Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Intracellular metabolites from an experimental manipulation of marine microorganisms

ABSTRACT: The marine environment holds one of the largest pools of reduced organic carbon on Earth. Within this organic carbon are metabolites produced as a result of microbial activity. This project considers the effects of predation and viral lysis on the metabolites found in the surface ocean. Using seawater from the surface ocean, we experimentally manipulated levels of predation and viral lysis. At the beginning and end of the experiment, we sampled the intracellular and extracellular metabolites. The extracts were analyzed using liquid chromatography-based targeted and untargeted metabolomics methods that we have modified for use with marine samples. The untargeted metabolomics data revealed a complex mixture of organic compounds in all of the experimental treatments. However, changes in the majority of the features could not be linked to viral lysis or predation. Within the targeted metabolomics data, increased intracellular levels of osmolytes (glycine betaine, dimethylsulfoniopropionate, proline, and ectoine) were observed under conditions with limited grazing or viral lysis. The molecular insights derived here will explicitly inform our understanding of microbial processes in the surface ocean and the subsequent impacts on the global carbon cycle.

OTHER RELATED OMICS DATASETS IN: PXD018322PXD006154

INSTRUMENT(S): Thermo Scientific LTQ FT Ultra

PROVIDER: MTBLS461 | MetaboLights | 2017-05-23

REPOSITORIES: MetaboLights

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	mtab_dilution_ft_100.RAW	Raw
	mtab_dilution_ft_59.RAW	Raw
	mtab_dilution_ft_61.RAW	Raw
	mtab_dilution_ft_62.RAW	Raw
	mtab_dilution_ft_64.RAW	Raw

Items per page:

1 - 5 of 41

Similar Datasets

MetaboLights MTBLS461 - GNPS Intracellular metabolites from an experimental manipulation of marine microorganisms

Project description:This data set was downloaded from MetaboLights (http://www.ebi.ac.uk/metabolights/) accession number MTBLS461 Abstract:The marine environment holds one of the largest pools of reduced organic carbon on Earth. Within this organic carbon are metabolites produced as a result of microbial activity. This project considers the effects of predation and viral lysis on the metabolites found in the surface ocean. Using seawater from the surface ocean, we experimentally manipulated levels of predation and viral lysis. At the beginning and end of the experiment, we sampled the intracellular and extracellular metabolites. The extracts were analyzed using liquid chromatography-based targeted and untargeted metabolomics methods that we have modified for use with marine samples. The untargeted metabolomics data revealed a complex mixture of organic compounds in all of the experimental treatments. However, changes in the majority of the features could not be linked to viral lysis or predation. Within the targeted metabolomics data, increased intracellular levels of osmolytes (glycine betaine, dimethylsulfoniopropionate, proline, and ectoine) were observed under conditions with limited grazing or viral lysis. The molecular insights derived here will explicitly inform our understanding of microbial processes in the surface ocean and the subsequent impacts on the global carbon cycle.

2018-08-07 | MSV000082777 | GNPS

Comparative proteomics of Alteromonas macleodii cultured with sulfoquinovose

Project description:Sulfoquinovose (SQ) and sulfoquinovosyl glycerol (SQGro), derived from abundant membrane sulfolipids termed sulfoquinovosyl diacylglycerols (SQDG) produced by photosynthetic organisms, serve as sources of carbon and sulfur for bacteria. The conversion processes of these sulfoquinovosyl compounds (SQ, SQGro, and SQDG) within marine ecosystems, and their quantitative contributions to the marine organic matter pool, are poorly understood. We have identified Alteromonas macleodii, a cosmopolitan marine bacterium, as a novel organism capable of metabolizing SQ and SQGro. A. macleodii possesses a sulfoquinovosidase that converts SQGro to SQ, and is a member of a distinct clade within glycoside hydrolase family 31 distinct from other sulfoqinovosidases. The ubiquitous presence of sulfoquinovosidases and their transcripts throughout marine environments suggests active metabolism of sulfoquinovose glycosides, particularly in the sunlit surface ocean. Complementing these observations, we demonstrate that marine algae and cyanobacteria produce significant quantities of SQGro, and field samples from coastal and open ocean environments enabled estimation of the annual turnover of SQGro in the teragram range. Together with SQDG and SQ, these sulfoquinovosyl compounds constitute a substantial portion of the marine organic sulfur, estimated at around 1.5 petagrams of carbon turnover per annum. These findings reveal a vast, previously unappreciated pool of organosulfonates within the microbial food web that contributes significantly to the marine carbon and sulfur cycles.

2025-08-25 | PXD058686 | Pride

Comparative proteomics of Alteromonas macleodii cultured with sulfoquinovosyl glycerol

2025-08-25 | PXD058710 | Pride

Gene expression response to copper toxicity between coastal and open ocean strains of marine Synechococcus

2009-07-01 | GSE13910 | GEO

Analysis of sulfur-related transcription by Roseobacter communities using a taxon-specific functional gene microarray

Project description:The fraction of dissolved dimethylsulfoniopropionate (DMSPd) converted by marine bacterioplankton into the climate-active gas dimethylsulfide (DMS) varies widely in the ocean, with the factors that determine this value still largely unknown. One current hypothesis is that the ratio of DMS formation:DMSP demethylation is determined by DMSP availability, with 'availability' in both an absolute sense (i.e., concentration in seawater) and in a relative sense (i.e., proportionally to other labile organic S compounds) being proposed as the critical factor. We investigated these models during an experimentally-induced phytoplankton bloom using an environmental microarray targeting DMSP-related gene expression in the Roseobacter group, a taxon of marine bacteria known to play an important role in the surface ocean sulfur cycle. The array consisted of 1,578 probes to 431 genes, including those previously linked to DMSP degradation as well as core genes common in sequenced Roseobacter genomes. The prevailing pattern of Roseobacter gene expression showed depletion of DMSP-related transcripts during the peak of the bloom, despite the fact that absolute concentrations and flux of DMSP-related compounds were increasing. A likely interpretation is that DMSPd was assimilated by Roseobacter populations in proportion to its relative abundance in the organic matter pool (the “relative sense” hypothesis), and that it is not taken up in preference to other sources of labile organic sulfur or carbon produced during the bloom. The relative investment of the Roseobacter community in DMSP demethylation did not predict the fractional conversion of DMSP to DMS, however, suggesting a complex regulatory process that may involve multiple fates of DMSPd.

2010-08-05 | GSE21325 | GEO

Effects of nutrient enrichment on surface microbial community gene expression in the oligotrophic North Pacific Subtropical Gyre

Project description:Marine microbial communities are critical for biogeochemical cycles and the productivity of ocean ecosystems. Primary productivity, at the base of marine food webs, is constrained by nutrient availability in the surface ocean, and nutrient advection from deeper waters can fuel photosynthesis. In this study, we compared the transcriptional responses by surface microbial communities after experimental deep water mixing to the transcriptional patterns of in situ microbial communities collected with high-resolution automated sampling during a bloom in the North Pacific Subtropical Gyre. Transcriptional responses were assayed with the MicroTOOLs (Microbiological Targets for Ocean Observing Laboratories) marine environmental microarray, which targets all three domains of life and viruses. The experiments showed that mixing of deep and surface waters substantially affects the transcription of photosystem and nutrient response genes among photosynthetic taxa within 24 hours, and that there are specific responses associated with the addition of deep water containing particles (organisms and detritus) compared to filtered deep water. In situ gene transcription was most similar to that in surface water experiments with deep water additions, showing that in situ populations were affected by mixing of nutrients at the six sampling sites. Together, these results show the value of targeted metatranscriptomes for assessing the physiological status of complex microbial communities.

2018-09-03 | GSE109218 | GEO

Gene expression response to copper toxicity between coastal and open ocean strains of marine Synechococcus

Project description:Marine cyanobacteria are thought to be the most sensitive of the phytoplankton groups to copper toxicity, yet little is known of the transcriptional response of marine Synechococcus to copper shock. Global transcriptional response to two levels of copper shock was assayed in both a coastal and an open ocean strain of marine Synechococcus using whole genome expression microarrays. Both strains showed an osmoregulatory-like response, perhaps as a result of increasing membrane permeability. This could have implications for marine carbon cycling if copper shock leads to dissolved organic carbon leakage in Synechococcus. The two strains additionally showed a reduction in photosynthetic gene transcripts. Contrastingly, the open ocean strain showed a typical stress response whereas the coastal strain exhibited a more specific oxidative or heavy metal type response. In addition, the coastal strain activated more regulatory elements and transporters, many of which are not conserved in other marine Synechococcus strains and may have been acquired by horizontal gene transfer. Thus, tolerance to copper shock in some marine Synechococcus may in part be a result of an increased ability to sense and respond in a more specialized manner. In this series four conditions have been analyzed. These are moderate copper shock for Synechococcus sp. WH8102 and CC9311 (pCu 11.1 and pCu 10.1, respectively), and high copper shock for WH8102 and CC9311 (pCu 10.1 and pCu 9.1, respectively). For each slide, an experimental RNA sample was labeled with Cy3 or Cy5 and was hybridized with a reference RNA from a non-copper-shocked sample labeled with the other Cy dye. There are six or eight slides per condition, each with two biological replicates. There are three or four technical replicates for each biological replicate including at least one flip-dye comparison. Each slide contains six replicate spots per gene.

2010-05-17 | E-GEOD-13910 | biostudies-arrayexpress

Morphological plasticity in a sulfur-oxidizing bacterium from the SUP05 clade enhances dark carbon fixation

Project description:Sulfur-oxidizing bacteria from the SUP05 clade are abundant in anoxic and oxygenated marine waters that appear to lack reduced sources of sulfur for cell growth. This raises questions about how these chemosynthetic bacteria survive across oxygen and sulfur gradients and how their mode of survival impacts the environment. Here we use growth experiments, proteomics and cryo-electron tomography to show that a SUP05 isolate, Ca. Thioglobus autotrophicus, is several times larger, amorphous in shape and stores considerably more intracellular sulfur when it respires oxygen. We also show that these cells can use diverse sources of reduced organic and inorganic sulfur at submicromolar concentrations. Enhanced cell size, carbon content and metabolic activity of the aerobic phenotype are likely facilitated by a stabilizing surface-layer (S-layer) and an uncharacterized form of FtsZ-less cell division that supports morphological plasticity. The additional sulfur storage provides an energy source that allows cells to continue metabolic activity when exogenous sulfur sources are not available. This metabolic flexibility leads to the production of more organic carbon in the ocean than estimates that are based solely on their anaerobic phenotype.

2019-05-22 | PXD013243 | Pride

Insights into the controls on metabolite distributions along a latitudinal transect of the western Atlantic Ocean

Project description:<p>Metabolites, or the small organic molecules that are synthesized by cells during metabolism, comprise a complex and dynamic pool of carbon in the ocean. They are an essential form of information, linking genotype to phenotype at the individual, population and community levels of biological organization. Characterizing metabolite distributions inside microbial cells and dissolved in seawater is essential to understanding the controls on their production and fate, as well as their roles in shaping marine microbial food webs. Here, we apply a targeted metabolomics method to quantify particulate and dissolved distributions of a suite of biologically relevant metabolites including vitamins, amino acids, nucleic acids, osmolytes, and intermediates in biosynthetic pathways along a latitudinal transect in the western Atlantic Ocean. We find that, in the euphotic zone, most particulate or intracellular metabolites positively co-vary with the most abundant microbial taxa. In contrast, dissolved metabolites exhibited greater variability with differences in distribution between ocean regions. Although fewer particulate metabolites were detected below the euphotic zone, molecules identified in the deep ocean may be linked to preservation of organic matter or adaptive physiological strategies of deep-sea microbes. Based on the identified metabolite distributions, we propose relationships between certain metabolites and microbial populations, and find that dissolved metabolite distributions are not directly related to their particulate abundances.</p>

2021-08-27 | MTBLS1752 | MetaboLights

Purple sea urchin larvae alter their transcriptome in response to ocean acidification

Project description:In this research we present a transcriptomics analysis of the physiological response of a marine calcifier, Strongylocentrotus purpuratus, to ocean acidification, a decline in ocean pH that results from the absorption of anthropogenic carbon dioxide (CO2). Larvae were raised from fertilization to prism stage in seawater with elevated CO2 conditions based upon IPCC emissions scenario B1 (540ppm CO2) and A1FI (1020ppm CO2).

2009-08-14 | GSE13777 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data