Fortes, A. M. | bioRxiv Science

bioRxiv2026

Unraveling grapevine taxonomic and functional soil microbiome under different edaphic conditions within a vineyard plot.

Grapevine, mainly Vitis vinifera, occupies an elite position among crops worldwide. Soil and plant rhizosphere microbiomes are known to act as promoters of plant growth and health status. Plant root systems can select microbial communities through root exudates, while soil physicochemical parameters influence the structure and composition of the microbial community. In this work, we characterize the taxonomic composition and potential functional microbiome in combination with a large set of physicochemical parameters from the same soil samples collected at short distance (250 m) within a conventionally managed commercial vineyard plot. Metabarcoding and metagenome analysis, using amplicon and shotgun sequencing, allowed us to explore the structure and composition of the microbiomes and their functional activity. Soil microbial structure and functionality, as well as physicochemical parameters, differed between the two locations. Levels of locations elevation, boron, and sodium showed high correlation with the sample distribution of microbial community and functional genes suggesting they could affect directly the microbial community and their interaction with grapevine roots. Elevation variable, which includes a set of stochastic and deterministic factors, could have exacerbated further the differences in the microbial community and functionality. As a result, Burkholderia-Caballeronia-Paraburkholderia, Pseudomonas, Pseudoxanthomonas, and Streptomyces genera, which were described to effectively improve plant growth and resistance to abiotic stresses, were significantly more abundant in one location presenting lower levels of boron, zinc and active limestone and higher levels of sodium (within safe ranges). Microbial activity points out to have higher positive plant interactions in the same location registering genes associated with biofilm formation and quorum sensing pathways together with lipopolysaccharide biosynthesis and membrane transport. Altogether this data contributes to a better understanding of complex systems such as grapevine soil since soil physicochemical properties and microbial communities present significant variation within the vineyard, which can eventually impact wine quality.

microbiology↗

bioRxiv2019

Evolutionary insights into PtdIns3P signaling through FYVE and PHOX effector proteins from the moss Physcomitrella patens.

Phosphatidylinositol 3-phosphate (PtdIns3P) is one of the five different phosphoinositides (PPIs) species in plant cells, which regulate several aspects of plant growth and development, as well as responses to biotic and abiotic stresses. The mechanistic insights underlying PtdIns3P mode of action, specifically through PtdIns3P-binding effectors such as FYVE and PHOX proteins have been partially explored in plants with main focus on Arabidopsis thaliana. Additionally, they have been underexplored in other plant organisms such as bryophytes, the earliest diverging group of terrestrial flora.\n\nIn this study, we searched for genes coding for FYVE and PHOX domains containing sequences from different photosynthetic organisms in order to gather evolutionary insights on these PPI binding domains, followed by an in silico characterization of the FYVE and PHOX gene family in the moss Physcomitrella patens. Phylogenetic analysis showed that PpFYVE proteins can be grouped in 7 subclasses, with an additional subclass whose FYVE domain was lost during evolution to higher plants. On the other hand, PpPHOX proteins are classified into 5 subclasses. Expression analyses based on RNAseq data together with the analysis of cis-acting regulatory elements and transcription factor binding sites in promoter regions suggest the importance of these proteins in regulating stress responses but mainly developmental processes in P. patens. The results provide valuable information and robust candidate genes for future functional analysis aiming to further explore the role of this signaling pathway mainly during growth and development of tip growing cells and during the transition from 2D to 3D growth, which could provide ancestral regulatory players undertaken during plant evolution.

plant biology↗