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«IZVESTIYA IRKUTSKOGO GOSUDARSTVENNOGO UNIVERSITETA». SERIYA «BIOLOGIYA. ECOLOGIYA»
«THE BULLETIN OF IRKUTSK STATE UNIVERSITY». SERIES «BIOLOGY. ECOLOGY»
ISSN 2073-3372 (Print)

List of issues > Series «Biology. Ecology». 2025. Vol 54

Metagenomic Analysis of the Native Microbial Community Transformation in a Lignocellulosic Substrate by a Phosphorus-Nitrogen-Containing Ionic Liquid

Author(s)

D. A. Yarygin1, V. L. Mikhailenko1, Yu. S. Bukin1, 3, S. I. Verkhoturova2, A. A. Orlova1, A. A. Sigova1, G. V. Yurinova1, V. P. Salovarova1

1Irkutsk State University, Irkutsk, Russian Federation

2A. E. Favorsky Institute of Chemistry SB RAS, Irkutsk, Russian Federation 

3Limnological Institute SB RAS, Irkutsk, Russian Federation

Abstract
The pretreatment of lignocellulosic biomass with ionic liquids (ILs) is a promising strategy to enhance its subsequent bioconversion. However, the impact of these green solvents on the structure and diversity of the native microbial communities inhabiting the substrate remains poorly understood. This study investigates the effect of pretreatment with a phosphorus-nitrogen-containing ionic liquid (glycinium phosphate) on the taxonomic diversity of the indigenous microbiota of a lignocellulosic substrate (mixed-species bark) during a short-term (7-day) composting process at 30°C. The IL was synthesized via acid-base neutralization of glycine and phosphoric acid, and its structure was confirmed by ¹³C and ³¹P NMR spectroscopy. The substrate was treated with a 1% (w/w) aqueous solution of the IL, with untreated substrate serving as a control. Total community DNA was extracted from both control and treated samples and analyzed using whole-metagenome shotgun sequencing on an Illumina NovaSeq platform. Bioinformatic analysis, including taxonomic classification with Kraken2 and abundance estimation with Bracken, revealed a profound restructuring of the microbial community following IL treatment. A dramatic shift was observed at the phylum level, with a sharp decline in the relative abundance of Pseudomonadota (from 78.23% in the control to 22.77% in the treated sample) and a concurrent, substantial increase in Actinomycetota (from 17.10% to 68.57%). At the family and genus levels, this was characterized by a significant enrichment of Streptomycetaceae (Streptomyces spp.) and Microbacteriaceae (Leifsonia sp.), alongside a reduction in typically dominant taxa such as Burkholderiaceae and Nitrobacteraceae. Alpha diversity analysis indicated a decrease in community evenness at the genus level and an increase in species richness, suggesting both a selective pressure against sensitive taxa and the creation of niches for ILtolerant, spore-forming, or metabolically versatile actinobacteria. The observed selection of actinobacterial taxa, many of which are renowned for their lignocellulolytic potential, suggests that IL pretreatment may act as a modulator of the resident microbiota, potentially influencing subsequent decomposition processes. Further functional studies are required to confirm this hypothesis.
About the Authors

Yarygin Dmitriy Andreevich, Undergraduate Irkutsk State University 1, K. Marx st., Irkutsk, 664003, Russian Federation e-mail: mr.dmitry.yarygin@gmail.com

Mikhailenko Valentina Lvovna, Candidate of Science (Chemistry), Associate Professor Irkutsk State University 1, K. Marx st., Irkutsk, 664003, Russian Federation e-mail: mival63@gmail.com

Bukin Yuri Sergeevich, Candidate of Science (Biology), Senior Research Scientist Limnological Institute SB RAS 3, Ulan-Batorskaya st., Irkutsk, 664033, Russian Federation Associate Professor Irkutsk State University 1, K. Marx st., Irkutsk, 664003, Russian Federation e-mail: bukinyura@mail.ru

Verkhoturova Svetlana Ilyasovna, Candidate of Sciences (Chemistry), Senior Research Scientist A. E. Favorsky Irkutsk Institute of Chemistry SB RAS 1, Favorsky st., Irkutsk, 664033, Russian Federation e-mail: verkhoturova@irioch.irk.ru

Orlova Anastasiya Alekseevna, Undergraduate Irkutsk State University 1, K. Marx st., Irkutsk, 664003, Russian Federation e-mail: nastay.orlowa2002@yandex.ru

Sigova Anna Alexandrovna, Undergraduate Irkutsk State University 1, K. Marx st., Irkutsk, 664003, Russian Federation e-mail: sigovaann02@gmail.com

Yurinova Galina Valerievna, Candidate of Sciences (Biology), Associate Professor Irkutsk State University 1, K. Marx st., Irkutsk, 664003, Russian Federation e-mail: yurinova@yandex.ru

Salovarova Valentina Petrovna, Doctor of Sciences (Biology), Professor, Head of Department Irkutsk State University 1, K. Marx st., Irkutsk, 664003, Russian Federation e-mail: vsalovarova@gmail.com

For citation
Yarygin D.A., Mikhailenko V.L., Bukin Yu.S., Verkhoturova S.I., Orlova A.A., Sigova A.A., Yurinova G.V., Salovarova V.P. Metagenomic Analysis of the Native Microbial Community Transformation in a Lignocellulosic Substrate by a Phosphorus-Nitrogen-Containing Ionic Liquid. The Bulletin of Irkutsk State University. Series Biology. Ecology, 2025, vol. 54, pp. 23-37. https://doi.org/10.26516/2073-3372.2025.54.23 (in Russian)
Keywords
lignocellulosic substrate, ionic liquids, indigenous microbiota, metagenomics, Actinobacteria, Pseudomonadota, composting.
UDC
579.64:579.26:577.2.083
DOI
https://doi.org/10.26516/2073-3372.2025.54.23
References
  1. Chen H., Liu J., Chang X., Chen D., Xue Y., Liu P., Lin H., Han S. A review on the pretreatment of lignocellulose for high-value chemicals. Fuel Process. Technol., 2017, vol. 160, pp. 196-206. https://doi.org/10.1016/j.fuproc.2016.12.007
  2. Bolger A.M., Lohse M., Usadel B. Trimmomatic: A flexible trimmer for Illumina sequence data. Bioinformatics, 2014, vol. 30, no. 15, pp. 2114-2120. https://doi.org/10.1093/bioinformatics/btu170
  3. Lu J., Breitwieser F.P., Thielen P., Salzberg S.L. Bracken: Estimating species abundance in metagenomics data. PeerJ Comput. Sci., 2017, vol. 3, e104. https://doi.org/10.7717/peerj-cs.104
  4. Silva J.P., Ticona A.R.P., Hamann P.R.V., Quirino B.F., Noronha E.F. Deconstruction of Lignin: From Enzymes to Microorganisms. Molecules, 2021, vol. 26, no. 8, art. 2299. https://doi.org/10.3390/molecules26082299
  5. Hua B., Lü Y., Wang J., Wen B., Cao Y., Wang X., Cui Z. Dynamic changes in the composite microbial system MC1 during and following its rapid degradation of lignocellulose. Appl. Biochem. Biotechnol., 2014, vol. 172, no. 2, pp. 951-962. https://doi.org/10.1007/s12010-013-0566-7
  6. Deng Y., Wang S., Beadham I., Gao X., Ji M., Wang G., Zhang C., Ruan W. Effect of Soil Washing with an Amino-Acid-Derived Ionic Liquid on the Properties of Cd-Contaminated Paddy Soil. Toxics, 2023, vol. 11, no. 3, 288. https://doi.org/10.3390/toxics11030288
  7. Ma H., Beadham I., Ruan W., Zhang C., Deng Y. Enhancing rice straw compost with an amino acid-derived ionic liquid as additive. Biores. Technol., 2022, vol. 345, art. 126387. https://doi.org/10.1016/j.biortech.2021.126387
  8. Batista-García R.A., Del Rayo Sánchez-Carbente M., Talia P., Jackson S.A., O'Leary N.D., Dobson A.D.W., Folch-Mallol J.L. From lignocellulosic metagenomes to lignocellulolytic genes: Trends, challenges and future prospects. Biofuels, Bioproducts and Biorefining, 2016, vol. 10, no. 6, pp. 864-882. https://doi.org/10.1002/bbb.1709
  9. Fu D., Mazza G., Tamaki Y. Lignin Extraction from Straw by Ionic Liquids and Enzymatic Hydrolysis of the Cellulosic Residues. J. Agric. Food Chem., 2010, vol. 58, no. 5, pp. 2915-2922. https://doi.org/10.1021/jf903616y
  10. Lee S.H., Doherty T.V., Linhardt R.J., Dordick J.S. Ionic liquid-mediated selective extraction of lignin from wood leading to enhanced enzymatic cellulose hydrolysis. Biotechnol. Bioengineer., 2009, vol. 102, no. 5, pp. 1368-1376. https://doi.org/10.1002/bit.22179
  11. Kirchhecker S., Esposito D. Amino acid based ionic liquids: A green and sustainable perspective. Curr. Opin. Green Sustain. Chem., 2016, vol. 2, pp. 28-33. https://doi.org/10.1016/j.cogsc.2016.09.001
  12. Langmead B., Salzberg S.L. Fast gapped-read alignment with Bowtie 2. Nat. Meth., 2012, vol. 9, no. 4, pp. 357-359. https://doi.org/10.1038/nmeth.1923
  13. Yang H., Huang Y., Li K., Zhu P., Wang Y., Li X., Meng Q., Niu Q., Wang S., Li Q. Lignocellulosic depolymerization induced by ionic liquids regulating composting habitats based on metagenomics analysis. Environ. Sci. Pollut. Res., 2022, vol. 29, no. 50, pp. 76298-76309. https://doi.org/10.1007/s11356-022-21148-3
  14. Uju, Nakamoto A., Shoda Y., Goto M., Tokuhara W., Noritake Y., Katahira S., Ishida N., Ogino C., Kamiya N. Low melting point pyridinium ionic liquid pretreatment for enhancing enzymatic saccharification of cellulosic biomass. Bioresour. Technol., 2013, vol. 135, pp. 103-108. https://doi.org/10.1016/j.biortech.2012.06.096
  15. Wang C., Dong D., Wang H., Müller K., Qin Y., Wang H., Wu W. Metagenomic analysis of microbial consortia enriched from compost: New insights into the role of Actinobacteria in lignocellulose decomposition. Biotechnology for Biofuels, 2016, vol. 9, no. 1, art. 22. https://doi.org/10.1186/s13068-016-0440-2
  16. Antunes L.P., Martins L.F., Pereira R.V., Thomas A.M., Barbosa D., Lemos L.N., Silva G.M.M., Moura L.M.S., Epamino G.W.C., Digiampietri L.A., Lombardi K.C., Ramos P.L., Quaggio R.B., De Oliveira J.C.F., Pascon R.C., Cruz J.B.D., Da Silva A.M., Setubal J.C. Microbial community structure and dynamics in thermophilic composting viewed through metagenomics and metatranscriptomics. Sci. Rep., 2016, vol. 6, no. 1, 38915. https://doi.org/10.1038/srep38915
  17. Himmel M.E., Xu Q., Luo Y., Ding S.-Y., Lamed R., Bayer E.A. Microbial enzyme systems for biomass conversion: Emerging paradigms. Biofuels, 2010, vol. 1, no. 2, pp. 323-341. https://doi.org/10.4155/bfs.09.25
  18. Hou X. D., Smith T. J., Li N., Zong M. H. Novel renewable ionic liquids as highly effective solvents for pretreatment of rice straw biomass by selective removal of lignin. Biotechnol. Bioengineer., 2012, vol. 109, no. 10, p. 2484-2493. https://doi.org/10.1002/bit.24522
  19. Ojo A. An Overview of Lignocellulose and Its Biotechnological Importance in High-Value Product Production. Fermentation, 2023, vol. 9, no. 11, art. 990. https://doi.org/10.3390/fermentation9110990
  20. Oksanen J., Blanchet F.G., Kindt R., Legendre P., Minchin P.R., O’hara R.B., Simpson G.L., Solymos P., Stevens M.H.H., Szoecs E., Wagner H., Oksanen M.J. Package 'vegan'. Community Ecology Package, v. 2(9), 2013, pp. 1-295. Available at: https://github.com/vegandevs/vegan
  21. Hou Q., Ju M., Li W., Liu L., Chen Y., Yang Q. Pretreatment of Lignocellulosic Biomass with Ionic Liquids and Ionic Liquid-Based Solvent Systems. Molecules, 2017, vol. 22, no. 3, art. 490. https://doi.org/10.3390/molecules22030490
  22. Czarny J., Piotrowska-Cyplik A., Lewicki A., Zgoła-Grześkowiak A., Wolko Ł., Galant N., Syguda A., Cyplik P. The Toxic Effect of Herbicidal Ionic Liquids on Biogas-Producing Microbial Community. Int. J. Environ. Res. Publ. Health, 2019, vol. 16, no. 6, art. 916. https://doi.org/10.3390/ijerph16060916
  23. Vangeel T., Neiva D.M., Quilhó T., Costa R.A., Sousa V., Sels B.F., Pereira H. Tree bark characterization envisioning an integrated use in a biorefinery. Biomass Conversion and Biorefinery, 2023, vol. 13, no. 3, pp. 2029-2043. https://doi.org/10.1007/s13399-021-01362-8
  24. Wingett S.W., Andrews S. FastQ Screen: A tool for multi-genome mapping and quality control. F1000Research, 2018, vol. 7, art. 1338. https://doi.org/10.12688/f1000research.15931.2
  25. Wood D.E., Lu J., Langmead B. Improved metagenomic analysis with Kraken 2. Genome Biol., 2019, vol. 20, no. 1, art. 257. https://doi.org/10.1186/s13059-019-1891-0

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