The hidden world within plants: metatranscriptomics unveils the complexity of wood microbiomes

Abstract

The importance of plants as complex entities influenced by genomes of the associated microorganisms is now seen as a new source of variability for a more sustainable agriculture, also in the light of ongoing climate change. For this reason, we investigated through metatranscriptomics whether the taxa profile and behaviour of microbial communities associated with the wood of 20-year-old grapevine plants are influenced by the health status of the host. We report for the first time a metatranscriptome from a complex tissue in a real environment, highlighting that this approach is able to define the microbial community better than referenced transcriptomic approaches. In parallel, the use of total RNA enabled the identification of bacterial taxa in healthy samples that, once isolated from the original wood tissue, displayed potential biocontrol activities against a wood-degrading fungal taxon. Furthermore, we revealed an unprecedented high number of new viral entities (~120 new viral species among 180 identified) associated with a single and limited environment and with potential impact on the whole holobiont. Taken together, our results suggest a complex multitrophic interaction in which the viral community also plays a crucial role in raising new ecological questions for the exploitation of microbial-assisted sustainable agriculture.

Coevolutionary legacies for plant decomposition

“…Furthermore, the microbial community in living leaves and wood will affect plant performance and vice versa [62][63][64][65]. The presence of seed-mediated transmission of microbes across plant generations suggests long-term co-evolution between plants and their microbiota [66].…”

Microbe-assisted crop improvement: a sustainable weapon to restore holobiont functionality and resilience

“…The use of multi-omics approaches ( i.e. so called holo-omics [ 93 ]) to study the functionality of plant-microbiome ecosystems led to the generation of data on multiple levels [ 92 ], focusing on diverse targets (DNA, RNA, protein or metabolites), as well as to the characterization the plant associated microbiota [ 62 , 94 ]. These data are particularly relevant, resulting in obtaining information on the ability of specific genotypes to recruit specialized microbial strain(s) or consortia and providing information that might be useful in the manipulation of these interactions.…”

The road to molecular identification and detection of fungal grapevine trunk diseases

“…The main benefit of such methods is the wide microbiome analysis in each sample, allowing it to be applied in several samples simultaneously without the need to isolate the detected agents. These methodologies also allow to identify and relatively quantify the presence of each microbial agent (Eichmeier et al, 2018;Morales-Cruz et al, 2018b;Nerva et al, 2022). Additionally, distinct NGS approaches can have several outcomes, such as the perception of the role of the genes in the infectious process by RNA sequencing (Morales-Cruz et al, 2015, 2018aPaolinelli et al, 2022), the prevalence of certain pathogens in distinct environments and grapevine cultivars by environmental microbiome metasequencing (Maree et al, 2012;Eichmeier et al, 2018;del Frari et al, 2019;Azevedo-Silva et al, 2021), and the role of other microbial agents toward GTD-causing fungal pathogens (Berlanas et al, 2019;Saccà et al, 2019;Niem et al, 2020;Bekris et al, 2021;Cobos et al, 2022).…”