Project description:A high-density oligonucleotide microarray that targets functional genes in marine microbial community was designed as a result of a multi-institutional effort. The design is based on nucleotide sequence data obtained with metagenomics and metatranscriptomics. The chip targets ~20000 gene sequences represented by 145 gene categories relevant to microbial metabolism in the open ocean and coastal environments. The three domains of life and also viruses are represented on the chip. Using this microarray we were able to compare the functional responses of microbial communities to iron and phosphate enrichments in samples from the North Pacific Subtropical Gyre. The response was attributed to individual lineages of microorganisms including uncharacterized strains. Transcription of 68% of the gene probes was detected from a variety of microorganisms, and the patterns of gene transcription indicated a relief from iron limitation and transition into nitrogen limitation. When combined with physicochemical descriptions of each system, the use of microarrays can help to develop a comprehensive understanding of the changes in microbially-driven processes. We analyzed three samples amended with phosphate and two sample amended with iron (III) after 48h of incubation
Project description:Pioneering studies (PXD014844) have identified many interesting molecules by LC-MS/MS proteomics, but the protein databases used to assign mass spectra were based on short Illumina reads of the Amblyomma americanum transcriptome and may not have captured the diversity and complexity of longer transcripts. Here we apply long-read Pacific Bioscience technologies to complement the previously reported short-read Illumina transcriptome-based proteome in an effort to increase spectrum assignments. Our dataset reveals a small increase in assignable spectra to supplement previously released short-read transcriptome-based proteome.
Project description:Pioneering studies (PXD014844) have identified many interesting molecules in tick saliva by LC-MS/MS proteomics, but the protein databases used to assign mass spectra were based on short Illumina reads of the Amblyomma americanum transcriptome and may not have captured the diversity and complexity of longer transcripts. Here we apply long-read Pacific Bioscience technologies to complement the previously reported short-read Illumina transcriptome-based proteome in an effort to increase spectrum assignments. Our dataset reveals a small increase in assignable spectra to supplement the previously released short-read transcriptome-based proteome.
Project description:The diazotroph Trichodesmium is an important contributor to marine dinitrogen (N2) fixation, supplying so-called new N to phytoplankton in typically N-limited ocean regions. Identifying how iron (Fe) and phosphorus (P) influence Trichodesmium activity and biogeography is an ongoing area of study, where predicting patterns of resource stress is complicated in part by the uncertain bioavailability of organically complexed Fe and P. Here, a comparison of 26 metaproteomes from picked Trichodesmium colonies identified significantly different patterns between three ocean regions: the western tropical South Pacific, the western North Atlantic, and the North Pacific Subtropical Gyre. Trichodesmium metaproteomes across these regions significantly differed in KEGG submodule signals, and vector fitting showed that dissolved Fe, phosphate, and temperature significantly correlated with regional proteome patterns. Populations in the western tropical South Pacific appeared to modulate their proteomes in response to both Fe and P stress, including a comparatively low relative abundance of the N2 fixation marker protein, NifH. Significant increases in the relative abundance of both Fe and P stress marker proteins previously validated in culture studies suggested that Trichodesmium populations in the western North Atlantic and North Pacific were P-stressed and Fe-stressed, respectively. These patterns recapitulate established regional serial and co-limitation patterns of resource stress on phytoplankton communities. Evaluating community stress patterns may therefore predict resource controls on diazotroph biogeography. These data highlight how Trichodesmium modulates its metabolism in the field and provide an opportunity to more accurately constrain controls on Trichodesmium biogeography and N2 fixation.
