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. 2018 Aug 23;8(1):12712.
doi: 10.1038/s41598-018-31168-0.

Marchantia liverworts as a proxy to plants' basal microbiomes

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Marchantia liverworts as a proxy to plants' basal microbiomes

Luis D Alcaraz et al. Sci Rep. .

Abstract

Microbiomes influence plant establishment, development, nutrient acquisition, pathogen defense, and health. Plant microbiomes are shaped by interactions between the microbes and a selection process of host plants that distinguishes between pathogens, commensals, symbionts and transient bacteria. In this work, we explore the microbiomes through massive sequencing of the 16S rRNA genes of microbiomes two Marchantia species of liverworts. We compared microbiomes from M. polymorpha and M. paleacea plants collected in the wild relative to their soils substrates and from plants grown in vitro that were established from gemmae obtained from the same populations of wild plants. Our experimental setup allowed identification of microbes found in both native and in vitro Marchantia species. The main OTUs (97% identity) in Marchantia microbiomes were assigned to the following genera: Methylobacterium, Rhizobium, Paenibacillus, Lysobacter, Pirellula, Steroidobacter, and Bryobacter. The assigned genera correspond to bacteria capable of plant-growth promotion, complex exudate degradation, nitrogen fixation, methylotrophs, and disease-suppressive bacteria, all hosted in the relatively simple anatomy of the plant. Based on their long evolutionary history Marchantia is a promising model to study not only long-term relationships between plants and their microbes but also the transgenerational contribution of microbiomes to plant development and their response to environmental changes.

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Conflict of interest statement

The authors declare no competing interests.

Figures

Figure 1
Figure 1
Marchantia microbiomes are the product of soil microbiomes and other environmental sources. Most bacteria in a plant microbiome are introduced to their soil as minor contributors from other environmental sources, such as rain and wind propagated microbes. Essential bacteria should be present in microbiomes from Marchantia grown in both the wild and in vitro conditions. By comparing M. paleacea and M. polymorpha under wild and in vitro conditions, we aimed to identify key plant-associated bacteria.
Figure 2
Figure 2
Phyla diversity in Marchantia microbiomes and a concise comparison of plant-related microbiomes. (A) M. paleacea and M. polymorpha microbiomes. Proteobacteria was the most abundant phylum for both wild M. paleacea and M. polymorpha, but Firmicutes dominated the microbiome diversity of in vitro M. polymorpha. (B) Proteobacteria was the most abundant phylum in the plant microbiomes analyzed but each microbiome had different frequencies, spanning from 30% up to 90%. Plant microbiomes were ordered according to their phylogenetic distances. Sphagnum moss served a representative for bryophytes (along with Marchantia species); Pinus represented gymnosperms; rice and maize represented monocots; and the carnivorous plant Utricularia gibba and Arabidopsis represented dicots (see Methods).
Figure 3
Figure 3
Comparison of plant microbiomes. (A) Weighted Unifrac distances for the Marchantia microbiomes were tested in this work. Diversity reduction in wild M. polymorpha (mpolyfl) showed a larger distance to its soil source when compared to M. paleacea (mpalafl). (B) Constrained analysis of principal coordinates (CAP) using weighted Unifrac distances with 9,999 permutational multivariate ANOVA showed significant (p > 1e-04) differences between in vitro, soil, and M. polymorpha microbial communities. (C) CAP of comparative literature plant-associated microbiomes using Bray-Curtis dissimilarities showed significant differences (p > 0.001) between microbial communities of different host plant species. Larger differences were found in Pinus, rice, and Marchantia species of this work.
Figure 4
Figure 4
Venn diagrams of microbiomes from M. paleacea, M. polymorpha and their soils. Above, OTUs are compared from in vitro, wild and soil microbiomes of each Marchantia species. Below, wild and soil microbiomes are compared from the two Marchantia species.
Figure 5
Figure 5
Relative abundance of the bacteria associated with Marchantia. The genera with significant (padj = 0.01) log2 fold changes are shown. “Other” corresponds to OTUs whose genera could not be assigned. Each dot represents an OTU. The OTUs prevalent in the Marchantia species are located on top of the plot while the OTUs prevalent in soil are located at the bottom. The majority of the OTUs were not assigned to a known genus, and are shown as “Others” in the plots. Shared genera between both Marchantia species are highlighted in blue.

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