Environmental Microbial Community Proteomics: Status, Challenges and Perspectives

Microbial community proteomics, also termed metaproteomics, is an emerging field within the area of microbiology, which studies the entire protein complement recovered directly from a complex environmental microbial community at a given point in time. Although it is still in its infancy, microbial community proteomics has shown its powerful potential in exploring microbial diversity, metabolic potential, ecological function and microbe-environment interactions. In this paper, we review recent advances achieved in microbial community proteomics conducted in diverse environments, such as marine and freshwater, sediment and soil, activated sludge, acid mine drainage biofilms and symbiotic communities. The challenges facing microbial community proteomics are also discussed, and we believe that microbial community proteomics will greatly enhance our understanding of the microbial world and its interactions with the environment.

[1]  T. Williams,et al.  Marine metaproteomics: deciphering the microbial metabolic food web. , 2014, Trends in microbiology.

[2]  Erin B. Taylor,et al.  Metaproteomic characterization of a soil microbial community following carbon amendment , 2010 .

[3]  Richard D. Smith,et al.  Transport functions dominate the SAR11 metaproteome at low-nutrient extremes in the Sargasso Sea , 2009, The ISME Journal.

[4]  A. Stensballe,et al.  Metaproteomics: Evaluation of protein extraction from activated sludge , 2014, Proteomics.

[5]  Dazhi Wang,et al.  Marine metaproteomics: current status and future directions. , 2014, Journal of proteomics.

[6]  Christine L. Sun,et al.  Community Genomic and Proteomic Analyses of Chemoautotrophic Iron-Oxidizing “Leptospirillum rubarum” (Group II) and “Leptospirillum ferrodiazotrophum” (Group III) Bacteria in Acid Mine Drainage Biofilms , 2009, Applied and Environmental Microbiology.

[7]  Gary J. Vora,et al.  Method development for metaproteomic analyses of marine biofilms. , 2012, Analytical chemistry.

[8]  Martin A. Jünger,et al.  Targeted proteome investigation via selected reaction monitoring mass spectrometry. , 2012, Journal of proteomics.

[9]  Andreas Richter,et al.  Proteome analysis of fungal and bacterial involvement in leaf litter decomposition , 2010, Proteomics.

[10]  Matthew Z. DeMaere,et al.  Metaproteogenomic analysis of a dominant green sulfur bacterium from Ace Lake, Antarctica , 2010, The ISME Journal.

[11]  D. Benndorf,et al.  Functional metaproteome analysis of protein extracts from contaminated soil and groundwater , 2007, The ISME Journal.

[12]  Sheng Lin,et al.  Characterization of metaproteomics in crop rhizospheric soil. , 2011, Journal of proteome research.

[13]  Manesh Shah,et al.  Environmental proteomics reveals early microbial community responses to biostimulation at a uranium‐ and nitrate‐contaminated site , 2013, Proteomics.

[14]  S. Ong,et al.  Comparing SILAC- and Stable Isotope Dimethyl-Labeling Approaches for Quantitative Proteomics , 2014, Journal of proteome research.

[15]  Jizhong Zhou,et al.  GeoChip-Based Analysis of the Functional Gene Diversity and Metabolic Potential of Microbial Communities in Acid Mine Drainage , 2010, Applied and Environmental Microbiology.

[16]  Matthew Z. DeMaere,et al.  An integrative study of a meromictic lake ecosystem in Antarctica , 2011, The ISME Journal.

[17]  Manesh Shah,et al.  Environmental proteomics of microbial plankton in a highly productive coastal upwelling system , 2011, The ISME Journal.

[18]  Ivan Mijakovic,et al.  Protein phosphorylation in bacterial signal transduction. , 2011, Biochimica et biophysica acta.

[19]  K. Riedel,et al.  Environmental proteomics: Analysis of structure and function of microbial communities , 2010, Proteomics.

[20]  M. Dai,et al.  Metaproteomic characterization of dissolved organic matter in the water column of the South China Sea , 2011 .

[21]  T. Urich,et al.  Microbial community structure and functioning in marine sediments associated with diffuse hydrothermal venting assessed by integrated meta-omics. , 2014, Environmental microbiology.

[22]  Kenneth H. Williams,et al.  Proteogenomic Monitoring of Geobacter Physiology during Stimulated Uranium Bioremediation , 2009, Applied and Environmental Microbiology.

[23]  Matthias Mann,et al.  Use of stable isotope labeling by amino acids in cell culture as a spike-in standard in quantitative proteomics , 2011, Nature Protocols.

[24]  J. Banfield,et al.  Proteogenomic approaches for the molecular characterization of natural microbial communities. , 2005, Omics : a journal of integrative biology.

[25]  Vincent J. Denef,et al.  Proteomics-inferred genome typing (PIGT) demonstrates inter-population recombination as a strategy for environmental adaptation. , 2009, Environmental microbiology.

[26]  M. Wagner,et al.  Use of Stable-Isotope Probing, Full-Cycle rRNA Analysis, and Fluorescence In Situ Hybridization-Microautoradiography To Study a Methanol-Fed Denitrifying Microbial Community , 2004, Applied and Environmental Microbiology.

[27]  I. Singleton,et al.  The potential of soil protein-based methods to indicate metal contamination , 2003 .

[28]  Paul Wilmes,et al.  A decade of metaproteomics: Where we stand and what the future holds , 2015, Proteomics.

[29]  E. Delong,et al.  Single-cell enabled comparative genomics of a deep ocean SAR11 bathytype , 2014, The ISME Journal.

[30]  L. Chan,et al.  Shotgun proteomics: Tools for analysis of marine particulate proteins , 2009 .

[31]  F. Bastida,et al.  Tracing changes in the microbial community of a hydrocarbon-polluted soil by culture-dependent proteomics. , 2010 .

[32]  Natalia Ivanova,et al.  Metagenomic analysis of two enhanced biological phosphorus removal (EBPR) sludge communities , 2006, Nature Biotechnology.

[33]  L. Choe,et al.  Metaproteomic analysis of a bacterial community response to cadmium exposure. , 2007, Journal of proteome research.

[34]  E. Delong,et al.  Microbial community transcriptomes reveal microbes and metabolic pathways associated with dissolved organic matter turnover in the sea , 2010, Proceedings of the National Academy of Sciences.

[35]  Jacque C. Young,et al.  Metaproteomics of a gutless marine worm and its symbiotic microbial community reveal unusual pathways for carbon and energy use , 2012, Proceedings of the National Academy of Sciences.

[36]  Vincent J. Denef,et al.  Systems Biology: Functional analysis of natural microbial consortia using community proteomics , 2009, Nature Reviews Microbiology.

[37]  M. Dai,et al.  Characterization of particulate organic matter in the water column of the South China Sea using a shotgun proteomic approach , 2010 .

[38]  Martin Taubert,et al.  Combining metagenomics with metaproteomics and stable isotope probing reveals metabolic pathways used by a naturally occurring marine methylotroph. , 2015, Environmental microbiology.

[39]  N. Jehmlich,et al.  Deforestation fosters bacterial diversity and the cyanobacterial community responsible for carbon fixation processes under semiarid climate: A metaproteomics study , 2015 .

[40]  Emanuel Schmid,et al.  Soil metaproteomics – Comparative evaluation of protein extraction protocols , 2012, Soil biology & biochemistry.

[41]  D. Walsh,et al.  Metaproteomic analysis of a winter to spring succession in coastal northwest Atlantic Ocean microbial plankton , 2014, The ISME Journal.

[42]  Joan García,et al.  Short-term harmful effects of ammonia nitrogen on activated sludge microfauna. , 2005, Water research.

[43]  T. Williams,et al.  A metaproteomic assessment of winter and summer bacterioplankton from Antarctic Peninsula coastal surface waters , 2012, The ISME Journal.

[44]  Alison S. Waller,et al.  Role for urea in nitrification by polar marine Archaea , 2012, Proceedings of the National Academy of Sciences.

[45]  R. Hettich,et al.  Geochemical, metagenomic and metaproteomic insights into trace metal utilization by methane-oxidizing microbial consortia in sulphidic marine sediments. , 2014, Environmental microbiology.

[46]  Aleksandar Cvetkovic,et al.  Microbial metalloproteomes are largely uncharacterized , 2010, Nature.

[47]  Jörg Bernhardt,et al.  Metaproteomics to unravel major microbial players in leaf litter and soil environments: Challenges and perspectives , 2013, Proteomics.

[48]  Timothy L. Tickle,et al.  Computational meta'omics for microbial community studies , 2013, Molecular systems biology.

[49]  E. Taylor,et al.  Microbial Protein in Soil: Influence of Extraction Method and C Amendment on Extraction and Recovery , 2010, Microbial Ecology.

[50]  Giacomo R. DiTullio,et al.  Multiple nutrient stresses at intersecting Pacific Ocean biomes detected by protein biomarkers , 2014, Science.

[51]  J. Casado-Vela,et al.  Differential plant proteome analysis by isobaric tags for relative and absolute quantitation (iTRAQ). , 2014, Methods in molecular biology.

[52]  R. Amann,et al.  Single-cell identification in microbial communities by improved fluorescence in situ hybridization techniques , 2008, Nature Reviews Microbiology.

[53]  F. Azam,et al.  Microbial structuring of marine ecosystems , 2007, Nature Reviews Microbiology.

[54]  J. Andersen,et al.  Comparative proteomics and activity of a green sulfur bacterium through the water column of Lake Cadagno, Switzerland. , 2011, Environmental microbiology.

[55]  Etienne Yergeau,et al.  Metaproteomics of aquatic microbial communities in a deep and stratified estuary , 2015, Proteomics.

[56]  E. Garman,et al.  A complex iron-calcium cofactor catalyzing phosphotransfer chemistry , 2014, Science.

[57]  J. Yates,et al.  The application of mass spectrometry to membrane proteomics , 2003, Nature Biotechnology.

[58]  Anders F. Andersson,et al.  Community proteogenomics highlights microbial strain-variant protein expression within activated sludge performing enhanced biological phosphorus removal , 2008, The ISME Journal.

[59]  Paul Wilmes,et al.  Metaproteomics Provides Functional Insight into Activated Sludge Wastewater Treatment , 2008, PloS one.

[60]  P. Wilmes,et al.  The application of two-dimensional polyacrylamide gel electrophoresis and downstream analyses to a mixed community of prokaryotic microorganisms. , 2004, Environmental microbiology.

[61]  David R Goodlett,et al.  Comparative metaproteomics reveals ocean-scale shifts in microbial nutrient utilization and energy transduction , 2010, The ISME Journal.

[62]  J. Bunkenborg,et al.  Identification of thioredoxin disulfide targets using a quantitative proteomics approach based on isotope-coded affinity tags. , 2008, Journal of proteome research.

[63]  P. Baldrian,et al.  Microbial genomics, transcriptomics and proteomics: new discoveries in decomposition research using complementary methods , 2014, Applied Microbiology and Biotechnology.

[64]  T. Williams,et al.  A metagenomic assessment of winter and summer bacterioplankton from Antarctica Peninsula coastal surface waters , 2012, The ISME Journal.

[65]  Steven P Gygi,et al.  Comparative evaluation of mass spectrometry platforms used in large-scale proteomics investigations , 2005, Nature Methods.

[66]  Vincent J. Denef,et al.  Strain-resolved community proteomics reveals recombining genomes of acidophilic bacteria , 2007, Nature.

[67]  C. Moore,et al.  Microbial proteins and oceanic nutrient cycles , 2014, Science.

[68]  F. Bastida,et al.  Metaproteomics of soils from semiarid environment: functional and phylogenetic information obtained with different protein extraction methods. , 2014, Journal of proteomics.

[69]  M. Rillig,et al.  Improving soil protein extraction for metaproteome analysis and glomalin‐related soil protein detection , 2009, Proteomics.

[70]  I. Hewson,et al.  Metaproteomic Survey of Six Aquatic Habitats: Discovering the Identities of Microbial Populations Active in Biogeochemical Cycling , 2014, Microbial Ecology.

[71]  H. Haflidason,et al.  Integrated metagenomic and metaproteomic analyses of an ANME-1-dominated community in marine cold seep sediments. , 2012, Environmental microbiology.

[72]  Sonya T. Dyhrman,et al.  Molecular approaches to diagnosing nutritional physiology in harmful algae: Implications for studying the effects of eutrophication , 2008 .

[73]  Manesh Shah,et al.  Metaproteomics Reveals Abundant Transposase Expression in Mutualistic Endosymbionts , 2013, mBio.

[74]  Paul Wilmes,et al.  Metaproteomics: studying functional gene expression in microbial ecosystems. , 2006, Trends in microbiology.

[75]  R. Helm,et al.  Investigating the Fate of Activated Sludge Extracellular Proteins in Sludge Digestion Using Sodium Dodecyl Sulfate Polyacrylamide Gel Electrophoresis , 2008, Water environment research : a research publication of the Water Environment Federation.

[76]  Andreas Richter,et al.  Who is who in litter decomposition? Metaproteomics reveals major microbial players and their biogeochemical functions , 2012, The ISME Journal.

[77]  P. Pevzner,et al.  Efficient de novo assembly of single-cell bacterial genomes from short-read data sets , 2011, Nature Biotechnology.

[78]  S. Mazard,et al.  Stable isotope probing to study functional components of complex microbial ecosystems. , 2014, Methods in molecular biology.

[79]  F. Chen,et al.  Metaproteomic analysis of Chesapeake Bay microbial communities , 2005, Saline systems.

[80]  D. recherche,et al.  Environmental OMICS: Current Status and Future Directions , 2013 .

[81]  N. Jehmlich,et al.  The ecological and physiological responses of the microbial community from a semiarid soil to hydrocarbon contamination and its bioremediation using compost amendment. , 2016, Journal of proteomics.

[82]  Timothy J Griffin,et al.  Deep metaproteomic analysis of human salivary supernatant , 2012, Proteomics.

[83]  Haibin Wang,et al.  Comparative Metaproteomic Analysis on Consecutively Rehmannia glutinosa-Monocultured Rhizosphere Soil , 2011, PloS one.

[84]  J. Banfield,et al.  Community Proteomics of a Natural Microbial Biofilm , 2005, Science.

[85]  J. Bettmer.  Application of isotope dilution ICP–MS techniques to quantitative proteomics , 2010, Analytical and bioanalytical chemistry.

[86]  Véronique Monnet,et al.  Shotgun metaproteomic profiling of biomimetic anaerobic digestion processes treating sewage sludge , 2015, Proteomics.

[87]  Christopher S. Miller,et al.  Fluctuations in Species-Level Protein Expression Occur during Element and Nutrient Cycling in the Subsurface , 2013, PloS one.

[88]  William A. Siebold,et al.  SAR11 clade dominates ocean surface bacterioplankton communities , 2002, Nature.