UDC 636.085:579.62/.63:577.21:579.083.1

doi: 10.15389/agrobiology.2015.6.832eng

Supported by grant of Russian Science Foundation, project № 14-16-00114


E.A. Yildirim1, G.Yu. Laptev1, L.A. Il’ina1, I.N. Nikonov1, V.A. Filippovav1, V.V. Soldatova1, E.A. Brazhnik1, N.I. Novikova1, T.Yu. Gagkaeva2

1Biotrof+ Ltd, 7-N,8, lit. A,
Malinovskaya ul., St. Petersburg, 196602 Russia,
е-mail deniz@biotrof.ru, laptev@biotrof.ru, ilina@biotrof.ru, nikonov@biotrof.ru, dumova@biotrof.ru, biotrof@biotrof.ru, bea@biotrof.ru;
2All-Russian Research Institute of Plant Protection, Federal Agency of Scientific Organizations,
3, sh. Podbel’skogo, St. Petersburg, 196608 Russia,
e-mail t.gagkaeva@mail.ru

Received June 30, 2015

The composition of plant and silage microflora affects the fermentation processes in the silage and its final quality. To date, reports about studying fodder plants and silage microbiota by means of molecular genetic methods are few and limited to descriptions of composition and function of some groups of microorganisms. Moreover, the NGS (next generation sequencing) data on diversity of epiphytic microflora and silage microbiocoenosis are not still reported. We first used this approach in studying phyllosphere and silage microbiom, and reported it to be rather rich in composition and abundance that is in contrast with conventional understanding. At that, the pathogenic and non-culturable microbes were detected in the microbiota, including specific inhabitants of mammalian gastrointestinal tract. So using NGS we examined the structure and diversity of bacterial community of Dactylis glomerata L. harvested plants and the biomass ensilaged with chemical preservative AIV 2000 Plus («KEMIRA OYJ, Inc.», Finland) composed of mixture of formic, propionic and benzoic acids. Assays were carried out on days 3, 7, 14 and 30 of ensilaging. The results showed that the bacterial community of silage from D. glomerata sharply differed from the composition of foliage microorganisms and varied greatly in the course of successive changes which occurred during maturation of silage preserved by mixture of organic acids. The composition of plant microorganisms and silage were found to be very various in contrast with a traditional view. Among foliar microorganisms of D. glomerata there were mostly the bacteria of phylum Proteobacteria (94.1 %), and in the silage the bacteria of phylums Bacteroidetes and Firmicutes were main representatives (up to 59.5 % and 74.9 %, respectively). In taxonomic diversity of the order Lactobacillales, mainly involved in ensilaging, there were genera Lactobacillus (up to 39.6%), Enterococcus (up to 36.36 %), Lactococcus (up to 14.4 %), Pediococcus (to 1.45 %) and the family Leuconostocaceae (to 3.52 %). Interestingly, in the silage there were the bacteria of phylum Bacteroidetes, families Ruminococcaceae, Lachnospiraceae and Selenomonadales considered the common inhabitants of the mammals’ gastrointestinal tract, and also the uncultured and pathogenic microorganisms. Particularly, these were 15 genera of family Enterobacteriaceae,including genera Klebsiella, Salmonella, Yersinia, etc., among which the dangerous mammalian pathogens are frequent. On days 3 and 7, the phylum Bacteroidetes prevailed (59.53 and 48.91 %, respectively). On days 14 and 30, the phylum Firmicutes was dominant (up to 74.85 %) with the facultative aerobic bacteria of order Lactobacillales mostly found (up to 74.76 %). Using NGS, a total of 70 genera were attributed in the plant phyloshere, and in the silage there were 84 genera on day 3, 96 genera on day 7, 51 genera on day 14, and 69 genera on day 30. Classical microbiology methods are not enough to detect these bacteria among silage microbiota.

Keywords: silage microorganisms, epiphytic microflora, NGS-sequencing, organic acids.


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