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Proteomics of Candidatus Thiodiazotropha endoloripes, the chemosynthetic symbiont of the lucinid clam Loripes lucinalis from the Bay of Fetovaia

ABSTRACT: The Lucinidae is a large family of marine bivalves. They occur in diverse habitats from shallow-water seagrass sediments to deep-sea hydrothermal vents. All members of this family so far investigated host intracellular sulfur-oxidizing symbionts that belong to the Gammaproteobacteria. We recently discovered the capability for nitrogen fixation in draft genomes of the symbionts of Loripes lucinalis from the Bay of Fetovaia, Elba, Italy. With proteomics, we investigated whether the genes for nitrogen fixation are expressed by the symbionts.

OTHER RELATED OMICS DATASETS IN: PRJNA314435

INSTRUMENT(S): Q Exactive

ORGANISM(S): Bacteria

SUBMITTER: Manuel Kleiner

LAB HEAD: Jillian Petersen

PROVIDER: PXD004536 | Pride | 2016-08-19

REPOSITORIES: Pride

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			Action	DRS
	80-gill_FDR_5percent.txt	Txt
	81-gill_FDR_5percent.txt	Txt
	82-gill_FDR_5percent.txt	Txt
	83-gill_FDR_5percent.txt	Txt
	84-gill_FDR_5percent.txt	Txt

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Publications

Chemosynthetic symbionts of marine invertebrate animals are capable of nitrogen fixation.

Petersen Jillian M JM Kemper Anna A Gruber-Vodicka Harald H Cardini Ulisse U van der Geest Matthijs M Kleiner Manuel M Bulgheresi Silvia S Mußmann Marc M Herbold Craig C Seah Brandon K B BK Antony Chakkiath Paul CP Liu Dan D Belitz Alexandra A Weber Miriam M

Nature microbiology 20161024

Chemosynthetic symbioses are partnerships between invertebrate animals and chemosynthetic bacteria. The latter are the primary producers, providing most of the organic carbon needed for the animal host's nutrition. We sequenced genomes of the chemosynthetic symbionts from the lucinid bivalve Loripes lucinalis and the stilbonematid nematode Laxus oneistus. The symbionts of both host species encoded nitrogen fixation genes. This is remarkable as no marine chemosynthetic symbiont was previously kno ...[more]

PMID: 27775707

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Proteomics of Cycloclasticus endosymbiont of deep-sea mussel Bathymodiolus heckerae from Campeche Knolls, southern Gulf of Mexico

Project description:Bathymodiolin mussels are a group of bivalves associated with deep-sea reducing habitats, such as hydrothermal vents and cold seeps. These mussels usually engage in an obligatory symbiosis with sulfur and/or methane oxidizing Gammaproteobacteria. In addition to these bacteria, Bathymodiolus heckerae that inhabit gas and oil seeps in Campeche Bay, the southern Gulf of Mexico, host bacteria phylogenetically with the Cycloclasticus genus. We recently discovered the capability for short-chain alkane degradation in draft genomes of symbiotic Cycloclasticus. With proteomics, we investigated whether the genes required for this process are expressed by the symbionts.

2016-12-05 | PXD005351 | Pride

Proteomics of Ca. Riegeria standrea – the chemosynthetic symbionts of the marine flatworm Paracatenula from the Bay of Sant´Andrea (Elba, Italy)

Project description:Paracatenula are marine catenulid flatworms occuring in shallow water sediments. Adult Paracatenula lack a mouth and a digestive system. Instead, a trophosome containing intracellular alphaproteobacterial symbionts, namely Ca. Riegeria fill most of the worm´s body (Gruber-Vodicka et al., 2011). Paracatenula sp. ‘standrea’ that harbor Ca. Riegeria sp. 812A (standrea) were sampled in Elba, Italy in April 2016. Based on the genome of Ca. Riegeria sp. 812A (standrea) we discovered a versatile combination of storage and biosynthesis and a convergence with unrelated intracellular thiotrophic symbionts. Proteomic analyses were performed to investigate which symbiont genes related to the host nutrition were expressed.

2019-03-26 | PXD009856 | 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.

2022-12-30 | PXD024174 | Pride

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

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

Project description: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).

2017-05-12 | PXD006343 | 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

Repetition of comparison of sample preservation methods for field collection of animal-microbe symbioses for metaproteomic analyses

Project description:When studying gene expression in microbe-animals symbioses collected in the field it is essential to quickly and efficiently preserve in situ symbiont and host protein abundance patterns. One of the most commonly used sample preservation methods for samples targeted for proteomic analyses is flash freezing, however, liquid nitrogen or dry ice needed for flash freezing are often not available at remote field sites. We replicated our experiment from PXD014591 to test if RNAlater allows preserving proteins in animal-microbe symbioses as efficiently as flash freezing and without introducing issues with downstream processing. We used the marine gutless oligochaete Olavius algarvensis as a model for testing. Olavius algarvensis lives in shallow water sediments off the coast of Elba, Italy. It has no digestive and excretory system and harbors five bacterial symbionts that fulfill its nutritional and waste recycling needs (Kleiner et al., 2012, PNAS 109(19):1173-82). We compared six RNAlater preserved and eight flash frozen samples in terms of the number of identified proteins, abundances of individual proteins and potential biases against specific protein or taxonomic groups. Six worms were incubated in RNAlater for 24 hours. After incubation, RNAlater was removed and samples were stored at -80°C. Eight worms were directly flash frozen in liquid nitrogen and stored at -80 °C immediately after preservation.

2021-11-03 | PXD026631 | Pride

Metaproteomes of intestinal microbiomes from mice fed different sources of dietary protein

Project description:Diet plays a major role in altering the composition and function of the gut microbiota. Previously most studies have focused on the effects of fiber, fat, and different amounts of protein on the gut microbiota. In this study we investigated how different sources of protein affect the gut microbiota of mice. We fed conventional and germ-free C57BL/6J mice a series of defined diets where the source of dietary protein was the key difference, which made up twenty or forty percent of the diet. The dietary protein sources used were purified protein. The diets were fed to the same mice for one week each with a fecal sample collected at the end of each week. The diets were fed in this order: standard chow, 20% soy, 20% casein, 20% rice, 40% soy, 20% yeast, 40% casein, 20% pea, 20% egg white protein, 20% chicken bone broth, and lastly at the end of the experiment half of the mice were fed the 20% soy and half the mice the 20% casein diet again as a control. We did not collect fecal samples for the chicken bone broth diet as the diet was stopped prematurely due to diet intolerance. 12 germ-free mice (6 female, 6 male) in four cages were used. 12 mice with a conventional gut microbiota in four cages were used (6 female, 6 male). One germ-free mouse was found dead after diet 5 (20% yeast) and one conventional mouse was sacrificed after the second diet (20% casein). No sample could be collected from one of the conventional mice after the 20% egg white diet.

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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.

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Labeling Escherichia coli to saturation with 2.5 % of 15N ammonium in two conditions (aerobic and anaerobic) 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 after labeling them with stable isotope-labeled substrates. For this dataset Escherichia coli cultures were labeled with 2.5 % of 15N-labeled NH4Cl and grown either anaerobically or aerobically. Cultures of E. coli were grown in M9 minimal medium in which 2.5 % of the ammonium was replaced with 15N-labeled NH4Cl for >10 generations to achieve close to complete labeling of cells. Triplicate cultures were grown. Please note that the unlabeled ammonium that was used of course had a natural content of 15N of around 0.4 %, thus the 0% added label samples have an actual 15N content of 0.4 % 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.

2022-02-16 | PXD024288 | Pride

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