Project description:High-throughput sequencing of endogenous small RNAs from the moss Physcomitrella patens. This dataset encompasses microRNAs and other small RNAs of ~20-24 nucleotides expressed in the moss P. patens. SAMPLES UPDATED JULY 9, 2007 TO INCLUDE DATA ON SEQUENCED SMALL RNAS THAT DO NOT MATCH THE P. PATENS GENOME Keywords: High throughput small RNA sequencing
Project description:4plex_physco_2014-05 - ppmax2 response to gr24 - How does the Ppmax2 moss mutant respond to Strigolactone (GR24)? - Two moss genotypes are used: WT and the Ppmax2 mutant. Moss tissues are fragmented, then plated on medium (Petri dish with cellophane disks) and cultivated for 3 weeks. Moss tissues are then transfered for 6 hours on acetone-containing medium (control treatment, for WT and Ppmax2) or GR24 (1 microM, in acetone)-containing medium (for Ppmax2). After 6 hours, the moss tissues are collected, quickly forzen in liquid nitrogen. RNA are isolated using the Quiagen RNeasy Plant mini kit (including a RNase-free DNase treatment on column). Two similar experiments (T1 and T2) have been led.
Project description:Transcription profiling of Physcomitrella patens Reute strain gametophore, mature sporophyte and spore stage. These samples are part of an large-scale expression data set for the model moss Physcomitrella patens.
Project description:<p>Background:</p><p>Primary succession is predicted to proceed through shifts from stress-tolerant to competitive to cooperative ecological strategies as resource availability increases, yet molecular evidence for these transitions in microbial systems remains limited. Here, we used an integrated multi-omics approach to investigate how microbial functional traits and chemical outputs change across early ecosystem development using experimental basaltic hillslopes spanning succession from bare rock through biocrust to moss-dominated communities.</p><p> </p><p>Results:</p><p>Genome-resolved analyses revealed stress-tolerant pioneer communities enriched in oxidative and temperature stress-response genes on nitrogen-limited and physically unstable basalt. These communities were replaced by competitive nitrogen-fixing cyanobacteria that formed biocrusts enriched in carbon and nitrogen fixation pathways while stabilizing substrates through exopolysaccharide production. This stabilization enabled the establishment of functionally diverse moss-associated communities characterized by complete biogeochemical cycling and cooperative metabolic interactions. Metabolomic profiling linked these functional transitions to distinct chemical signatures across succession. Early stages were enriched in organic nitrogen- and sulfur-containing compounds, intermediate stages accumulated nucleosides and organic acids, and later stages were characterized by complex lipids and secondary metabolites. Metabolites discriminated successional stages with substantially higher accuracy than taxonomic markers, indicating that functional outputs in this system more reliably capture ecosystem state than community composition. While microbial community assembly shifted from stochastic to deterministic processes over succession, metabolite assembly remained predominantly deterministic throughout.</p><p> </p><p>Conclusions:</p><p>Integration across genomic and metabolomic data demonstrates that cyanobacterial nitrogen fixation coupled with substrate stabilization alleviates nutrient limitation and modifies physical habitat conditions, driving successional progression through ecological strategy shifts. These results advance succession theory by showing that biogeochemical and physical processes operate in tandem rather than sequentially. These molecular insights provide the first comprehensive evidence for predicted ecological strategy shifts at the molecular level and offer a framework for ecosystem monitoring and restoration, with stage specific metabolic signatures serving as quantitative biomarkers for assessing recovery trajectories.</p>