Regulation of Water Use in the Southernmost European Fir (Abies pinsapo Boiss.): Drought Avoidance Matters

Under Stress: Searching for Genes Involved in the Response of Abies pinsapo Boiss to Climate Change

Currently, Mediterranean forests are experiencing the deleterious effects of global warming, which mainly include increased temperatures and decreased precipitation in the region. Relict Abies pinsapo fir forests, endemic in the southern Iberian Peninsula, are especially sensitive to these recent environmental disturbances, and identifying the genes involved in the response of this endangered tree species to climate-driven stresses is of paramount importance for mitigating their effects. Genomic resources for A. pinsapo allow for the analysis of candidate genes reacting to warming and aridity in their natural habitats. Several members of the complex gene families encoding late embryogenesis abundant proteins (LEAs) and heat shock proteins (HSPs) have been found to exhibit differential expression patterns between wet and dry seasons when samples from distinct geographical locations and dissimilar exposures to the effects of climate change were analyzed. The observed changes were more perceptible in the roots of trees, particularly in declining forests distributed at lower altitudes in the more vulnerable mountains. These findings align with previous studies and lay the groundwork for further research on the molecular level. Molecular and genomic approaches offer valuable insights for mitigating climate stress and safeguarding this endangered conifer.

Warming appears as the main risk of non-adaptedness for western Mediterranean relict fir forests under expected climate change scenarios

Circum-Mediterranean firs are considered among the most drought-sensitive species to climate change. Understanding the genetic basis of trees' adaptive capacity and intra-specific variability to drought avoidance is mandatory to define conservation measures, thus potentially preventing their extinction. We focus here on Abies pinsapo and Abies marocana, both relict tree species, endemic from south Spain and north Morocco, respectively. A total of 607 samples were collected from eight nuclei: six from Spanish fir and two from Moroccan fir. A genotyping by sequencing technique called double digestion restriction site-associated DNA sequencing (ddRAD-seq) was performed to obtain a genetic matrix based on single-nucleotide polymorphisms (SNPs). This matrix was utilized to study the genetic structure of A. pinsapo populations and to carry out selection signature studies. In order to understand how Spanish fir and Moroccan fir cope with climate change, genotype-environment associations (GEAs) were identified. Further, the vulnerability of these species to climate variations was estimated by the risk of non-adaptedness (RONA). The filtering of the de novo assembly of A. pinsapo provided 3,982 SNPs from 504 out of 509 trees sequenced. Principal component analysis (PCA) genetically separated Grazalema from the rest of the Spanish populations. However, FST values showed significant differences among the sampling points. We found 51 loci potentially under selection. Homolog sequences were found for some proteins related to abiotic stress response, such as dehydration-responsive element binding transcription factor, regulation of abscisic acid signaling, and methylation pathway. A total of 15 associations with 11 different loci were observed in the GEA studies, with the maximum temperature of the warmest month being the variable with the highest number of associated loci. This temperature sensitivity was also supported by the risk of non-adaptedness, which yielded a higher risk for both A. pinsapo and A. marocana under the high emission scenario (Representative Concentration Pathway (RCP) 8.5). This study sheds light on the response to climate change of these two endemic species.

Contrasting transcriptomic patterns reveal a genomic basis for drought resilience in the relict fir Abies pinsapo Boiss

Climate change challenges the adaptive capacity of several forest tree species in the face of increasing drought and rising temperatures. Therefore, understanding the mechanistic connections between genetic diversity and drought resilience is highly valuable for conserving drought-sensitive forests. Nonetheless, the post-drought recovery in trees from a transcriptomic perspective has not yet been studied by comparing contrasting phenotypes. Here, experimental drought treatments, gas-exchange dynamics and transcriptomic analysis (RNA-seq) were performed in the relict and drought-sensitive fir Abies pinsapo Boiss. to identify gene expression differences over immediate (24 h) and extended drought (20 days). Post-drought responses were investigated to define resilient and sensitive phenotypes. Single nucleotide polymorphisms (SNPs) were also studied to characterize the genomic basis of A. pinsapo drought resilience. Weighted gene co-expression network analysis showed an activation of stomatal closing and an inhibition of plant growth-related genes during the immediate drought, consistent with an isohydric dynamic. During the extended drought, transcription factors, as well as cellular damage and homeostasis protection-related genes prevailed. Resilient individuals activate photosynthesis-related genes and inhibit aerial growth-related genes, suggesting a shifting shoot/root biomass allocation to improve water uptake and whole-plant carbon balance. About, 152 fixed SNPs were found between resilient and sensitive seedlings, which were mostly located in RNA-activity-related genes, including epigenetic regulation. Contrasting gene expression and SNPs were found between different post-drought resilience phenotypes for the first time in a forest tree, suggesting a transcriptomic and genomic basis for drought resilience. The obtained drought-related transcriptomic profile and drought-resilience candidate genes may guide conservation programs for this threatened tree species.

De novo transcriptome sequencing and gene co-expression reveal a genomic basis for drought sensitivity and evidence of a rapid local adaptation on Atlas cedar (Cedrus atlantica)

Introduction

Understanding the adaptive capacity to current climate change of drought-sensitive tree species is mandatory, given their limited prospect of migration and adaptation as long-lived, sessile organisms. Knowledge about the molecular and eco-physiological mechanisms that control drought resilience is thus key, since water shortage appears as one of the main abiotic factors threatening forests ecosystems. However, our current background is scarce, especially in conifers, due to their huge and complex genomes.

Methods

Here we investigated the eco-physiological and transcriptomic basis of drought response of the climate change-threatened conifer Cedrus atlantica. We studied C. atlantica seedlings from two locations with contrasting drought conditions to investigate a local adaptation. Seedlings were subjected to experimental drought conditions, and were monitored at immediate (24 hours) and extended (20 days) times. In addition, post-drought recovery was investigated, depicting two contrasting responses in both locations (drought resilient and non-resilient). Single nucleotide polymorphisms (SNPs) were also studied to characterize the genomic basis of drought resilience and investigate a rapid local adaptation of C. atlantica.

Results

De novo transcriptome assembly was performed for the first time in this species, providing differences in gene expression between the immediate and extended treatments, as well as among the post-drought recovery phenotypes. Weighted gene co-expression network analysis showed a regulation of stomatal closing and photosynthetic activity during the immediate drought, consistent with an isohydric dynamic. During the extended drought, growth and flavonoid biosynthesis inhibition mechanisms prevailed, probably to increase root-to-shoot ratio and to limit the energy-intensive biosynthesis of secondary metabolites. Drought sensitive individuals failed in metabolism and photosynthesis regulation under drought stress, and in limiting secondary metabolite production. Moreover, genomic differences (SNPs) were found between drought resilient and sensitive seedlings, and between the two studied locations, which were mostly related to transposable elements.

Discussion

This work provides novel insights into the transcriptomic basis of drought response of C. atlantica, a set of candidate genes mechanistically involved in its drought sensitivity and evidence of a rapid local adaptation. Our results may help guide conservation programs for this threatened conifer, contribute to advance drought-resilience research and shed light on trees' adaptive potential to current climate change.

Unexpected resilience in relict Abies pinsapo Boiss forests to dieback and mortality induced by climate change

Acute and early symptoms of forest dieback linked to climate warming and drought episodes have been reported for relict Abies pinsapo Boiss. fir forests from Southern Spain, particularly at their lower ecotone. Satellite, orthoimages, and field data were used to assess forest decline, tree mortality, and gap formation and recolonization in the lower half of the altitudinal range of A. pinsapo forests (850-1550 m) for the last 36 years (1985-2020). Field surveys were carried out in 2003 and in 2020 to characterize changes in stand canopy structure and mortality rates across the altitudinal range. Time series of the Normalized Difference Vegetation Index (NDVI) at the end of the dry season (derived from Landsat 5 and 7 imagery) were used for a Dynamic Factor Analysis to detect common trends across altitudinal bands and topographic solar incidence gradients (SI). Historical canopy cover changes were analyzed through aerial orthoimages classification. Here we show that extensive decline and mortality contrast to the almost steady alive basal area for 17 years, as well as the rising photosynthetic activity derived from NDVI since the mid-2000s and an increase in the forest canopy cover in the late years at mid and high altitudes. We hypothesized that these results suggest an unexpected resilience in A. pinsapo forests to climate change-induced dieback, that might be promoted by compensation mechanisms such as (i) recruitment of new A. pinsapo individuals; (ii) facilitative effects on such recruitment mediated by revegetation with other species; and (iii) a 'release effect' in which surviving trees can thrive with fewer resource competition. Future research is needed to understand these compensation mechanisms and their scope in future climate change scenarios.

Physiological and Shoot Growth Responses of Abies holophylla and Abies koreana Seedlings to Open-Field Experimental Warming and Increased Precipitation

Projected changes in temperature and precipitation in mid-latitude wet regions are expected to significantly affect forest ecosystems. We studied the physiological and shoot growth responses of Abies holophylla and Abies koreana seedlings to warming (3 °C above ambient temperature) and increased precipitation (irrigation with 40% of rainfall) treatments under open-field conditions. The physiological parameters, quantified by the net photosynthetic rate, transpiration rate, stomatal conductance, and total chlorophyll content, were monitored from July to October 2018. Shoot growth (i.e., root collar diameter and height) was assessed in August and December 2018. Irrespective of the treatments, the physiological parameters of both species decreased from July to August under warming treatment due to heat stress before recovering in September and October. Warming alone (W) and warming along with increased precipitation (W*P) decreased the physiological activities of both species in July, August, and September, with more pronounced effects on A. koreana compared with A. holophylla. Increased precipitation resulted in the increased chlorophyll content of both species in October. Shoot growth was not generally affected by the treatments, except for a subtle reduction in height under W*P for A. koreana. A. holophylla had consistently higher values for the physiological parameters and shoot growth than A. koreana. Our results indicate that the physiological activities of the Abies species could be seriously reduced under climate change, with a more severe impact on A. koreana. Among the two species, A. holophylla appears to be a more robust candidate for future forest planting.

Challenges and Perspectives in the Epigenetics of Climate Change-Induced Forests Decline

Forest tree species are highly vulnerable to the effects of climate change. As sessile organisms with long generation times, their adaptation to a local changing environment may rely on epigenetic modifications when allele frequencies are not able to shift fast enough. However, the current lack of knowledge on this field is remarkable, due to many challenges that researchers face when studying this issue. Huge genome sizes, absence of reference genomes and annotation, and having to analyze huge amounts of data are among these difficulties, which limit the current ability to understand how climate change drives tree species epigenetic modifications. In spite of this challenging framework, some insights on the relationships among climate change-induced stress and epigenomics are coming. Advances in DNA sequencing technologies and an increasing number of studies dealing with this topic must boost our knowledge on tree adaptive capacity to changing environmental conditions. Here, we discuss challenges and perspectives in the epigenetics of climate change-induced forests decline, aiming to provide a general overview of the state of the art.

Linkages between Climate, Radial Growth and Defoliation in Abies pinsapo Forests from Southern Spain

Systematic forest networks of health monitoring have been established to follow changes in tree vigor and mortality. These networks often lack long-term growth data, but they could be complemented with tree ring data, since both defoliation and radial growth are proxies of changes in tree vigor. For instance, a severe water shortage should reduce growth and increase tree defoliation in drought-prone areas. However, the effects of climatic stress and drought on growth and defoliation could also depend on tree age. To address these issues, we compared growth and defoliation data with recent climate variability and drought severity in Abies pinsapo old and young trees sampled in Southern Spain, where a systematic health network (Andalucía Permanent Plot Network) was established. Our aims were: (i) to assess the growth sensitivity of old and young A. pinsapo trees and (ii) to test if relative changes in radial growth were related with recent defoliation, for instance, after severe droughts. We also computed the resilience indices to quantify how old and young trees recovered growth after recent droughts. Wet-cool conditions during the prior autumn and the current early summer improved the growth of old trees, whereas late-spring wet conditions enhanced the growth of young trees. Old trees were more sensitive to wet and sunny conditions in the early summer than young trees. Old and young trees were more responsive to the Standardized Precipitation-Evapotranspiration Index drought index of June–July and July–August calculated at short (one–three months) and mid (three–six months) time scales, respectively. Old trees presented a higher resistance to a severe drought in 1995 than young trees. A positive association was found between stand defoliation and relative growth. Combining monitoring and tree ring networks is useful for the detection of early warning signals of dieback in similar drought-prone forests.

Carbon Limitation and Drought Sensitivity at Contrasting Elevation and Competition of Abies pinsapo Forests. Does Experimental Thinning Enhance Water Supply and Carbohydrates?

Stand-level competition and local climate influence tree responses to increased drought at the regional scale. To evaluate stand density and elevation effects on tree carbon and water balances, we monitored seasonal changes in sap-flow density (SFD), gas exchange, xylem water potential, secondary growth, and non-structural carbohydrates (NSCs) in Abies pinsapo. Trees were subjected to experimental thinning within a low-elevation stand (1200 m), and carbon and water balances were compared to control plots at low and high elevation (1700 m). The hydraulic conductivity and the resistance to cavitation were also characterized, showing relatively high values and no significant differences among treatments. Trees growing at higher elevations presented the highest SFD, photosynthetic rates, and secondary growth, mainly because their growing season was extended until summer. Trees growing at low elevation reduced SFD during late spring and summer while SFD and secondary growth were significantly higher in the thinned stands. Declining NSC concentrations in needles, branches, and sapwood suggest drought-induced control of the carbon supply status. Our results might indicate potential altitudinal shifts, as better performance occurs at higher elevations, while thinning may be suitable as adaptive management to mitigate drought effects in endangered Mediterranean trees.

Climate extremes and predicted warming threaten Mediterranean Holocene firs forests refugia

Warmer and drier climatic conditions are projected for the 21st century; however, the role played by extreme climatic events on forest vulnerability is still little understood. For example, more severe droughts and heat waves could threaten quaternary relict tree refugia such as Circum-Mediterranean fir forests (CMFF). Using tree-ring data and a process-based model, we characterized the major climate constraints of recent (1950-2010) CMFF growth to project their vulnerability to 21st-century climate. Simulations predict a 30% growth reduction in some fir species with the 2050s business-as-usual emission scenario, whereas growth would increase in moist refugia due to a longer and warmer growing season. Fir populations currently subjected to warm and dry conditions will be the most vulnerable in the late 21st century when climatic conditions will be analogous to the most severe dry/heat spells causing dieback in the late 20th century. Quantification of growth trends based on climate scenarios could allow defining vulnerability thresholds in tree populations. The presented predictions call for conservation strategies to safeguard relict tree populations and anticipate how many refugia could be threatened by 21st-century dry spells.