Advances in metaproteomic profiling of molecular microbiology and environmental responses

Kavya Dashora1,a, Vijai Kumar Gupta2, Gyan Datta Tripathi1, Zoya Javed1, Meghana Gattupalli1

Systems Microbiology and Biomanufacturing ›› 2024, Vol. 4 ›› Issue (2) : 463-472. DOI: 10.1007/s43393-023-00231-x
Review

Advances in metaproteomic profiling of molecular microbiology and environmental responses

  • Kavya Dashora1,a, Vijai Kumar Gupta2, Gyan Datta Tripathi1, Zoya Javed1, Meghana Gattupalli1
Author information +
History +

Abstract

In the present review, the application of metaproteomics is highlighted to understand the microbial species under different environmental conditions. As the environmental conditions are changing because of natural and anthropogenic activities, the molecular microbiology of the environment is also affected. The proteins are essential molecules expressed by the microorganism under environmental stresses, which are extracted and analyzed for the studies. Metaproteomics based on the molecular microbial ecology is still at the very incipient stage but has a strong potential over other non-omics and omics methods.

Keywords

Protein / Environment / Mass spectrophotometry / Microbiology

Cite this article

Download citation ▾
Kavya Dashora, Vijai Kumar Gupta, Gyan Datta Tripathi, Zoya Javed, Meghana Gattupalli. Advances in metaproteomic profiling of molecular microbiology and environmental responses. Systems Microbiology and Biomanufacturing, 2024, 4(2): 463‒472 https://doi.org/10.1007/s43393-023-00231-x

References

1.
Abiraami TV, Singh S, Nain L. Soil metaproteomics as a tool for monitoring functional microbial communities: promises and challenges. Rev Environ Sci Bio/Technology, 2020, 19(1): 73-102
2.
Starke R, Jehmlich N, Bastida F. Using proteins to study how microbes contribute to soil ecosystem services: the current state and future perspectives of soil metaproteomics. J Proteomics, 2019, 198: 50-58,
3.
Dominati E, Patterson M, Mackay A. A framework for classifying and quantifying the natural capital and ecosystem services of soils. Ecol Econ, 2010, 69(9): 1858-1868,
4.
Bastida F, Moreno JL, Nicolas C, Hernandez T, Garcia C. Soil metaproteomics: a review of an emerging environmental science. Significance, methodology and perspectives. Eur J Soil Sci, 2009, 60(6): 845-859
5.
Mueller RS, Pan C. Chapter Fifteen - Sample Handling and Mass Spectrometry for Microbial Metaproteomic Analyses. In: DeLong EFBTM in E, ed. Microbial Metagenomics, Metatranscriptomics, and Metaproteomics. Vol 531. Academic Press; 2013:289–303. doi:https://doi.org/10.1016/B978-0-12-407863-5.00015-0
6.
Shrestha HK, Appidi MR, Villalobos Solis MI, et al.. Metaproteomics reveals insights into microbial structure, interactions, and dynamic regulation in defined communities as they respond to environmental disturbance. BMC Microbiol, 2021, 21(1): 1-17
7.
Bharagava RN, Purchase D, Saxena G, Mulla SI. Chapter 26 - Applications of Metagenomics in Microbial Bioremediation of Pollutants: From Genomics to Environmental Cleanup. In: Das S, Dash HRBTMD in the GE, eds. Academic Press; 2019:459–477. doi:https://doi.org/10.1016/B978-0-12-814849-5.00026-5
8.
Dashora K, Gattupalli M, Javed Z, et al.. Leveraging multiomics approaches for producing lignocellulose degrading enzymes. Cell Mol Life Sci, 2022, 79(2): 1-15,
9.
Junge K, Cameron K, Nunn B. Chapter 12 - Diversity of Psychrophilic Bacteria in Sea and Glacier Ice Environments—Insights Through Genomics, Metagenomics, and Proteomics Approaches. In: Das S, Dash HRBTMD in the GE, eds. Academic Press; 2019:197–216. doi:https://doi.org/10.1016/B978-0-12-814849-5.00012-5
10.
Srivastava N, Gupta B, Gupta S, Danquah MK, Sarethy IP. Chapter 6 - Analyzing Functional Microbial Diversity: An Overview of Techniques. In: Das S, Dash HRBTMD in the GE, eds. Academic Press; 2019:79–102. doi:https://doi.org/10.1016/B978-0-12-814849-5.00006-X
11.
Panigrahi S, Velraj P, Subba Rao T. Chapter 21 - Functional Microbial Diversity in Contaminated Environment and Application in Bioremediation. In: Das S, Dash HRBTMD in the GE, eds. Academic Press; 2019:359–385. doi:https://doi.org/10.1016/B978-0-12-814849-5.00021-6
12.
Zampieri E, Chiapello M, Daghino S, Bonfante P, Mello A. Soil metaproteomics reveals an inter-kingdom stress response to the presence of black truffles. Sci Rep, 2016, 6: 25773, pmcid: 4861934
13.
Vogel TM, Hirsch PR, Simonet P, et al.. Advantages of the metagenomic approach for soil exploration: reply from Vogel et al.. Nat Rev Microbiol, 2009, 7(10): 756-757
14.
Qian C, Hettich RL. Optimized extraction method to remove humic acid interferences from soil samples prior to microbial proteome measurements. J Proteome Res, 2017, 16(7): 2537-2546,
15.
Lau MCY, Harris RL, Oh Y, Yi MJ, Behmard A, Onstott TC. Taxonomic and functional compositions impacted by the quality of metatranscriptomic assemblies. Front Microbiol. Published online 2018:1235
16.
Gutleben J, Chaib De Mares M, Van Elsas JD, Smidt H, Overmann J, Sipkema D. The multi-omics promise in context: from sequence to microbial isolate. Crit Rev Microbiol, 2018, 44(2): 212-229,
17.
Picotti P, Aebersold R. Selected reaction monitoring–based proteomics: workflows, potential, pitfalls and future directions. Nat Methods, 2012, 9(6): 555-566,
18.
Kleiner M. Metaproteomics: much more than measuring gene expression in microbial communities. Msystems, 2019, 4(3): e00115-e119, pmcid: 6529545
19.
Muth T, Renard BY, Martens L. Metaproteomic data analysis at a glance: advances in computational microbial community proteomics. Expert Rev Proteomics, 2016, 13(8): 757-769,
20.
Murray AE, Freudenstein J, Gribaldo S, et al.. Roadmap for naming uncultivated Archaea and bacteria. Nat Microbiol, 2020, 5(8): 987-994, pmcid: 7381421
21.
Bahram M, Hildebrand F, Forslund SK, et al.. Structure and function of the global topsoil microbiome. Nature, 2018, 560(7717): 233-237,
22.
Parks DH, Rinke C, Chuvochina M, et al.. Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life. Nat Microbiol, 2017, 2(11): 1533-1542,
23.
Ogunseitan OA. Direct extraction of proteins from environmental samples. J Microbiol Methods, 1993, 17(4): 273-281
24.
Singleton I, Merrington G, Colvan S, Delahunty JS. The potential of soil protein-based methods to indicate metal contamination. Appl Soil Ecol, 2003, 23(1): 25-32
25.
Wilmes P, Wexler M, Bond PL. Metaproteomics provides functional insight into activated sludge wastewater treatment. PLoS ONE, 2008, 3(3), pmcid: 2289847
26.
Callister SJ, Fillmore TL, Nicora CD, et al.. Addressing the challenge of soil metaproteome complexity by improving metaproteome depth of coverage through two-dimensional liquid chromatography. Soil Biol Biochem, 2018, 125: 290-299
27.
Speda J, Johansson MA, Carlsson U, Karlsson M. Assessment of sample preparation methods for metaproteomics of extracellular proteins. Anal Biochem, 2017, 516: 23-36,
28.
Redmile-Gordon MA, Armenise E, White RP, Hirsch PR, Goulding KWT. A comparison of two colorimetric assays, based upon Lowry and Bradford techniques, to estimate total protein in soil extracts. Soil Biol Biochem, 2013, 67: 166-173, pmcid: 3819989
29.
Michalski WP, Shiell BJ. Strategies for analysis of electrophoretically separated proteins and peptides. Anal Chim Acta, 1999, 383(1–2): 27-46
30.
Graves PR, Haystead TAJ. Molecular biologist’s guide to proteomics. Microbiol Mol Biol Rev, 2002, 66(1): 39-63, pmcid: 120780
31.
Patton WF. A thousand points of light: the application of fluorescence detection technologies to two-dimensional gel electrophoresis and proteomics. Electrophor An Int J, 2000, 21(6): 1123-1144
32.
Criquet S, Farnet A, Ferre E. Protein measurement in forest litter. Biol Fertil Soils, 2002, 35(5): 307-313,
33.
Link AJ, Eng J, Schieltz DM, et al.. Direct analysis of protein complexes using mass spectrometry. Nat Biotechnol, 1999, 17(7): 676-682,
34.
Bakker PAHM, Berendsen RL, Doornbos RF, Wintermans PCA, Pieterse CMJ. The rhizosphere revisited: root microbiomics. Front Plant Sci, 2013, 4: 165, pmcid: 3667247
35.
McNear DH Jr. The rhizosphere-roots, soil and everything in between. Nat Educ Knowl, 2013, 4(3): 1
36.
Vives-Peris V, de Ollas C, Gómez-Cadenas A, Pérez-Clemente RM. Root exudates: from plant to rhizosphere and beyond. Plant Cell Rep, 2020, 39(1): 3-17,
37.
Bais HP, Weir TL, Perry LG, Gilroy S, Vivanco JM. The role of root exudates in rhizosphere interactions with plants and other organisms. Annu Rev Plant Biol, 2006, 57(1): 233-266,
38.
Saleh D, Sharma M, Seguin P, Jabaji S. Organic acids and root exudates of Brachypodium distachyon: effects on chemotaxis and biofilm formation of endophytic bacteria. Can J Microbiol, 2020, 66(10): 562-575,
39.
Olanrewaju OS, Ayangbenro AS, Glick BR, Babalola OO. Plant health: feedback effect of root exudates-rhizobiome interactions. Appl Microbiol Biotechnol, 2019, 103(3): 1155-1166,
40.
Tartaglia M, Bastida F, Sciarrillo R, Guarino C. Soil metaproteomics for the study of the relationships between microorganisms and plants: a review of extraction protocols and ecological insights. Int J Mol Sci, 2020, 21(22): 8455, pmcid: 7697097
41.
Han X, He L, Xin L, Shan B, Ma B. PeaksPTM: mass spectrometry-based identification of peptides with unspecified modifications. J Proteome Res, 2011, 10(7): 2930-2936,
42.
Rrj A, Bm A, Mb B, et al.. Genome-Resolved Metaproteomics Decodes the Microbial and Viral Contributions to Coupled Carbon and Nitrogen Cycling in River Sediments. mSystems, 2022,
43.
Rane NR, Tapase S, Kanojia A, et al.. Molecular insights into plant–microbe interactions for sustainable remediation of contaminated environment. Bioresour Technol, 2022, 344,
44.
Liu D, Li M, Xi B, et al.. Metaproteomics reveals major microbial players and their biodegradation functions in a large-scale aerobic composting plant. Microb Biotechnol, 2015, 8(6): 950-960, pmcid: 4621448
45.
Guazzaroni ME, Herbst FA, Lores I, et al.. Metaproteogenomic insights beyond bacterial response to naphthalene exposure and bio-stimulation. ISME J, 2013, 7(1): 122-136,
46.
Chiapello M, Zampieri E, Mello A. A small effort for researchers, a big gain for soil metaproteomics. Front Microbiol, 2020, 11: 88, pmcid: 7010931
47.
Murase A, Yoneda M, Ueno R, Yonebayashi K. Isolation of extracellular protein from greenhouse soil. Soil Biol Biochem, 2003, 35(5): 733-736
48.
Chen S, Rillig MC, Wang W. Improving soil protein extraction for metaproteome analysis and glomalin-related soil protein detection. Proteomics, 2009, 9(21): 4970-4973,
49.
Chourey K, Jansson J, VerBerkmoes N, et al.. Direct cellular lysis/protein extraction protocol for soil metaproteomics. J Proteome Res, 2010, 9(12): 6615-6622,
50.
Mandalakis M, Panikov NS, Polymenakou PN, Sizova MV, Stamatakis A. A simple cleanup method for the removal of humic substances from soil protein extracts using aluminum coagulation. Environ Sci Pollut Res, 2018, 25: 23845-23856
51.
Gupta SK, Rai AK, Sarim KM, et al.. Metaproteomic data of maize rhizosphere for deciphering functional diversity. Data Br, 2019, 27
52.
Heyer R, Schallert K, Zoun R, Becher B, Saake G, Benndorf D. Challenges and perspectives of metaproteomic data analysis. J Biotechnol, 2017, 261: 24-36,
53.
Artursson V, Finlay RD, Jansson JK. Combined bromodeoxyuridine immunocapture and terminal-restriction fragment length polymorphism analysis highlights differences in the active soil bacterial metagenome due to Glomus mosseae inoculation or plant species. Environ Microbiol, 2005, 7(12): 1952-1966,
54.
Singer E, Wagner M, Woyke T. Capturing the genetic makeup of the active microbiome in situ. ISME J, 2017, 11(9): 1949-1963, pmcid: 5563950
55.
Saito MA, Bertrand EM, Duffy ME, et al.. Progress and challenges in ocean metaproteomics and proposed best practices for data sharing. J Proteome Res, 2019, 18(4): 1461-1476, pmcid: 7575043
56.
Lacerda CMR, Reardon KF. Environmental proteomics: applications of proteome profiling in environmental microbiology and biotechnology. Briefings Funct Genomics Proteomics, 2009, 8(1): 75-87

Accesses

Citations

Detail

Sections
Recommended

/