Project description:16s RNA gene sequencing data from seawater, bed sediment and steel corrosion samples from Shoreham Harbour, UK, collected to allow bacterial species comparisons between microbially influenced corrosion, the surrounding seawater, and the sea bed sediment at the seafloor and 50cm depth below seafloor.
Project description:Chemical analysis of the compounds present in sediment, although informative, often is not indicative of the downstream biological effects that these contaminants exert on resident aquatic organisms. More direct molecular methods are needed to determine if marine life is affected by exposure to sediments. In this study, we used an aquatic multispecies microarray and q-PCR to investigate the effects on gene expression in juvenile sea bream (Sparus aurata) of two contaminated sediments defined as sediment 1 and 2 respectively, from marine areas in Northern Italy.
Project description:non-targeted metabolic profiling of 26 soybean varieties using liquid chromatography-mass spectrometry (LC-MS) including 15 wild black soybeans (WBS) and 11 cultivated black soybeans (CBS), combined with multivariate analysis, revealed significant differences in 25 differential metabolites
Project description:Non-targeted metabolic profiling of 26 soybean varieties using liquid chromatography-mass spectrometry (LC-MS) including 15 wild black soybeans (WBS) and 11 cultivated black soybeans (CBS), combined with multivariate analysis, revealed significant differences in 25 differential metabolites
Project description:Marine algae convert a substantial fraction of the carbon dioxide they fix into various polysaccharides. Bacteria specialized on the remineralization of these polysaccharides often feature genomic clusters, termed polysaccharide utilization loci (PULs). Such PULs are often prevalent in, but not limited to, marine Flavobacteriia. Since knowledge on extant PUL diversity is sparse, we sequenced the genomes of 53 North Sea Flavobacteriia. We obtained 400 PULs, suggesting usage of a large array of polysaccharides, including laminarin, α- and β-mannans, fucose-, xylose-, galactose-, rhamnose- and arabinose-containing substrates, pectins, and chitins. Many of the PULs were novel, some indicating substrates that have rarely been described in marine environments. PUL repertoires of isolates often differed significantly within genera, corroborating ecological niche-associated glycan partitioning. Polysaccharide uptake in Flavobacteriia is mediated by SusCD. Respective protein trees revealed clustering according to polysaccharide specificities. Analysis of SusCD expression in multiyear phytoplankton bloom-associated metaproteomes indicated changes in microbial utilization of glucan, ß-mannan and sulfated xylan, suggesting that distinct substrates are temporarily abundant.
Project description:Our goal is to convert methane efficiently into liquid fuels that may be more readily transported. Since aerobic oxidation of methane is less efficient, we focused on anaerobic processes to capture methane, which are accomplished by anaerobic methanotrophic archaea (ANME) in consortia. However, no pure culture capable of oxidizing and growing on methane anaerobically has been isolated. In this study, Methanosarcina acetivorans, an archaeal methanogen, was metabolically engineered to take up methane, rather than to generate it. To capture methane, we cloned the DNA coding for the enzyme methyl-coenzyme M reductase (Mcr) from an unculturable archaeal organism from a Black Sea mat into M. acetivorans to effectively run methanogenesis in reverse. The engineered strain produces primarily acetate, and our results demonstrate that pure cultures can grow anaerobically on methane. Differential gene analysis of two growth conditions (three biological replicates each) was performed: (i) M. acetivorans/pES1-MATmcr3 grown on methane and (ii) M. acetivorans/pES1-MATmcr3 grown on methanol. All starter cultures (200 mL) were grown on methanol for 5 days, and harvested by centrifugation. Cell pellets were washed three times with HS medium, and resuspended using 5 mL HS medium, 2 µg/mL puromycin, and 0.1 mM FeCl3. For condition (i), methane was filled into the headspace of the cultures. For condition (ii), 150 mM methanol was added. All cultures were incubated at 37C for 5 days, followed by rapid centrifugation in the presence of 50 µL RNAlater solution (Ambion, Austin, TX) per mL of culture. Total RNA was isolated using RNeasy Mini kit (Qiagen, Valencia, CA) were then digested with terminator 5’-phosphate-dependent exonuclease (Epicentre, Madison, WI) to partially remove ribosomal RNA. Digested RNA were cleaned up using AgenCourt RNAClean XP beads (AgenCourt Bioscience, Beverly, MA) and used for cDNA library construction using the TruSeq Stranded mRNA Library kit (Illumina). Pooled and barcoded cDNA library was then sequenced on a HiSeq sequencing platform (Illumina). Obtained reads were mapped to the reference genome of M. acetivorans (Genbank accession NC_003552.1) using STAR. The mapped reads were assembled using Cufflink v2.2.1 to identify potential novel transcripts. Assembled, unannotated novel transcripts for all the strains were combined with the list of known genes. Differential expression of genes and potential novel transcripts were determined using Cuffdiff at a significance cutoff at q < 0.07 with a false discovery rate of 0.05. Expression levels of gene transcripts are expressed as fragments per kilobase of transcript per million mapped fragments (FPKM), and expression changes are determined by the ratio of FPKM of culture replicates grown on methane to FPKM of culture replicates grown on methanol.