Host selection shapes crop microbiome assembly and network complexity

Chao Xiong, Yong-Guan Zhu, Jun-Tao Wang, Brajesh Singh, Li-Li Han, Ju-Pei Shen, Pei-Pei Li, Gui-Bao Wang, Chuan-Fa Wu, An-Hui Ge, Li-Mei Zhang, Ji-Zheng He

Research output: Contribution to journalArticlepeer-review

422 Citations (Scopus)

Abstract

Plant microbiomes are essential to host health and productivity but the ecological processes that govern crop microbiome assembly are not fully known. Here we examined bacterial communities across 684 samples from soils (rhizosphere and bulk soil) and multiple compartment niches (rhizoplane, root endosphere, phylloplane, and leaf endosphere) in maize (Zea mays)-wheat (Triticum aestivum)/barley (Hordeum vulgare) rotation system under different fertilization practices at two contrasting sites. Our results demonstrate that microbiome assembly along the soil-plant continuum is shaped predominantly by compartment niche and host species rather than by site or fertilization practice. From soils to epiphytes to endophytes, host selection pressure sequentially increased and bacterial diversity and network complexity consequently reduced, with the strongest host effect in leaf endosphere. Source tracking indicates that crop microbiome is mainly derived from soils and gradually enriched and filtered at different plant compartment niches. Moreover, crop microbiomes were dominated by a few dominant taxa (c. 0.5% of bacterial phylotypes), with bacilli identified as the important biomarker taxa for wheat and barley and Methylobacteriaceae for maize. Our work provides comprehensive empirical evidence on host selection, potential sources and enrichment processes for crop microbiome assembly, and has important implications for future crop management and manipulation of crop microbiome for sustainable agriculture.
Original languageEnglish
Pages (from-to)1091-1104
Number of pages14
JournalNew Phytologist
Volume229
Issue number2
DOIs
Publication statusPublished - 2021

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