Modern progress in soil biology is associated with the use of new molecular biology methods based on the isolation of total DNA from soil and its further analysis. The two main approaches to the study of soil microbial DNA are metabarcoding, the identification of the community composition via analysis of the sequences of barcode marker genes, and metagenomics, the analysis of the collective genomes of the community. These two methods provide direct access to the enormous genetic diversity of the “uncultivated majority” of soil microorganisms and have become an essential part of many soil biology studies. The review considers the application of these research methods to the study of the ecology and diversity of soil microorganisms. The methodological limitations of molecular genetics methods due to soil specificity as an object of research are discussed. The achievements, challenges, and prospects of metabarcoding and metagenomics in soil ecology research, as well as their combination with other research approaches, are considered.
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Abia, A.L.K., Alisoltani, A., Ubomba-Jaswa, E., and Dippenaar, M.A., Microbial life beyond the grave: 16S rRNA gene-based metagenomic analysis of bacteria diversity and their functional profiles in cemetery environments, Sci. Total Environ., 2019, vol. 655, pp. 831–841.
Angly, F.E., Dennis, P.G., Skarshewski, A., Vanwonterghem, I., Hugenholtz, P., and Tyson, G.W., CopyRighter: a rapid tool for improving the accuracy of microbial community profiles through lineage-specific gene copy number correction, Microbiome, 2014, vol. 2, p. 11.
Bailey, V.L., Smith, J.L., and Bolton, H., Jr., Fungal-to-bacterial ratios in soils investigated for enhanced C sequestration, Soil Biol. Biochem., 2002, vol. 34, no. 7, pp. 997–1007.
Bakker, P.A., Berendsen, R.L., Doornbos, R.F., Wintermans, P.C., and Pieterse, C.M., The rhizosphere revisited: root microbiomics, Front. Plant Sci., 2013, vol. 4, p. 165.
Baldrian, P., The known and the unknown in soil microbial ecology, FEMS Microbiol. Ecol., 2019, vol. 95, no. 2, art. ID fiz005.
Baldrian, P., Kolarik, M., Stursova, M., Kopecky, J., Valaskova, V., et al., Active and total microbial communities in forest soil are largely different and highly stratified during decomposition, ISME J., 2012, vol. 6, no. 2, pp. 248–258.
Balvociute, M. and Huson, D.H., SILVA, RDP, Greengenes, NCBI and OTT—how do these taxonomies compare? BMC Genome, 2017, vol. 18, no. 2, p. 114.
Banerjee, S., Schlaeppi, K., and Heijden, M.G., Keystone taxa as drivers of microbiome structure and functioning, Nat. Rev. Microbiol., 2018, vol. 16, pp. 567–576.
Banerjee, S., Walder, F., Buchi, L., Meyer, M., Held, A.Y., et al., Agricultural intensification reduces microbial network complexity and the abundance of keystone taxa in roots, ISME J., 2019, vol. 13, pp. 1722–1736.
Barberan, A., Bates, S.T., Casamayor, E.O., and Fierer, N., Using network analysis to explore co-occurrence patterns in soil microbial communities, ISME J., 2012, vol. 6, no. 2, pp. 343–351.
Bardgett, R.D., Bowman, W.D., Kaufmann, R., and Schmidt, S.K., A temporal approach to linking aboveground and belowground ecology, Trends Ecol. Evol., 2005, vol. 20, no. 11, pp. 634–641.
Bernard, L., Mougel, C., Maron, P.A., Nowak, V., Lévêque, J., et al., Dynamics and identification of soil microbial populations actively assimilating carbon from 13C-labelled wheat residue as estimated by DNA- and RNA-SIP techniques, Environ. Microbiol., 2007, vol. 9, no. 3, pp. 752–764.
Blagodatskaya, E. and Kuzyakov, Y., Active microorganisms in soil: critical review of estimation criteria and approaches, Soil Biol. Biochem., 2013, vol. 67, pp. 192–211.
Blagodatskaya, E.V., Semenov, M.V., and Yakushev, A.V., Aktivnost’ i biomassa pochvennykh mikroorganizmov v izmenyayushchikhsya usloviyakh okruzhayushchei sredy (Activity and Biomass of Soil Microorganisms in Changing of Environmental Conditions), Moscow: KMK, 2016.
Bohan, D.A., Vacher, C., Tamaddoni-Nezhad, A., Raybould, A., Dumbrell, A.J., and Woodward, G., Next-generation global biomonitoring: large-scale, automated reconstruction of ecological networks, Trends Ecol. Evol., 2017, vol. 32, no. 7, pp. 477–487.
Bouchez, T., Blieux, A.L., Dequiedt, S., Domaizon, I., Dufresne, A., et al., Molecular microbiology methods for environmental diagnosis, Environ. Chem. Lett., 2016, vol. 14, no. 4, pp. 423–441.
Callahan, B.J., McMurdie, P.J., and Holme, S.P., Exact sequence variants should replace operational taxonomic units in marker-gene data analysis, ISME J., 2017, vol. 11, no. 12, pp. 2639–2943.
Carini, P., Marsden, P.J., Leff, J.W., Morgan, E.E., Strickland, M.S., and Fierer, N., Relic DNA is abundant in soil and obscures estimates of soil microbial diversity, Nat. Microbiol., 2017, vol. 2, p. 16242.
Carugati, L., Corinaldesi, C., Dell’Anno, A., and Danovaro, R., Metagenetic tools for the census of marine meiofaunal biodiversity: an overview, Mar. Genomics, 2015, vol. 24, pp. 11–20.
Chen, C., Zhang, J., Lu, M., Qin, C., Chen, Y., et al., Microbial communities of an arable soil treated for 8 years with organic and inorganic fertilizers, Biol. Fertil. Soils, 2016, vol. 52, no. 4, pp. 455–467.
Coissac, E., Riaz, T., and Puillandre, N., Bioinformatic challenges for DNA metabarcoding of plants and animals, Mol. Ecol., 2012, vol. 21, no. 8, pp. 1834–1847.
D’Amore, R., Ijaz, U.Z., Schirmer, M., Kenny, J.G., Gregory, R., et al., A comprehensive benchmarking study of protocols and sequencing platforms for 16S rRNA community profiling, BMC Genome, 2016, vol. 17, p. 55.
da Rocha, U.N., Andreote, F.D., de Azevedo, J.L., van Elsas, J.D., and van Overbeek, L.S., Cultivation of hitherto-uncultured bacteria belonging to the Verrucomicrobia subdivision 1 from the potato (Solanum tuberosum L.) rhizosphere, J. Soils Sediments, 2010, vol. 10, no. 2, pp. 326–339.
Delmont, T.O., Prestat, E., Keegan, K.P., Faubladier, M., Robe, P., et al., Structure, fluctuation and magnitude of a natural grassland soil metagenome, ISME J., 2012, vol. 6, no. 9, pp. 1677–1687.
Ding, J., Zhang, Y., Deng, Y., Cong, J., Lu, H., et al., Integrated metagenomics and network analysis of soil microbial community of the forest timberline, Sci. Rep., 2015, vol. 5, p. 7994.
Eilers, K.G., Debenport, S., Anderson, S., and Fierer, N., Digging deeper to find unique microbial communities: the strong effect of depth on the structure of bacterial and archaeal communities in soil, Soil Biol. Biochem., 2012, vol. 50, pp. 58–65.
Esposito, A. and Kirschberg, M., How many 16S-based studies should be included in a metagenomic conference? It may be a matter of etymology, FEMS Microbiol. Lett., 2014, vol. 351, no. 2, pp. 145–146.
Fan, K., Weisenhorn, P., Gilbert, J.A., and Chu, H., Wheat rhizosphere harbors a less complex and more stable microbial co-occurrence pattern than bulk soil, Soil Biol. Biochem., 2018, vol. 125, pp. 251–260.
Fierer, N., Leff, J.W., Adams, B.J., Nielsen, U.N., Bates, S.T., et al., Cross-biome metagenomic analyses of soil microbial communities and their functional attributes, Proc. Natl. Acad. Sci. U.S.A., 2012. vol. 109, no. 52, pp. 21390–21395.
Fierer, N., Ladau, J., Clemente, J.C., Leff, J.W., Owens, S.M., et al., Reconstructing the microbial diversity and function of pre-agricultural tallgrass prairie soils in the United States, Science, 2013, vol. 342, no. 6154, pp. 621–624.
Fonseca, V.G., Nichols, B., Lallias, D., Quince, C., Carvalho, G.R., et al., Sample richness and genetic diversity as drivers of chimera formation in nSSU metagenetic analyses, Nucleic Acids Res., 2012, vol. 40, no. 9, p. e66.
Geisen, S., Laros, I., Vizcaíno, A., Bonkowski, M., and de Groot, G.A., Not all are free-living: high-throughput DNA metabarcoding reveals a diverse community of protists parasitizing soil metazoan, Mol. Ecol., 2015, vol. 24, no. 17, pp. 4556–4569.
Gorbacheva, M.A., Melnikova, N.V., Chechetkin, V.R., Kravatsky, Y.V., and Tchurikov, N.A., DNA sequencing and metagenomics of cultivated and uncultivated chernozems in Russia, Geoderma Reg., 2018, vol. 14, p. e00180.
Grundmann, G.L., Spatial scales of soil bacterial diversity—the size of a clone, FEMS Microbiol. Ecol., 2004, vol. 48, no. 2, pp. 119–127.
Hamady, M. and Knight, R., Microbial community profiling for human microbiome projects: tools, techniques, and challenges, Genome Res., 2009, vol. 19, no. 7, pp. 1141–1152.
Handelsman, J., Metagenetics: spending our inheritance on the future, Microb. Biotechnol., 2009, vol. 2, no. 2, pp. 138–139.
Handelsman, J., Rondon, M.R., Brady, S.F., Clardy, J., and Goodman, R.M., Molecular biological access to the chemistry of unknown soil microbes: a new frontier for natural products, Chem. Biol., 1998, vol. 5, no. 10, pp. 245–249.
Hesse, C.N., Mueller, R.C., Vuyisich, M., Gallegos-Graves, L.V., Gleasner, C.D., et al., Forest floor community metatranscriptomes identify fungal and bacterial responses to N deposition in two maple forests, Front. Microbiol., 2015, vol. 6, p. 337.
Hirsch, P.R., Gilliam, L.M., Sohi, S.P., Williams, J.K., Clark, I.M., and Murray, P.J., Starving the soil of plant inputs for 50 years reduces abundance but not diversity of soil bacterial communities, Soil Biol. Biochem., 2009, vol. 41, no. 9, pp. 2021–2024.
Hug, L.A., Baker, B.J., Anantharaman, K., Brown, C.T., Probst, A.J., et al., A new view of the tree of life, Nat. Microbiol., 2016, vol. 1, p. 16048.
Ibáñez de Aldecoa, A.L., Zafra, O., and González-Pastor, J.E., Mechanisms and regulation of extracellular DNA release and its biological roles in microbial communities, Front. Microbiol., 2017, vol. 8, p. 1390.
Ji, Y., Ashton, L., Pedley, S.M., Edwards, D.P., Tang, Y., et al., Reliable, verifiable and efficient monitoring of biodiversity via meta-barcoding, Ecol. Lett., 2013, vol. 16, no. 10, pp. 1245–1257.
Kang, S. and Mills, A.L., The effect of sample size in studies of soil microbial community structure, J. Microbiol. Methods, 2006, vol. 66, no. 2, pp. 242–250.
Karimi, B., Terrat, S., Dequiedt, S., Saby, N.P., Horrigue, W., et al., Biogeography of soil bacteria and archaea across France, Sci. Adv., 2018, vol. 4, no. 7, art. ID eaat1808.
Keegan, K.P., Glass, E.M., and Meyer, F., MG-RAST, a metagenomics service for analysis of microbial community structure and function, in Microbial Environmental Genomics (MEG), New York: Humana, 2016, pp. 207–233.
Knight, R., Vrbanac, A., Taylor, B.C., Aksenov, A., Callewaert, C., et al., Best practices for analysing microbiomes, Nat. Rev. Microbiol., 2018, vol. 16, no. 7, pp. 410–422.
Kuikman, P.J., van Elsas, J.D., Jansen, A.G., Burgers, S.L., and van Veen, J.A., Population dynamics and activity of bacteria and protozoa in relation to their spatial distribution in soil, Soil Biol. Biochem., 1990, vol. 22, no. 8, pp. 1063–1073.
Kumar, V., AlMomin, S., Al-Aqeel, H., Al-Salameen, F., Nair, S., and Shajan, A., Metagenomic analysis of rhizosphere microflora of oil-contaminated soil planted with barley and alfalfa, PLoS One, 2018, vol. 13, no. 8, p. e0202127.
Langille, M.G., Zaneveld, J., Caporaso, J.G., McDonald, D., Knights, D., et al., Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences, Nat. Biotechnol., 2013, vol. 31, no. 9, pp. 814–821.
Lauber, C.L., Ramirez, K.S., Aanderud, Z., Lennon, J., and Fierer, N., Temporal variability in soil microbial communities across land-use types, ISME J., 2013, vol. 7, no. 8, pp. 1641–1650.
Ling, N., Chen, D., Guo, H., Wei, J., Bai, Y., et al., Differential responses of soil bacterial communities to long-term N and P inputs in a semi-arid steppe, Geoderma, 2017, vol. 292, pp. 25–33.
Loeppmann, S., Semenov, M., Kuzyakov, Y., and Blagodatskaya, E., Shift from dormancy to microbial growth revealed by RNA:DNA ratio, Ecol. Indic., 2018, vol. 85, pp. 603–612.
Lombard, N., Prestat, E., van Elsas, J.D., and Simonet, P., Soil-specific limitations for access and analysis of soil microbial communities by metagenomics, FEMS Microbiol. Ecol., 2011, vol. 78, no. 1, pp. 31–49.
Lorenz, P. and Eck, J., Metagenomics and industrial applications, Nat. Rev. Microbiol., 2005, vol. 3, no. 6, pp. 510–516.
Louca, S., Doebeli, M., and Parfrey, L.W., Correcting for 16S rRNA gene copy numbers in microbiome surveys remains an unsolved problem, Microbiome, 2018, vol. 6, no. 1, p. 41.
Mendes, L.W., Tsai, S.M., Navarrete, A.A., de Hollander, M., van Veen, J.A., and Kuramae, E.E., Soil-borne microbiome: linking diversity to function, Microb. Ecol., 2015, vol. 70, no. 1, pp. 255–265.
Mummey, D., Holben, W., Six, J., and Stahl, P., Spatial stratification of soil bacterial populations in aggregates of diverse soils, Microb. Ecol., 2006, vol. 51, no. 3, pp. 404–411.
Murali, A., Bhargava, A., and Wright, E.S., IDTAXA: a novel approach for accurate taxonomic classification of microbiome sequences, Microbiome, 2018, vol. 6, no. 1, p. 140.
Navarrete, A.A., Soares, T., Rossetto, R., van Veen, J.A., Tsai, S.M., and Kuramae, E.E., Verrucomicrobial community structure and abundance as indicators for changes in chemical factors linked to soil fertility, Antonie Leeuwenhoek, 2015, vol. 108, no. 3, pp. 741–752.
Nesme, J., Achouak, W., Agathos, S.N., Bailey, M., Baldrian, P., et al., Back to the future of soil metagenomics, Front. Microbiol., 2016, vol. 7, p. 73.
Niimi, H., Mori, M., Tabata, H., Minami, H., Ueno, T., et al., A novel eukaryote-made thermostable DNA polymerase which is free from bacterial DNA contamination, J. Clin. Microbiol., 2011, vol. 49, no. 9, pp. 3316–3320.
Osnovnye dostizheniya i perspektivy pochvennoi metagenomiki (General Achievements and Prospects of Soil Metagenomics), Pershina, E.V., Kutova, O.V., Kogut, B.M., and Andronov, E.E., Eds., St. Petersburg: Inform-Navigator, 2004.
Pester, M., Schleper, C., and Wagner, M., The Thaumarchaeota: an emerging view of their phylogeny and ecophysiology, Curr. Opin. Microbiol., 2011, vol. 14, no. 3, pp. 300–306.
Pham, V.H. and Kim, J., Cultivation of unculturable soil bacteria, Trends Biotechnol., 2012, vol. 30, no. 9, pp. 475–484.
Placella, S.A., Brodie, E.L., and Firestone, M.K., Rainfall-induced carbon dioxide pulses result from sequential resuscitation of phylogenetically clustered microbial groups, Proc. Natl. Acad. Sci. U.S.A., 2012, vol. 109, no. 27, pp. 10931–10936.
Porazinska, D.L., Giblin-Davis, R.M., Esquivel, A., Powers, T.O., Sung, W.A.Y., and Thomas, W.K., Ecometagenetics confirm high tropical rainforest nematode diversity, Mol. Ecol., 2010, vol. 19, no. 24, pp. 5521–5530.
Prosser, J.I., Dispersing misconceptions and identifying opportunities for the use of ‘omics’ in soil microbial ecology, Nat. Rev. Microbiol., 2015, vol. 13, no. 7, pp. 439–446.
Ranjard, L. and Richaume, A., Quantitative and qualitative microscale distribution of bacteria in soil, Res. Microbiol., 2001, vol. 152, no. 8, pp. 707–716.
Riesenfeld, C.S., Schloss, P.D., and Handelsman, J., Metagenomics: genomic analysis of microbial communities, Annu. Rev. Genet., 2004, vol. 38, pp. 525–552.
Rutherford, P.M. and Juma, N.G., Influence of texture on habitable pore space and bacterial-protozoan populations in soil, Biol. Fertil. Soils, 1992, vol. 12, no. 4, pp. 221–227.
Salter, S.J., Cox, M.J., Turek, E.M., Calus, S.T., Cookson, W.O., et al., Reagent and laboratory contamination can critically impact sequence-based microbiome analyses, BMC Biol., 2014, vol. 12, no. 1, p. 87.
Schloss, P.D., Gevers, D., and Westcott, S.L., Reducing the effects of PCR amplification and sequencing artifacts on 16S rRNA-based studies, PLoS One, 2011, vol. 6, no. 12, p. e27310.
Schmieder, R. and Edwards, R., Insights into antibiotic resistance through metagenomic approaches, Future Microbiol., 2012, vol. 7, no. 1, pp. 73–89.
Schoch, C.L., Seifert, K.A., Huhndorf, S., Robert, V., Spouge, J.L., et al., Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi, Proc. Natl. Acad. Sci. U.S.A., 2012, vol. 109, no. 16, pp. 6241–6246.
Semenov, M.V., Stolnikova, E.V., Ananyeva, N.D., and Ivashchenko, K.V., Structure of the microbial community in soil catena of the right bank of the Oka River, Biol. Bull. (Moscow), 2013, vol. 40, no. 3, pp. 266–274.
Semenov, M., Blagodatskaya, E., Stepanov, A., and Kuzyakov, Y., DNA-based determination of soil microbial biomass in alkaline and carbonaceous soils of semi-arid climate, J. Arid Environ., 2018a, vol. 150, pp. 54–61.
Semenov, M.V., Chernov, T.I., Tkhakakhova, A.K., Zhelezova, A.D., Ivanova, E.A., Kolganova, T.V., and Kutovaya, O.V., Distribution of prokaryotic communities throughout the Chernozem profiles under different land uses for over a century, Appl. Soil Ecol., 2018b, vol. 127, pp. 8–18.
Senechkin, I.V., Speksnijder, A.G., Semenov, A.M., van Bruggen, A.H.C., and van Overbeek, L.S., Isolation and partial characterization of bacterial strains on low organic carbon medium from soils fertilized with different organic amendments, Microb. Ecol., 2010, vol. 60, no. 4, pp. 829–839.
Souza, R.C., Hungria, M., Cantao, M.E., Vasconcelos, A.T.R., Nogueira, M.A., and Vicente, V.A., Metagenomic analysis reveals microbial functional redundancies and specificities in a soil under different tillage and crop-management regimes, Appl. Soil Ecol., 2015, vol. 86, pp. 106–112.
Staley, J.T. and Konopka, A., Measurement of in situ activities of nonphotosynthetic microorganisms in aquatic and terrestrial habitats, Annu. Rev. Microbiol., 1985, vol. 39, pp. 321–346.
Stoddard, S.F., Smith, B.J., Hein, R., Roller, B.R., and Schmidt, T.M., Rrn DB: Improved tools for interpreting rRNA gene abundance in bacteria and archaea and a new foundation for future development, Nucleic Acids Res., 2015, vol. 43, no. 1, pp. D593–D598.
Taberlet, P., Coissac, E., Pompanon, F., Brochmann, C., and Willerslev, E., Towards next-generation biodiversity assessment using DNA metabarcoding, Mol. Ecol., 2012, vol. 21, no. 8, pp. 2045–2050.
Terrat, S., Horrigue, W., Dequietd, S., Saby, N.P., Lelièvre, M., et al., Mapping and predictive variations of soil bacterial richness across France, PLoS One, 2017, vol. 12, no. 10, p. e0186766.
Tian, J., He, N., Kong, W., Deng, Y., Feng, K., et al., Deforestation decreases spatial turnover and alters the network interactions in soil bacterial communities, Soil Biol. Biochem., 2018, vol. 123, pp. 80–86.
Torsvik, V. and Ovreas, L., Microbial diversity and function in soil: from genes to ecosystems, Curr. Opin. Microbiol., 2002, vol. 5, no. 3, pp. 240–245.
Torsvik, V., Goksoyr, J., and Daae, F.L., High diversity in DNA of soil bacteria, Appl. Environ. Microbiol., 1990, vol. 56, no. 3, pp. 782–787.
Trevors, J.T., One gram of soil: a microbial biochemical gene library, Antonie Leeuwenhoek, 2010, vol. 97, no. 2, pp. 99–106.
Tveit, A.T., Urich, T., and Svenning, M.M., Metatranscriptomic analysis of arctic peat soil microbiota, Appl. Environ. Microbiol., 2014, vol. 80, no. 18, pp. 5761–5772.
Valentine, D.L., Adaptations to energy stress dictate the ecology and evolution of the archaea, Nat. Rev. Microbiol., 2007, vol. 5, no. 4, pp. 316–323.
van der Bom, F., Nunes, I., Raymond, N.S., Hansen, V., Bonnichsen, L., et al., Long-term fertilisation form, level and duration affect the diversity, structure and functioning of soil microbial communities in the field, Soil Biol. Biochem., 2018, vol. 122, pp. 91–103.
Vester, J.K., Glaring, M.A., and Stougaard, P., Improved cultivation and metagenomics as new tools for bioprospecting in cold environments, Extremophiles, 2015, vol. 19, no. 1, pp. 17–29.
Vetrovsky, T. and Baldrian, P., The variability of the 16S rRNA gene in bacterial genomes and its consequences for bacterial community analyses, PLoS One, 2013, vol. 8, no. 2, p. e57923.
Vogel, T.M., Simonet, P., Jansson, J.K., Hirsch, P.R., Tiedje, J.M., et al., TerraGenome: a consortium for the sequencing of a soil metagenome, Nat. Rev. Microbiol., 2009, vol. 7, p. 252.
Will, C., Thürmer, A., Wollherr, A., Nacke, H., Herold, N., et al., Horizon-specific bacterial community composition of German grassland soils, as revealed by pyrosequencing-based analysis of 16S rRNA genes, Appl. Environ. Microbiol., 2010, vol. 76, no. 20, pp. 6751–6759.
Wilson, I.G., Inhibition and facilitation of nucleic acid amplification, Appl. Environ. Microbiol., 1997, vol. 63, no. 10, pp. 3741–3751.
Wolinska, A., Kuzniar, A., Zielenkiewicz, U., Banach, A., and Blaszczyk, M., Indicators of arable soils fatigue— Bacterial families and genera: a metagenomic approach, Ecol. Indic., 2018, vol. 93, pp. 490–500.
Wright, D.A., Killham, K., Glover, L.A., and Prosser, J.I., The effect of location in soil on protozoal grazing of a genetically modified bacterial inoculum, Geoderma, 1993, vol. 56, pp. 633–640.
Xu, J., Fungal DNA barcoding, Genome, 2016, vol. 59, no. 11, pp. 913–932.
Zifcakova, L., Vetrovsky, T., Lombard, V., Henrissat, B., Howe, A., and Baldrian, P., Feed in summer, rest in winter: microbial carbon utilization in forest topsoil, Microbiome, 2017, vol. 5, no. 1, p. 122.
Zvyagintsev, D.G., Bab’eva, I.P., and Zenova, G.M., Biologiya pochv (Soil Biology), Moscow: Mosk. Gos. Univ., 2005.
The author thanks Academician V.V. Rozhnov and O.L. Makarova for the opportunity to present this material at the XXV Sukachev Lectures, “Metagenomics and metabarcoding in ecological studies: a methodological breakthrough?!”.
This study was supported by the Russian Foundation for Basic Research, project no. 19-04-00315.
Conflict of interests. The authors declare that they have no conflicts of interest.
Statement on the welfare of humans or animals. This article does not contain any studies involving animals performed by any of the authors.
Translated by M. Bibov
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Semenov, M.V. Metabarcoding and Metagenomics in Soil Ecology Research: Achievements, Challenges, and Prospects. Biol Bull Rev 11, 40–53 (2021). https://doi.org/10.1134/S2079086421010084