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A robust metaproteomics pipeline for a holistic taxonomic and functional characterization of microbial communities from marine particles

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1002/mbo3.92openalex-snapshot

Taxonomic composition of the particle‐attached and free‐living bacterial assemblages in the N orthwest M editerranean S ea analyzed by pyrosequencing of the 16S rRNA

inferredcites →https://doi.org/10.1002/pmic.200900450openalex-snapshot

Environmental proteomics: Analysis of structure and function of microbial communities

inferredcites →https://doi.org/10.1002/pmic.201000590openalex-snapshot

Metaproteome analysis of sewage sludge from membrane bioreactors

inferredcites →https://doi.org/10.1002/pmic.201000679openalex-snapshot

Structure and function of the symbiosis partners of the lung lichen ( Lobaria pulmonaria L. Hoffm.) analyzed by metaproteomics

inferredcites →https://doi.org/10.1002/pmic.201500222openalex-snapshot

Proteomics of the Roseobacter clade, a window to the marine microbiology landscape

inferredcites →https://doi.org/10.1002/pmic.201700241openalex-snapshot

Impact of Extraction Methods on the Detectable Protein Complement of Metaproteomic Analyses of Marine Sediments

inferredcites →https://doi.org/10.1007/978-1-4939-8695-8_21openalex-snapshot

Sample Preparation for Metaproteome Analyses of Soil and Leaf Litter

inferredcites →https://doi.org/10.1007/s00248-006-9189-7openalex-snapshot

Diel and Seasonal Variations in Abundance, Activity, and Community Structure of Particle-Attached and Free-Living Bacteria in NW Mediterranean Sea

inferredcites →https://doi.org/10.1007/s11270-006-9196-9openalex-snapshot

Heavy Metals Pollution of the Atlantic Marine Environment by the Moroccan Phosphate Industry, as Observed through their Bioaccumulation in Ulva Lactuca

inferredcites →https://doi.org/10.1016/0967-0637(93)90129-qopenalex-snapshot

The abundance and significance of a class of large, transparent organic particles in the ocean

inferredcites →https://doi.org/10.1016/j.femsec.2005.01.008openalex-snapshot

Colonization and community dynamics of class Flavobacteria on diatom detritus in experimental mesocosms based on Southern Ocean seawater⋆

inferredcites →https://doi.org/10.1016/j.funeco.2017.08.009openalex-snapshot

Algal polysaccharide utilisation by saprotrophic planktonic marine fungi

inferredcites →https://doi.org/10.1016/j.gca.2012.01.002openalex-snapshot

Identifying and tracking proteins through the marine water column: Insights into the inputs and preservation mechanisms of protein in sediments

inferredcites →https://doi.org/10.1016/j.gene.2015.10.035openalex-snapshot

Databases of the marine metagenomics

inferredcites →https://doi.org/10.1016/j.gpb.2015.10.001openalex-snapshot

Marine Metagenome as a Resource for Novel Enzymes

inferredcites →https://doi.org/10.1016/j.jprot.2013.08.024openalex-snapshot

Marine metaproteomics: Current status and future directions

inferredcites →https://doi.org/10.1016/j.ymeth.2016.02.020openalex-snapshot

MEGAHIT v1.0: A fast and scalable metagenome assembler driven by advanced methodologies and community practices

inferredcites →https://doi.org/10.1021/ac025747hopenalex-snapshot

Empirical Statistical Model To Estimate the Accuracy of Peptide Identifications Made by MS/MS and Database Search

inferredcites →https://doi.org/10.1021/ac0341261openalex-snapshot

A Statistical Model for Identifying Proteins by Tandem Mass Spectrometry

inferredcites →https://doi.org/10.1021/ac801707sopenalex-snapshot

Experimental Approach for Deep Proteome Measurements from Small-Scale Microbial Biomass Samples

inferredcites →https://doi.org/10.1021/acs.jproteome.8b00761openalex-snapshot

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

inferredcites →https://doi.org/10.1021/pr100787qopenalex-snapshot

Direct Cellular Lysis/Protein Extraction Protocol for Soil Metaproteomics

inferredcites →https://doi.org/10.1023/a:1015809708632openalex-snapshot

Chemical and Biological Studies of Particulate Organic Matter in the Ocean

inferredcites →https://doi.org/10.1038/ismej.2010.4openalex-snapshot

Comparative metaproteomics reveals ocean-scale shifts in microbial nutrient utilization and energy transduction

inferredcites →https://doi.org/10.1038/ismej.2012.11openalex-snapshot

Who is who in litter decomposition? Metaproteomics reveals major microbial players and their biogeochemical functions

inferredcites →https://doi.org/10.1038/ismej.2012.169openalex-snapshot

Ecology of marine Bacteroidetes: a comparative genomics approach

inferredcites →https://doi.org/10.1038/ismej.2012.28openalex-snapshot

A metaproteomic assessment of winter and summer bacterioplankton from Antarctic Peninsula coastal surface waters

inferredcites →https://doi.org/10.1038/ismej.2013.144openalex-snapshot

Metagenomic analysis of size-fractionated picoplankton in a marine oxygen minimum zone

inferredcites →https://doi.org/10.1038/ismej.2016.113openalex-snapshot

Eukaryotic microbes, principally fungi and labyrinthulomycetes, dominate biomass on bathypelagic marine snow

inferredcites →https://doi.org/10.1038/ismej.2017.165openalex-snapshot

Recurrent patterns of microdiversity in a temperate coastal marine environment

inferredcites →https://doi.org/10.1038/nature02152openalex-snapshot

Contributions of microbial biofilms to ecosystem processes in stream mesocosms

inferredcites →https://doi.org/10.1038/nrmicro1747openalex-snapshot

Microbial structuring of marine ecosystems

inferredcites →https://doi.org/10.1038/nrmicro1935openalex-snapshot

Molecular eco-systems biology: towards an understanding of community function

inferredcites →https://doi.org/10.1038/s41396-018-0242-6openalex-snapshot

Polysaccharide utilization loci of North Sea Flavobacteriia as basis for using SusC/D-protein expression for predicting major phytoplankton glycans

inferredcites →https://doi.org/10.1046/j.1365-2958.1998.01062.xopenalex-snapshot

Flagellar and twitching motility are necessary for Pseudomonas aeruginosa biofilm development

inferredcites →https://doi.org/10.1073/pnas.1101591108openalex-snapshot

Bacterial community assembly based on functional genes rather than species

inferredcites →https://doi.org/10.1073/pnas.1708779115openalex-snapshot

Organic matter processing by microbial communities throughout the Atlantic water column as revealed by metaproteomics

inferredcites →https://doi.org/10.1074/mcp.m114.043463openalex-snapshot

A Metaproteomics Approach to Elucidate Host and Pathogen Protein Expression during Catheter-Associated Urinary Tract Infections (CAUTIs)

inferredcites →https://doi.org/10.1089/omi.2005.9.301openalex-snapshot

Proteogenomic Approaches for the MolecularCharacterization of Natural Microbial Communities

inferredcites →https://doi.org/10.1093/bioinformatics/btu153openalex-snapshot

Prokka: rapid prokaryotic genome annotation

inferredcites →https://doi.org/10.1093/nar/gky1106openalex-snapshot

The PRIDE database and related tools and resources in 2019: improving support for quantification data

inferredcites →https://doi.org/10.1099/ijs.0.02689-0openalex-snapshot

Kordia algicida gen. nov., sp. nov., an algicidal bacterium isolated from red tide

inferredcites →https://doi.org/10.1099/mic.0.034827-0openalex-snapshot

Involvement of motility and flagella in Bacillus cereus biofilm formation

inferredcites →https://doi.org/10.1101/gr.213959.116openalex-snapshot

metaSPAdes: a new versatile metagenomic assembler

inferredcites →https://doi.org/10.1111/1462-2920.12466openalex-snapshot

Comparison of bacterial communities on limnic versus coastal marine particles reveals profound differences in colonization

inferredcites →https://doi.org/10.1111/j.1462-2920.2005.00759.xopenalex-snapshot

Marine diatom species harbour distinct bacterial communities

inferredcites →https://doi.org/10.1111/j.1462-2920.2006.01152.xopenalex-snapshot

Whole genome analysis of the marine Bacteroidetes ‘ Gramella forsetii ’ reveals adaptations to degradation of polymeric organic matter

inferredcites →https://doi.org/10.1111/j.1462-2920.2007.01244.xopenalex-snapshot

High local and global diversity of Flavobacteria in marine plankton

inferredcites →https://doi.org/10.1111/j.1462-2920.2011.02555.xopenalex-snapshot

Genomic content of uncultured Bacteroidetes from contrasting oceanic provinces in the North Atlantic Ocean

inferredcites →https://doi.org/10.1111/j.1758-2229.2010.00179.xopenalex-snapshot

Ecological consequences of bacterioplankton lifestyles: changes in concepts are needed

inferredcites →https://doi.org/10.1126/science.1109070openalex-snapshot

Community Proteomics of a Natural Microbial Biofilm

inferredcites →https://doi.org/10.1126/science.1114057openalex-snapshot

Genome Streamlining in a Cosmopolitan Oceanic Bacterium

inferredcites →https://doi.org/10.1126/science.1140516openalex-snapshot

Signals from chloroplasts converge to regulate nuclear gene expression.

inferredcites →https://doi.org/10.1126/science.1218344openalex-snapshot

Substrate-Controlled Succession of Marine Bacterioplankton Populations Induced by a Phytoplankton Bloom

inferredcites →https://doi.org/10.1126/science.218.4574.795openalex-snapshot

Heterotrophic Bacteria and Bacterivorous Protozoa in Oceanic Macroaggregates

inferredcites →https://doi.org/10.1126/science.280.5364.694openalex-snapshot

Microbial Control of Oceanic Carbon Flux: The Plot Thickens

inferredcites →https://doi.org/10.1126/science.281.5374.200openalex-snapshot

Biogeochemical Controls and Feedbacks on Ocean Primary Production

inferredcites →https://doi.org/10.1126/science.281.5374.237openalex-snapshot

Primary Production of the Biosphere: Integrating Terrestrial and Oceanic Components

inferredcites →https://doi.org/10.1128/aem.62.2.316-322.1996openalex-snapshot

DNA recovery from soils of diverse composition

inferredcites →https://doi.org/10.1128/aem.66.2.578-587.2000openalex-snapshot

Dynamics of Bacterial Community Composition and Activity during a Mesocosm Diatom Bloom

inferredcites →https://doi.org/10.1128/aem.67.11.5134-5142.2001openalex-snapshot

Isolation of Novel Pelagic Bacteria from the German Bight and Their Seasonal Contributions to Surface Picoplankton

inferredcites →https://doi.org/10.1128/aem.70.11.6753-6766.2004openalex-snapshot

Changes in Bacterioplankton Composition under Different Phytoplankton Regimens

inferredcites →https://doi.org/10.1128/jb.01967-06openalex-snapshot

Flagellar Motility Is Critical for Listeria monocytogenes Biofilm Formation

inferredcites →https://doi.org/10.1128/mmbr.00007-12openalex-snapshot

Interactions between Diatoms and Bacteria

inferredcites →https://doi.org/10.1186/1471-2105-11-119openalex-snapshot

Prodigal: prokaryotic gene recognition and translation initiation site identification

inferredcites →https://doi.org/10.1371/journal.pbio.1001889openalex-snapshot

The Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP): Illuminating the Functional Diversity of Eukaryotic Life in the Oceans through Transcriptome Sequencing

inferredcites →https://doi.org/10.1371/journal.pone.0001426openalex-snapshot

A Model for Carbohydrate Metabolism in the Diatom Phaeodactylum tricornutum Deduced from Comparative Whole Genome Analysis

inferredcites →https://doi.org/10.1371/journal.pone.0001778openalex-snapshot

Metaproteomics Provides Functional Insight into Activated Sludge Wastewater Treatment

inferredcites →https://doi.org/10.3354/ame018275openalex-snapshot

Different community structure and temperature optima of heterotrophic picoplankton in various regions of the Southern Ocean

inferredcites →https://doi.org/10.3354/ame019001openalex-snapshot

Interactions between marine bacteria and axenic diatoms (Cylindrotheca fusiformis, Nitzschia laevis, and Thalassiosira weissflogii) incubated under various conditions in the lab

inferredcites →https://doi.org/10.3354/ame028175openalex-snapshot

Microbial ecology of organic aggregates in aquatic ecosystems

inferredcites →https://doi.org/10.3354/meps010257openalex-snapshot

The Ecological Role of Water-Column Microbes in the Sea

inferredcites →https://doi.org/10.3354/meps249069openalex-snapshot

Microbial dynamics on diatom aggregates in Øresund, Denmark

inferredcites →https://doi.org/10.3389/fmicb.2012.00035openalex-snapshot

Effects of Resource Chemistry on the Composition and Function of Stream Hyporheic Biofilms

inferredcites →https://doi.org/10.3389/fmicb.2012.00096openalex-snapshot

Redox Transformations of Iron at Extremely Low pH: Fundamental and Applied Aspects

inferredcites →https://doi.org/10.3389/fmicb.2017.00442openalex-snapshot

Complementary Metaproteomic Approaches to Assess the Bacterioplankton Response toward a Phytoplankton Spring Bloom in the Southern North Sea

inferredcites →https://doi.org/10.3389/fmicb.2019.00238openalex-snapshot

More Is Not Always Better: Evaluation of 1D and 2D-LC-MS/MS Methods for Metaproteomics

inferredcites →https://doi.org/10.4319/lo.1993.38.5.0924openalex-snapshot

Phylogenetic diversity of aggregate‐attached vs. free‐living marine bacterial assemblages

inferredcites →https://doi.org/10.7554/elife.11888openalex-snapshot

Recurring patterns in bacterioplankton dynamics during coastal spring algae blooms

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1016/j.jenvman.2025.124292openalex-snapshot

Advancing sustainable agriculture through multi-omics profiling of biosolids for safe application: A review

inferred← citeshttps://doi.org/10.1186/s12866-022-02441-0openalex-snapshot

Sediment-associated microbial community profiling: sample pre-processing through sequential membrane filtration for 16S rRNA amplicon sequencing

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