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Metaproteomics of phototrophic biomats from two soda lakes in the Canadian Rocky Mountains

ABSTRACT: This data is a case study done in the context of developing methods for assessing the taxonomic composition of microbial communities using metaproteomics. For this study with analyzed phototrophic biomats from two Soda Lakes in the Canadian Rocky Mountains using metaproteomics. For protein identification we generated a metagenome from which we predicted and annotated the protein sequences used to analyze the metaproteomes. The database is available in this PRIDE submission. Lake1 refers to Goodenough Lake (GEM, 51°19'47.64"N 121°38'28.90"W) and Lake2 referes to Last Chance Lake (LCM, 51°19'39.3" N 121°37'59.3"W).

OTHER RELATED OMICS DATASETS IN: PRJEB19901

INSTRUMENT(S): Q Exactive

ORGANISM(S): Archaea Bacteria Viruses Eukaryota (eucaryotes)

SUBMITTER: Manuel Kleiner

LAB HEAD: Marc Strous

PROVIDER: PXD006343 | Pride | 2017-05-12

REPOSITORIES: Pride

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Dataset's files

Source:

			Action	DRS
	GEM-01.pep.xml	Pepxml
	GEM.msf	Msf
	LCM-01.pep.xml	Pepxml
	LCM.msf	Msf
	Run1_1000ng_LCM.raw	Raw

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Publications

Assessing species biomass contributions in microbial communities via metaproteomics.

Kleiner Manuel M Thorson Erin E Sharp Christine E CE Dong Xiaoli X Liu Dan D Li Carmen C Strous Marc M

Nature communications 20171116 1

Microbial community structure can be analyzed by quantifying cell numbers or by quantifying biomass for individual populations. Methods for quantifying cell numbers are already available (e.g., fluorescence in situ hybridization, 16-S rRNA gene amplicon sequencing), yet high-throughput methods for assessing community structure in terms of biomass are lacking. Here we present metaproteomics-based methods for assessing microbial community structure using protein abundance as a measure for biomass ...[more]

PMID: 29146960

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Metaproteomes of phototrophic mats from four soda lakes found in the Cariboo Plateau region of British Columbia, Canada

Project description:In this study we used metaproteomics to discern the metabolism and physiology of the microorganisms occurring in the phototrophic mats of four soda lakes in the interior of British Columbia, Canada. Binned and assembled metagenomes were used as the database for protein identification.

2019-07-29 | PXD011230 | Pride

Optimization of protein extraction methods for root-associated microbes in maize

Project description:The goal of this study was to optimize protein extraction methods to study root-associated bacteria in maize. For this we inoculated sterile maize plants with a synthetic community composed of seven different bacteria (Ben Niu et al. PNAS 2017, vol 114, n 12). Then, we extracted proteins from maize roots using eight different protein extraction methods in triplicates. These methods were a combination of different extraction buffers (SDS or Triton-based) and mechanical disruption methods (bead-beating, N2 grinding, glass homogenizer and freeze-thaw cycles). We found that vortexing maize roots with glass beads in PBS yielded the highest numbers of microbial protein identification.

2022-09-08 | PXD026369 | Pride

Metaproteomes of cyanobacterial consortium collected from photobioreactors enriched from soda lake microbial mats in BC, Canada

Project description:In this work we used metaproteomics to study the effect of pH and nitrogen source on cyanobacterial growth of the laboratory cultures. The database for protein identification was obtained from assembled metagenomes.

2021-11-02 | PXD024393 | Pride

Quantification of mock microbial communities with metagenomes, 16S rRNA gene amplicons and metaproteomics

Project description:In this study we developed metaproteomics based methods for quantifying taxonomic composition of microbiomes (microbial communities). We also compared metaproteomics based quantification to other quantification methods, namely metagenomics and 16S rRNA gene amplicon sequencing. The metagenomic and 16S rRNA data can be found in the European Nucleotide Archive (Study number: PRJEB19901). For the method development and comparison of the methods we analyzed three types of mock communities with all three methods. The communities contain between 28 to 32 species and strains of bacteria, archaea, eukaryotes and bacteriophage. For each community type 4 biological replicate communities were generated. All four replicates were analyzed by 16S rRNA sequencing and metaproteomics. Three replicates of each community type were analyzed with metagenomics. The "C" type communities have same cell/phage particle number for all community members (C1 to C4). The "P" type communities have the same protein content for all community members (P1 to P4). The "U" (UNEVEN) type communities cover a large range of protein amounts and cell numbers (U1 to U4). We also generated proteomic data for four pure cultures to test the specificity of the protein inference method. This data is also included in this submission.

2017-05-12 | PXD006118 | Pride

Metaproteomics of the marine gutless oligochaete Olavius algarvensis and its symbionts to determine stable isotope fingerprints using Direct Protein-SIF

Project description:We developed a method that allows measuring the stable carbon isotope composition of individual species in microbial communities using metaproteomics. We call this methods “Direct Protein-SIF”. We validated and tested the method extensively using pure cultures (PXD006762) and mock communities (PXD006118, https://www.ebi.ac.uk/pride/archive/projects/PXD006118). As a case study we applied Direct Protein-SIF to the Olavius algarvensis symbiosis. Olavius algarvensis is a marine worm that lives in shallow-water sediments off the coast of Elba, Italy. The worm has no digestive and excretory system, instead it harbors five bacterial symbionts that fulfill its nutritional and waste recycling needs (http://www.pnas.org/content/109/19/E1173.short). For this project we generated metaproteomes of 14 O. algarvensis individuals. A total of 18 LC-MS/MS runs were generated. For Direct Protein-SIF the data from all runs was combined. In this submission we are including the Direct Protein-SIF specific isotope pattern file as well as the .mzML files and PSM file required as input for the Direct Protein-SIF software (Calis-p). In addition to the Olavius algarvensis samples a protein reference material (MKH files) was measured. The respective .raw files and isotopic pattern files are available through project PXD006762 (see publication for details on how the reference material is used to calibrate the method).

2018-05-21 | PXD007510 | Pride

Optimization of protein extraction methods for root-associated microbes in Arabidopsis

Project description:The goal of this study was to optimize protein extraction methods to study root-associated bacteria in Arabidopsis. For this we inoculated Arabidopsis seedlings grown in agar plates with a synthetic community (SynSom) composed of four different strains (Variovorax paradoxus, Arthrobacter sp, Agrobacterium sp. and Pseudomonas sp.. Twelve days after inoculation we extracted proteins from the roots using six different protein extraction methods each in triplicates. These methods were a combination of different extraction buffers (SDS or Triton-based) and mechanical disruption methods (bead-beating, N2 grinding, glass homogenizer and freeze-thaw cycles) We found that bead-beating the roots with lysing matrix E in SDT lysis buffer yielded the highest numbers of microbial protein identification and enhanced the detection of proteins derived from gram positive bacteria.

2022-09-08 | PXD026330 | Pride

Stable isotope probing with 13C-labeled bicarbonate/proteomics of cyanobacterial consortium collected from photobioreactors enriched from soda lake microbial mats in BC, Canada

Project description:In this work we used stable isotope probing/proteomics to study uptake of carbon sources by members of the cyanobacterial consortium. The database for protein identification was obtained from assembled metagenomes.

2022-01-21 | PXD028578 | Pride

Effect of nitroprusside on the proteomic expression of Desulfovibrio vulgaris Hildenborough

Project description:In this study, the effect of nitroprusside on protein expression of the model sulfate reducing bacterial isolate (Desulfovibrio vulgaris Hildenborough) was investigated. Three different experiments were done with different exposure time to nitroprusside (30 min, 1 hour, and 3 hours). In each experiment, the culture was grown in quadruplet of serum bottles containing 40 ml complex medium (Postgate medium B) under anaerobic condition at 30oC. At mid-log growth phase, each of the quadruplet culture was divided into two (20 ml each) and nitroprusside (0.25 mM) was added to one of each bottle while the other bottles were used as controls. After 30 min, 1 hour, and 3 hours of exposure to nitroprusside, the culture (1 ml) was pelleted and used for proteomic analysis.

2018-05-17 | PXD007623 | Pride

Mock microbial community with spike-ins of 13C-labeled Escherichia coli cells for benchmarking of protein-based stable isotope probing proteomics (Protein-SIP)

Project description:This dataset is part of a study aimed at developing algorithms for the quantification of stable isotope content in microorganisms in microbial communities after labeling them with stable isotope-labeled substrates. For this dataset Escherichia coli cultures were labeled with different percentages (1, 5 and 10%) of fully labeled 13C glucose (13C1-6) and spiked-in into a mock microbial community consisting of 32 species of bacteria, archaea, eukaryote and bacteriophages (UNEVEN Community described in Kleiner et al. 2017 Nat Communications 8(1):1558). The community also contained unlabeled E. coli cells and labeled/unlabeled E. coli cells in the spike-in sample were at a 1:1 ratio. Cultures of E. coli were grown in M9 minimal medium in which a percentage of the glucose was replaced with 13C1-6 glucose for >10 generations to achieve close to complete labeling of cells. The following percentages of 13C1-6 glucose were added 1, 5 and 10%. Triplicate cultures were grown for each percentage. Please note that the unlabeled glucose that was used of course had a natural content of 13C of around 1.1%, thus the 0% added label samples have an actual 13C content of 1.1% and all added label is on top of this value. We included a tab delimited table with this submission providing details on all raw files.

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