Progress and Challenges in Ocean Metaproteomics and Proposed Best Practices for Data Sharing

Saito, Mak A.; Bertrand, Erin M.; Duffy, Megan; Gaylord, David A.; Held, Noelle A.; Hervey, W. Judson; Hettich, Robert L.; Jagtap, Pratik; Janech, Michael G.; Kinkade, Danie; Leary, Dagmar H.; McIlvin, Matthew R.; Moore, Elizabeth Hernández; Morris, Robert M.; Neely, Benjamin A.; Nunn, Brook L.; Saunders, Jaclyn K.; Shepherd, Adam; Symmonds, Nicholas; Walsh, David A.

doi:10.1021/acs.jproteome.8b00761

Cited by 75 publications

(74 citation statements)

References 98 publications

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“…2) with 13 C 6 -lysine label to identify the newly synthesized proteins. Because analyses of metaproteomic libraries remain challenging 41 , we used flow sorting that guaranteed us targeted proteomic analyses of the two most abundant populations of sheath-water bacterioplankton (the 1 st and 2 nd population, Fig. 4a) enabling direct metabolic and growth assessment of the bacterioplankton majority.…”

Section: Proteins Synthesized In Situ By Dominant Cells Of the Sheathmentioning

confidence: 99%

Bacterioplankton reveal years-long retention of Atlantic deep-ocean water by the Tropic Seamount

Giljan

Kamennaya

Otto³

et al. 2020

Sci Rep

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Seamounts, often rising hundreds of metres above surrounding seafloor, obstruct the flow of deepocean water. While the retention of deep-water by seamounts is predicted from ocean circulation models, its empirical validation has been hampered by large scale and slow rate of the interaction. to overcome these limitations we use the growth of planktonic bacteria to assess the retention time of deep-ocean water by a seamount. the selected tropic Seamount in the north-eastern Atlantic is representative for the majority of isolated seamounts, which do not affect the surface ocean waters. We prove deep-water is retained by the seamount by measuring 2.4× higher bacterial concentrations in the seamount-associated or 'sheath'-water than in deep-ocean water unaffected by seamounts. Genomic analyses of flow-sorted, dominant sheath-water bacteria confirm their planktonic origin, whilst proteomic analyses of the sheath-water bacteria, isotopically labelled in situ, indicate their slow growth. According to our radiotracer experiments, it takes the sheath-water bacterioplankton 1.5 years to double their concentration. therefore, the seamount should retain the deep-ocean water for 1.8 years for the deep-ocean bacterioplankton to grow to the 2.4× higher concentration in the sheathwater. We propose that turbulent mixing of the seamount sheath-water stimulates bacterioplankton growth by increasing cell encounter rate with ambient dissolved organic molecules.The 1,000-year-long global thermohaline circulation 1 connects the bulk deep water of the modern World Ocean, irrespective of barriers erected by continents, islands and thousands of seamounts 2-4 . While continents and islands shape the circulation, seamounts affect this deep-water flow by creating enclosed circulation cells 5 , thereby reducing exchange between the so-called 'sheath-water' retained by seamounts and the surrounding deep water.This does not, however, mean that the sheath-water is stagnant. The interaction of seamounts with deep water currents and waves (internal and tidal) causes complex sheath-water dynamics 6 , specified by the unique geometry of individual seamounts 5 . The complexity arises from interactions of parallel, rapid, turbulent mixing at centimetre-scales on seamount slopes 7,8 and much slower flowing circulations (including Taylor columns) at the seamount-scale 9 . The complex sheath-water dynamics shapes seamount habitats for resident benthos and plankton 5,10,11 , causes erosion, controls sedimentation and affects ferromanganese crust formation on seamount slopes 12 .A number of seamounts peak close to the ocean surface and mix nutrient-rich deep water with the nutrient-poor surface water enhancing local phytoplankton growth 13 and causing a surface seamount effect 5,13,14 ; retention of the produced organic matter in the seamount proximity raises productivity and enriches diversity of the entire seamount-associated ecosystem 9,10,[15][16][17][18][19] . The majority of seamounts do not cause the surface seamount effect because their summits are ...

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Section: Proteins Synthesized In Situ By Dominant Cells Of the Sheathmentioning

confidence: 99%

Bacterioplankton reveal years-long retention of Atlantic deep-ocean water by the Tropic Seamount

Giljan

Kamennaya

Otto³

et al. 2020

Sci Rep

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“…However, DDA analysis methods seldom consider multiple peptides per MS/MS, which commonly occur in congested regions of LC gradients 10 or with complicated or mixed proteomes such as ocean, soil, or gut metaproteomics studies. 11 Despite the wide appeal of DIA for quantitative proteomics, one drawback is that many approaches commonly require generating comprehensive DDA-based spectrum libraries 12 before interpreting any DIA data. 9,13,14 While this approach produces high-performance libraries by guest on October 4, 2020…”

Section: Introductionmentioning

confidence: 99%

Acquiring and Analyzing Data Independent Acquisition Proteomics Experiments without Spectrum Libraries

Pino

Just²,

MacCoss

et al. 2020

Molecular & Cellular Proteomics

208

259

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Data independent acquisition (DIA) is an attractive alternative to standard shotgun proteomics methods for quantitative experiments. However, most DIA methods require collecting exhaustive, sample-specific spectrum libraries with data dependent acquisition (DDA) to detect and quantify peptides. In addition to working with non-human samples, studies of splice junctions, sequence variants, or simply working with small sample yields can make developing DDA-based spectrum libraries impractical. Here we illustrate how to acquire, queue, and validate DIA data without spectrum libraries, and provide a workflow to efficiently generate DIA-only chromatogram libraries using gas-phase fractionation (GPF). We present best-practice methods for collecting DIA data using Orbitrap-based instruments and develop an understanding for why DIA using an Orbitrap mass spectrometer should be approached differently than when using time-of-flight instruments. Finally, we discuss several methods for analyzing DIA data without libraries.

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“…Marine oligotrophic waters present significant challenges for metaproteomics study as protein extraction is hampered by the low bacterial biomass, which requires to filter important volume of water [23,24]. In situ physicochemical measurement confirmed the oligotrophic environmental conditions in which the studied picoplanktonic communities were sampled (Supplementary Information 1), therefore large volumes of water (60L/sample) were sequentially filtered onto both 0.8 and 0.2µm pore-size filters.…”

Section: Discussionmentioning

confidence: 83%

Diel Rhythms of Marine Picoplanktonic Communities Assessed by Comparative Metaproteomics

Géron

Werner

Wattiez

et al. 2020

Preprint

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Background Diel cycle is of enormous biological importance in that it imposes temporal structure on ecosystem productivity. In the world oceans, microorganisms form complex communities that carry out about half of photosynthesis and the bulk of life-sustaining nutrient cycling. Within these natural microbial assemblages, photoautotrophs, such as Cyanobacteria , display diel rhythmicity in gene expression. To what extent autotrophs and heterotrophs are impacted by light and dark oscillations and how this collectively influences community structure and functionality remains poorly documented. In this study, we compared eight day/night metaproteome profiles of Cyanobacteria and both free-living and attached bacterial fractions from picoplanktonic communities sampled over two consecutive days from the surface north-west Mediterranean Sea. Results Our results showed similar taxonomic structure in both free-living and particle-attached bacteria, dominated by Alphaproteobacteria and Gammaproteobacteria . Temporal rhythmicity in protein expression was observed in both Synechococcales and Rhodobacterales in light-dependent processes such as photosynthesis or UV-stress response. Other biological processes, such as phosphorus or amino acid metabolisms, were also found to cycle in phototrophs. In contrast, proteins from the ubiquitous Pelagibacterales remained stable independently of the day/night oscillations. Conclusion This work integrated for the first time diel comparative metaproteomics on both free-living and particle attached bacterial fractions in coastal oligotrophic environment. Our findings demonstrated a taxa-specific response to diel cycle with a more controlled protein regulation for phototrophs. This study provided additional evidences that timekeeping mechanisms might be widespread among bacteria, broadening our knowledge on diel microbial assemblage dynamics.

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Progress and Challenges in Ocean Metaproteomics and Proposed Best Practices for Data Sharing

Cited by 75 publications

References 98 publications

Bacterioplankton reveal years-long retention of Atlantic deep-ocean water by the Tropic Seamount

Bacterioplankton reveal years-long retention of Atlantic deep-ocean water by the Tropic Seamount

Acquiring and Analyzing Data Independent Acquisition Proteomics Experiments without Spectrum Libraries

Diel Rhythms of Marine Picoplanktonic Communities Assessed by Comparative Metaproteomics

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