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.

A Novel Penicillium sp. Causes Rot in Stored Sugar Beet Roots in Idaho

“…On stored sugar beet roots, P. vulpinum has been shown to be the most prevalent Penicillium species in older literature, while other Penicillium species have also been documented to occur: P. cyclopium, P. duclauxii, P. expansum, P. funiculosum [now T. funiculosus], P. paneum, P. rubrum, P. stoloniferum, and P. variable [now T. variabilis] (Bugbee 1975, Bugbee and Nielsen 1978, Fugate and Campbell 2009, Liebe et al 2016, Morotchkovsky 1936, Samson et al 2011, Visagie et al 2014. In a recent fungicide study (Strausbaugh et al 2015) in a Table 2.…”

“…Penicillium species involved in storage rot have frequently been associated with wounds and are prevalent, but not necessarily the most damaging pathogen present (Bugbee 1975(Bugbee , 1982(Bugbee , 1993Nielsen 1978, Fugate andCampbell 2009;Liebe et al 2016;Mumford and Wyse 1976). In the 1970s in the Red River Valley, P. vulpinum and Phoma betae were isolated more than 70% of the time, but P. betae was considered the more damaging pathogen because it decayed roots at a faster rate (Bugbee 1982).…”

“…A fungicide storage study from the 1970s targeted at the Pacific Northwest focused on P. vulpinum and B. cinerea indicating Penicillium was important in that region as well (Mumford and Wyse 1976). In Europe, Penicillium was recently acknowledged as being one the dominant fungal species in storage (Liebe et al 2016, Liebe andVarrelmann 2014).…”

The potential of plant microbiota in reducing postharvest food loss

“…More recently, Liebe et al . (2016) reported shifts in the fungal and oomycete community composition associated with storage soft rot development in different sugar beet hybrids from different environments stored at different temperatures. Interestingly, while the genotypes showed differences in the susceptibility to soft rot, the shifts in the microbial community of sugar beet were genotype independent.…”

“…Interestingly, while the genotypes showed differences in the susceptibility to soft rot, the shifts in the microbial community of sugar beet were genotype independent. The authors suggested an unspecific resistance mechanism slowing down the spread of pathogens in more resistant genotypes but not preventing infection (Liebe et al ., 2016). However, the study focused on fungi and oomycetes and the dynamics of bacteria community during storage soft rot development of sugar beet and its putative role in disease expression remains elusive.…”