Abstract
The diversity indices used in ecology for assessing the metagenomes of soil prokaryotic communities at different phylogenetic levels were compared. The following indices were considered: the number of detected taxa and the Shannon, Menhinick, Margalef, Simpson, Chao1, and ACE indices. The diversity analysis of the prokaryotic communities in the upper horizons of a typical chernozem (Haplic Chernozem (Pachic)), a dark chestnut soil (Haplic Kastanozem (Chromic)), and an extremely arid desert soil (Endosalic Calcisol (Yermic)) was based on the analysis of 16S rRNA genes. The Menhinick, Margalef, Chao1, and ACE indices gave similar results for the classification of the communities according to their diversity levels; the Simpson index gave good results only for the high-level taxa (phyla); the best results were obtained with the Shannon index. In general, all the indices used showed a decrease in the diversity of the soil prokaryotes in the following sequence: chernozem > dark chestnut soil > extremely arid desert soil.
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References
E. E. Andronov, A. G. Pinaev, E. V. Pershina, and E. P. Chizhevskaya, Isolation of DNA from Soil Samples: Methodological Guidelines (All-Russia Research Institute of Agricultural Microbiology, St. Petersburg, 2011) [in Russian].
E. S. Vasilenko, O. V. Kutovaya, A. K. Tkhakakhova, and A. S. Martynov, “Changes in the intensity of soil biological processes as dependent on the size of aggregates in the migration-micellar chernozem,” Byull. Pochv. Inst. im. V.V. Dokuchaeva, No. 73, 85–97 (2014).
Yu. G. Evstifev, “Soils of extremely arid regions in the People’s Republic of Mongolia,” in The V Congress of Soviet Soil Science Society, Abstracts of Papers (Minsk, 1977), No. 6, pp. 172–175.
Unified State Register of Soil Resources of Russia, Ver. 1.0 (Dokuchaev Soil Science Institute, Moscow, 2014) [in Russian].
Classification and Diagnostics of Soils in the Soviet Union (Kolos, Moscow, 1977) [in Russian].
O. V. Kutovaya, E. S. Vasilenko, and M. P. Lebedeva, “Microbiological and micromorphological characteristics of extremely arid desert soils in the Ili Depression (Kazakhstan),” Eurasian Soil Sci. 45(12), 1147–1158 (2012).
A. Magurran, Ecological Diversity and Its Measurement (Princeton University Press, New Jersey, 1988).
V. V. Parfenova, A. S. Gladkikh, and O. I. Belykh, “Comparative analysis of biodiversity in the planktonic and biofilm bacterial communities in Lake Baikal,” Microbiology (Moscow) 82(1), 91–101 (2013).
E. V. Pershina, G. S. Tamazyan, A. S. Dol’nik, A. G. Pinaev, N. Kh. Sergaliev, and E. E. Andronov, “Analysis of the structure of microbial community in saline soils using high-performance sequencing,” Ekol. Genet. 10(2), 31–38 (2012).
E. L. Chirak, E. V. Pershina, A. S. Dol’nik, O. V. Kutovaya, E. S. Vasilenko, B. M. Kogut, Ya. V. Merzlyakova, and E. E. Andronov, “Taxonomic structure of microbial communities in different types of soils according to the high-performance sequencing of the libraries of 16S rRNA gene,” Sel’skokhoz. Biol., No. 3, 100–109 (2013).
V. K. Shitikov and G. S. Rozenberg, “Analysis of biological diversity: an attempt of formal generalization, in Structural Analysis of Ecological Systems. Quantitative Methods Applied in Ecology and Hydrobiology (Samara Scientific Center, Russian Academy of Sciences, Tolyatti, 2005), pp. 91–129.
S. Bates, D. Berg-Lyons, J. G. Caporaso, W. A. Walters, R. Knight, and N. Fierer, “Examining the global distribution of dominant archaeal populations in soil,” ISME J., No. 5, 908–917 (2011).
A. Chao, “Nonparametric estimation of the number of classes in a population,” Scand. J. Stat. 11, 265–270 (1984).
A. Chao, M.-C. Ma, and M. C. K. Yang, “Stopping rules and estimation for recapture debugging with unequal failure rates,” Biometrika 80, 193–201 (1993).
R. K. Colwell and J. A. Coddington, “Estimating terrestrial biodiversity through extrapolation,” Philos. Trans. R. Soc., B 345(1311), 101–118 (1994).
J. Hortal, P. A. V. Borges, and C. Gaspar, “Evaluating the performance of species richness estimators: sensitivity to sample grain size,” J. Anim. Ecol. 75, 274–287 (2006). doi: 10.1111/j.1365-2656.2006.01048.x
IUSS Working Group WRB, World Reference Base for Soil Resources 2014. International Soil Classification System for Naming Soils and Creating Legends for Soil Maps, in World Soil Resources Reports No. 106 (FAO, Rome, 2014).
K. S. Kakirde, L. C. Parsley, and M. R. Liles, “Size does matter: application-driven approaches for soil metagenomics,” Soil Biol. Biochem. 42, 1911–1923 (2010). doi: 10.1016/j.soilbio.2010.07.021
S.-M. Lee and A. Chao, “Estimating population size via sample coverage for closed capture-recapture models,” Biometrics 50, 88–97 (1994).
L. F. W. Roesch, R. R. Fulthorpe, A. Riva, et al., “Pyrosequencing enumerates and contrasts soil microbial diversity,” ISME J 1, 283–290 (2007).
S. G. Tringe and P. Hugenholtz, “A renaissance for the pioneering 16S rRNA gene,” Curr. Opin. Microbiol. 11, 442–446 (2008). doi: 10.1016/j.mib.2008.09.011
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Original Russian Text © T.I. Chernov, A.K. Tkhakakhova, O.V. Kutovaya, 2015, published in Pochvovedenie, 2015, No. 4, pp. 462–468.
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Chernov, T.I., Tkhakakhova, A.K. & Kutovaya, O.V. Assessment of diversity indices for the characterization of the soil prokaryotic community by metagenomic analysis. Eurasian Soil Sc. 48, 410–415 (2015). https://doi.org/10.1134/S1064229315040031
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DOI: https://doi.org/10.1134/S1064229315040031