Dominant bacterial genera of microbiota of chernozems of the forest-steppe zone

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Abstract

BACKGROUND: Bacterial community plays a significant role in maintaining homeostasis and fertility of chernozems. Analysis of its components allows us to identify the dominant taxonomic groups, the ecological preferences of the species that form their basis, and helps to focus efforts on creating biological products and tests aimed at monitoring and enhancing fertility.

AIM: The aim of this study is to identify bacterial genera that dominate the microbiota of Chernozems in the forest-steppe zone of the European part of Russia, and to trace the influence of land use, summer season phase, agrochemical parameters and interactions with each other on their abundance.

MATERIALS AND METHODS: In the Belgorod region, 10 samples of arable and non-arable chernozems were taken twice during the summer. Based on metabarcoding data, the percentages of genera in bacterial communities were obtained. An agrochemical analysis was carried out with the calculation of correlation coefficients between the chemical indicators of chernozems and the proportions of bacterial genera. An analysis of correlations between bacterial genera was carried ut as well.

RESULTS: Dominant genera include Sphingomonas, Rubrobacter, Gemmatimonas, Bradyrhizobium, Haliangium and others. Under soil conditions, the proportion of representatives of the genera Sphingomonas and Gemmatimonas shows a strong positive correlation with nitrate nitrogen concentration, and the proportion of the genus Bradyrhizobium shows a strong negative correlation with phosphorus concentration. The largest number of positive correlation interactions with other genera was found for Nocardioides, Mycobacterium, Streptomyces, and Solirubrobacter.

CONCLUSIONS: The stability of the set of bacterial genera dominant in the chernozems of the forest-steppe zone of Russia in different environmental conditions (plowed and unplowed areas), as well as over time (June and August) was shown. A number of representatives belonging to the genera Sphingomonas, Gemmatimonas, Bradyrhizobium and others are strongly dependent on the concentrations of nitrogen and phosphorus fertilizer components. Representatives of actinomycetes and mycobacteria are closely involved in positive correlation interactions among bacterial genera.

About the authors

Wentao Zheng

Belgorod State University

Email: zhengwentaoo@126.com
ORCID iD: 0009-0003-3460-8401
Russian Federation, Belgorod

Konstantin S. Boyarshin

Belgorod State University

Email: ulmus-04@yandex.ru
ORCID iD: 0000-0002-2960-0670
SPIN-code: 6002-9327

Cand. Sci. (Biology)

Russian Federation, Belgorod

Valeria V. Adamova

Belgorod State University

Email: adamova@bsu.edu.ru
ORCID iD: 0000-0001-8329-4670
SPIN-code: 8985-6005

Cand. Sci. (Biology)

Russian Federation, Belgorod

Ekaterina V. Nikitinskaya

Cherepovets State University

Email: nikitinskajacat@yandex.ru
Russian Federation, Cherepovets

Olga Yu. Obukhova

Belgorod State University

Author for correspondence.
Email: 1064261@bsu.edu.ru
ORCID iD: 0009-0007-5139-0394
SPIN-code: 9138-2276
Russian Federation, Belgorod

Marina V. Kolkova

Belgorod State University

Email: mvk3105@mail.ru
ORCID iD: 0009-0008-3849-3564
Russian Federation, Belgorod

Olga S. Bespalova

Belgorod State University

Email: olga9078@mail.ru
Russian Federation, Belgorod

Violetta V. Klyueva

Belgorod State University

Email: klyueva@bsu.edu.ru
ORCID iD: 0000-0002-9509-5115
SPIN-code: 8265-0423
Russian Federation, Belgorod

Kristina A. Degtyareva

Belgorod State University

Email: degtyareva@bsu.edu.ru
ORCID iD: 0000-0003-4474-0919
SPIN-code: 6439-6568
Russian Federation, Belgorod

Lyubov V. Nesteruk

Belgorod State University

Email: nesteruk@bsu.edu.ru
ORCID iD: 0000-0003-3189-8178
SPIN-code: 3616-4039

Cand. Sci. (Biology)

Russian Federation, Belgorod

Yulia N. Kurkina

Belgorod State University

Email: kurkina@bsu.edu.ru
ORCID iD: 0000-0001-9180-1257
SPIN-code: 5292-6973

Cand. Sci. (Biology)

Russian Federation, Belgorod

Olesya A. Makanina

Belgorod State University

Email: makanina@bsu.edu.ru
ORCID iD: 0009-0006-7571-2493
SPIN-code: 9678-8458

Cand. Sci. (Biology)

Russian Federation, Belgorod

Elena S. Ivanova

Cherepovets State University

Email: stepinaelena@yandex.ru
ORCID iD: 0000-0002-6976-1452
SPIN-code: 5997-3738

Cand. Sci. (Biology)

Russian Federation, Cherepovets

Irina V. Batlutskaya

Belgorod State University

Email: bat@bsu.edu.ru
ORCID iD: 0000-0003-0068-6586
SPIN-code: 2555-6176

Dr. Sci. (Biology)

Russian Federation, Belgorod

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Supplementary files

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2. Fig. 4. The scheme of correlations between the proportions of bacterial genera in the microbiota of chernozems. Statistically significant correlations with the Spearman coefficient modulus greater than 0.5 are shown. Positive values correspond to the colors of the arrows in shades of red and pink, negative values correspond to shades of blue. Pink and light blue indicate correlations explained by common correlations of the proportions of genera with the chemical parameters of soil (Fig. 3, Supplement 4), red and blue — not explained by them. The size of the alphabetic characters is proportional to the proportion (abundance) of the corresponding bacterial genus

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3. Fig. 5. The scheme of correlations between the proportions of bacterial genera in the microbiota of chernozems. Statistically significant correlations are shown, which are not explained from common reliable correlations of the proportions of genera with the chemical parameters of soil. Positive values correspond to the colors of the arrows in shades of red and pink, negative values correspond to shades of blue. Pink and blue indicate correlations that might be explained by statistically insignificant common trends towards correlation with chemical parameters (Fig. 3, Supplement 4), red and dark blue — not explained by them. The names of the genera are shown in Fig. 4

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4. suppl. 1 Place and time of sampling and quantity of samples of arable and non-arable chernozems
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5. suppl. 2 Statistics on the classification of sequences obtained by sequencing amplicons of a fragment of the 16S rRNA gene
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6. suppl. 3 Average percentages of bacterial genera in the community in arable and non-arable chernozems with standard deviations
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7. suppl. 4 Correlation coefficients of the percentages of genera in bacterial communities of chernozem with chemical parameters of the soil, p ≤ 0.05
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8. suppl. 5 Correlation coefficients of the percentages of 30 bacterial genera in chernozem communities with each other
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9. Fig. 1. Places where soil samples were collected on the territory of the Belgorod region of Russia. Pentagons correspond to Haplic Chernozem, rhombuses mean Luvic Chernozem, triangles are for southern variety of Haplic Chernozem (Ordinary Chernozem). An asterisk marks Haplic Chernozem on the border of the protected area

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10. Fig. 2. The effect of the month of sample collection and agricultural processing on the proportion of genera in the soil bacterial community. The colors indicate how many times the value deviates from the average for a given genus. Statistically significant excess depending on the month (И — June, A — August) and agricultural processing (П — arable areas, Н. п. — non-arable) are marked with letter designations. Numerical data are given in Supplement 3 (doi: 10.17816/ecogen634581-4318801)

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11. Fig. 3. A heat map of the values of the correlation coefficient of the percentages of the 30 most numerous bacterial genera in the communities of chernozems with the chemical parameters of the soil, as well as with each other. Humidity is indicated as ωH2O, the mass fraction of organic matter as ωорг. Data on the statistical reliability of the obtained values are given in Supplements 4 and 5 (doi: 10.17816/ecogen634581-4318802, doi: 10.17816/ecogen634581-4318803)

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