Бактериальное сообщество сельскохозяйственных почв, используемых для возделывания картофеля в Свердловской области

На урожайность картофеля и других сельскохозяйственных культур оказывает влияние множество факторов, один из главнейших – комплексное состояние почвы. В исследованиях почв чаще делают акцент на определение ее физико-химических свойств, но редко учитывают бактериальное сообщество и его разнообразие. В работе проведена оценка бактериальной микробиоты почв, на которых возделывается картофель. С помощью метабаркодирования и полнофрагментного секвенирования участка 16S рРНК, методом нанопорового секвенирования в 2022 г. был проведён первичный скрининг бактериального сообщества полей в трёх административных районах Свердловской области: город Екатеринбург, Белоярский и Сысертский районы. В результате до уровня вида была определена 2371 операционная таксономическая единица (ОТЕ). Более половины относительного бактериального обилия занимал филум Proteobacteria. Более трети всего бактериального сообщества приходилось на три порядка: Burkholderiales, Hyphomicrobiales и Acidobacteriales. Наиболее распространены в обрабатываемых сельскохозяйственных почвах Свердловской области рода бактерий: Bradyrhizobium, Massilia, Gaiella, Sphingomonas, Lysobacter и Gemmatimonas. Полученные результаты анализа альфа- и бета-разнообразия позволили заключить, что, несмотря на статистически значимую разницу в численности обнаруженных ОТЕ между некоторыми полями, различие в их разнообразии по объектам исследования в административных районах Свердловской области отсутствует.

1. Young I. M., Crawford J. W. Interactions and self-organization in the soil-microbe complex. Science. 2004;304(5677):1634-1637. DOI: https://www.science.org/doi/10.1126/science.1097394

2. Roger-Estrade J., Christel A., Bertrand M., Richard G. Tillage and soil ecology: Partners for sustainable agriculture. Soil and Tillage Research. 2010;111(1):33-40. DOI: https://doi.org/10.1016/j.still.2010.08.010

3. Brussaard L., Ruiter P., Brown G. Soil biodiversity for agricultural sustainability. Agriculture, Ecosystems & Environment. 2007;121(3):233-244. DOI: https://doi.org/10.1016/j.agee.2006.12.013

4. Zelles L. Fatty acids patterns of phospholipids and lipopolysacharides in the characterisation of microbial communities in soil: a review. Biology and Fertility of Soils. 1999;29:111-129. DOI: https://doi.org/10.1007/s003740050533

5. Zornoza R., Guerrero C., Mataix-Solera J., Scow K. M., Arcenegui V., Mataix-Beneyto J. Changes in soil microbial community structure following the abandonment of agricultural terraces in mountainous areas of Eastern Spain. Appl Soil Ecol. 2009:42(3);315-323. DOI: https://doi.org/10.1016/j.apsoil.2009.05.011

6. Fürnkranz M., Lukesch B., Müller H., Huss H., Grube M., Berg G. Microbial diversity inside pumpkins: Microhabitat-specific communities display a high antagonistic potential against phytopathogens. Microbial Ecology. 2012;63:418-428. DOI: https://doi.org/10.1007/s00248-011-9942-4

7. Glassner H., Zchori-Fein E., Compant S., Sessitsch A., Katzir N., Portnoy V., Yaron S. Characterization of endophytic bacteria from cucurbit fruits with potential benefits to agriculture in melons (Cucumis melo L.). FEMS Microbiology Ecology. 2015;91(7):fiv074. DOI: https://doi.org/10.1093/femsec/fiv074

8. Kõiv V., Roosaare M., Vedler E., Ann Kivistik P., Toppi K., Schryer D. W., Remm M., Tenson T., Mäe A. Microbial population dynamics in response to Pectobacteriumatrosepticum infection in potato tubers. SciRep. 2015;5:11606. DOI: https://doi.org/10.1038/srep11606

9. EFSA Panel on Plant Protection Products and their Residues (PPR), Ockleford C., Adriaanse P., Berny P., Brock T., Duquesne S., Grilli S., Hernandez-Jerez A. F., Bennekou S. H., Klein M., Kuhl M., Laskowski R., Machera K., Pelkonen O., Pieper S., Stemmer M., Sundh I., Teodorovic I., Tiktak A., Topping C. J., Wolterink G., Craig P., de Jong F., Manachini B., Sousa P., Swarowsky K., Auteri D., Arena M., Rob S. Scientific Opinion addressing the state of the science on risk assessment of plant protection products for in-soil organisms. EFSA Journal. 2017;15(2):e04690. DOI: https://doi.org/10.2903/j.efsa.2017.4690

10. Inceoglu Ö., van Overbeek L. S., Falcão Salles J., van Elsas J. D. Normal operating range of bacterial communities in soil used for potato cropping. Applied and Environmental Microbiology. 2013;79(4):1160-1170. DOI: https://doi.org/10.1128/AEM.02811-12

11. Gu S., Xiong X., Tan L., Deng Y., Du X., Yang X., Hu Q. Soil microbial community assembly and stability are associated with potato (Solanum tuberosum L.) fitness under continuous cropping regime. Front Plant Sci. 2022;13:1000045. DOI: https://doi.org/10.3389/fpls.2022.1000045

12. Buchholz F., Antonielli L., Kostić T., Sessitsch A., Mitter B. The bacterial community in potato is recruited from soil and partly inherited across generations. PLoS One. 2019;14(11):e0223691. DOI: https://doi.org/10.1371/journal.pone.0223691

13. Kracmarova M., Karpiskova J., Uhlik O., Strejcek M., Szakova J., Balik J., Demnerova K., Stiborova H. Microbial communities in soils and endosphere of Solanum tuberosum L. and their response to long-term fertilization. Microorganisms. 2020;8(9):1377. DOI: https://doi.org/10.3390/microorganisms8091377

14. Qin S., Yeboah S., Xu X., Liu Y., Yu B. Analysis on fungal diversity in rhizosphere soil of continuous cropping potato subjected to different furrow-ridge mulching managements. Frontiers in Microbiology. 2017;(8):845. DOI: https://doi.org/10.3389/fmicb.2017.00845

15. Linz A. M., Crary B. C., Shade A., Owens S., Gilbert J. A., Knight R., McMahon K. D. Bacterial community composition and dynamics spanning five years in freshwater bog lakes. ASM Journals. MSphere. 2017;2(3):e00169. DOI: https://doi.org/doi:10.1128/mSphere.00169-17

16. McMurdie P. J., Holmes S. Phyloseq: An R package for reproducible interactive analysis and graphics of microbiome census data. PLoS One. 2013;8(4):e61217. DOI: https://doi.org/10.1371/journal.pone.0061217

17. Shin J., Lee S., Go M. J., Lee S. Y., Kim S. C., Lee C. H., Cho B. K. Analysis of the mouse gut microbiome using full-length 16S rRNA amplicon sequencing. Scientific Reports. 2016;6:29681. DOI: https://doi.org/10.1038/srep29681

18. Johnson J. S., Spakowicz D. J., Hong B. Y., Petersen L. M., Demkowicz P., Chen L., Leopold S. R., Hanson B. M., Agresta H. O., Gerstein M., Sodergren E., Weinstock G. M. Evaluation of 16S rRNA gene sequencing for species and strain-level microbiome analysis. Nature Communications. 2019;10(1):5029. DOI: https://doi.org/10.1038/s41467-019-13036-1

19. Penton C. R., Gupta V. V., Yu J., Tiedje J. M. Size matters: assessing optimum soil sample size for fungal and bacterial community structure analyses using high throughput sequencing of rRNA gene amplicons. Frontirs in Microbiology. 2016;7:824. DOI: https://doi.org/10.3389/fmicb.2016.00824

20. Morita H., Akao S. The effect of soil sample size, for practical DNA extraction, on soil microbial diversity in different taxonomic ranks. PLoS One. 2021;16(11):e0260121. DOI: https://doi.org/10.1371/journal.pone.0260121

21. Větrovský T., Baldrian P. The variability of the 16S rRNA gene in bacterial genomes and its consequences for bacterial community analyses. PLoS One. 2013;8(2):e57923. DOI: https://doi.org/10.1371/journal.pone.0057923

22. Louca S., Doebeli M., Parfrey L. W. Correcting for 16S rRNA gene copy numbers in microbiome surveys remains an unsolved problem. Microbiome 2018;6:41. DOI: https://doi.org/10.1186/s40168-018-0420-9

23. Klappenbach J. A., Saxman P. R., Cole J. R., Schmidt T. M. Rrndb: the ribosomal RNA operon copy number database. Nucleic Acids Research. 2001;29(1):181-184. DOI: https://doi.org/10.1093/nar/29.1.181

24. Starke R., Pylro V. S., Morais D. K. 16S rRNA gene copy number normalization does not provide more reliable conclusions in metataxonomic surveys. Microbial Ecology. 2021;81:535-539. DOI: https://doi.org/10.1007/s00248-020-01586-7

25. Gao Y., Wu M. Accounting for 16S rRNA copy number prediction uncertainty and its implications in bacterial diversity analyses. ISME Communications. 2023;3(1):59. DOI: https://doi.org/10.1038/s43705-023-00266-0

26. Charkowski A., Sharma K., Parker M. L., Secor G. A., Elphinstone J. Bacterial diseases of potato. In: Campos H., Ortiz O. (eds) The Potato Crop. Springer, Cham. 2020. pp. 351-388. DOI: https://doi.org/10.1007/978-3-030-28683-5_10

27. Voronina O. L., Kunda M. S., Ryzhova N. N., Aksenova E. I., Semenov A. N., Lasareva A. V., Amelina E. L., Chuchalin A. G., Lunin V. G., Gintsburg A. L. The variability of the order Burkholderiales representatives in the healthcare units. BioMed Research International. 2015;2015:680210. DOI: https://doi.org/10.1155/2015/680210

28. Volpiano C. G., Sant'Anna F. H., Ambrosini A., de São José J. F. B., Beneduzi A., Whitman W. B., de Souza E. M., Lisboa B. B., Vargas L. K., Passaglia L. M. P. Genomic metrics applied to Rhizobiales (Hyphomicrobiales): species reclassification, identification of unauthentic genomes and false type strains. Frontiers in Microbiology. 2021;12:614957. DOI: https://doi.org/10.3389/fmicb.2021.614957

29. Quaiser A., Ochsenreiter T., Lanz C., Schuster S. C., Treusch A. H., Eck J., Schleper C. Acidobacteria form a coherent but highly diverse group within the bacterial domain: evidence from environmental genomics. Molecular Microbiology. 2003;50(2):563-575. DOI: https://doi.org/10.1046/j.1365-2958.2003.03707.x

30. Tian B., Yang J., Zhang K. Q. Bacteria used in the biological control of plant-parasitic nematodes: populations, mechanisms of action, and future prospects. FEMS Microbiology Ecology. 2007;61(2):197-213. DOI: https://doi.org/10.1111/j.1574-6941.2007.00349.x

31. Postma J., Schilder M. T., Bloem J., Van Leeuwen-Haagsma W. K. Soil suppressiveness and functional diversity of the soil microflora in organic farming systems. Soil Biology and Biochemistry, 2008;40(9):2394-2406. DOI: https://doi.org/10.1016/j.soilbio.2008.05.023

32. Duran D., Rey L., Navarro A., Busquets A., Imperial J., Ruiz-Argüeso T. Bradyrhizobiumvalentinum sp. nov., isolated from effective nodules of Lupinus mariae-josephae, a lupine endemic of basic-lime soils in Eastern Spain. Systematic and Applied Microbiology. 2014;37(5):336-341. DOI: https://doi.org/10.1016/j.syapm.2014.05.002

33. Helene L. C. F., Delamuta J. R. M., Ribeiro R. A., Hungria M. Bradyrhizobiummercantei sp. nov., a nitrogen-fixing symbiont isolated from nodules of Degueliacostata (syn. Lonchocarpuscostatus). International Journal of Systematic and Evolutionary Microbiology. 2017;67(6):1827-1834. DOI: https://doi.org/10.1099/ijsem.0.001870

34. 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. International Journal of Systematic and Evolutionary Microbiology. 2003;53(4):1155-1163. DOI: https://doi.org/10.1099/ijs.0.02520-0

35. Ofek M., Hadar Y., Minz D. Ecology of root colonizing Massilia (Oxalobacteraceae). PLoS One. 2012;7(7):e40117. DOI: https://doi.org/10.1371/journal.pone.0040117

36. Macchi M., Martinez M., NemeTauil R. M., Valacco M. P., Morelli I. S., Coppotell B. M. Insights into the genome and proteome of Sphingomonas paucimobilis strain 20006FA involved in the regulation of polycyclic aromatic hydrocarbon degradation. World Journal of Microbiology and Biotechnology. 2017;34(1):7. DOI: https://doi.org/10.1007/s11274-017-2391-6

37. Li R., Dörfler U., Munch J. C., Schroll R. Enhanced degradation of isoproturon in an agricultural soil by a Sphingomonas sp. strain and a microbial consortium. Chemosphere. 2017;168:1169-1176. DOI: https://doi.org/10.1016/j.chemosphere.2016.10.084

38. Mazoyon C., Hirel B., Pecourt A., Catterou M., Gutierrez L., Sarazin V., Dubois F., Duclercq J. Sphingomonasse diminicola is an end osymbiotic bacterium able to induce the formation of root nodules in pea (Pisum sativum L.) And to enhance plant biomass production. Microorganisms. 2023;11(1):199. DOI: https://doi.org/10.3390/microorganisms11010199

39. Ahn J. H., Lee S. A., Kim J. M., Kim M. S., Song J., Weon H. Y. Dynamics of bacterial communities in rice field soils as affected by different long-term fertilization practices. Journal of Microbiology. 2016;54(11):724-731. DOI: https://doi.org/10.1007/s12275-016-6463-3

40. Cordero J., de Freitas J. R., Germida J. J. Bacterial microbiome associated with the rhizosphere and root interior of crops in Saskatchewan, Canada. Canadian Journal of Microbiology. 2020;66(1):71-85. DOI: https://doi.org/10.1139/cjm-2019-0330

41. Kim H., Park Y. H., Yang J. E., Kim H. S., Kim S. C., Oh E. J., Moon J., Cho W., Shin W., Yu C. Analysis of major bacteria and diversity of surface soil to discover biomarkers related to soil health. Toxics. 2022;10(3):117. DOI: https://doi.org/10.3390/toxics10030117