Duckweed hosts a taxonomically similar bacterial assemblage as the terrestrial leaf microbiome.

Kenneth Acosta,Eric Lam,Sarah Gilbert,Thomas Brinkman,Jenny Xu,Sarah Lebeis,Elizabeth Denison,Ulrich Melcher

doi:10.1371/journal.pone.0228560

Kenneth Acosta, Eric Lam + Show 6 more

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https://doi.org/10.1371/journal.pone.0228560

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Abstract

Culture-independent characterization of microbial communities associated with popular plant model systems have increased our understanding of the plant microbiome. However, the integration of other model systems, such as duckweed, could facilitate our understanding of plant microbiota assembly and evolution. Duckweeds are floating aquatic plants with many characteristics, including small size and reduced plant architecture, that suggest their use as a facile model system for plant microbiome studies. Here, we investigated the structure and assembly of the duckweed bacterial microbiome. First, a culture-independent survey of the duckweed bacterial microbiome from different locations in New Jersey revealed similar phylogenetic profiles. These studies showed that Proteobacteria is a dominant phylum in the duckweed bacterial microbiome. To observe the assembly dynamics of the duckweed bacterial community, we inoculated quasi-gnotobiotic duckweed with wastewater effluent from a municipal wastewater treatment plant. Our results revealed that duckweed strongly shapes its bacterial microbiome and forms distinct associations with bacterial community members from the initial inoculum. Additionally, these inoculation studies showed the bacterial communities of different duckweed species were similar in taxa composition and abundance. Analysis across the different duckweed bacterial communities collected in this study identified a set of "core" bacterial taxa consistently present on duckweed irrespective of the locale and context. Furthermore, comparison of the duckweed bacterial community to that of rice and Arabidopsis revealed a conserved taxonomic structure between the duckweed microbiome and the terrestrial leaf microbiome. Our results suggest that duckweeds utilize similar bacterial community assembly principles as those found in terrestrial plants and indicate a highly conserved structuring effect of leaf tissue on the plant microbiome.

Highlights

Terrestrial plants harbor a multitude of microorganisms that can confer fitness advantages either through plant growth promotion or disease protection [1]
They observed a majority of bacteria enriched in the rhizoplane/endosphere were enriched in the rhizosphere
While many bacteria decreased in abundance along this nexus, bacteria enriched on duckweed were enriched in ambient wastewater when compared to wastewater without duckweed (Fig 5)

Summary

Introduction

Terrestrial plants harbor a multitude of microorganisms that can confer fitness advantages either through plant growth promotion or disease protection [1]. To improve our understanding of these interactions, a number of culture-independent studies, using next-generation sequencing technologies, have been conducted on terrestrial plants to characterize the plant microbiome. In addition to culture-independent studies, reductionist approaches using gnotobiotic plants, culture collections of plant microbiota, and sterile soil matrix have begun to resolve the complexity of interactions occurring in the plant microbiome [11,12]. While these approaches have mainly used terrestrial plants, implementation of other model systems could facilitate our understanding of the plant microbiome and the mechanisms that are involved in shaping its population structure

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