response in Bd-susceptible toads.
2023-10-04 | GSE244617 | GEO
Project description:Rocky Mountain Fire Chronosequence
Project description:<p>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.</p>
Project description:Global warming has shifted climate zones poleward or upward. However, understanding the responses and mechanism of microbial community structure and functions relevant to natural climate zone succession is challenged by the high complexity of microbial communities. Here, we examined soil microbial community in three broadleaved forests located in the Wulu Mountain (WLM, temperate climate), Funiu Mountain (FNM, at the border of temperate and subtropical climate zones), or Shennongjia Mountain (SNJ, subtropical climate).Soils were characterized for geochemistry, Illumina sequencing was used to determine microbial taxonomic communities and GeoChips 5.0 were used to determine microbial functional genes.
Project description:Strains of R. rickettsii, the agent of Rocky Mountain spotted fever, differ greatly in the severity of the disease caused. The genetic differences responsible for this disparity are only now being uncovered. An avirulent, laboratory adapted strain of R. rickettsii fails to proteolytically process several large surface protein antigens. We have identified a protease that cleaves the protein precursors to their mature form. The gene encoding this protease is mutated in the avirulent strain. Complementation of the active form of the gene identifies proteolytic processing of surface antigens as important to virulence.
Project description:Drought is an increasing threat to soybean (Glycine max) production worldwide. In addition to methods such as breeding and genetic modification, inoculation of plants or soils with single microbes and microbial consortia are being explored to mitigate the impacts of drought stress on crop plants. One criterion for selecting microbes within a consortium is to select hub taxa, which are those whose abundances appear to be highly correlated with abundances of other taxa in the microbiome. To assess the impact of microbial inoculations with hub taxa on soybean, I identified five hub taxa from soybean roots which were then used to inoculate soybeans grown in 75% sand and 25% no-till soil from the KBS LTER. No-till soil was used to match the environment from which hub taxa were identified and isolated, and because no-till soils are known to confer resilience to low-moisture stress. Inoculated and control plants were then exposed to low-moisture stress as seedlings. Selected hub taxa included two fungi (Humicola sp., and Gibellulopsis sp.) and three bacteria (Streptomyces sp., Massilia sp., and Caulobacter segnis). The impact of inoculation on plant hosts was assessed with phenotype measures (aboveground and belowground) and plant functional measures (transcriptomics and non-target metabolomics of roots). The impact on the microbiome was assessed using amplicon sequencing of DNA as well as cDNA created from RNA extracted from roots. Inoculation had a minor impact on the microbiome that was most apparent when a more active fraction of the microbiome was analyzed using cDNA. cDNA amplicon sequencing demonstrated that Bradyrhizobium was enriched earlier in inoculated samples compared to control samples and that Glomus was enriched earlier in control samples. Transcriptomics of soybean roots demonstrated that genes related to nodulation were upregulated in inoculated samples, and non-targeted metabolomics appeared to show a possible signal of increased nodulation related metabolites in inoculated samples. Molecular and metabolomics data agreed with phenotypic data which showed increases in nodulation as well as increased aboveground growth, likely related to increased nitrogen fixation activity. Experiments using field soils and enriching individual hub taxa revealed that this effect of increased resilience to drought and nodulation was reproducible with both Caulobacter segnis and Streptomyces treatments. Overall, these results support the hypothesis that hub taxa can be used as inocula to improve the performance and resilience of the host plants.
Project description:Isolation and characterization of two recently isolated Novosphingobium oxfordensis sp. nov. and Novosphingobium mississippiensis sp. nov. strains from soil, with LCMS and genome-based investigation of their glycosphingolipid productions