ena-STUDY-Natural Resources Institute Finland (Luke)-22-09-2020-08:23:06:151-132
Soil bacterial community in potato tuberosphere following repeated applications of a common scab suppressive antagonist
Bacterial communities in tuberosphere, i.e., the soil adjacent to potato tubers, were analyzed by next generation sequencing (NGS). The aim was to compare bacterial communities in untreated control plots to those in which seed tubers were treated with antagonist Str272 in one or several growing seasons.The experiment situated in Lumijoki (64º 85' N 25º 17' E), Northern Finland. The field was naturally infested with scab-causing Streptomyces spp. and had documented problems with common scab. The experiment included four treatments with the following applications: i) untreated control (C0), ii) one application of Str272 in 2012 (A1), iii) three applications of Str272 in the previous three years, but no application in 2012 (A3), iv) three applications of Str272 in the previous three years and with a further application in 2012 (A4) (Fig. 1A). In 2012, the treatments that did not receive an antagonist application (C0, A3), were treated with an equivalent volume of water. In 2013, no antagonist treatments were applied. Each treatment was repeated in four replicate plots nested within the treatments. The experiment and treatments were fixed to the same position in all years.In both years (2012 and 2013) the soil samples were collected from the potato tuberospheres 6 weeks after planting at early tuber development, when the tubers are most susceptible to infection. Soil samples were collected by a spoon no further than 1 cm from a potato tuber. Five subsamples were collected from each plot, pooled to form a composite sample per plot.From each composite sample three specimens (1 g) were taken. The three specimens per replicate were processed individually through DNA extraction and subsequent sequencing.DNA was extracted using the E.Z.N.A. Soil Extraction Kit. A 364-nucleotides long region of the bacterial 16S rRNA genes, including the hypervariable regions V3 and V4, was amplified from the soil DNA samples and sequenced using Illumina MiSeq paired-ends 250-nucleotide chemistry in the Institute of Molecular Medicine Finland. The forward primer 340F (5'-TCCTACGGGAGGCAGCAGT-3') and reverse primer 704R (5'-TCTRCGMATTYCACYKCTACAC-3') were optimized for amplification of the 16S rRNA gene sequences of soil bacteria.
Bacterial communities in tuberosphere, i.e., the soil adjacent to potato tubers, were analyzed by next generation sequencing (NGS). The aim was to compare bacterial communities in untreated control plots to those in which seed tubers were treated with antagonist Str272 in one or several growing seasons.The experiment situated in Lumijoki (64º 85' N 25º 17' E), Northern Finland. The field was naturally infested with scab-causing Streptomyces spp. and had documented problems with common scab. The experiment included four treatments with the following applications: i) untreated control (C0), ii) one application of Str272 in 2012 (A1), iii) three applications of Str272 in the previous three years, but no application in 2012 (A3), iv) three applications of Str272 in the previous three years and with a further application in 2012 (A4) (Fig. 1A). In 2012, the treatments that did not receive an antagonist application (C0, A3), were treated with an equivalent volume of water. In 2013, no antagonist treatments were applied. Each treatment was repeated in four replicate plots nested within the treatments. The experiment and treatments were fixed to the same position in all years.In both years (2012 and 2013) the soil samples were collected from the potato tuberospheres 6 weeks after planting at early tuber development, when the tubers are most susceptible to infection. Soil samples were collected by a spoon no further than 1 cm from a potato tuber. Five subsamples were collected from each plot, pooled to form a composite sample per plot.From each composite sample three specimens (1 g) were taken. The three specimens per replicate were processed individually through DNA extraction and subsequent sequencing.DNA was extracted using the E.Z.N.A. Soil Extraction Kit. A 364-nucleotides long region of the bacterial 16S rRNA genes, including the hypervariable regions V3 and V4, was amplified from the soil DNA samples and sequenced using Illumina MiSeq paired-ends 250-nucleotide chemistry in the Institute of Molecular Medicine Finland. The forward primer 340F (5'-TCCTACGGGAGGCAGCAGT-3') and reverse primer 704R (5'-TCTRCGMATTYCACYKCTACAC-3') were optimized for amplification of the 16S rRNA gene sequences of soil bacteria.