Surveying the sweetpotato rhizosphere, endophyte, and surrounding soil microbiomes at two North Carolina farms reveals underpinnings of sweetpotato microbiome community assembly

Farmers grow sweetpotatoes worldwide and some sub-Saharan African and Asian diets include sweetpotato as a staple, yet the sweetpotato microbiome is conspicuously less studied relative to crops such as maize, soybean, and wheat. Studying sweetpotato microbiome ecology may reveal paths to engineer the microbiome to improve sweetpotato yield, and/or combat sweetpotato pests and diseases. We sampled sweetpotatoes and surrounding soil from two North Carolina farms. We took samples from sweetpotato fields under two different land management regimes, conventional and organic, and collected two sweetpotato cultivars, 'Beauregard' and 'Covington'. By comparing SSU rRNA gene amplicon sequence profiles from sweetpotato storage root skin, rhizosphere, and surrounding soil we found the skin microbiome possessed the least composition heterogeneity among samples and lowest alpha-diversity and was significantly nested by the rhizosphere in amplicon sequence variant (ASV) membership. Many ASVs were specific to a single field and/or only found in either the skin, rhizosphere, or surrounding soil. Notably, sweetpotato skin enriched for Planctomycetaceae in relative abundance at both farms. This study elucidates underpinnings of sweetpotato microbiome community assembly, quantifies microbiome composition variance within a single farm, and reveals microorganisms associated with sweetpotato skin that belong to common but uncultured soil phylotypes.

全球范围内均有农户种植甘薯（sweetpotato），部分撒哈拉以南非洲与亚洲地区的膳食结构将甘薯作为主食，但相较于玉米（maize）、大豆（soybean）与小麦（wheat）等大宗作物，甘薯微生物组的相关研究仍显著匮乏。探究甘薯微生物组生态学或可揭示调控微生物组的可行路径，进而提升甘薯产量、抵御甘薯病虫害。本研究从北卡罗来纳州的两处农场采集甘薯及其周边土壤样本，在采用常规耕作与有机耕作两种不同土地管理模式的甘薯田中开展采样，并选取了博雷加德（Beauregard）与科文顿（Covington）两个甘薯品种。通过比对甘薯块根表皮、根际（rhizosphere）及周边土壤的小亚基核糖体RNA（SSU rRNA）基因扩增子序列谱，我们发现块根表皮的微生物组样本组成异质性最低、α多样性（alpha-diversity）也最低，且其扩增子序列变异体（amplicon sequence variant, ASV）的成员组成显著被根际所嵌套。诸多扩增子序列变异体仅特异性存在于单个农场，或仅见于块根表皮、根际或周边土壤中的某一类生境。值得注意的是，两处农场的甘薯块根表皮均显著富集浮霉菌科（Planctomycetaceae）的相对丰度。本研究阐明了甘薯微生物组群落的组装机制，量化了单个农场内微生物组组成的变异程度，并揭示了与甘薯块根表皮相关的、属于常见但未培养土壤系统发育型的微生物类群。