Host-specific and tissue-dependent orchestration of microbiome community structure in traditional rice paddy ecosystems

Weijuan Huang,Sarah Lebeis,Sarah Gilbert,Kenneth Acosta,Eric Lam,Chunlin Long,Alexander Poulev

doi:10.1007/s11104-020-04568-3

Abstract

Background and aimRice and duckweed are two monocotyledonous plants that naturally coexist in paddy fields. While the presence of duckweed in paddy fields significantly improves rice productivity, the interplay between soil microbes and the two plant hosts in this agroecosystem remains unexplored.MethodsWe compared the bacterial community structure between duckweed, rice and soil from multiple rice paddies. We also isolated bacteria from these communities and characterized their modes of bacterial colonization and plant growth-promotion using model plants.ResultsOur data indicate that host-specific and tissue-dependent factors reproducibly orchestrate the bacterial community structure associated with their plant hosts. This is corroborated by results from culture-dependent approaches in which the dominant genus Pantoea isolated from rice aerial tissues can strongly attach and colonize gnotobiotic duckweed in spite of the low representation of this bacterial genus in the natural duckweed microbiome. Our study identified a core of 254 bacterial taxa that are consistently found in all rice and duckweed tissue samples from rice paddy fields. Furthermore, characterizing auxin-producing bacteria isolates from both plant species identified potential plant growth-promoting bacteria that may improve growth for both duckweed and rice in paddy fields.ConclusionsResults from this work provide evidence for the importance of the host tissue and species context in determining plant colonization by microbes in the paddy field system. The resources generated in this study could facilitate the agronomic deployment of microbes for more sustainable rice production.

Highlights

Paddy field farming became the dominant form of rice cultivation across the globe from Asia to South America during the 20th Century
Our data indicate that host-specific and tissuedependent factors reproducibly orchestrate the bacterial community structure associated with their plant hosts
This is corroborated by results from culture-dependent approaches in which the dominant genus Pantoea isolated from rice aerial tissues can strongly attach and colonize gnotobiotic duckweed in spite of the low representation of this bacterial genus in the natural duckweed microbiome

Summary

Introduction

Paddy field farming became the dominant form of rice cultivation across the globe from Asia to South America during the 20th Century. The presence of duckweed in flooded rice fields is a common phenomenon (Kumura 2005) and inclusion of duckweed (Lemna minor) in rice paddy agroecosystems has been reported to reduce nitrogen loss from 20–54% (Li et al 2009). In addition to enhancing rice production, duckweed may suppress rice diseases, reduce the greenhouse gas footprint associated with rice cultivation and remediate heavy metal contaminants in paddy fields (Wang et al 2015; Ng et al 2017). While the presence of duckweed in paddy fields significantly improves rice productivity, the interplay between soil microbes and the two plant hosts in this agroecosystem remains unexplored

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Results

Conclusion