doi: 10.15389/agrobiology.2013.5.85eng
UDC 579.6/.8:631.46:574.24:575.852'1
THE MAIN TRENDS IN DYNAMICS OF SOIL MICROBIOM DURING A LONG-TERM FIELD EXPERIMENT AS INDICATED BY HIGH THROUGHPUT SEQUENCING THE 16S-rRNA GENE LIBRARIES
V.A. Dumova, E.V. Pershina, Ya.V. Merzlyakova, Yu.V. Kruglov, E.E. Andronov
All-Russian Research Institute of Agricultural Microbiology, Russian Academy of Agricultural Sciences,
3, sh. Podbelskogo, Saint Petersburg-Pushkin, 196608 Russia,
e-mail: doumova@gmail.com
Received June 28, 2012
A biodiversity of soil microbial communities now is being widely studied. Since 1912, the influence of different agrotechnical factors on soil is being examined in the stationary field experiment in the Moscow Agricultural Academy. We investigated an effect of different combination of three factors, i.e. plants (flax and winter rye), crop rotation and soil acidity, to the soil microbiom. To estimate a biodiversity, the throughput sequencing was used. Also an original approach, the binary sampling, was suggested to analyze the data of throughput sequencing. It was shown the number of microorganisms which changed under the influence of studied factor is approximately equal to those staying unchanged. But a taxonomic composition of these two groups differed, and the impacted group was more uniform. Thus, we can conclude that the less part of microorganism is sensitive to the acting factors, and the rest ones keep their number unchanged, more or less. The taxonomic groups of microorganisms, sensitive to each of studied factors, were revealed. The binary sampling, suggested herein, allows finding out a relation between an action of some ecological factor and varying taxonomic structure of microbial population.
Keywords: soil microbiom, high throughput sequencing.
REFERENCES
1. Pace N.R. Mapping the tree of life: progress and prospects. Microbiology and Molecular Biology Reviews, 2009, 73(4): 565-576.
2. Tyson G.W., Banfield J.F. Cultivating the uncultivated: a community genomics perspective. Trends in Microbiology, 2005, 9(13): 411-415.
3. Kakirde K.S., Parsley L.C., Liles M.R. Size does matter: application-driven approaches for soil metagenomics. Soil Biol. Biochem., 2010, 42: 1911-1923.
4. Lombard N., Prestat E., Elsas J.D.V., Simonet P. Soil-specific limitations for access and analysis of soil microbial communities by metagenomics. FEMS Microbiol. Ecol., 2011, 78: 31-49.
5. Wooley J.C., Ye Y. Metagenomics: Facts and artifacts, and computational challenges. Journal of Computer Science and Technology, 2010, 1(25): 71-81.
6. Mardis E.R. Next-generation DNA sequencing methods. Annual Review of Genomics and Human Genetics, 2008, 9: 211-219.
7. Bates S.T.D., Berg-Lyons J.G., Caporaso W.A. et al. Examining the global distribution of dominant archaeal populations in soil. ISME Journal, 2010, 5: 908-917.
8. Cole J.R., Wang Q., Cardenas E. et al. The Ribosomal Database Project: improved alignments and new tools for rRNA analysis. Nucl. Acids Res., 2009, 37: D141-D145.
9. Lauber C.L., Strickland M.S., Bradford M.A., Fierer N. The influence of soil properties on the structure of bacterial and fungal communities across land-use types. Soil Biol. Biochem., 2008, 40: 2407-2415.
10. Zhang H., Sekiguchi Y., Hanada S. et al. 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 Microbioly, 2003, 53(4): 1155-1163.
