Sel’skokhozyaistvennaya Biologiya [Agricultural Biology], 2017, Vol. 52, № 3, p. 588-596.
(how to cite this article)

doi: 10.15389/agrobiology.2017.3.588eng

UDC 631.461:577.2

Acknowledgements:
Soil sampling and chemical analyzes of soils and substrates (cellulose and straw) were supported financially by the Program of Basic Research of the Presidium of the Russian Academy of Sciences. DNA study (isolation, sequencing and bioinformatic analysis) was supported by Russian Science Foundation (grant № 14-26-00094)

 

DYNAMICS OF CHERNOZEM MICROBIAL COMMUNITY DURING
BIODEGRADATION OF CELLULOSE AND BARLEY STRAW

E.L. Chirak1, O.V. Orlova1, T.S. Aksenova1, A.A. Kichko1, E.R. Chirak1 ,
N.A. Provorov1, E.E. Andronov1, 2, 3

1All-Russian Research Institute for Agricultural Microbiology, Federal Agency of Scientific Organizations, 3, sh. Podbel’skogo, St. Petersburg, 196608 Russia,
e-mail biologartillerist@gmail.com, arriam2008@yandex.ru (corresponding authors);
2Saint-Petersburg State University, 7-9 Universitetskaya nab., St. Petersburg, 199034 Russia;
3V.V. Dokuchaev Soil Science Institute, 7/2, Pyzhevskii per., Moscow, 397463 Russia

ORCID:
Chirak E.L. orcid.org/0000-0001-9167-5000
Orlova O.V. orcid.org/0000-0002-2154-503X
Aksenova T.S. orcid.org/0000-0002-0002-9538
Kichko A.A. orcid.org/0000-0002-8482-6226
Chirak E.R. orcid.org/0000-0002-1610-8935
Provorov N.A. orcid.org/0000-0001-9091-9384
Andronov E.E. orcid.org/0000-0002-5204-262X

Received June 14, 2016

 

Study of cellulose decomposition is an extremely important for the agricultural sciences, as straw is one of the most affordable organic fertilizers. In this area, a large number of research works devoted to biochemical mechanisms of cellulose destruction, as well as study of the cellulolytic microorganisms’ taxonomic diversity were conducted. However, the composition of the microbial community was estimated only by the methods based on cultivation and thus describing only a very small part of the soil microbiome. With the advent of «new generation sequencing» methods the analysis of whole microbial communities found in the soil became possible. The main objective of this work was the implementation of an integrated approach, combining agrochemical techniques of biodegradation processes intensity estimation with modern molecular methods (soil metagenome analysis of 16S rRNA) in the process of cellulose decomposition in two substrates (straw and filter paper). It was first shown by the method of high-throughput sequencing that the introduction of a straw in soil caused dipper changes in the structure of the microbial community than the introduction of chemically pure cellulose. The model experiment was carried out on typical chernozem, sampled in the Voronezh region in fallow areas from a depth of 2-15 cm. Chemically pure cellulose (very fine-chopped filter paper) and crushed straw of barley were added at 1 g per 100 g of soil. Analyzes were performed on days 0, 7, 14, 21 and 28. CO2 emission, the content of nitrates, ammonium nitrogen, labile carbon, and microbial biomass were estimated. During the first 7 days, microbial mass and respiration increased when straw was added. For cellulose, an increase in biomass was not significant, and respiration was activated with a delay. The introduction of cellulose and straw reduced the soil level of nitrate nitrogen compared to control, and with straw, the indicator lowered to a lesser extent. In this work, some taxa were found, the proportion of which increased (Chthoniobacteraceae, Xanthomonadaceae, Chitinophagaceae), and decreased (Gaiellaceae). Among the microorganisms whose proportion increased after the introduction of cellulose, we found classic cellulose destructors (Chitinophaga and representatives of the families Streptosporangiaceae and Micromonosporaceae), and microorganisms whose ability to decompose cellulose had not previously been reported yet (Chthoniobacter, Chitinophaga). Community homeostasis was found (i.e. significant changes in the composition of microbiome on day 14 of the experiment returned to the original state on day 28). Agrochemical analysis (dynamics of nitrate nitrogen content, the rate of release of carbon dioxide, dynamics of bacterial biomass) fully agreed with the analysis of metagenomic data in fact that the microbial community actively respond to the introduction of straw as opposed to the introduction of pure cellulose.

Keywords: microbiome, soil, metagenome, straw, cellulose, biodegradation.

 

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