Comparison of rhizosphere and endophytic microbial communities of Chinese leek through high-throughput 16S rRNA gene Illumina sequencing

Chinese leek（Allium tuberosum Rottler ex Sprengel） is a common vegetable in China. In our previous study, Chinese leek in rotation was found to have significant antifungal and nematicidal activity. This study＇s aim was to investigate the potential antifungal and nematicidal activity associated with rhizosphere or endophytic microbes of Chinese leek. Thus, a total of 79 261 high-quality sequences were obtained from Chinese leek rhizosphere soil, leaf and root samples. In the rhizosphere soil, the bacterial community comprised five dominant phyla： Proteobacteria（37.85%）, Acidobacteria（10.99%）, Bacteroidetes（8.24%）, Cyanobacteria（7.79%） and Planctomycetes（7.1%）. The leaf and root bacterial communities comprised two dominant phyla： Cyanobacteria（83.42% in leaf and 75.44% in root） and Proteobacteria（14.75% in leaf and 21.04% in root）. Microbial diversity, richness and evenness in the rhizosphere soil bacterial community were higher than that in the endophytic bacterial communities. The rhizosphere bacterial community was significantly different from the endophytic bacterial communities. The endophytic bacterial communities from the leaf and the root were slightly, but not significantly different from each other. This study＇s findings would contribute to the isolation and identification of nematicidal and antifungal bacterial communities in Chinese leek.

Effect of long-term fertilization on bacterial communities in wheat endosphere

Fertilization has been shown to exert a significant influence on soil microorganisms and directly and indirectly influences plant growth and survival in agroecosystems. However, it is unknown whether fertilization affects endophytic microbial communities, which are ubiquitous and intimately associated with plant growth and health. Herein, we investigated endophytic bacterial communities in wheat leaves and roots under different long-term fertilization regimes,including NPK chemical fertilizer and NPK chemical fertilizer combined with wheat straw, pig manure, or cow manure. Endophytic bacterial community composition considerably differed in leaves and roots. Although different fertilization treatments did not affect the endophytic bacterial species richness or phylogenetic diversity in either leaves or roots, the community composition was significantly altered, particularly in roots. The endophytic bacterial co-occurrence network in leaves was more complex and stable than that in roots. Furthermore, many of the keystone species that were identified by their topological positions in the co-occurrence networks of leaves and roots were involved in plant growth and fitness. The total relative abundance of keystone species was the highest in the NPK plus cow manure treatment in both leaves and roots. Overall, our results suggest that different fertilization regimes can strongly affect endophytic bacterial communities, and the combination of NPK fertilizer and cow manure promoted the relative abundance of the key endophytic bacterial microbiota in both leaves and roots, which might be beneficial for plants in agroecosystems.