Beyond the surface: exploring the mycobiome of Norway spruce under drought stress and with Heterobasidion parviporum.

The mycobiome, comprising fungi inhabiting plants, potentially plays a crucial role in tree health and survival amidst environmental stressors like climate change and pathogenic fungi. Understanding the intricate relationships between trees and their microbial communities is essential for developing effective strategies to bolster the resilience and well-being of forest ecosystems as we adopt more sustainable forest management practices. The mycobiome can be considered an integral aspect of a tree's biology, closely linked to its genotype. To explore the influence of host genetics and environmental factors on fungal composition, we examined the mycobiome associated with phloem and roots of Norway spruce (Picea abies (L.) Karst.) cuttings under varying watering conditions. To test the "mycobiome-associated-fitness" hypothesis, we compared seedlings artificially inoculated with Heterobasidion parviporum and control plants to evaluate mycobiome interaction on necrosis development. We aimed to 1) identify specific mycobiome species for the Norway spruce genotypes/families within the phloem and root tissues and their interactions with H. parviporum and 2) assess stability in the mycobiome species composition under abiotic disturbances (reduced water availability). The mycobiome was analyzed by sequencing the ribosomal ITS2 region. Our results revealed significant variations in the diversity and prevalence of the phloem mycobiome among different Norway spruce genotypes, highlighting the considerable impact of genetic variation on the composition and diversity of the phloem mycobiome. Additionally, specific mycobiome genera in the phloem showed variations in response to water availability, indicating the influence of environmental conditions on the relative proportion of certain fungal genera in Norway spruce trees. In the root mycobiome, key fungi such as Phialocephala fortinii and Paraphaeosphaeria neglecta were identified as conferring inhibitory effects against H. parviporum growth in Norway spruce genotypes. Furthermore, certain endophytes demonstrated greater stability in root ecosystems under low water conditions than ectomycorrhizal fungi. This knowledge can contribute to developing sustainable forest management practices that enhance the well-being of trees and their ecosystems, ultimately bolstering forest resilience.

Three years of warming and rainfall reduction alter leaf physiology but not relative abundance of an annual species in a Mediterranean savanna.

Increasing air temperatures and decreasing rainfall can alter Mediterranean ecosystems, where summer heat and drought already limit plant regeneration. Manipulative field studies can help to understand and anticipate community responses to climate changes. In a Mediterranean oak wooded pasture, we have investigated the effects of warming (W, via open-top chambers increasing 1.4 °C mean air temperature), reduced rainfall (D, via gutters removing 33% of rainfall) and the combination of both factors (WD) on the winter-annual Geranium dissectum L. We measured reproductive phenology and output, leaf physiology during the reproductive phase, and plant relative abundance. Warming had a positive effect on plant height and little effects on leaf physiology. Rainfall reduction enhanced leaf water use efficiency. However, the most noticeable effects occurred in WD plants, which exhibited lower leaf predawn water potential and earlier flowering phenology in the first year of treatment, and a higher ratio of leaf dark respiration (R) to net CO2 assimilation (Pn) at comparable temperatures in the third year, compared to control plants. Leaf R at ambient temperature was similar across climatic treatments. The relative abundance of G. dissectum decreased by 23% over three years, but similarly across treatments. A short life cycle helps G. dissectum to escape severe late-spring heat and drought stress. Moreover, stomata closure and thermal acclimation of R can attenuate plant stress impact on reproduction. Adaptability of the short-lived annual G. dissectum could mitigate climate change impact on community composition over short periods (e.g. three years); however, a reduction in net carbon gain could eventually affect its reproductive success and persistence in the community.

Epigenetic responses of hare barley (Hordeum murinum subsp. leporinum) to climate change: an experimental, trait-based approach.

The impact of reduced rainfall and increased temperatures forecasted by climate change models on plant communities will depend on the capacity of plant species to acclimate and adapt to new environmental conditions. The acclimation process is mainly driven by epigenetic regulation, including structural and chemical modifications on the genome that do not affect the nucleotide sequence. In plants, one of the best-known epigenetic mechanisms is cytosine-methylation. We evaluated the impact of 30% reduced rainfall (hereafter "drought" treatment; D), 3 °C increased air temperature ("warming"; W), and the combination of D and W (WD) on the phenotypic and epigenetic variability of Hordeum murinum subsp. leporinum L., a grass species of high relevance in Mediterranean agroforestry systems. A full factorial experiment was set up in a savannah-like ecosystem located in southwestern Spain. H. murinum exhibited a large phenotypic plasticity in response to climatic conditions. Plants subjected to warmer conditions (i.e., W and WD treatments) flowered earlier, and those subjected to combined stress (WD) showed a higher investment in leaf area per unit of leaf mass (i.e., higher SLA) and produced heavier seeds. Our results also indicated that both the level and patterns of methylation varied substantially with the climatic treatments, with the combination of D and W inducing a clearly different epigenetic response compared to that promoted by D and W separately. The main conclusion achieved in this work suggests a potential role of epigenetic regulation of gene expression for the maintenance of homoeostasis and functional stability under future climate change scenarios.

TOA: A software package for automated functional annotation in non-model plant species.

The increase of sequencing capacity provided by high-throughput platforms has made it possible to routinely obtain large sets of genomic and transcriptomic sequences from model and non-model organisms. Subsequent genomic analysis and gene discovery in next-generation sequencing experiments are, however, bottlenecked by functional annotation. One common way to perform functional annotation of sets of sequences obtained from next-generation sequencing experiments, is by searching for homologous sequences and accessing the related functional information deposited in genomic databases. Functional annotation is especially challenging for non-model organisms, like many plant species. In such cases, existing free and commercial general-purpose applications may not offer complete and accurate results. We present TOA (Taxonomy-oriented annotation), a Python-based user-friendly open source application designed to establish functional annotation pipelines geared towards non-model plant species that can run in Linux/Mac computers, HPCs and cloud servers. TOA performs homology searches against proteins stored in the PLAZA databases, NCBI RefSeq Plant, Nucleotide Database and Non-Redundant Protein Sequence Database, and outputs functional information from several ontology systems: Gene Ontology, InterPro, EC, KEGG, Mapman and MetaCyc. The software performance was validated by comparing the runtimes, total number of annotated sequences and accuracy of the functional information obtained for several plant benchmark data sets with TOA and other functional annotation solutions. TOA outperformed the other software in terms of number of annotated sequences and accuracy of the annotation and constitutes a good alternative to improve functional annotation in plants. TOA is especially recommended for gymnosperms or for low quality sequence data sets of non-model plants.

Proliferation of axial parenchymatic xylem cells is a key step in wound closure of girdled stems in Pinus canariensis.

BACKGROUND: Wounds caused by fire, herbivorism, rock impacts, etc. cause the direct loss of photosynthetic, storage and/or vascular tissue. In addition, they may entail other damages, such as desiccation of the exposed internal parts, or become a gateway to infection by fungi and other pathogens. To successfully overcome such injuries, plants must reorganize their meristems or even differentiate new ones, producing new traumatic tissues to cover the wound and restore the vascular connection. RESULTS: In this work we analyse the anatomical growth response in conifers after debarking and injuring the vascular cambium, using Pinus canariensis as model species, due to its high wound recovery ability. Conversely to angiosperm woody species, this process is initiated and largely driven by the damaged vascular cambium and not by proliferation in the wound surface. We have detected alterations and switches in the divisions of cambial cells, associated to their position relative to the surface and edges of the wound, resulting in disordered traumatic xylem. We also describe the formation of column-like structures, after girdling, which are in part formed by the proliferation of xylem parenchymatous cells, associated to axial resin ducts. CONCLUSIONS: Abundant resinosis on the wound surface, typical of conifers, is an efficient barrier against opportunistic fungi, insects, etc. but it also hinders the healing process directly from the surface. Thus, wound closure must be largely carried out from the wound margins, being a much slower process, which very often remains unconcluded for long years. This work also describes for the first time the proliferation of inner parenchymatous cells to form column-like structures, which accelerates wound closure in girdled P. canariensis. Irregularities in the surface of the healing edge or column-like structures result in the production of disordered vascular tissues, compromising their future functionality, and which must be overcome through the fast restoration of the proper polarity in vascular cambium.