Gonzalez-Sanz, C. | bioRxiv Science

bioRxiv2024

A compendium of bona fide reference markers of plant-derived extracellular vesicles and their degree of phylogenetic conservation

Although the field of plant EVs (PEVs) is experiencing exponential growth, rigorous characterisation complying with MISEV guidelines has not been yet implemented due to the lack of bona fide reference markers. In this work, we have paved the way for the standardisation of PEV markers, providing the most profound proteomic data so far from apoplastic washing fluid-EVs, a sample enriched in genuine extracellular vesicles from plant tissue of two reference plant species: Arabidopsis thaliana (Arath-EVs) and Brassica oleracea (Braol-EVs). Besides, we analysed the protein content of the soluble fraction of the apoplast and calculated the enrichment of the potential markers studied in EVs. Additionally, we have conducted an exhaustive analysis of the proteomic data available so far from genuine EVs from any plant species, evaluating current potential markers, together with those found in our proteomic analyses. Our results provide evidence supporting the potential use of the following families as PEV markers: aquaporins, vacuolar-type ATPase complex subunits, some fasciclin-like arabinogalactan proteins (FLAs), tetraspanins, syntaxins, germin-like proteins and calreticulins. Next, we analysed the presence of orthologues and their degree of conservation throughout plant taxa, as well as in 2 reference species from the animal kingdom: human and mouse. Their degree of conservation was compared with that of current animal EV: CD63, CD81 and CD9. Among the protein families with potential to be used as PEV markers, 2 were found to be plant-specific: FLAs and germin-like proteins. On the other hand, aquaporins and vacuolar-type ATPase complex subunits showed the greatest degree of conservation across plant and animal kingdoms. Our results provide key insights on several aspects of classical and novel protein identity markers for PEVs to assist in the selection of the best candidates for standardisation: 1) species-specific abundance, 2) specificity for PEVs, and 3) conservation and plant specificity.

molecular biology↗

bioRxiv2024

Maize associated bacterial and fungal microbiomes show contrasting conformation patterns that are resilient to water availability

Plant-associated microorganisms can help crops to alleviate water stress and increase the resilience of agricultural ecosystems to climate change. However, we still lack knowledge on the dynamics of bacterial and fungal microbial kingdoms within the soil and plant microbiomes and the response of these communities to different conditions such us, for example, water restrictions. This information is essential for the development of microbiome-based solutions to improve crop resilience to stressors associated to climate change. In this work, we explored: i) the conformation of the bacterial and fungal assemblages of different soil and plant compartments (bulk soil, rhizosphere, roots, leaves and grains) along the crop cycle of maize in an open field trial; and ii) the effect of water restriction on the maize microbiome comparing optimal irrigation with a 30% reduction of water supply. Our results show that microbial communities are highly structured along soil and plant compartments, with contrasting patterns for bacteria and fungi that were intensified towards the end of the plant cycle. Root showed the most differentiated bacterial assemblage while fungi conformed a very distinct community in the leaf, suggesting a relevant contribution of aerial fungal propagules to the microbiome of this plant organ. Despite the reductions in plant growth and yield, the microbiome of limited-watered plants did not show severe alterations. Still, significant impacts were observed within compartments, being fungi more responsive to limited watering than bacteria. Network analysis suggest that bacteria and fungi may play different roles in the shifts observed under water stress.

microbiology↗