title: Taxonomic analysis of the microbial community in stored sugar beets using high-throughput sequencing of different marker genes.
abstract: Post-harvest colonization of sugar beets accompanied by rot development is a serious problem due to sugar losses and negative impact on processing quality. Studies on the microbial community associated with rot development and factors shaping their structure are missing. Therefore, high-throughput sequencing was applied to describe the influence of environment, plant genotype and storage temperature (8°C and 20°C) on three different communities in stored sugar beets, namely fungi (internal transcribed spacers 1 and 2), Fusarium spp. (elongation factor-1α gene fragment) and oomycetes (internal transcribed spacers 1). The composition of the fungal community changed during storage mostly influenced by the storage temperature followed by a weak environmental effect. Botrytis cinerea was the prevalent species at 8°C whereas members of the fungal genera Fusarium and Penicillium became dominant at 20°C. This shift was independent of the plant genotype. Species richness within the genus Fusarium also increased during storage at both temperatures whereas the oomycetes community did not change. Moreover, oomycetes species were absent after storage at 20°C. The results of the present study clearly show that rot development during sugar beet storage is associated with pathogens well known as causal agents of post-harvest diseases in many other crops.
authors.affiliation: Institute of Sugar Beet Research, D-37077 Göttingen, Germany.
authors.forename: Sebastian
authors.initials: S
authors.lastname: Liebe
authors.affiliation: Institute for Genome Research and Systems Biology, CeBiTec, Bielefeld University, D-33501 Bielefeld, Germany.
authors.forename: Daniel
authors.initials: D
authors.lastname: Wibberg
authors.affiliation: Institute for Genome Research and Systems Biology, CeBiTec, Bielefeld University, D-33501 Bielefeld, Germany.
authors.forename: Anika
authors.initials: A
authors.lastname: Winkler
authors.affiliation: Institute for Genome Research and Systems Biology, CeBiTec, Bielefeld University, D-33501 Bielefeld, Germany.
authors.forename: Alfred
authors.initials: A
authors.lastname: Pühler
authors.affiliation: Institute for Genome Research and Systems Biology, CeBiTec, Bielefeld University, D-33501 Bielefeld, Germany.
authors.forename: Andreas
authors.initials: A
authors.lastname: Schlüter
authors.affiliation: Institute of Sugar Beet Research, D-37077 Göttingen, Germany varrelmann@ifz-goettingen.de.
authors.forename: Mark
authors.initials: M
authors.lastname: Varrelmann
mesh_terms: D001483:Base Sequence; D027461:Beta vulgaris / Q000382:microbiology*; D020171:Botrytis / Q000145:classification / Q000235:genetics* / Q000254:growth & development; D002241:Carbohydrates; D018556:Crops, Agricultural / Q000382:microbiology*; D021901:DNA, Intergenic / Q000235:genetics; D004777:Environment; D005670:Fusarium / Q000145:classification / Q000235:genetics* / Q000254:growth & development; D005819:Genetic Markers / Q000235:genetics; D059014:High-Throughput Nucleotide Sequencing; D009868:Oomycetes / Q000145:classification / Q000235:genetics*; D010407:Penicillium / Q000145:classification / Q000235:genetics* / Q000254:growth & development; D017422:Sequence Analysis, DNA; D013696:Temperature
chemical_list: D002241:Carbohydrates; D021901:DNA, Intergenic; D005819:Genetic Markers
keywords: Botrytis cinerea; bioinformatic analysis pipeline; environment; genotype; post-harvest disease; storage temperature