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Kimeklis A.K., Dmitrakova Ya.A., Pershina E.A., Ivanova E.A., Zverev A.O., Gladkov G.V., Kichko A.A., Andronov E.E., Abakumov E.V. Analysis of microbiome of recultivated soils of the kingisepp area of phosphorite mining. Sel'skokhozyaistvennaya Biologiya [Agricultural Biology], 2020, Vol. 55, № 1, p. 137-152.
(how to cite this article)

doi: 10.15389/agrobiology.2020.1.137eng

UDC: 631.618:631.46:577.2

Acknowledgements:
Supported financially by Russian Science Foundation, grant No. 17-16-01030

 

ANALYSIS OF MICROBIOME OF RECULTIVATED SOILS
OF THE KINGISEPP AREA OF PHOSPHORITE MINING

A.K. Kimeklis1, 2, Ya.A. Dmitrakova1, E.A. Pershina1, 2,
E.A. Ivanova1, 2, 3, A.O. Zverev1, 2, G.V. Gladkov1, 2, A.A. Kichko2,
E.E. Andronov1, 2, 4, E.V. Abakumov1

1Saint-Petersburg State University, 7-9, Universitetskaya nab., St. Petersburg, 199034 Russia, e mail kimeklis@gmail.com (✉ corresponding author), dmitrakovay.a@gmail.com, microbioliza@gmail.com, ektrnivanova@gmail.com, azver.bio@gmail.com, ruginodis@gmail.com, eeandr@gmail.com, e_abakumov@mail.ru;
2All-Russian Research Institute for Agricultural Microbiology, 3, sh. Podbel’skogo, St. Petersburg, 196608 Russia, e-mail 2014arki@gmail.com;
3Agrophysical Research Institute, 14, Grazhdanskii pr., St. Petersburg, 195220 Russia;
4Dokuchaev Soil Science Institute, 7/str. 2, Pyzhyovskii per., Moscow, 119017 Russia

ORCID:
Kimeklis A.K. orcid.org/0000-0003-0348-7021
Gladkov G.V. orcid.org/0000-0002-5248-9018
Dmitrakova Ya.A. orcid.org/0000-0002-6980-4854
Kichko A.A. orcid.org/0000-0002-8482-6226
Pershina E.A. orcid.org/0000-0003-0834-3211
Andronov E.E. orcid.org/0000-0002-5204-262X
Ivanova E.A. orcid.org/0000-0003-1589-9875
Abakumov E.V. orcid.org/0000-0002-5248-9018
Zverev A.O. orcid.org/0000-0002-5315-8632

Received May 15, 2019

 

The microbial composition of reclaimed disturbed soil covers may indicate the degree of their recovery and the processes occurring in them, as well as their suitability for further use in agriculture. Kingisepp phosphorte quarry was developed in the 1960s, and at the end of the 1970s reclamation was performed. This object is unique because its soil physical parameters were monitored for 29 years and the reclamation was performed with the planting of three plant cultures — spruce, larch and pine. In the area with spruce it was leveled with an addition of peaty-mineral mixture, and in areas with larch and pine only mineral substrate without peat was added. However, the analysis of the microbiome composition of the soil cover at the reclamation sites has not yet been carried out. Our study showed that the structure of the studied soil microbiome did not depend on the physicochemical parameters of the soil, the diversity of the soil microbiome did not correlate with the main mineral nutrients, and the dominant plant species did not significantly affect the structure of the microbiome. The aim of the work was to study the microbiome of these sites using high-throughput sequencing of amplicon libraries of the 16S rRNA gene, as well as to search for the connection between the microbiome composition and the type of remediation and physical and chemical parameters of the soil. For three plots, descriptions of vegetation cover and soil cuts were made, and soil samples were taken to determine their physical and chemical parameters and DNA extraction. The granulometric composition of the samples, pH levels, substrate induced and basal respiration, as well as the content of organic carbon, mobile compounds of phosphorus and potassium, exchangeable ammonium and nitrates were measured. Quantity of bacteria, archaea and fungi was determined using real-time PCR. For the analysis of microbial communities, the level of their alpha and beta diversity was measured, their taxonomic structure was determined, as well as their relationship with the soil biochemical parameters and vegetation cover. According to the results of the studies, the soil parameters were similar for all plots, and the levels of basal and substrate-induced respiration were very low (around 0.02-0.05 µg CO2/g per hour). The plot under the spruce showed a more acidic soil extract reaction (pH 6.5) than the plots under larch and pine (pH 7.6 and 7.1, respectively). The type of vegetation was not a sufficiently strong ecological factor and microbial communities turned out to be close in structure. The quantitative composition of microorganisms did not differ significantly between the three experimental plots, except for the lower content of archaea in the plot with spruce. The level of alpha-diversity of the prokaryotic community in all three plots was also similar, but the area under the spruce differed from others by a higher diversity of actinobacteria. Proteobacteria, Actinobacteria and Acidobacteria phyla were dominant in all samples. The most numerous taxon in all plots was Pseudomonas, in the plot with spruce dominated Actinobacteria, Rhizobiaceae, Kouleothrixaceae, Ellin6529, N1423WL, with pine — Rhodoplanesand Sinobacteraceae, with larch — IS-44. Pine plot was also characterized by a relative low content of Micrococcaceae and Ellin6075, and spruce plot — of RB41. In general, in the studied microbiomes, bacteria are identified that belong to both oligotrophic slow-growing forms characteristic of stabilized soil communities with a full carbon cycle, and to fast-growing copyotrophic, often associated with a rhizosphere niche. In this regard, this stage of overgrowing of reclaimed soils of the Kingisepp phosphorite deposit can be attributed to pre-climax.

Keywords: reclamation, soil microbiome, alpha and beta diversity, high throughput sequencing, 16S rRNA.

 

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