Marchantia liverworts as a proxy to plants’ basal microbiomes

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.

Testing the two-step model of plant root microbiome acquisition under multiple plant species and soil sources

“…Marchantia polymorpha and M. paleacea (Alcaraz et al 2018); both showed less diversity in their root analogs (bladders, and rhizoids) than their soil sources, supporting the two-step model. The Marchantia microbiomes even allowed us to perform an extreme microbial selection due to the in vitro propagation of these plants, highlighting a reduced core of closely related microbial inhabitants (Alcaraz et al 2018). Testing multiple plants, wild and domesticated, could reduce the gaps in understanding the microbiome structure loss as a domestication trade-off.…”

“…The 16S rRNA protocol used in this work had been used previously and is detailed at GitHub (Alcaraz et al, 2018; https://genomica-fciencias-unam.github.io/SOP/). In summary, gene amplicon libraries were quality inspected using Fastx Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/) and trimmed to a 250 bp length.…”

Station and train surface microbiomes of Mexico City’s metro (subway/underground)

“…We used a previously reported protocol for 16S rRNA gene amplicons analysis 34 , which is detailed at GitHub (https://genomica-fciencias-unam.github.io/SOP/). Briefly, sequencing pair-ended reads were merged, using a minimum of 470 bp, a 15 bp of minimum overlapping, and with a quality threshold of 0.95 using PANDASEQ 35 .…”

The holobiont concept before Margulis

“…This includes the question how their components assemble, how they interact, how holobionts evolve, and what role they might play in speciation and macroevolution (Collens et al, 2019; Parker, Dury, & Moczek, 2019; Sevellec, Derome, & Bernatchez, 2018; Zilber‐Rosenberg & Rosenberg, 2008). Moreover, the very species studied by Meyer‐Abich are currently used again as model organisms to investigate the development and evolution of holobionts and other host‐microbiotes collectives: lichens (Aschenbrenner, Cernava, Berg, & Grube, 2016; Cernava et al, 2019), sponges (Pita, Fraune, & Hentschel, 2016; Webster & Thomas, 2016) and various plants, ranging from mosses, like Marchantia spp., to orchid species (Alcaraz et al, 2018; Hassani, Durán, & Hacquard, 2018; Jacquemyn, Waud, Merckx, Lievens, & Brys, 2015; Vandenkoornhuyse, Quaiser, Duhamel, Van, & Dufresne, 2015). Remarkably, current views of holobionts, both in evo‐devo and microbiology, share with Meyer‐Abich the assumption of the phylogenetic ubiquitous nature and evolutionary centrality of holobiosis (Gilbert, 2019; Gilbert et al, 2012; McFall‐Ngai et al, 2013; Rosenberg & Zilber‐Rosenberg, 2018).…”