Evidence for quorum sensing and differential metabolite production by a marine bacterium in response to DMSP

Johnson, Winifred M.; Soule, Melissa C. Kido; Kujawinski, Elizabeth B.

doi:10.1038/ismej.2016.6

Cited by 122 publications

(121 citation statements)

References 62 publications

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“…It was estimated that on average 40% of the mangrove production is decomposed in the soil, 30% is exported from the forest, 10% is stored in the soil, and 9% is consumed by herbivores (Duarte and Cebrian, 1996). Hence, a major part of primary mangrove production is decomposed locally.…”

Section: Introductionmentioning

confidence: 99%

Potential for Sulfate Reduction in Mangrove Forest Soils: Comparison between Two Dominant Species of the Americas

2016

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Avicennia and Rhizophora are globally occurring mangrove genera with different traits that place them in different parts of the intertidal zone. It is generally accepted that the oxidizing capacity of Avicennia roots is larger than that of Rhizophora roots, which initiates more reduced conditions in the soil below the latter genus. We hypothesize that the more reduced conditions beneath Rhizophora stands lead to more active sulfate-reducing microbial communities compared to Avicennia stands. To test this hypothesis, we measured sulfate reduction traits in soil samples collected from neighboring Avicennia germinans and Rhizophora mangle stands at three different locations in southern Florida. The traits measured were sulfate reduction rates (SRR) in flow-through reactors containing undisturbed soil layers in the absence and presence of easily degradable carbon compounds, copy numbers of the dsrB gene, which is specific for sulfate-reducing microorganisms, and numbers of sulfate-reducing cells that are able to grow in liquid medium on a mixture of acetate, propionate and lactate as electron donors. At the tidal locations Port of the Islands and South Hutchinson Islands, steady state SRR, dsrB gene copy numbers and numbers of culturable cells were higher at the A. germinans than at the R. mangle stands, although not significantly for the numbers at Port of the Islands. At the non-tidal location North Hutchinson Island, results are mixed with respect to these sulfate reduction traits. At all locations, the fraction of culturable cells were significantly higher at the R. mangle than at the A. germinans stands. The dynamics of the initial SRR implied a more in situ active sulfate-reducing community at the intertidal R. mangle stands. It was concluded that in agreement with our hypothesis R. mangle stands accommodate a more active sulfate-reducing community than A. germinans stands, but only at the tidal locations. The differences between R. mangle and A. germinans stands were absent at the non-tidal, impounded location.

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Section: Introductionmentioning

confidence: 99%

Potential for Sulfate Reduction in Mangrove Forest Soils: Comparison between Two Dominant Species of the Americas

2016

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“…New categories of nonpredatory microbial alliances that release organic compounds into seawater are also being recognized. These include molecules in microbial cytosols and exudates (39,68) that serve as substrates, signaling molecules, and allelochemicals to neighboring microbes (69,70). Genes able to mediate microbial interactions have also been uncovered (71,72), including a high prevalence of virulence gene homologs in marine bacteria and archaea that could facilitate direct contact with eukaryotic plankton (73).…”

Section: How Do Microbe−microbe Relationships Influence Dom?mentioning

confidence: 99%

“…Correspondingly, nontargeted workflows are helping us to discover new molecules we didn't know to look for (33,39,70,105,135). Newly developed informatics approaches are supporting data mining across multiple studies and systems (136,137) (see Box 1).…”

Section: The Next Step: Prototypical Molecules Of the Marine Carbon Cmentioning

confidence: 99%

Deciphering ocean carbon in a changing world

Moran

Kujawinski

Stubbins

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

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266

233

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Dissolved organic matter (DOM) in the oceans is one of the largest pools of reduced carbon on Earth, comparable in size to the atmospheric CO 2 reservoir. A vast number of compounds are present in DOM, and they play important roles in all major element cycles, contribute to the storage of atmospheric CO 2 in the ocean, support marine ecosystems, and facilitate interactions between organisms. At the heart of the DOM cycle lie molecular-level relationships between the individual compounds in DOM and the members of the ocean microbiome that produce and consume them. In the past, these connections have eluded clear definition because of the sheer numerical complexity of both DOM molecules and microorganisms. Emerging tools in analytical chemistry, microbiology, and informatics are breaking down the barriers to a fuller appreciation of these connections. Here we highlight questions being addressed using recent methodological and technological developments in those fields and consider how these advances are transforming our understanding of some of the most important reactions of the marine carbon cycle.dissolved organic matter | marine microbes | cyberinfrastructure

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“…Targeted metabolomic studies focus on individual, well-characterized substrates whose concentrations and cycling can be followed precisely in incubations and in field settings. Advantages of such an approach are clear -in general, targeted work is quantitative, precise, and the metabolic role of identified substrates may already be well established (Amin et al, 2015;Johnson et al, 2016;Repeta et al, 2016;Heal et al, 2017).…”

Section: Introductionmentioning

confidence: 99%

“…These molecules have been identified in culture experiments and/or detected in field samples to highlight some of the important microbial interactions in the surface ocean (Amin et al, 2015;Johnson et al, 2016;Repeta et al, 2016;Heal et al, 2017;Kujawinski et al, 2017). Targeted metabolomic studies focus on individual, well-characterized substrates whose concentrations and cycling can be followed precisely in incubations and in field settings.…”

Section: Introductionmentioning

confidence: 99%

High-Resolution Liquid Chromatography Tandem Mass Spectrometry Enables Large Scale Molecular Characterization of Dissolved Organic Matter

et al. 2017

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Dissolved organic matter (DOM) is arguably one of the most complex exometabolomes on earth, and is comprised of thousands of compounds, that together contribute more than 600 × 10 15 g carbon. This reservoir is primarily the product of interactions between the upper ocean's microbial food web, yet abiotic processes that occur over millennia have also modified many of its molecules. The compounds within this reservoir play important roles in determining the rate and extent of element exchange between inorganic reservoirs and the marine biosphere, while also mediating microbe-microbe interactions. As such, there has been a widespread effort to characterize DOM using high-resolution analytical methods including nuclear magnetic resonance spectroscopy (NMR) and mass spectrometry (MS). To date, molecular information in DOM has been primarily obtained through calculated molecular formulas from exact mass. This approach has the advantage of being non-targeted, accessing the inherent complexity of DOM. Molecular structures are however still elusive and the most commonly used instruments are costly. More recently, tandem mass spectrometry has been employed to more precisely identify DOM components through comparison to library mass spectra. Here we describe a data acquisition and analysis workflow that expands the repertoire of high-resolution analytical approaches available to access the complexity of DOM molecules that are amenable to electrospray ionization (ESI) MS. We couple liquid chromatographic separation with tandem MS (LC-MS/MS) and a data analysis pipeline, that integrates peak extraction from extracted ion chromatograms (XIC), molecular formula calculation and molecular networking. This provides more precise structural characterization. Although only around 1% of detectable DOM compounds can be annotated through publicly available spectral libraries, community-wide participation in populating and annotating DOM datasets could rapidly increase the annotation rate and should be broadly encouraged. Our analysis also identifies shortcomings of the current Petras et al. LC-MS/MS Analysis of DOMdata analysis workflow that need to be addressed by the community in the future. This work will lay the foundation for an integrative, non-targeted molecular analysis of DOM which, together with next generation sequencing, meta-proteomics and physical data, will pave the way to a more comprehensive understanding of the role of DOM in structuring marine ecosystems.

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Evidence for quorum sensing and differential metabolite production by a marine bacterium in response to DMSP

Cited by 122 publications

References 62 publications

Potential for Sulfate Reduction in Mangrove Forest Soils: Comparison between Two Dominant Species of the Americas

Potential for Sulfate Reduction in Mangrove Forest Soils: Comparison between Two Dominant Species of the Americas

Deciphering ocean carbon in a changing world

High-Resolution Liquid Chromatography Tandem Mass Spectrometry Enables Large Scale Molecular Characterization of Dissolved Organic Matter

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