Preliminary Study into the Application of Metabolomics in Soil Discrimination
Article Sidebar
Page Numbers:
258-278
Digital Object Identifier:
10.58578/kijst.v2i2.6486
Viewed: 188 times
Downloaded: 105 times
LYAS Publisher cordially invites qualified professionals to serve as Editors or Reviewers. Your expertise will make an important contribution to maintaining and strengthening the academic quality of our publications. Interested applicants are kindly requested to complete the application form at the following link: Editors & Reviewers
Please feel free to contact us if you need any further information about the submission process or if you have any additional questions.
Authors:
Abdulwasiu Olawale Salaudeen1, Yemisi Ajoke Olawore2, Aishat Abdulkareem Yetunde3, Hajara Yakubu4, Abubakar Umar Dewa5 
Copyright :
Authors retain copyright and grant the journal right of first publication.
Main Article Content
Abstract
Soil metabolomics provides a comprehensive analysis of small-molecule metabolites (≤1.5 kDa) present in soil and offers insights into how environmental processes influence soil conditions. Although this technique has been applied to various soil-related studies, it remains underrepresented in the broader field of metabolomics, highlighting the need for further research. This study aims to characterize the soil metabolome across contrasting soil sites to evaluate the discriminating capacity of soil metabolomics and its potential as a soil quality indicator. Soil metabolites were extracted using methanol and dichloromethane and analyzed with an Agilent 1260 Infinity II liquid chromatography–mass spectrometry platform. A total of 307 compounds were positively identified, including steroids, saponins, amino acids, organothiophosphorus compounds, and fatty acids. Multivariate statistical tools, such as Partial Least Squares Discriminant Analysis (PLS-DA) score and loading plots, Variable Importance in Projection (VIP) scores, Significance Analysis of Microarrays (SAM), and heat mapping successfully discriminated the soil samples from four distinct sites. Among the identified metabolites, prolyl-hydroxyproline (ID 1817) had the highest VIP score (≈2.62) and emerged as a potential biomarker for differentiating soil types. These findings underscore the utility of metabolomics in soil characterization and its potential application in environmental monitoring and soil quality assessment.
Downloads
Article Details
Authors retain copyright and grant the journal right of first publication with the work simultaneously licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License that allows others to share the work with an acknowledgement of the work's authorship and initial publication in this journal.
References
Brown, R.W.; Chadwick, D.R.; Zang, H.; Jones, D.L. Use of Metabolomics to Quantify Changes in Soil Microbial Function in Response to Fertiliser Nitrogen Supply and Extreme Drought. Soil Biol. Biochem. 2021, 160, 108351. https://doi.org/10.1016/j.soilbio.2021.108351.
Chomel, M.; Guittonny‐Larchevêque, M.; Fernandez, C.; Gallet, C.; DesRochers, A.; Paré, D.; Jackson, B.G.; Baldy, V. Plant Secondary Metabolites: A Key Driver of Litter Decomposition and Soil Nutrient Cycling. J. Ecol. 2016, 104, 1527–1541. https://doi.org/10.1111/1365-2745.12644.
Jones, O.A.H.; Sdepanian, S.; Lofts, S.; Svendsen, C.; Spurgeon, D.J.; Maguire, M.L.; Griffin, J.L. Metabolomic Analysis of Soil Communities Can Be Used for Pollution Assessment. Environ. Toxicol. Chem. 2014, 33, 61–64. https://doi.org/10.1002/etc.2418.
Lehmann, J.; Bossio, D.A.; Kögel-Knabner, I.; Rillig, M.C. The Concept and Future Prospects of Soil Health. Nat. Rev. Earth Environ. 2020, 1, 544–553. https://doi.org/10.1038/s43017-020-0080-8.
Pereira, P.; Bogunovic, I.; Muñoz-Rojas, M.; Brevik, E.C. Soil Ecosystem Services, Sustainability, Valuation and Management. Curr. Opin. Environ. Sci. Health 2018, 5, 7–13. https://doi.org/10.1016/j.coesh.2017.12.003.
Bünemann, E.K.; Bongiorno, G.; Bai, Z.; Creamer, R.E.; De Deyn, G.; de Goede, R.; Fleskens, L.; Geissen, V.; Kuyper, T.W.; Mäder, P.; et al. Soil Quality–A Critical Review. Soil Biol. Biochem. 2018, 120, 105–125. https://doi.org/10.1016/j.soilbio.2018.01.030.
Prăvălie, R. Exploring the Multiple Land Degradation Pathways across the Planet. Earth-Sci. Rev. 2021, 220, 103689. https://doi.org/10.1016/j.earscirev.2021.103689.
Borrelli, P.; Robinson, D.A.; Panagos, P.; Lugato, E.; Yang, J.E.; Alewell, C.; Wuepper, D.; Montanarella, L.; Ballabio, C. Land Use and Climate Change Impacts on Global Soil Erosion by Water (2015–2070). Proc. Natl. Acad. Sci. USA 2020, 117, 21994–22001. https://doi.org/10.1073/pnas.2001403117.
Kikuchi, J.; Ito, K.; Date, Y. Environmental Metabolomics with Data Science for Investigating Ecosystem Homeostasis. Prog. Nucl. Magn. Reson. Spectrosc. 2018, 104, 56–88. https://doi.org/10.1016/j.pnmrs.2017.11.003.
Matich, E.K.; Chavez Soria, N.G.; Aga, D.S.; Atilla-Gokcumen, G.E. Applications of Metabolomics in Assessing Ecological Effects of Emerging Contaminants and Pollutants on Plants. J. Hazard. Mater. 2019, 373, 527–535. https://doi.org/10.1016/j.jhazmat.2019.02.084.
Pétriacq, P.; Williams, A.; Cotton, A.; McFarlane, A.E.; Rolfe, S.A.; Ton, J. Metabolite Profiling of Non‐Sterile Rhizosphere Soil. Plant J. 2017, 92, 147–162. https://doi.org/10.1111/tpj.13639.
van Dam, N.M.; Bouwmeester, H.J. Metabolomics in the Rhizosphere: Tapping into Belowground Chemical Communication. Trends Plant Sci. 2016, 21, 256–265. https://doi.org/10.1016/j.tplants.2016.01.008.
Bell, M.A.; McKim, U.; Sproule, A.; Tobalt, R.; Gregorich, E.; Overy, D.P. Extraction Methods for Untargeted Metabolomics Influence Enzymatic Activity in Diverse Soils. Sci. Total Environ. 2022, 828, 154433. https://doi.org/10.1016/j.scitotenv.2022.154433.
Swenson, T.L.; Jenkins, S.; Bowen, B.P.; Northen, T.R. Untargeted Soil Metabolomics Methods for Analysis of Extractable Organic Matter. Soil Biol. Biochem. 2015, 80, 189–198. https://doi.org/10.1016/j.soilbio.2014.10.007.
Simpson, M.J.; McKelvie, J.R. Environmental Metabolomics: New Insights into Earthworm Ecotoxicity and Contaminant Bioavailability in Soil. Anal. Bioanal. Chem. 2009, 394, 137–149. https://doi.org/10.1007/s00216-009-2612-4.
Rodríguez, A.; Castrejón-Godínez, M.L.; Salazar-Bustamante, E.; Gama-Martínez, Y.; Sánchez-Salinas, E.; Mussali-Galante, P.; Tovar-Sánchez, E.; Ortiz-Hernández, M.L. Omics Approaches to Pesticide Biodegradation. Curr. Microbiol. 2020, 77, 545–563. https://doi.org/10.1007/s00284-020-01916-5.
Patti, G.J.; Yanes, O.; Siuzdak, G. Innovation: Metabolomics: The Apogee of the Omics Trilogy. Nat. Rev. Mol. Cell Biol. 2012, 13, 263–269. https://doi.org/10.1038/nrm3314.
Wilson, I.; Plumb, R.; Granger, J.; Major, H.; Williams, R.; Lenz, E. HPLC-MS-Based Methods for the Study of Metabonomics. J. Chromatogr. B 2005, 817, 67–76. https://doi.org/10.1016/j.jchromb.2004.07.045.
Jones, O.A.H.; Maguire, M.L.; Griffin, J.L.; Dias, D.A.; Spurgeon, D.J.; Svendsen, C. Metabolomics and Its Use in Ecology. Aust. Ecol. 2013, 38, 713–720. https://doi.org/10.1111/aec.12019.
Tang, J. Microbial Metabolomics. Curr. Genom. 2011, 12, 391–403. https://doi.org/10.2174/138920211797248619.
Lehmann, J.; Hansel, C.M.; Kaiser, C.; Kleber, M.; Maher, K.; Manzoni, S.; Nunan, N.; Reichstein, M.; Schimel, J.P.; Torn, M.S.; et al. Persistence of Soil Organic Carbon Caused by Functional Complexity. Nat. Geosci. 2020, 13, 529–534. https://doi.org/10.1038/s41561-020-0612-3.
Fischer, H.; Meyer, A.; Fischer, K.; Kuzyakov, Y. Carbohydrate and Amino Acid Composition of Dissolved Organic Matter Leached from Soil. Soil Biol. Biochem. 2007, 39, 2926–2935. https://doi.org/10.1016/j.soilbio.2007.06.014.
Warren, C.R. Response of Osmolytes in Soil to Drying and Rewetting. Soil Biol. Biochem. 2014, 70, 22–32. https://doi.org/10.1016/j.soilbio.2013.12.008.
Kakumanu, M.L.; Cantrell, C.L.; Williams, M.A. Microbial Community Response to Varying Magnitudes of Desiccation in Soil: A Test of the Osmolyte Accumulation Hypothesis. Soil Biol. Biochem. 2013, 57, 644–653. https://doi.org/10.1016/j.soilbio.2012.08.014.
Roth, V.-N.; Dittmar, T.; Gaupp, R.; Gleixner, G. The Molecular Composition of Dissolved Organic Matter in Forest Soils as a Function of pH and Temperature. PLoS ONE 2015, 10, e0119188. https://doi.org/10.1371/journal.pone.0119188.
Baran, R.; Brodie, E.L.; Mayberry-Lewis, J.; Hummel, E.; Da Rocha, U.N.; Chakraborty, R.; Bowen, B.P.; Karaoz, U.; Cadillo-Quiroz, H.; Garcia-Pichel, F.; et al. Exometabolite Niche Partitioning among Sympatric Soil Bacteria. Nat. Commun. 2015, 6, 8289. https://doi.org/10.1038/ncomms9289.
Sumner, L.W.; Amberg, A.; Barrett, D.; Beale, M.H.; Beger, R.; Daykin, C.A.; Fan, T.W.-M.; Fiehn, O.; Goodacre, R.; Griffin, J.L.; et al. Proposed Minimum Reporting Standards for Chemical Analysis. Metabolomics 2007, 3, 211–221. https://doi.org/10.1007/s11306-007-0082-2.
Wellerdiek, M.; Winterhoff, D.; Reule, W.; Brandner, J.; Oldiges, M. Metabolic Quenching of Corynebacterium glutamicum: Efficiency of Methods and Impact of Cold Shock. Bioproc. Biosyst. Eng. 2009, 32, 581–592. https://doi.org/10.1007/s00449-008-0280-y.
Swenson, T.L.; Jenkins, S.; Bowen, B.P.; Northen, T.R. Untargeted Soil Metabolomics Methods for Analysis of Extractable Organic Matter. Soil Biol. Biochem. 2015, 80, 189–198. https://doi.org/10.1016/j.soilbio.2014.10.007.
Yao, X.; Nie, J.; Bai, R.; Sui, X. Amino Acid Transporters in Plants: Identification and Function. Plants 2020, 9, 972. https://doi.org/10.3390/plants9080972.
Li, F.; Dong, C.; Yang, T.; Bao, S.; Fang, W.; Lucas, W.J.; Zhang, Z. The Tea Plant CsLHT1 and CsLHT6 Transporters Take up Amino Acids, as a Nitrogen Source, from the Soil of Organic Tea Plantations. Hortic. Res. 2021, 8, 178. https://doi.org/10.1038/s41438-021-00615-x.
Feng, H.; Fan, X.; Miller, A.J.; Xu, G. Plant Nitrogen Uptake and Assimilation: Regulation of Cellular pH Homeostasis. J. Exp. Bot. 2020, 71, 4380–4392. https://doi.org/10.1093/jxb/eraa150.
Hamano, Y. Occurrence, Biosynthesis, Biodegradation, and Industrial and Medical Applications of a Naturally Occurring ε-Poly-L-Lysine. Biosci. Biotechnol. Biochem. 2011, 75, 1226–1233. https://doi.org/10.1271/bbb.110201.
Kielland, K. Landscape Patterns of Free Amino Acids in Arctic Tundra Soils. Biogeochemistry 1995, 31, 113–132. https://doi.org/10.1007/BF00000940.
Neshich, I.A.P.; Kiyota, E.; Arruda, P. Genome-Wide Analysis of Lysine Catabolism in Bacteria Reveals New Connections with Osmotic Stress Resistance. ISME J. 2013, 7, 2400–2410. https://doi.org/10.1038/ismej.2013.123.
Mohapatra, S.; Ahuja, A.K.; Deepa, M.; Sharma, D. Residues of Acephate and Its Metabolite Methamidophos in/on Mango Fruit (Mangifera indica L.). Bull. Environ. Contam. Toxicol. 2011, 86, 101–104. https://doi.org/10.1007/s00128-010-0154-2.
Syed, J.H.; Alamdar, A.; Mohammad, A.; Ahad, K.; Shabir, Z.; Ahmed, H.; Ali, S.M.; Sani, S.G.A.S.; Bokhari, H.; Gallagher, K.D.; et al. Pesticide Residues in Fruits and Vegetables from Pakistan: A Review of the Occurrence and Associated Human Health Risks. Environ. Sci. Pollut. Res. 2014, 21, 13367–13393. https://doi.org/10.1007/s11356-014-3117-z.