AUTHOR=Wang Juanying , Wu Hongmiao , Wu Linkun , Liu Ye , Letuma Puleng , Qin Xianjin , Chen Ting , Rensing Christopher , Lin Sheng , Lin Wenxiong 

TITLE=Revealing Microbiome Structure and Assembly Process in Three Rhizocompartments of Achyranthes bidentata Under Continuous Monoculture Regimes

JOURNAL=Frontiers in Microbiology

VOLUME=12

YEAR=2021

URL=https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2021.677654

DOI=10.3389/fmicb.2021.677654

ISSN=1664-302X

ABSTRACT=<p>The complex composition and interaction of root-associated microbes are critical to plant health and performance. In this study, we presented a detailed characterization of three rhizocompartment (rhizosphere, rhizoplane, and root) microbiomes of <italic>Achyranthes bidentata</italic> under different years of consecutive monoculture by deep sequencing in order to determine keystone microorganisms <italic>via</italic> co-occurrence network analysis. The network analysis showed that multiple consecutive monoculture (MCM, represented 5Y and 10Y) soils generated some distinct beneficial bacterial taxa such as <italic>Bacillus</italic>, <italic>Fictibacillus</italic>, <italic>Bradyrhizobium</italic>, <italic>Shinella</italic>, and <italic>Herbaspirillum</italic>. For fungi, <italic>Mortierella</italic> substituted for <italic>Fusarium</italic> in occupying an important position in different rhizocompartments under <italic>A. bidentate</italic> monoculture. Quantitative PCR analysis confirmed a significant increase in <italic>Bacillus</italic>, <italic>Pseudomonas</italic>, and <italic>Burkholderia</italic> spp. The results of the inoculation assay showed that addition of beneficial bacteria <italic>Bacillus subtilis</italic> 74 and <italic>Bacillus halodurans</italic> 75 significantly increased the root length and fresh weight of <italic>A. bidentata.</italic> Furthermore, three types of phytosterones, as the main allochemicals, were identified both in the rhizosphere soil and in culture medium under sterile conditions by LC-MS/MS. When looking at <italic>in vitro</italic> interactions, it was found that phytosterones displayed a positive interaction with dominant beneficial species (<italic>Bacillus amyloliquefaciens</italic> 4 and <italic>B. halodurans</italic> 75) and had a negative effect on the presence of the pathogenic fungi <italic>Fusarium solani</italic> and <italic>Fusarium oxysporum</italic>. Overall, this study demonstrated that consecutive monoculture of <italic>A. bidentata</italic> can alter the bacterial and fungal community by secreting root exudates, leading to recruitment of beneficial microbes and replacement of plant-specific pathogenic fungi with plant beneficial fungi.</p>