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Lisina T.O., Zverev A.O., Gladkov G.V., Kimeklis A.K., Orlova O.V., Kichko A.A., Andronov E.E. Metagenomic analysis of pro- and eukaryotic components of microbiota of biologically active preparation BAGS. Sel'skokhozyaistvennaya Biologiya [Agricultural Biology], 2025, Vol. 60, № 1, p. 96-109.
(how to cite this article)

doi: 10.15389/agrobiology.2025.1.96eng

UDC: 579.64:631.461.61:631.879.42

Acknowledgements:
We express our sincere gratitude to L.N. Paromenskaya for consultations on the history of the BAGS.
The research was performed using equipment of the Core Centrum Genomic Technologies, Proteomics and Cell Biology (ARRIAM).
Funded by the Russian Science Foundation, grant No. 23-16-00147

 

METAGENOMIC ANALYSIS OF PRO- AND EUKARYOTIC COMPONENTS OF MICROBIOTA OF BIOLOGICALLY ACTIVE PREPARATION BAGS

T.O. Lisina✉, A.O. Zverev, G.V. Gladkov, A.K. Kimeklis,
O.V. Orlova, A.A. Kichko, E.E. Andronov

All-Russian Research Institute for Agricultural Microbiology, 3, sh. Podbel’skogo, St. Petersburg, 196608 Russia, e-mail lisina-to@yandex.ru (✉ corresponding author), azver.bio@gmail.com, grgladkov@arriam.ru, kimeklis@gmail.com, falenki@hotmail.com, 2014arki@gmail.com, eeandr@gmail.com

Lisina T.O. orcid.org/0000-0003-1268-4166
Orlova O.V. orcid.org/0000-0002-2154-503Х
Zverev A.O. orcid.org/0000-0002-5315-8632
Kichko A.A. orcid.org/0000-0002-8482-6226
Gladkov G.V. orcid.org/0000-0002-5489-1414
Andronov E.E. orcid.org/0000-0002-5204-262Х
Kimeklis A.K. orcid.org/0000-0003-0348-7021

Final revision received September 13, 2024
Accepted November 29, 2024

The vast majority of microbial preparations are based on pure cultures of microorganisms. The use of such preparations is quite reasonable and effective for such functions as nitrogen fixation in symbiosis of rhizobia with legumes or biocontrol properties of bacilli. However, when it comes to soil processes that determine the cycle of biogenic elements, in particular the transformation of plant residues, the microbial preparations based on pure cultures are not stable and sufficiently effective, even when consortia containing a mixture of several microbial species are used. This is due to the fact that microbiological processes in soil are carried out not by individual species, but by microbial communities with complex network organization. Therefore, a more effective alternative is the mobilization of native cellulose-degrading communities in the form of microbial preparations. This is exactly the case with the microbial preparation BAGS (biologically active substrate on straw), the development of the precursor of which began at the All-Russian Research Institute of Agricultural Microbiology in the 1930s. In the present work the metagenomic data on the taxonomic composition of prokaryotic and eukaryotic communities of two consecutive batches of BAGS preparation, one of which acted as an inoculum, are presented for the first time. In addition, comparison of the microbial composition of mature BAGS, the major components used in its preparation (peat, straw) and soil as a source of humate-degrading bacteria made it possible to suggest the origin of major prokaryotic components of the microbiota of the preparation. The aim of the work was to use a metagenomic approach to study the taxonomic composition of the microbial consortium in two batches of BAGS and components for its production. We used ready mature BAGS microbial preparation obtained by composting peat-silage-mineral mixture with inoculum for 11 months which was the last of a series of perennial periodic renewals for at least 20 years, and mature BAGS from the previous 15-month composting that served as inoculum. Lme-softened sphagnum peat (village of Fornosovo, Leningrad Province) was 15 % decomposed, dry oat straw was shredded; soil was sod-podzolic light loamy (Belogorka settlement, Leningrad Province). For BAGS preparation, the peat was added with dolomite meal to pH 6.4, oat straw (10 % of peat weight), Azophoska (10 g of nitrogen/kg of straw) and inoculum (20 % of peat weight). The mixture was moistened to 60 % of full moisture capacity, mixed, packed into plastic 90 l containers and incubated for 11 months at 28 °С, periodically moistening and mixing. Microbiological analysis, including bacterial and fungal components, was performed by deep sequencing of the 16S rRNA gene (prokaryotes) and ITS (fungi) amplicon libraries. Data were analyzed using the dada2 package, and basic analyses (alpha and beta diversity, bar graphs and heatmaps) were performed using the phyloseq package and tidyverse in the R software environment. PERMANOVA analysis was performed using the vegan package. According to the analysis of the taxonomic composition of BAGS, the main components of bacterial communities of both batches of BAGS preparation, one of which acted as an inoculum, belonged to representatives of phyla Pseudomonadota (27-32 %), Planctomycetota (11-14 %) and Bacteroidota (10-11 %), and the main components of fungal communities were representatives of classes Sordariomycetes, Mucoromycetes and Leotiomycetes. By the end of the composting period, the bacterial part of the BAGS community appeared to be more stable than the fungal one and very close to the composition of the inoculum, while the eukaryotic communities were influenced by the peat microbiome. Meanwhile, years of BAGS reproduction have shaped its own unique microbiome. Approximately 12 % of all taxa in BAGS were unique and specific to it, and the microbial mass of unique taxa in the preparation community accounted for 93 % of their total number.

Keywords: BAGS preparation, inoculum, microbial community, prokaryotes, eukaryotes.

 

REFERENCES

  1. Kaminsky L.M., Trexler R.V., Malik R.J., Hockett K.L., Bell T.H. The inherent conflicts in developing soil microbial inoculants. Trends in Biotechnology, 2019, 37(2): 140-151 CrossRef
  2. Lazarev N.M. V sbornike: Trudy Vsesoyuznogo nauchno-issledovatel’skogo instituta sel’skokhozyaystvennoy mikrobiologii za 1941-1945 gg. [In: Proceedings of the All-Union Research Institute of Agricultural Microbiology for 1941-1945]. Moscow, 1949, 1: 5-22 (in Russ.).
  3. Bylinkina V.N. V sbornike: Trudy Vsesoyuznogo nauchno-issledovatel’skogo instituta sel’skokhozyaystvennoy mikrobiologii za 1941-1945 gg. [In: Proceedings of the All-Union Research Institute of Agricultural Microbiology for 1941-1945]. Moscow, 1949, 1: 59-69 (in Russ.).
  4. Datta R. Enzymatic degradation of cellulose in soil: a review. Heliyon, 2024, 10(1): e24022 CrossRef
  5. Meng L., Xu C., Wu F., Huhe. Microbial co-occurrence networks driven by low-abundance microbial taxa during composting dominate lignocellulose degradation. Science of The Total Environment, 2022, 845: 157197 CrossRef
  6. Miao Y., Lin Y., Chen Z., Zheng H., Niu Y., Kuzyakov Y., Liu D., Ding W. Fungal key players of cellulose utilization: Microbial networks in aggregates of long-term fertilized soils disentangled using 13C-DNA-stable isotope probing. Science of The Total Environment, 2022, 832: 155051 CrossRef
  7. Tom L. M., Aulitto M., Wu Y.-W., Deng K., Gao Y., Xiao N., Rodriguez B.G., Louime C., Northen T.R., Eudes A., Mortimer J.C., Adams P.D., Scheller H.V., Simmons B.A., Ceja-Navarro J.A., Singer S.W. Low-abundance populations distinguish microbiome performance in plant cell wall deconstruction. Microbiome, 2022, 10(1): 183 CrossRef
  8. Li T., Mazéas L., Sghir A., Leblon G., Bouchez T. Insights into networks of functional microbes catalysing methanization of cellulose under mesophilic conditions. Environmental Microbiology, 2009, 11(4): 889-904 CrossRef
  9. Schellenberger S., Kolb S., Drake H.L. Metabolic responses of novel cellulolytic and saccharolytic agricultural soil Bacteria to oxygen. Environmental Microbiology, 2010, 12(4): 845-861 CrossRef
  10. Schiml V.C., Delogu F., Kumar P., Kunath B., Batut B., Mehta S., Johnson J.E., Grüning B., Pope P.B., Jagtap P.D., Griffin T.J., Arntzen M.Ø. Integrative meta-omics in Galaxy and beyond. Environmental Microbiome, 2023, 18(1): 56 CrossRef
  11. Gladkov G.V., Kimeklis A.K., Afonin A.M., Lisina T.O., Orlova O.V., Aksenova T.S., Kichko A.A., Pinaev A.G., Andronov E.E. The structure of stable cellulolytic consortia isolated from natural lignocellulosic substrates. International Journal of Molecular Sciences, 2022, 23(18): 10779 CrossRef
  12. Provorov N.A., Andronov E.E., Kimeklis A.K., Onishchuk O.P., Igolkina A.A., Karasev E.S. Microevolution, speciation and macroevolution in rhizobia: Genomic mechanisms and selective patterns. Frontiers in Plant Science, 2022, 13: 1026943 CrossRef
  13. Hu J., Xue Y., Guo H., Gao M., Li J., Zhang S., Tsang Y.F. Design and composition of synthetic fungal-bacterial microbial consortia that improve lignocellulolytic enzyme activity. Bioresource Technology, 2017, 227: 247-255 CrossRef
  14. Puentes-Téllez P.E., Falcao Salles J. Construction of effective minimal active microbial consortia for lignocellulose degradation. Microbial Ecology, 2018, 76(2): 419 CrossRef
  15. Rodríguez C.A.D., Díaz-García L., Bunk B., Spröer C., Herrera K., Tarazona N.A., Rodriguez R.L.M., Overmann J., Jiménez D.J. Novel bacterial taxa in a minimal lignocellulolytic consortium and their potential for lignin and plastics transformation. ISME Communications, 2022, 2(1): 89 CrossRef
  16. Vinogradskiy S.N. Mikrobiologiya pochvy. Problemy i metody. 50 let issledovaniy [Soil microbiology. Problems and methods. 50 years of research]. Moscow, 1952 (in Russ.).
  17. Shul’gina O.N. V sbornike: Itogi nauchno-issledovatel’skikh rabot vsesoyuznogo instituta sel’skokhozyaystvennoy mikrobiologii za 1939 [In: Results of research work of the All-Union Institute of Agricultural Microbiology for 1939]. Leningrad, 1941: 35-67 (in Russ.).
  18. Lazarev N.M., Gladilovich B.R., Nikitina E.A. V sbornike: Dostizheniya nauki — sel’skokhozyaystvennomu proizvodstvu. Polevodstvo [In: Achievements of science — agricultural production. Field cultivation]. Leningrad, 1953: 122-126 (in Russ.).
  19. Beresneva V.N, Lazarev N.M. V sbornike: Mikrobiologiya na sluzhbe sel’skomu khozyaystvu [In: Microbiology in the service of agriculture]. Moscow, 1959: 44-51 (in Russ.).
  20. Bylinkina V.N., Movchan N.A. V sbornike: Trudy Vsesoyuznogo nauchno-issledovatel’skogo instituta sel’skokhozyaystvennoy mikrobiologii [In: Proceedings of the All-Union Research Institute of Agricultural Microbiology]. Moscow, 1960, XVI: 202-215 (in Russ.).
  21. Bylinkina V.N. Tezisy dokladov Vsesoyuznoy konferentsii po sel’skokhozyaystvennoy mikrobiologii [Abstracts of the All-Union Conference on Agricultural Microbiology]. Leningrad, 1963: 27-28 (in Russ.).
  22. Lazarev N.M, Rogacheva P.U., Timofeev S.G., Ponomarev I.P. Sposob polucheniya biologicheski aktivnogo grunta. A.s. 320471 MPK S05F 11/02,S05F 11/08. Vses. nauch.-issl. in-t sel’skokhozyaystvennoy mikrobiologii (RF). № 1333522/30-15. Zayavl. 26.05.69. Opubl. 04.11.1971. Byul. № 34 [Method for obtaining biologically active soil. A.s. 320471 IPC C05F 11//02, C05F 11//08. All-Russian Research Institute of Agricultural Microbiology (Russian Federation). No. 1333522/30-15. Claimed 05/26/69. Publ. 11/04/1971. Bull. No. 34](in Russ.).
  23. Gersh N.B., Kruglov Yu.V. V sb.: Trudy Vsesoyuznogo nauchno-issledovatel’skogo instituta sel’skokhozyaystvennoy mikrobiologii [In: Proceedings of the All-Union Research Institute of Agricultural Microbiology]. Leningrad, 1986, 56: 101-106 (in Russ.).
  24. Afanas’ev V.N., Gamova M.V., Garan’kina N.G., Kruglov Yu.V., Maksimov G.A., Paromenskaya L.N. Sposob polucheniya mikrobnogo preparata dlya utilizatsii pestitsidov, sposob utilizatsii pestitsidov (varianty) i ustroystvo dlya utilizatsii pestitsidov. A.s. 2279325 MPK V09S 1/10; S12M 1/00; S12M 1/10. Vses. nauch.-issl. in-t sel’skokhozyaystvennoy mikrobiologii (RU). № 2002114831/13. Zayavl. 06.06.2002. Opubl. 10.07.2006. Byul. № 19 [Method for obtaining a microbial preparation for pesticide utilization, a method for pesticide utilization (variants) and a device for pesticide utilization. A.s. 2279325 IPC B09C 1/10; C12M 1/00; C12M 1/10. All-Russian Research Institute of Agricultural Microbiology (RU). No. 2002114831/13. Claimed 06/06/2002. Publ. 07/10/2006. Bull. No. 19] (in Russ.).
  25. Dumova V.A., Osudar R.L., Paromenskaya L.N., Gamova M.V. Materialy VI Mezhdunarodnoy nauchnoy konferentsii «Sovremennoe sostoyanie i perspektivy razvitiya mikrobiologii i biotekhnologii» [Proc. VI Int. Conf. «Current state and development prospects of microbiology and biotechnology»]. Minsk, 2008, tom 1: 139-142 (in Russ.).
  26. Rusakova I.V., Oskovkin V.V. Agrokhimiya, 2016, 8: 56-61 (in Russ.).
  27. Rusakova I.V. Vladimirskiy zemledelets, 2021, 2(96): 34-40 (in Russ.).
  28. Pinaev A.G., Kichko A.A., Aksenova T.S., Safronova V.I., Kozhenkova E.V., Andronov E.E. RIAM: A universal accessible protocol for the isolation of high purity DNA from various soils and other humic substances. Methods and Protocols, 2022, 5(6): 99 CrossRef
  29. Caporaso J.G., Lauber C.L. Walters W.A., Berg-Lyons D., Lozupone C.A., Turnbaugh P.J., Fierer N., Knight R. Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample. Proceedings of the National Academy of Sciences, 2011, 108(Suppl_1): 4516-4522 CrossRef
  30. Toju H., Tanabe A.S., Yamamoto S., Sato H. High-coverage ITS primers for the DNA-based identification of ascomycetes and basidiomycetes in environmental samples. PLoS ONE, 2012, 7(7): e40863 CrossRef
  31. Callahan B.J., McMurdie P.J., Rosen M.J., Han A.W., Johnson A.J.A., Holmes S.P. DADA2: High-resolution sample inference from Illumina amplicon data. Nature Methods, 2016, 13: 581-583 CrossRef
  32. McMurdie P.J., Holmes S. phyloseq: An R package for reproducible interactive analysis and graphics of microbiome census data. PLoS ONE, 2013, 8(4): e61217 CrossRef
  33. Wickham H., Averick M., Bryan J., Chang W., McGowan L.D, François R., Grolemund G., Hayes A., Henry L., Hester J., Kuhn M., Pedersen T.L., Miller E., Bache S.M., Müller K., Ooms J., Robinson D., Seidel D.P., Spinu V., Takahashi K., Vaughan D., Wilke C., Woo K., Yutani H. Welcome to the Tidyverse. Journal of Open Source Software, 2019, 4(43): 1686 CrossRef
  34. Oksanen J., Simpson G., Blanchet F., Kindt R., Legendre P., Minchin P., O'Hara R., Solymos P., Stevens M., Szoecs E., Wagner H., Barbour M., Bedward M., Bolker B., Borcard D., Borman T., Carvalho G., Chirico M., De Caceres M., Durand S., Evangelista H., FitzJohn R., Friendly M., Furneaux B., Hannigan G., Hill M., Lahti L., McGlinn D., Ouellette M., Ribeiro Cunha E., Smith T., Stier A., Ter Braak C., Weedon J. Vegan: Community Ecology Package. R package version 2.7-0. 2025. Available: https://github.com/vegandevs/vegan. No date.
  35. Orlova O.V., Gladkov G.V., Zverev A.O., Shapkin V.M., Lisina T.O., Kurchak N., Kichko A.A., Arkhipchenko I.A., Andronov E.E. Dynamics of the pro- and eukaryotic microbiome of straw during its destruction under surface application. Sel'skokhozyaistvennayabiologiya[AgriculturalBiology], 2025, 60(1): 82-95 CrossRef
  36. Kers J.G., Saccenti E. The power of microbiome studies some consideration on which alfa and beta metrics to use and how to report results. Front. Microbiol., 2022, 12: 796025 CrossRef
  37. Wang X., Chi Y., Song S. Important soil microbiota's effects on plants and soils: a comprehensive 30-year systematic literature review. Front. Microbiol., 2024, 15: 1347745 CrossRef
  38. Hannula S.E., Ma H.K., Pérez-Jaramillo J.E., Pineda A., Bezemer T.M. Structure and ecological function of the soil microbiome affecting plant-soil feedbacks in the presence of a soil-borne pathogen. Environ. Microbiol., 2020, 22(2): 660-676 CrossRef
  39. Sun L., Li G., Zhao J., Zhang T., Liu J., Zhang J. Core microbiota drive multi-functionality of the soil microbiome in the Cinnamomum camphora coppice planting. BMC Microbiol., 2024, 24(1): 18CrossRef
  40. Buckley D.H., Huangyutitham V., Nelson T.A., Rumberger A., Thies J.E. Diversity of Planctomycetes in soil in relation to soil history and environmental heterogeneity. Appl. Environ. Microbiol., 2006, 72(7): 4522-4531 CrossRef Erratum in: Appl. Environ. Microbiol., 2006, 72(9): 6429.
  41. Wiegand S., Jogler M., Boedeker C., Pinto D., Vollmers J., Rivas-Marín E., Kohn T., Peeters S.H., Heuer A., Rast P., Oberbeckmann S., Bunk B., Jeske O., Meyerdierks A., Storesund J.E., Kallscheuer N.., Lücker S.., Lage O.M., Pohl T., Merkel B.J., Hornburger P., Müller R.W., Brümmer F., Labrenz M., Spormann A.M., Op den Camp H.J.M., Overmann J., Amann R., Jetten M.S.M., Mascher T., Medema M.H., Devos D.P., Kaster A.K., Øvreås L., Rohde M., Galperin M.Y., Jogler C. Cultivation and functional characterization of 79 planctomycetes uncovers their unique biology. Nat. Microbiol., 2020, 5(1):126-140 CrossRef
  42. Kaboré O.D., Godreuil S., Drancourt M. Planctomycetes as host-associated bacteria: a perspective that holds promise for their future isolations, by mimicking their native environmental niches in clinical microbiology Laboratories. Front. Cell. Infect. Microbiol., 2020, 10: 519301 CrossRef
  43. Rusakova I.V. Juvenis Scientia, 2018, 9: 4-9 (in Russ.).
  44. Rowińska P., Gutarowska B., Janas R., Szulc J. Biopreparations for the decomposition of crop residues. Microb. Biotechnol., 2024, 17(8): e14534 CrossRef
  45. Chernov T.I., Semenov M.V.Pochvovedenie, 2021, 12: 1506-1522 CrossRef (in Russ.).
  46. Orlova O.V., Chirak E.L., Vorob’ev N.I., Sviridova O.V., Lisina T.O., Andronov E.E. Taxonomic composition and organization of the microbial community of soddy-podzolic soils after application of straw of cereal crops and using of the Barkon biopreparation. Sel'skokhozyaistvennaya biologiya [Agricultural Biology], 2019, 54(1): 47-64 CrossRef

 

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