Project description:Nitrate-reducing iron(II)-oxidizing bacteria are widespread in the environment contribute to nitrate removal and influence the fate of the greenhouse gases nitrous oxide and carbon dioxide. The autotrophic growth of nitrate-reducing iron(II)-oxidizing bacteria is rarely investigated and poorly understood. The most prominent model system for this type of studies is enrichment culture KS, which originates from a freshwater sediment in Bremen, Germany. To gain insights in the metabolism of nitrate reduction coupled to iron(II) oxidation under in the absence of organic carbon and oxygen limited conditions, we performed metagenomic, metatranscriptomic and metaproteomic analyses of culture KS. Raw sequencing data of 16S rRNA amplicon sequencing, shotgun metagenomics (short reads: Illumina; long reads: Oxford Nanopore Technologies), metagenome assembly, raw sequencing data of shotgun metatranscriptomes (2 conditions, triplicates) can be found at SRA in https://www.ncbi.nlm.nih.gov/bioproject/PRJNA682552. This dataset contains proteomics data for 2 conditions (heterotrophic and autotrophic growth conditions) in triplicates.
Project description:Pseudo-nitzschia multiseries (Ps-n) is a toxigenic marine diatom that produces the neurotoxin, domoic acid. We screened for candidate genes that may be involved in domoic acid production by determining changes in transcript profiles in Ps-n cultures that were in late exponential (low-domoic-acid-producing) vs. stationary (high-domoic-acid-producing) growth states. We also identified a number of candidate reference genes for future RT-qPCR studies, based on their stability in this study. Ps-n RNA was extracted from late exponential and stationary phase cultures. Experiments included one axenic culture, and two non-axenic cultures. Experiments were dye-swapped to account for differences in dye labeling and detection efficiencies: a) the axenic culture experiment included 4 technical replicate arrays (i.e., 2 dye-swapped experiments = 4 total hybridizations), and b) the non-axenic culture experiments each included 6 technical replicate arrays (i.e., 3 dye-swapped experiments = 6 total hybridizations).
Project description:We sequenced mRNA and small RNA (sRNA) profiles in the interaction between Brachypodium distachyon (Bd) and Serendipita indica (Si; syn. Piriformospora indica), at four (4) days post inoculation (DPI). sRNA sequencing reads of Si-colonized and non-colonized roots, as well as axenic fungal cultures were generated. Three biological samples of each were sequenced, with two technical replicates per sample (SE). Raw reads from sRNA sequencing were submitted to technical adapter trimming (Cutadapt) before upload.