Dominant Bacterial Taxa of Chernozems and Factors Affecting Their Abundance in the Bacterial Community

Cover Page

Cite item

Full Text

Open Access Open Access
Restricted Access Access granted
Restricted Access Subscription Access

Abstract

Families and genera of bacteria that dominate in the chernozems of the forest-steppe zone have been identified. Microbiological profiling of samples of arable and non-arable chernozems using the 16S rRNA gene sequencing was carried out in different phases of the vegetation period: in June and August. The changes in the proportion of individual bacterial families depending on land use and time are shown. Correlations between the prevalence of bacterial families and the chemical parameters of the soil have been revealed. The predominant role of nitrates in the formation of the community structure, in this process the content of organic carbon, soil moisture and its pH play an important role. Despite the revealed differences in the proportions of the studied families depending on land use and the time of sample collection, the set of dominant bacterial families in the studied samples remained stable. The first 6 dominant families make up about 1/4 of the entire community, and the first 20 make up about 40%. The obtained results create prerequisites for further study of the variability of the taxonomic composition of the bacterial community of chernozems in various biotic and agrochemical conditions.

About the authors

K. S. Boyarshin

Belgorod State University

Author for correspondence.
Email: kboyarshin@mail.ru
Russian Federation, Belgorod

V. V. Adamova

Belgorod State University

Email: kboyarshin@mail.ru
Russian Federation, Belgorod

W. Zheng

Belgorod State University

Email: kboyarshin@mail.ru
Russian Federation, Belgorod

E. V. Nikitinskaya

Cherepovets State University

Email: kboyarshin@mail.ru
Russian Federation, Cherepovets

O. Yu. Obukhova

Belgorod State University

Email: kboyarshin@mail.ru
Russian Federation, Belgorod

M. V. Kolkova

Belgorod State University

Email: kboyarshin@mail.ru
Russian Federation, Belgorod

V. A. Nesterenko

Dokuchaev Soil Science Institute

Email: kboyarshin@mail.ru
Russian Federation, Moscow

O. S. Bespalova

Belgorod State University

Email: kboyarshin@mail.ru
Russian Federation, Belgorod

V. V. Klyueva

Belgorod State University

Email: kboyarshin@mail.ru
Russian Federation, Belgorod

K. A. Degtyareva

Belgorod State University

Email: kboyarshin@mail.ru
Russian Federation, Belgorod

L. V. Nesteruk

Belgorod State University

Email: kboyarshin@mail.ru
Russian Federation, Belgorod

Yu. N. Kurkina

Belgorod State University

Email: kboyarshin@mail.ru
Russian Federation, Belgorod

O. A. Makanina

Belgorod State University

Email: kboyarshin@mail.ru
Russian Federation, Belgorod

E. S. Ivanova

Belgorod State University

Email: kboyarshin@mail.ru
Russian Federation, Belgorod

Zh. Li

Dezhou University

Email: kboyarshin@mail.ru
China, Dezhou

I. V. Batlutskaya

Belgorod State University

Email: kboyarshin@mail.ru
Russian Federation, Belgorod

References

  1. Авраменко П.М., Акулов П.Г., Атанов Ю.Г. Природные ресурсы и окружающая среда Белгородской области. Белгород: Белгород, 2007. 556 с.
  2. Григорьев Г.Н. География Белгородской области. Белгород: Изд-во БелГУ, 1996. 144 с.
  3. Докучаев В.В. Русский чернозем. СПб.: Типография Деклерона и Евдокимова, 1883. 376 с.
  4. Иванова Е.А., Кутовая О.В., Тхакахова А.К., Чернов Т.И., Першина Е.В., Маркина Л.Г., Андронов Е.Е., Когут Б.М. Структура микробного сообщества агрегатов чернозема типичного в условиях контрастных вариантов сельскохозяйственного использования // Почвоведение. 2015. № 11. С. 1367–1382. https://doi.org/10.7868/ S 0032180 X 15110088
  5. Чевердин Ю.И., Зборищук Ю.Н. Закономерности изменения показателей кислотности черноземов Каменной Степи // Вестник Моск. ун-та. Сер. 17, почвоведение. 2009. № 4. С. 22–25.
  6. Чернов Т.И., Тхакахова А.К., Иванова Е.А., Кутовая О.В., Турусов В.И. Сезонная динамика почвенного микробиома многолетнего агрохимического опыта на черноземах Каменной Степи // Почвоведение. 2015. № 12. С. 1483–1488. https://doi.org/10.7868/S0032180X15120059
  7. Anderson M.J. Permutational Multivariate Analysis of Variance (PERMANOVA) // Wiley StatsRef: Statistics Reference Online. Wiley, 2017. P. 1–15. https://doi.org/10.1002/9781118445112.stat07841
  8. Bennett L.T., Kasel S., Tibbits J. Non-parametric multivariate comparisons of soil fungal composition: Sensitivity to thresholds and indications of structural redundancy in T-RFLP data // Soil Biol. Biochem. 2008. V. 40(7). P. 1601–1611. https://doi.org/10.1016/j.soilbio.2008.01.008
  9. Boyarshin K.S., Adamova V.V., Zheng W., Obuhova O.Y., Kolkova M.V., Nesterenko V.A., Bespalova O.S., et al. The effect of long-term agricultural use on the bacterial microbiota of chernozems of the forest-steppe zone // Diversity. 2023. V. 15(2). P. 191. https://doi.org/10.3390/d15020191
  10. Caporaso J.G., Kuczynski J., Stombaugh J., Bittinger K., Bushman F.D., Costello E.K., Fierer N., et al. QIIME allows analysis of high-throughput community sequencing data // Nat. Methods. 2010. V. 7. P. 335–336. https://doi.org/10.1038/nmeth.f.303
  11. Chibilyov A.A. Ecology-geographical essay about steppes of northern Eurasia // Вопросы степеведения. 2000. № 2. P. 12–29.
  12. Coelho C., Mesquita N., Costa I., Soares F., Trovão J., Freitas H., Portugal A., Tiago I. Bacterial and archaeal structural diversity in several biodeterioration patterns on the limestone walls of the old cathedral of Coimbra // Microorganisms. 2021. V. 9(4). P. 709. https://doi.org/10.3390/microorganisms9040709
  13. Dedov A.V., Boluchevsky D.A. Influence of biological techniques for restoring soil fertility and methods of soil treatment on the fertility of typical chernozem and yield of winter wheat // Bull. Agric. Sci. 2014. V. 46(1). P. 38–41.
  14. Dixon P. VEGAN, a package of R functions for community ecology // J. Veg. Sci. 2003. V. 14(6). P. 927–930. https://doi.org/10.1111/j.1654-1103.2003.tb02228.x
  15. Ferreira A., Nobre M., Moore E., Rainey F.A., Battista J.R., da Costa M.S. Characterization and radiation resistance of new isolates of Rubrobacter radiotolerans and Rubrobacter xylanophilus // Extremophiles. 1999. V. 3. P. 235–238. https://doi.org/10.1007/s007920050121
  16. Fujita H., Ushio M., Suzuki K., Abe M.S., Yamamichi M., Okazaki Y., Canarini A., Hayashi I., Fukushima K., Fukuda Sh., Kiers E.T., Toju H. Metagenomic analysis of ecological niche overlap and community collapse in microbiome dynamics // bioRxiv.2023. P. 524457. https://doi.org/10.1101/2023.01.17.524457
  17. Glaeser S., Kämpfer P. The family Sphingomonadaceae // The Prokaryotes: Alphaproteobacteria and Betaproteobacteria. Springer, 2013. P. 641–707. https://doi.org/10.1007/978-3-642-30197-1_302
  18. Gorbacheva M.A., Melnikova N.V., Chechetkin V.R., Kravatsky Yu.V., Tchurikov N.A. DNA sequencing and metagenomics of cultivated and uncultivated chernozems in Russia // Geoderma Reg. 2018. V. 14. P. e00180. https://doi.org/10.1016/j.geodrs.2018.e00180
  19. Goryanin O., Chichkin A., Dzhangabaev B., Shcherbinina E. Scientific bases of the humus stabilization in ordinary chernozem in Russia // Geogr. Environ. Sustain. 2019. V. 52(1). P. 113–128. https://doi.org/10.17951/pjss.2019.52.1.113
  20. Hester E.R., Jetten M.S.M., Welte C.U., Lücker S. Metabolic overlap in environmentally diverse microbial communities // Front. Genet. 2019. V. 10. P. 989. https://doi.org/10.3389/fgene.2019.0098
  21. Kool J., Tymchenko L., Shetty S.A., Fuentes S. Reducing bias in microbiome research: Comparing methods from sample collection to sequencing // Front. Microbiol. 2023. V. 14. P. 1094800. https://doi.org/10.3389/fmicb.2023.1094800
  22. Kosako Y., Yabuuchi E., Naka T., Fujiwara N., Kobayashi K. Proposal of Sphingomonadaceae fam. nov., consisting of Sphingomonas Yabuuchi et al. 1990, Erythrobacter Shiba and Shimidu 1982, Erythromicrobium Yurkov et al. 1994, Porphyrobacter Fuerst et al. 1993, Zymomonas Kluyver and van Niel 1936, and Sandaracinobacter Yurkov et al. 1997, with the type genus Sphingomonas Yabuuchi et al. 1990 // Microbiol. Immunol. 2000. V. 44(7). P. 563 – 575. https://doi.org/ 10.1111/j.1348-0421.2000.tb02535.x
  23. Kruskal W.H., Wallis W.A. Use of Ranks in One-Criterion Variance Analysis // J. Am. Stat. Assoc. 1952. V. 47(260). P. 583–621. https://doi.org/10.2307/2280779
  24. Liu X., Burras C.L., Kravchenko Y.S., Duran A., Huffman T., Morrás H.J., Studdert G.A., Zhang X., Cruse R.M., Yuan X. Overview of Mollisols in the world: Distribution, land use and management // Can. J. Soil Sci. 2012. V. 92(3). P. 383–402. https://doi.org/10.1139/CJSS2010-058
  25. Mikhailova E.A., Post Ch. Organic carbon stocks in the Russian Chernozem // Eur. J. Soil Sci. 2005. V. 57(3). P. 330–336. https://doi.org/10.1111/j.1365-2389.2005.00741.x
  26. Oren A. The family Xanthobacteraceae // The Prokaryotes. Springer, 2014. P. 709–726. https://doi.org/10.1007/978-3-642-30197-1_258
  27. Quast C., Pruesse E., Yilmaz P., Gerken J., Schweer T., Yarza P., Peplies J., Glöckner F.O. The SILVA ribosomal RNA gene database project: Improved data processing and web-based tools // Nucleic Acids Res. 2013. V. 41. P. D590–D596. https://doi.org/ 10.1093/ nar / gks 1219
  28. Ricotta C., Szeidl L., Pavoine S. Towards a unifying framework for diversity and dissimilarity coefficients // Ecol. Indic. 2021. V. 129. P. 107971. https://doi.org/10.1016/j.ecolind.2021.107971.
  29. Roger B.J., Curtis J.T. An Ordination of the Upland Forest Communities of Southern Wisconsin // Ecol. Monogr. 1957. V. 27(4). P. 325–349. https://doi.org/10.2307/1942268
  30. Rosenberg E. The family Chitinophagaceae // The Prokaryotes. Springer, 2014. P. 493–495. https://doi.org/ 10.1007/978-3-642-38954-2_137
  31. Sangwan P., Chen X., Hugenholtz P., Janssen P.H. Chthoniobacter flavus gen. nov., sp. nov., the first pure-culture representative of subdivision two, Spartobacteria classis nov. of the phylum Verrucomicrobia // Appl. Environ. Microbiol. 2004. V. 70(10). P. 5875 – 5881. h ttps://doi.org/10.1128/AEM.70.10.5875-5881.2004
  32. Schoch C.L., Ciufo S., Domrachev M., Hotton C.L., Kannan S., Khovanskaya R., Leipe D., et al. NCBI Taxonomy: a comprehensive update on curation, resources and tools // Database (Oxford). 2020. P. baaa062. https://doi.org/10.1093/database/baaa062
  33. Semenov M.V., Chernov T.I., Tkhakakhova A.K., Zhelezova A.D., Ivanova E.A., Kolganova T.V., Kutovaya O.V. Distribution of prokaryotic communities throughout the Chernozem profiles under different land uses for over a century // Appl. Soil Ecol. 2018. V. 127. P. 8–18. https://doi.org/10.1016/j.apsoil.2018.03.002
  34. Silverman J.D., Bloom R.J., Jiang S., Durand H.K., Dallow E., Mukherjee S., David L.A. Measuring and mitigating PCR bias in microbiota datasets // PLoS Comput. Biol. 2021. V. 17(7). P. e1009113. https://doi.org/10.1371/journal.pcbi.1009113
  35. Six J., Feller Ch., Denef K., Ogle S., Carlos de Moraes Sa J., Albrecht A. Soil organic matter, biota and aggregation in temperate and tropical soils – Effects of no-tillage // Agronomie. 2002. V. 22(7–8). P. 755–775. https://doi.org/10.1051/agro:2002043
  36. Stanek-Tarkowska J., Pastuszczak M., Szpunar-Krok E., Kacaniova M., Kluz M., Czyż E., Pieniążek R., Skrobacz K., Pietrzyk K. Comparison of the effect of fertilization with ash from wood chips on bacterial community in podzolic and chernozem soils for the cultivation of winter oilseed rape: a preliminary study // Agronomy. 2022. V. 12(3). P. 576. https://doi.org/10.3390/agronomy12030576
  37. Stekolnikov K.E., Gasanova E.S., Stekolnikova N.V. Agrogenic transformation (degradation) of chernozems of the Central Chernozem Region // BIO Web Conf. 2021. V. 36. P. 03021. https://doi.org/10.1051/bioconf/20213603021
  38. Suzuki K., Collins M.D., Iijima E., Komagata K. Chemotaxonomic characterization of a radiotolerant bacterium, Arthrobacter radiotolerans: Description of Rubrobacter radiotolerans gen. nov., comb. nov. // FEMS Microbiol. Lett. 1988. V. 52(1 – 2). P. 33–39. https://doi.org/10.1111/j.1574-6968.1988.tb02568.x
  39. Szalay A. Cation exchange properties of humic acids and their importance in the geochemical enrichment of UO 2 ++ and other cations // Geochim. Cosmochim. Acta. 1964. V. 28(10–11). P. 1605–1614. https://doi.org/10.1016/0016-7037(64)90009-2
  40. Trofimov I.A., Trofimova L.S., Yakovleva E.P., Emelyanov A.V., Skripnikova E.V. Preserving the fertility of Russian chernozems. Status, trends, forecast // IOP Conf. Ser.: Earth Environ. Sci. 2021. V. 817. P. 012108. https://doi.org/10.1088/1755-1315/817/1/012108
  41. Van D.H. Cation binding of humic acids // Geoderma. 1971. V. 5(1). P. 53–67. https://doi.org/10.1016/0016-7061(71)90024-3
  42. Vysloužilová B., Ertlen D., Schwartz D., Šefrna L. Chernozem. From concept to classification: A review // Acta Univ. Carol. Geogr. 2016. V. 51(1). P. 85–95. https://doi.org/10.14712/23361980.2016.8
  43. Weaver B., Wuensch K.L. SPSS and SAS Programs for Comparing Pearson Correlations and OLS Regression Coefficients // Behav. Res. Methods. 2013. V. 45(3). P. 880–895. https://doi.org/10.3758/s13428-012-0289-7
  44. Wilcoxon F. Individual comparisons by ranking methods // Biomathem. Bull. 1945. V. 1(6). P. 80–83. https://doi.org/10.2307/3001968
  45. Zhang H., Sekiguchi Y., Hanada S., Hugenholtz P., Kim H., Kamagata Y., Nakamura K. Gemmatimonas aurantiaca gen. nov., sp. nov., a gram-negative, aerobic, polyphosphate-accumulating micro-organism, the first cultured representative of the new bacterial phylum Gemmatimonadetes phyl. nov. / / Int. J. Syst. Evol. Microbiol. 2003. V. 53. P. 1155–1163. https://doi.org/10.1099/ijs.0.02520-0

Supplementary files

Supplementary Files
Action
1. JATS XML
2. Fig. 1. Sampling points on the soil map of Belgorod region of Russia

Download (841KB)
3. Fig. 2. Chemical characteristics of arable (A) and non-arable (N/A) chernozems with their standard deviations: pH KCl, mass fraction of organic matter (Sorg, %), mass concentrations of exchangeable potassium in terms of K2O, exchangeable phosphorus in terms of P2O5, NO3- and NH4+ in terms of nitrogen

Download (250KB)

Copyright (c) 2024 Russian Academy of Sciences