Project description:Monitoring microbial communities can aid in understanding the state of these habitats. Environmental DNA (eDNA) techniques provide efficient and comprehensive monitoring by capturing broader diversity. Besides structural profiling, eDNA methods allow the study of functional profiles, encompassing the genes within the microbial community. In this study, three methodologies were compared for functional profiling of microbial communities in estuarine and coastal sites in the Bay of Biscay. The methodologies included inference from 16S metabarcoding data using Tax4Fun, GeoChip microarrays, and shotgun metagenomics.
Project description:Triplets of Lactobacullus plantarum strains were isolated from nine contrasting habitats. Without any passage through other culture media, isolation and cultivation were on model media that strictly reproduced the chemical and physical conditions and stressors of the habitats of origin. Here, we demonstrated how L. plantarum regulates and shapes its transcriptome in response to contrasting habitats. Firstly, multivariate clustering analysis of transcriptional data (RNA-Seq), complemented with metabolomics and phenomics, grouped the strains according to the habitats of origin. Subsequently, selected strains from each habitat switched to repeated cultivation on MRS medium and transcriptomes homogenized into a unique cluster. Adaptation to this common medium mainly relied on activation of genes for phage- and prophage-related proteins and transposases. Finally, the comparison of growth across model media and with respect to MRS medium showed that 44% of the overall 3,112 gene transcripts changed depending on the specific habitat. Regulation and shaping of transcriptomes mainly concerned carbohydrate acquisition, pyruvate catabolism, proteolytic system and amino acid, lipid and inorganic ion transport and metabolism, with contrasting responses for contrasting habitats. Pathways reconstruction demonstrated how the large genome size of L. plantarum imparts transcriptome and metabolic flexibility as the basic mechanism for a nomadic lifestyle.
2018-11-14 | GSE115448 | GEO
Project description:Seasonal and spatial patterns of freshwater microbial communities
| PRJNA588356 | ENA
Project description:Environmental DNA metabarcoding reveals spatial and seasonal in fish community in the Venice Lagoon
Project description:The aim of this study was to investigate ecotypic adaptation in Holcus lanatus in plants selected from two widely contrasting habitats, acid bog (pH 3.5) or limestone quarry spoil (pH 7.5), using a transcriptome based analysis approach including sequence analysis of root associated Glomeromycota. Differential gene expression in root and shoot of naturally occurring H. lanatus ecotypes, selected from either habitat and grown in a full factorial reciprocal soil transplant experiment were investigated and ecotype specific SNPs identified.
