AUTHOR=Wang Zongneng , Dai Qingzhong , Su Daifa , Zhang Zhenrong , Tian Yunxia , Tong Jiangyun , Chen Shanyan , Yan Congwen , Yang Junyu , Cui Xiaolong 

TITLE=Comparative analysis of the microbiomes of strawberry wild species Fragaria nilgerrensis and cultivated variety Akihime using amplicon-based next-generation sequencing

JOURNAL=Frontiers in Microbiology

VOLUME=15

YEAR=2024

URL=https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2024.1377782

DOI=10.3389/fmicb.2024.1377782

ISSN=1664-302X

ABSTRACT=<p><italic>Fragaria nilgerrensis</italic> is a wild strawberry species widely distributed in southwest China and has strong ecological adaptability. Akihime (<italic>F. × ananassa</italic> Duch. cv. Akihime) is one of the main cultivated strawberry varieties in China and is prone to infection with a variety of diseases. In this study, high-throughput sequencing was used to analyze and compare the soil and root microbiomes of <italic>F. nilgerrensis</italic> and <italic>Akihime.</italic> Results indicate that the wild species <italic>F. nilgerrensis</italic> showed higher microbial diversity in nonrhizosphere soil and rhizosphere soil and possessed a more complex microbial network structure compared with the cultivated variety Akihime. Genera such as <italic>Bradyrhizobium</italic> and <italic>Anaeromyxobacter</italic>, which are associated with nitrogen fixation and ammonification, and <italic>Conexibacter</italic>, which is associated with ecological toxicity resistance, exhibited higher relative abundances in the rhizosphere and nonrhizosphere soil samples of <italic>F. nilgerrensis</italic> compared with those of Akihime. Meanwhile, the ammonia-oxidizing archaea <italic>Candidatus Nitrososphaera</italic> and <italic>Candidatus Nitrocosmicus</italic> showed the opposite tendencies. We also found that the relative abundances of potential pathogenic genera and biocontrol bacteria in the Akihime samples were higher than those in the <italic>F. nilgerrensis</italic> samples. The relative abundances of <italic>Blastococcus, Nocardioides, Solirubrobacter,</italic> and <italic>Gemmatimonas</italic>, which are related to pesticide degradation, and genus Var<italic>iovorax</italic>, which is associated with root growth regulation, were also significantly higher in the Akihime samples than in the <italic>F. nilgerrensis</italic> samples. Moreover, the root endophytic microbiomes of both strawberry species, especially the wild <italic>F. nilgerrensis</italic>, were mainly composed of potential biocontrol and beneficial bacteria, making them important sources for the isolation of these bacteria. This study is the first to compare the differences in nonrhizosphere and rhizosphere soils and root endogenous microorganisms between wild and cultivated strawberries. The findings have great value for the research of microbiomes, disease control, and germplasm innovation of strawberry.</p>