Comparative Analysis of Microbial Communities of Contrasting Soil Types in Different Plant Communities
Abstract
Microbiomes were analyzed in samples of the major soil types of Russia and Western Kazakhstan region from different plant communities (fallow, forest, agrophytocenosis). The representatives of 42 bacterial and 2 archaeal phyla were identified in the samples, among which the dominant positions were occupied by representatives of ten phyla: nine bacterial (Actinobacteria (33.5%), Proteobacteria (28.4%), Acidobacteria (8.3%), Verrucomicrobia (7.7%), Bacteroidetes (4.2%), Chloroflexi (3.0%), Gemmatimonadetes (2.3%), Firmicutes (2.1%), Planctomycetes (2.0%)) and one archaeal Crenarchaeota (2.6%). Data analysis by the methods of multivariate statistics suggests that the taxonomic structure of microbiota is formed under the action of two main factors: the strongest factor is soil acidity, which determines the dynamics of the microbiome at the level of major taxa such as phylum, and the weaker factor is the type of vegetation, which determines the community structure at lower taxonomic level (order, family, genus). Detailed analysis of the samples of podzolic soil in Leningrad Region made it possible to identify bacterial taxa specifically associated both with the type of biome (fallow, forest, agrophytocenosis) and with the specific plant community (specific composition of plant synusia).
Keywords
soil microbiome high-throughput sequencing synusiaePreview
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References
- 1.Drenovsky, R.E., Vo, D., Graham, K.J., et al., Soil water content and organic carbon availability are major determinants of soil microbial community composition, Microb. Ecol., 2004, vol. 48, pp. 424–430.CrossRefPubMedGoogle Scholar
- 2.Lauber, C.L., Hamady, M., Knight, R., and 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. 15, no. 75, pp. 5111–5120.CrossRefGoogle Scholar
- 3.Lozupone, C.A. and Knight, R., Global patterns in bacterial diversity, Proc. Natl. Acad. Sci. U. S. A., 2007, vol. 104, no. 27, pp. 11436–11440.CrossRefPubMedPubMedCentralGoogle Scholar
- 4.Rousk, J., Baath, E., Brookes, P.C., et al., Soil bacterial and fungal communities across a Ph gradient in an arable soil, ISME J., 2010, vol. 4, pp. 1340–1351.CrossRefPubMedGoogle Scholar
- 5.Eisenhauer, N., Bebler, H., Scherber, C., et al., Plant diversity effects on soil microorganisms support the singular hypothesis, Ecology, 2010, vol. 91.Google Scholar
- 6.Schlatter, D.C., Bakker, M.G., Bradeen, J.M., and Kinkel, L.L., Plant community richness and microbial interactions structure bacterial communities in soil, Ecology, 2014, vol. 96, pp. 134–142.CrossRefGoogle Scholar
- 7.Prober, S.M., Leff, J.W., Bates, S.T., et al., Plant diversity predicts beta but not alpha diversity of soil microbes across grasslands worldwide, Ecol. Lett., 2015, vol. 18, pp. 85–95.CrossRefPubMedGoogle Scholar
- 8.Caporaso, J.G., Kuczynski, J., Stombaugh, J., et al., QIIME allows analysis of high-throughput community sequencing data, Nat. Methods, 2010, vol. 5, no. 7, pp. 335–336.CrossRefGoogle Scholar
- 9.Edgar, R.C., Search and clustering orders of magnitude faster than blast, Bioinformatics, 2010, vol. 26, no 19, pp. 2460–2461.CrossRefPubMedGoogle Scholar
- 10.Kurahashi, M., Fukunaga, Y., Sakiyama, Y., et al., Euzebya tangerina gen. nov., sp. nov., a deeply branching marine actinobacterium isolated from the sea cucumber Holothuria edulis, and proposal of Euzebyaceae fam. nov., Euzebyales ord. nov., and Nitriliruptoridae subclassis nov., Int. J. Syst. Evol. Microbiol., 2010, vol. 60, pp. 2314–2319.CrossRefPubMedGoogle Scholar
- 11.Acosta-Martinez, V., Dowd, S.E., Bell, C., et al., Microbial community comparison as affected by dryland cropping systems and tillage in a semiarid sandy soil, Diversity, 2010, vol. 2, pp. 910–931.CrossRefGoogle Scholar
- 12.The Family Paenibacillaceae, Zeigler, D.R., Ed., BGSC, 2013.Google Scholar
- 13.Singh, A.K., Singh, M., and Dubey, S.K., Changes in actinomycetes community structure under the influence of Bt transgenic brinjal crop in a tropical agroecosystem, BMC Microbiol., 2013, vol. 13, no. 122, pp. 1–12.Google Scholar
- 14.Schellenberger, S., Kolb, S., and Drake, H.L., Metabolic responses of novel cellulolytic and saccharolytic agricultural soil bacteria to oxygen, Environ. Microbiol., 2010, vol. 4, pp. 845–861.Google Scholar
- 15.Tkhakakhova, A.K., Vasilenko, E.S., and Kutovaya, O.V., Effect of mineral fertilizers on microbiological and biochemical characteristics of agrochernozem, Geophys. Res. Abstr. EGU General Assembly, 2013, vol. 15, pp. EGU2013–EGU1219.Google Scholar
- 16.Ding, G.-C., Piceno, Y.M., Heuer, H., et al., Changes of soil bacterial diversity as a consequence of agricultural land use in a semi-arid ecosystem, PLOS ONE, 2013, vol. 8, no. 3, pp. 1–10.Google Scholar
- 17.Pershina, E., Valkonen, J., Kurki, P., et al., Comparative analysis of prokaryotic communities associated with organic and conventional farming systems, PLOS ONE, 2015, vol. 10, no. 12, e0145072. doi 10.1371/journal. pone.0145072CrossRefPubMedPubMedCentralGoogle Scholar