Assessment of the effect of soil physico-chemical properties on the bacterial community structure
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Assessment of the effect of soil physico-chemical properties on the bacterial community structure

L.R. Biktasheva*, A.A. Saveliev**, S.Y. Selivanovskaya***, P.Y. Galitskaya****

Kazan Federal University, Kazan, 420008 Russia

E-mail: *biktasheval@mail.ru, **Anatoly.Saveliev.aka.saa@gmail.com, ***svetlana.selivanovskaya@kpfu.ru, ****gpolina33@yandex.ru

Received March 12, 2018

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Abstract

The physico-chemical properties of soils determine their potential as a habitat for living species. They influence the state of soil flora and fauna, the diversity of soil microbiome in particular. In the present study, particle size distribution, pH, and organic carbon content have been analyzed in 25 soil samples representing 8 different soil types. It has been found that the pH values vary in the range from 5.05 (sample no. 4) to 7.29 (sample no. 19), while the organic carbon content change from 0.72% (sample no. 2) to 4.54% (sample no. 19). According to the analysis of particle size distribution, particles of 2–50 μm in size dominate in the majority of samples and particles greater 50 μm occur in samples no. 5 and 6. The species composition and abundance of bacteria in the soil samples have been estimated by the Illumina MiSeq method. A total of 443 unique OTUs have been identified in 6 soil samples. The dominant taxa at the phylum level include Verrucomicrobia, Proteobacteria, Gemmatimonadetes, Bacteroidetes, Actinobacteria, Acidobacteria, while Chloroflexi phylym is also abundant in samples no. 18, 12, 19, and 23. The MDS (multidimentional scaling) method has been used to determine the similarities and differences between the soil samples based on: 1) their physico-chemical characteristics and 2) bacterial diversity. It has been shown that the physico-chemical characteristics are not the only determinants for the structure of soil bacterial community.

Keywords: physico-chemical characteristics of soils, soil microbial community, next-generation sequencing

Acknowledgments. The study was supported by the Russian Science Foundation (project no. 17-7420183).

Figure Captions

Fig. 1. Map of sampling sites.

Fig. 2. pH of water extracts from the soil samples under study.

Fig. 3. Total organic carbon content in the soil samples under study.

Fig. 4. MDS plots representing the diversity of soil samples on the basis of three physico-chemical characteristics.

Fig. 5. Structure of the bacterial community of soils under study.

Fig. 6. MDS plots representing the diversity of soil samples on the basis of bacterial community structure.

References

  1. Szoboszlay M., Dohrmann, A.B., Poeplau C., Axel D., Tebbe C.C. Impact of land-use change and soil organic carbon quality on microbial diversity in soils across Europe. FEMS Microbiol. Ecol., 2017, vol. 93, no. 12, pp. 1–12. doi: 10.1093/femsec/fix146.
  2. Chmolowska D., Elhottová D., Krištůfek V., Kozak M., Kapustka F., Zubek S. Functioning grouped soil microbial communities according to ecosystem type, based on comparison of fallows and meadows in the same region. Sci. Total Environ., 2017, vol. 599–600, pp. 981–991. doi: 10.1016/j.scitotenv.2017.04.220.
  3. Kang H. Gao H., Yu W., Yi Y., Wang Y., Ning M. Changes in soil microbial community structure and function after afforestation depend on species and age: Case study in a subtropical alluvial island. Sci. Total Environ., 2018, vol. 625, pp. 1423–1432. doi: 10.1016/j.scitotenv.2017.12.180.
  4. Ivanova E.A., Pershina E.V., Kutovaya A.V., Sergalieva N.Kh., Nagieva A.G., Zhiengaliev A.T., Provorov N.A., Andronov E.E. Comparative analysis of microbial communities of contrasting soil types in different phytocenoses. Ekologiya, 2018, no. 1, pp. 34–44. doi: 10.7868/S0367059718010043. (In Russian)
  5. Liu D., Huang Y., An Sh., Sun H., Bhople P., Chen Zh. Soil physicochemical and microbial characteristics of contrasting land-use types along soil depth gradients. Catena, 2018, vol. 162, pp. 345–353. doi: 10.1016/j.catena.2017.10.028.
  6. Sánchez-Marañón M., Miralles I., Aguirre-Garrido J.F., Anguita-Maeso M., Millán V., Ortega R., García-Salcedo J.A., Martínez-Abarca F., Soriano M. Changes in the soil bacterial community along a pedogenic gradient. Sci. Rep., 2017, vol. 7, no. 1, art. 14593, pp. 1–11. doi: 10.1038/s41598-017-15133-x.
  7. Fierer N., Jackson R.B. The diversity and biogeography of soil bacterial communities. Proc. Natl. Acad. Sci. U. S. A., 2006, vol. 103, no. 3, pp. 626–631. doi: 10.1073/pnas.0507535103.
  8. Lauber C.L., Hamady M., Knight R., Fierer N. Pyrosequencing-based assessment of soil pH as a predictor of soil bacterial community structure at the continental scale. Appl. Environ. Microbiol., 2009, vol. 75, no. 15, pp. 5111–5120. doi: 10.1128/AEM.00335-09.
  9. Jones R.T., Robeson M.S., Lauber C.L., Hamady M., Knight R., Fierer N. A comprehensive survey of soil acidobacterial diversity using pyrosequencing and clone library analyses. ISME J., 2009, vol. 3, no. 4, pp. 442–453. doi: 10.1038/ismej.2008.127.
  10. Fierer N., Lauber C.L., Ramirez K.S., Zaneveld J., Bradford M.A., Knight R. Comparative metagenomic, phylogenetic and physiological analyses of soil microbial communities across nitrogen gradients. ISME J., 2012, vol. 6, no. 5, pp. 1007–1017. doi: 10.1038/ismej.2011.159.
  11. Ma B., Wang H., Dsouza M., Lou J., He Y., Dai Zh., Brookes, P., Xu J., Gilbert J. Geographic patterns of co-occurrence network topological features for soil microbiota at continental scale in eastern China. ISME J., 2016, vol. 10, no. 8, pp. 1891–1901. doi: 10.1038/ismej.2015.261.
  12. Shinkarev A.A., Kornilova A.G., Trofimova F.A., Gordeev A.S., Ginijatullin K.G., Lygina T.Z., Comparison of sedimentometric analysis with laser grain size analysis for the determination of particle-size distribution of the soil clay fraction. Uchenye Zapiski Kazanskogo Universiteta. Seriya Estestvennye Nauki, 2010, vol. 152, no. 2, pp. 252–260. (In Russian)
  13. Bystrianský L., Štofik M., Gryndler M. Soil-derived organic particles and their effects on the community of culturable microorganisms. Folia Microbiol. (Praha), 2018, vol. 63, no. 1, pp. 69–72. doi: 10.1007/s12223-017-0537-4.
  14. Jurelevicius D., Cotta S., Peixoto R., Rosado A., Seldin L. Distribution of alkane-degrading bacterial communities in soils from King George Island, Maritime Antarctic. Eur. J. Soil Biol., 2012, vol. 51, pp. 37–44. doi: 10.1016/j.ejsobi.2012.03.006.
  15. Margesin R., Labbé D., Schinner F., Greer C.W., Whyte L.G. Characterization of hydrocarbon-degrading microbial populations in contaminated and pristine Alpine soils. Appl. Environ. Microbiol., 2003, vol. 69, no. 6, pp. 3085–3092. doi: 10.1128/AEM.69.6.3085-3092.2003.
  16. Noronha M.F., Lacerda J.G., Gilbert J., de Oliveira V. Taxonomic and functional patterns across soil microbial communities of global biomes. Sci. Total Environ., 2017, vol. 609, pp. 1064–1074. doi: 10.1016/j.scitotenv.2017.07.159.
  17. Blagodatskii S.A., Blagodatskaya E.V. Dynamics of microbial biomass and ratio of eukaryote and prokaryote microorganisms in grey forest soil. Pochvovedenie, 1996, no. 12, pp. 1485–1490. (In Russian)
  18. Velvis H. Evaluation of the selective respiratory inhibition method for measuring the ratio of fungal:bacterial activity in acid agricultural soils. Biol. Fertil. Soils, 1997, vol. 25, no. 4, pp. 354–360. doi: 10.1007/s003740050325.
  19. Schmidt N., Bolter M. Fungal and bacterial biomass in tundra soils along an arctic transect from Taimyr Peninsula, central Siberia. Polar Biol., 2002, vol. 25, no. 12, pp. 871–877. doi: 10.1007/s00300-002-0422-7.
  20. Li X., Lin X., Li P., Liu W., Wang L., Ma F., Chukwuka K.S. Biodegradation of the low concentration of polycyclic aromatic hydrocarbons in soil by microbial consortium during incubation. J. Hazard. Mater., 2009, vol. 172, nos. 2–3, pp. 601–605. doi: 10.1016/j.jhazmat.2009.07.044.
  21. Martens R. Current methods for measuring microbial biomass C in soil: Potentials and limitations. Biol. Fertil. Soils, 1995, vol. 19, nos. 2–3, pp. 87–99. doi: 10.1007/BF00336142.
  22. Colloff M.J. Wakelin S.A., Gomez D., Rogers S.L. Detection of nitrogen cycle genes in soils for measuring the effects of changes in land use and management. Soil Biol. Biochem., 2008, vol. 40, no. 7, pp. 1637–1645. doi: 10.1016/j.soilbio.2008.01.019.
  23. Macdonald C.A., Thomas N., Robinson L., Tate K., Ross D., Dando J., Singh B. Physiological, biochemical and molecular responses of the soil microbial community after afforestation of pastures with Pinus radiate. Soil Biol. Biochem., 2009, vol. 41, no. 8, pp. 1642–1651. doi: 10.1016/j.soilbio.2009.05.003.
  24. Anderson T.H., Domsch K.H. Soil microbial biomass: The eco-physiological approach. Soil Biol. Biochem., 2010. vol. 42, no. 12, pp. 2039–2043. doi: 10.1016/j.soilbio.2010.06.026.
  25. Ermolaev O.P., Igonin M.E., Bubnov A.Yu., Pavlova S.V. Landshafty Respubliki Tatarstan. Regional'nyi landshaftno-ekologicheskii analiz [Landscapes of Tatarstan Republic. Regional Landscape and Ecological Analysis]. Ermolaev O.P. (Еd.). Kazan, Slovo. 2007. 411 p. (In Russian)
  26. ISO 14235:1998(en). Soil quality – determination of organic carbon by sulfochromic oxidation. 1998. 5 p.
  27. ISO 10390:2005(E). Soil quality – determination of pH. 2005. 5 p.
  28. ISO 13320:2009(en). Particle size analysis – laser diffraction methods. 2009. 51 p.
  29. ISO/TS 17892-4:2004. Geotechnical investigation and testing – Laboratory testing of soil. Part 4: Determination of particle size distribution. 2010. 10 p.
  30. Caporaso J.G., Kuczynski J., Stombaugh J., Bittinger K., Bushman F.D., Costello E.K., Fierer N., Peña A.G., Goodrich J.K., Gordon J.I. QIIME allows analysis of high-throughput community sequencing data. Nat. Methods, 2010, vol. 7, no. 5, pp. 335–336. doi: 10.1038/nmeth.f.303.
  31. Edgar R.C. Search and clustering orders of magnitude faster than BLAST. Bioinformatics, 2010, vol. 26, no. 19, pp. 2460–2461. doi: 10.1093/bioinformatics/btq461.
  32. Wang Q., Garrity G., Tiedje J., Cole J. Naïve Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl. Environ. Microbiol., 2007, vol. 73, no. 16, pp. 5261–5267. doi: 10.1128/AEM.00062-07.
  33. Team R. R development core team. R A Lang. Environ. Stat. Comput., 2013, vol. 55, pp. 275–286.
  34. Faith D.P., Minchin P.R., Belbin L. Compositional dissimilarity as a robust measure of ecological distance. Vegetatio, 1987, vol. 69, nos. 1–3, pp. 57–68. doi: 10.1007/BF00038687.
  35. Vershinin A.A., Petrov A.M., Akaikin DV., Ignatev Yu.A Assessing the biological activity of oil-contaminated soddy-podzolic soils with different textures. Eurasian Soil Sci., 2014, no. 2, pp. 250–256. (In Russian)
  36. Soil Texture Triangle. In: Natural Resources Conservation Service Soils. United States Department of Agriculture. Available at: https://www.nrcs.usda.gov/wps/portal/nrcs/detail/soils/survey/ ?cid=nrcs142p2_054167.
  37. World Reference Base for Soils Resources. World Soil Resource Report No. 103. Rome, Italy, FAO, 2006. 145 p.
  38. Kovda V.A., Rozanov B.G. Pochvovedenie. Ch. 2. Tipy pochv, ikh geografiya i ispol'zovanie [Soil Science: Soil Types, Their Geography, and Use]. Moscow, Vyssh. Shk., 1988. 368 p. (In Russian)
  39. Ivanov A.L., Shoba S.A. Unified State Register of Soil Resources of Russia. Available at: http://infosoil.ru/reestr/content/1sem.php. (In Russian)
  40. Lefèvre C., Rekik F., Alcantara V., Wiese L. Soil Organic Carbon the Hidden Potential. Rome, Italy, FAO, 2017. 90 p.
  41. Villarino S.H., Studdert G., Laterra P., Cendoya M. Agricultural impact on soil organic carbon content: Testing the IPCC carbon accounting method for evaluations at county scale. Agric., Ecosyst. Environ., 2014, vol. 185, pp. 118–132. doi: 10.1016/j.agee.2013.12.021.
  42. Lauber C.L., Strickland M., Bradford M., Fierer N. The influence of soil properties on the structure of bacterial and fungal communities across land-use types. Soil Biol. Biochem., 2008, vol. 40, no. 9, pp. 2407–2415. doi: 10.1016/j.soilbio.2008.05.021.
  43. Dumova V.A., Pershina E.B., Merzlykova A.V., Kruglov Yu.V., Andronov E.E. The main trends in formation of the soil microbial community under the conditions of stationary field experiment from the data of next-generation sequencing of the 16S rRNA gene libraries. S-kh. Biol., 2013, no. 5, pp. 87–92. (In Russian)
  44. Brewer T.E, Handley K., Carini P., Gilbert J., Fierer N. Genome reduction in an abundant and ubiquitous soil bacterium “Candidatus Udaeobacter copiosus”. Nat. Microbiol., 2016, vol. 2, art. 16198, pp. 1–7. doi: 10.1038/nmicrobiol.2016.198.
  45. Sangwan P., Chen X., Hugenholtz P., Janssen P. 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, vol. 70, no. 10, pp. 5875–5881. doi: 10.1128/AEM.70.10.5875-5881.2004.
  46. Eichorst S.A., Varanasi P., Stavila V., Zemla M., Auer M., Singh S., Simmons B., Singer S. Community dynamics of cellulose-adapted thermophilic bacterial consortia. Environ. Microbiol., 2013, vol. 15, no. 9, pp. 2573–2587. doi: 10.1111/1462-2920.12159.
  47. Wu S.H., Huang B.H., Huang Ch.L., Li G., Liao P.Ch. The aboveground vegetation type and underground soil property mediate the divergence of soil microbiomes and the biological interactions. Microb. Ecol., 2018, vol. 75, no. 2, pp. 434–446. doi: 10.1007/s00248-017-1050-7.

 

For citation: Biktasheva L.R., Saveliev A.A., Selivanovskaya S.Y., Galitskaya P.Y. Assessment of the effect of soil physico-chemical properties on the bacterial community structure. Uchenye Zapiski Kazanskogo Universiteta. Seriya Estestvennye Nauki, 2018, vol. 160, no. 2, pp. 240–258. (In Russian)

 

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