Dataset Information

Columbia River sediment HUM-V (Hyporheic Uncultured Microbial and Viral) database metaproteome

ABSTRACT: Metaproteomic data for Rodriguez-Ramos, et al. interrogating microbial and viral communities of hyporheic river sediments within the Columbia River. Samples were digested with trypsin, and analyzed by LC-MS/MS. Data was searched with MS-GF+ using PNNL's DMS Processing pipeline.

INSTRUMENT(S): Q Exactive Plus

ORGANISM(S): Environmental Samples <bacteria> (ncbitaxon:48479)

SUBMITTER: Kelly Wrighton

PROVIDER: MSV000087330 | MassIVE | Wed Apr 28 18:20:00 BST 2021

SECONDARY ACCESSION(S): PXD025696

REPOSITORIES: MassIVE

ACCESS DATA

Publications

Genome-Resolved Metaproteomics Decodes the Microbial and Viral Contributions to Coupled Carbon and Nitrogen Cycling in River Sediments.

Rodríguez-Ramos Josué A JA Borton Mikayla A MA McGivern Bridget B BB Smith Garrett J GJ Solden Lindsey M LM Shaffer Michael M Daly Rebecca A RA Purvine Samuel O SO Nicora Carrie D CD Eder Elizabeth K EK Lipton Mary M Hoyt David W DW Stegen James C JC Wrighton Kelly C KC

mSystems 20220721 4

Rivers have a significant role in global carbon and nitrogen cycles, serving as a nexus for nutrient transport between terrestrial and marine ecosystems. Although rivers have a small global surface area, they contribute substantially to worldwide greenhouse gas emissions through microbially mediated processes within the river hyporheic zone. Despite this importance, research linking microbial and viral communities to specific biogeochemical reactions is still nascent in these sediment environmen ...[more]

PMID: 35861508

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Project description:Escaped domesticated individuals can introduce disadvantageous traits into wild populations due to both adaptive differences between population ancestors and human-induced changes during domestication. In contrast to their domesticated counterparts, some endangered wild Atlantic salmon populations encounter during their marine stage large amounts of suspended sediments, which may act as a selective agent. We used microarrays to elucidate quantitative transcriptional differences between a domesticated salmon strain, a wild population and their first-generation hybrids during their marine life stage, to describe transcriptional responses to natural suspended sediments, and to test for adaptive genetic variation in plasticity relating to a history of natural exposure or nonexposure to suspended sediments. We identified 67 genes differing in transcription level among salmon groups. Among these genes, processes related to energy metabolism and ion homoeostasis were over-represented, while genes contributing to immunity and actin-/myosin-related processes were also involved in strain differentiation. DomesticM-bM-^@M-^Swild hybrids exhibited intermediate transcription patterns relative to their parents for two-thirds of all genes that differed between their parents; however, genes deviating from additivity tended to have similar levels to those expressed by the wild parent. Sediments induced increases in transcription levels of eight genes, some of which are known to contribute to external or intracellular damage mitigation. Although genetic variation in plasticity did not differ significantly between groups after correcting for multiple comparisons, two genes (metallothionein and glutathione reductase) tended to be more plastic in response to suspended sediments in wild and hybrid salmon, and merit further examination as candidate genes under natural selection. Salmon of three genotypes (strains: 1. wild (Stewiacke River salmon), 2. domesticated (Saint John River salmon), and 3. first generation hybrids between the two strains, were exposed to two environments (treatment: 1. suspended sediments, 2. control: clear water), using eight biological replicates (individuals) of each of the six experimental groups, summing up to 48 individuals, each individual has two technical replicates , each technical replicate has been labelled with a different dye, each technical replicate appears on a different array, dye swaps are equilibrated for arrays that combine individuals from different genotypes and for arrays that combine individuals from the same genotype but different environments. Technical replicates of individuals always appear once on arrays that compare between environments and once on arrays that compare among genotypes. In total there are 48 arrays.

Dataset Information

Columbia River sediment HUM-V (Hyporheic Uncultured Microbial and Viral) database metaproteome

Publications

Genome-Resolved Metaproteomics Decodes the Microbial and Viral Contributions to Coupled Carbon and Nitrogen Cycling in River Sediments.

Similar Datasets

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