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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'skokhozyaistvennaya Biologiya [Agricultural Biology], 2025, Vol. 60, № 1, p. 82-95.
(how to cite this article)

doi: 10.15389/agrobiology.2025.1.82eng

UDC: 579.64:574.472:631.46

Acknowledgements:
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

 

DYNAMICS OF THE PRO- AND EUKARYOTIC MICROBIOME OF STRAW DURING ITS DESTRUCTION UNDER SURFACE APPLICATION

O.V. Orlova ✉, G.V. Gladkov, A.O. Zverev, V.M. Shapkin, T.O. Lisina,
N. Kurchak, A.A. Kichko, I.A. Arkhipchenko, E.E. Andronov

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

Orlova O.V. orcid.org/0000-0002-2154-503X
Kurchak N. orcid.org/0009-0009-5901-0354
Gladkov G.V. orcid.org/0000-0002-5489-1414
Kichko A.A. orcid.org/0000-0002-8482-6226
Zverev A.O. orcid.org/0000-0002-5315-8632
Arkhipchenko I.A. orcid.org/0009-0003-6312-7666
Shapkin V.M. orcid.org/0000-0002-8394-3009
Andronov E.E. orcid.org/0000-0002-5204-262X
Lisina T.O. orcid.org/0000-0003-1268-4166

Final revision received July 30, 2024
Accepted September 22, 2024

No-till technologies are becoming more widespread, as they allow for obtaining high yields at lower costs while reducing soil degradation (G.A. Thomas et al., 2007). One of the key issues in no-till farming is the regulation of the quantity and quality of mulch. No-till requires the use of herbicides and pesticides, which increases the risk of accumulating their residual amounts in mulch. The BAGS biopreparation developed at the All-Russian Research Institute of Agricultural Microbiology is capable of decomposing prometryn and possessing high cellulolytic activity. In this work, a significant change in the succession and composition of straw microbiomes under the influence of BAGS was shown for the first time; however, despite the increase in the activity of microorganisms, no significant increase in the efficiency of destruction in the variant with the biological preparation was detected over 68 days. The aim of the work was to study the dynamics of prokaryotic and eukaryotic microbiomes of straw when its decomposition occurs on the soil surface in the presence of BAGS. A laboratory experiment with composting oat straw (Avena sativa L.) on the soil surface was carried out in 1-liter plastic containers. Nylon fabric was laid on the soil surface, onto which 15 g of chopped straw was placed. The straw was pre-soaked for 2 h in an NH4NO3 solution at the rate of 5 g N/kg of straw. Straw without treatment with BAGS served as a control. In the experimental variant, 10 % BAGS was added to wet straw. At the beginning of the experiment (day 0) and in 30 and 68 days, the number of fungi and bacteria in the straw were determined using real-time PCR (RT-PCR), along with straw mass loss, nitrate content, water-soluble carbon, ash content, and respiration. Prokaryotic and eukaryotic microbial communities of straw were analyzed using deep sequencing of the 16S rRNA gene (prokaryotes) and ITS (eukaryotes) amplicon libraries. Oat straw decomposed quickly, on day 30, the mass loss was 31-35 %. The introduction of BAGS increased the emission of carbon dioxide on day 30 (569±36 vs 394±67 mg CO2·m-2·h-1 in the control), and on day 68, the difference was 8 %. The high activity of microorganisms led to greater consumption of readily available nutrients by them, which was evident from the decrease in the amount of water-soluble organic compounds by 1.6-1.8 times and nitrate nitrogen by 1.8-1.4 times vs the control. Probably, under the experimental conditions, the lack of mineral nitrogen was one of the factors contributing to the low efficiency of BAGS as a straw decomposer compared to the control: on day 68, the ash content was 11.6 % higher, and the loss of straw mass was 5 %. Recalculation of the absolute copy numbers of the 16S rRNA gene and ITS (RT-PCR) into the cell number showed that during straw destruction the number of bacteria exceeded the number of fungi by 3.6-4.1 times. However, if we take into account the difference in the mass and volume of prokaryotic and eukaryotic cells, the biomass of fungi can exceed bacterial biomass by hundreds times, up to 500-fold. Analysis of alpha diversity for fungi revealed a classic succession pattern, namely low Shannon index and a smaller number of species at the beginning of the experiment, followed by a subsequent growth of biodiversity, which can serve as indirect confirmation of the leading role of fungi in the straw destruction. It was shown that up to 60 % of the representatives of the initial prokaryotic and eukaryotic communities of straw did not play a significant role in its decomposition and were replaced by other microorganisms. The greatest changes in the composition of microbiomes occurred during the first 30 days, with small differences between days 30 and 68. During the analysis of eukaryotes (ITS), along with fungi, other representatives were identified, in particular plants, nematodes, and protists. Nematodes and protists appearing in the straw biotransformation occupied a noticeable place in the microbiome, up to 17.9 % and 21.4 %, respectively. The biopreparation BAGS had a significant effect on the eukaryotic community. The relative representation of protists increased by 4-10 times compared to the control, while the role of basidiomycetes decreased. On day 68, the ratio of ascomycetes and basidiomycetes was 1.49 and 4.30, respectively. The proportion of Coprinopsis radiata decreased 2-fold on day 30 and 11-fold on day 68. BAGS had little effect on the number of microorganisms and the rate of straw destruction over 68 days of our experiment. However, it was found that under its influence, the structure of prokaryotic and eukaryotic microbial communities and their succession changed significantly. Conditions for increasing the efficiency of BAGS application, given its potential for pesticide degradation, we plan to investigate in more details in further experiments.

Keywords: mulch, BAGS, 16S rRNA gene, ITS, real-time PCR, qPCR, high-performance sequencing, destruction of oat straw, succession of microbial communities.

 

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