Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

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

ABSTRACT: 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.

INSTRUMENT(S): Thermo Scientific LTQ FT Ultra

ORGANISM(S): Sea Water

SUBMITTER: Longnecker

PROVIDER: MSV000082777 | GNPS | Tue Aug 07 10:48:00 BST 2018

REPOSITORIES: GNPS

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Shared Molecules

Only show the datasets with similarity scores above: 0.5

Threshold

0.5

Similar Datasets

Intracellular metabolites from an experimental manipulation of marine microorganisms

Project description: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.

2017-05-23 | MTBLS461 | MetaboLights

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

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

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.

2009-07-01 | GSE13910 | GEO

Using network analysis to discern compositional patterns in ultrahigh resolution mass spectrometry data of dissolved organic matter

Project description:RATIONALE: Marine dissolved organic matter (DOM) has long been recognized as a large and dynamic component of the global carbon cycle. Yet, DOM is chemically varied and complex and these attributes present challenges to researchers interested in addressing questions about the role of DOM in global biogeochemical cycles.METHODS: Organic matter extracts from seawater were analyzed by direct infusion with electrospray ionization into a Fourier transform ion cyclotron resonance mass spectrometer. Network analysis was used to quantify the number of chemical transformations between mass-to-charge values in each sample. The network of chemical transformations was calculated using the MetaNetter plug-in within Cytoscape. The chemical transformations serve as markers for the shared structural characteristics of compounds within complex DOM.RESULTS: Network analysis revealed that transformations involving selected sulfur-containing moieties and isomers of amino acids were more prevalent in the deep sea than in the surface ocean. Common chemical transformations were not significantly different between the deep sea and surface ocean. Network analysis complements existing computational tools used to analyze ultrahigh-resolution mass spectrometry data.CONCLUSIONS: This combination of ultrahigh-resolution mass spectrometry with novel computational tools has identified new potential building blocks of organic compounds in the deep sea, including the unexpected importance of dissolved organic sulfur components. The method described here can be readily applied by researchers to analyze heterogeneous and complex DOM.

2016-10-31 | MTBLS366 | MetaboLights

Emergence of metabolic coupling to the heterotroph Alteromonas promotes dark survival in Prochlorococcus

Project description:Prochlorococcus is found throughout the euphotic zone in the oligotrophic open ocean. Deep mixing and sinking in aggregates or while attached to particles can, however, transport cells below this sunlit zone, depriving them of light for extended periods of time and influencing their circulation via ocean currents. Viability of these cells over extended periods of darkness could shape the ecology and evolution of the Prochlorococcus collective. We have shown that when co-cultured with a heterotrophic microbe and subjected to repeated periods of extended darkness, Prochlorococcus cells develop a heritable dark-tolerant phenotype – through an apparent epigenetic mechanism – such that they survive longer periods of darkness. Here we examine this adaptation at the level of physiology and metabolism in co-cultures of dark-tolerant and parent strains of Prochlorococcus, each grown with the heterotroph Alteromonas under diel light:dark conditions. The relative abundance of Alteromonas is higher in dark-tolerant than parental co-cultures, while dark tolerant Prochlorococcus cells are also larger, contain less chlorophyll, and are less synchronized to the light:dark cycle. Meta-transcriptome analysis of the cultures further suggests that dark-tolerant co-cultures undergo a coupled shift in which Prochlorococcus uses more organic carbon and less photosynthesis, and Alteromonas uses more organic acids and fewer sugars. Collectively, the data suggest that dark adaptation involves a loosening of the coupling between Prochlorococcus metabolism and the light:dark cycle and a strengthening of the coupling between the carbon metabolism of Prochlorococcus and Alteromonas.

2024-04-23 | GSE264347 | GEO

M. sedula transcriptional response under heterotrophic, autotrophic, and mixotrophic growth conditions

Project description:To study mixotrophy, it is desirable to have an organism capable of growth in the presence and absence of both organic and inorganic carbon sources, as well as organic and inorganic energy sources. Metallosphaera sedula is an extremely thermoacidophilic archaeon which has been shown to grow in the presence of inorganic carbon and energy source supplements (autotrophy), organic carbon and energy source supplements (heterotrophy), and in the presence of organic carbon and inorganic energy source supplements. The recent elucidation of M. sedula’s inorganic carbon fixation cycle and its genome sequence further facilitate its use in mixotrophic studies. In this study, we grow M. sedula heterotrophically in the presence of organic carbon and energy sources (0.1% tryptone), autotrophically in the presence of inorganic carbon and energy sources (H2 + CO2), and “mixotrophically” in the presence of both organic and inorganic carbon and energy sources (0.1% tryptone + H2 + CO2 ) to characterize the nature of mixotrophy exhibited.

2009-11-01 | GSE14978 | GEO

SAR11 Cells Rely on Enzyme Multifunctionality to Transport and Metabolize a Range of Polyamine Compounds

Project description:In the ocean surface layer and cell culture, the polyamine transport protein PotD of SAR11 bacteria is often one of the most abundant proteins detected. Polyamines are organic cations at seawater pH produced by all living organisms and are thought to be an important component of dissolved organic matter (DOM) produced in planktonic ecosystems. We hypothesized that SAR11 cells uptake and metabolize multiple polyamines and use them as sources of carbon and nitrogen. Metabolic footprinting and fingerprinting were used to measure the uptake of five polyamine compounds (putrescine, cadaverine, agmatine, norspermidine, and spermidine) in two SAR11 strains that represent the majority of SAR11 cells in the surface ocean environment, Ca. Pelagibacter st. HTCC7211 and C. P. ubique st. HTCC1062. Both strains took up all five polyamines and concentrated them to micromolar or millimolar intracellular concentrations. Both strains could use most of the polyamines to meet their nitrogen requirements, but polyamines did not fully substitute for their requirements of glycine (or related compounds) or pyruvate (or related compounds). Our data suggests that potABCD transports all five polyamines and that spermidine synthase, speE, is reversible, catalyzing the breakdown of spermidine and norspermidine, in addition to its usual biosynthetic role. These findings provide support for the hypothesis that enzyme multifunctionality enables streamlined cells in planktonic ecosystems to increase the range of DOM compounds they metabolize.

2021-09-09 | MTBLS3146 | MetaboLights

Primed primary metabolism in systemic leaves: a functional systems analysis

Project description:During their co-evolution, plants have learned to counteract bacterial infection by preparing yet uninfected tissues for an enhanced defence response, the so-called systemic acquired resistance or priming response. Primed leaves express a wide range of genes that enhance the defence response once an infection takes place. While hormone-driven defence signalling and generation of defensive metabolites has been well studied, less focus has been set on the reorganization of primary metabolism in systemic leaves. Since primary metabolism plays an essential role for fuelling and optimizing defences in terms of providing energy and chemical building blocks, we investigated medium-term primed changes in primary metabolism at RNA and metabolite levels in systemic leaves of Arabidopsis thaliana plants that were locally infected with Pseudomonas syringae. While known defence genes were still activated 3-4 days after infection, we also found several parts of primary metabolism to be significantly altered. Nitrogen (N)-metabolism and content of amino acids and other N-containing metabolites were significantly reduced, whereas the organic acids fumarate and malate were strongly increased. We suggest that reduction of N-metabolites in systemic, yet non-infected leaves primes defence against bacterial infection by reducing the nutritional value of systemic tissue. The increased organic acids serve as a quickly available metabolic resource of energy and carbon-building blocks for the production of defence metabolites during subsequent secondary infections.

2018-02-13 | GSE101839 | GEO

SynWH7803_DOM

Project description:Dissolved organic matter prepared via PPL SPE from cultures of Synechococcus WH7803. Biological triplicate samples were prepared of DOM released via exudation, mechanical lysis, and viral lysis by phage S-SM1.

2018-01-26 | MSV000081980 | MassIVE

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