Mechanistic links between physiology and spectral reflectance enable previsual detection of oak wilt and drought stress.

Tree mortality due to global change-including range expansion of invasive pests and pathogens-is a paramount threat to forest ecosystems. Oak forests are among the most prevalent and valuable ecosystems both ecologically and economically in the United States. There is increasing interest in monitoring oak decline and death due to both drought and the oak wilt pathogen (Bretziella fagacearum). We combined anatomical and ecophysiological measurements with spectroscopy at leaf, canopy, and airborne levels to enable differentiation of oak wilt and drought, and detection prior to visible symptom appearance. We performed an outdoor potted experiment with Quercus rubra saplings subjected to drought stress and/or artificially inoculated with the pathogen. Models developed from spectral reflectance accurately predicted ecophysiological indicators of oak wilt and drought decline in both potted and field experiments with naturally grown saplings. Both oak wilt and drought resulted in blocked water transport through xylem conduits. However, oak wilt impaired conduits in localized regions of the xylem due to formation of tyloses instead of emboli. The localized tylose formation resulted in more variable canopy photosynthesis and water content in diseased trees than drought-stressed ones. Reflectance signatures of plant photosynthesis, water content, and cellular damage detected oak wilt and drought 12 d before visual symptoms appeared. Our results show that leaf spectral reflectance models predict ecophysiological processes relevant to detection and differentiation of disease and drought. Coupling spectral models that detect physiological change with spatial information enhances capacity to differentiate plant stress types such as oak wilt and drought.

Karyotype and LTR-RTs analysis provide insights into oak genomic evolution.

BACKGROUND: Whole-genome duplication and long terminal repeat retrotransposons (LTR-RTs) amplification in organisms are essential factors that affect speciation, local adaptation, and diversification of organisms. Understanding the karyotype projection and LTR-RTs amplification could contribute to untangling evolutionary history. This study compared the karyotype and LTR-RTs evolution in the genomes of eight oaks, a dominant lineage in Northern Hemisphere forests. RESULTS: Karyotype projections showed that chromosomal evolution was relatively conservative in oaks, especially on chromosomes 1 and 7. Modern oak chromosomes formed through multiple fusions, fissions, and rearrangements after an ancestral triplication event. Species-specific chromosomal rearrangements revealed fragments preserved through natural selection and adaptive evolution. A total of 441,449 full-length LTR-RTs were identified from eight oak genomes, and the number of LTR-RTs for oaks from section Cyclobalanopsis was larger than in other sections. Recent amplification of the species-specific LTR-RTs lineages resulted in significant variation in the abundance and composition of LTR-RTs among oaks. The LTR-RTs insertion suppresses gene expression, and the suppressed intensity in gene regions was larger than in promoter regions. Some centromere and rearrangement regions indicated high-density peaks of LTR/Copia and LTR/Gypsy. Different centromeric regional repeat units (32, 78, 79 bp) were detected on different Q. glauca chromosomes. CONCLUSION: Chromosome fusions and arm exchanges contribute to the formation of oak karyotypes. The composition and abundance of LTR-RTs are affected by its recent amplification. LTR-RTs random retrotransposition suppresses gene expression and is enriched in centromere and chromosomal rearrangement regions. This study provides novel insights into the evolutionary history of oak karyotypes and the organization, amplification, and function of LTR-RTs.

Rhytidome- and cork-type barks of holm oak, cork oak and their hybrids highlight processes leading to cork formation.

BACKGROUND: The periderm is basic for land plants due to its protective role during radial growth, which is achieved by the polymers deposited in the cell walls. In most trees, like holm oak, the first periderm is frequently replaced by subsequent internal periderms yielding a heterogeneous outer bark made of a mixture of periderms and phloem tissues, known as rhytidome. Exceptionally, cork oak forms a persistent or long-lived periderm which results in a homogeneous outer bark of thick phellem cell layers known as cork. Cork oak and holm oak distribution ranges overlap to a great extent, and they often share stands, where they can hybridize and produce offspring showing a rhytidome-type bark. RESULTS: Here we use the outer bark of cork oak, holm oak, and their natural hybrids to analyse the chemical composition, the anatomy and the transcriptome, and further understand the mechanisms underlying periderm development. We also include a unique natural hybrid individual corresponding to a backcross with cork oak that, interestingly, shows a cork-type bark. The inclusion of hybrid samples showing rhytidome-type and cork-type barks is valuable to approach cork and rhytidome development, allowing an accurate identification of candidate genes and processes. The present study underscores that abiotic stress and cell death are enhanced in rhytidome-type barks whereas lipid metabolism and cell cycle are enriched in cork-type barks. Development-related DEGs showing the highest expression, highlight cell division, cell expansion, and cell differentiation as key processes leading to cork or rhytidome-type barks. CONCLUSION: Transcriptome results, in agreement with anatomical and chemical analyses, show that rhytidome and cork-type barks are active in periderm development, and suberin and lignin deposition. Development and cell wall-related DEGs suggest that cell division and expansion are upregulated in cork-type barks whereas cell differentiation is enhanced in rhytidome-type barks.

Identification of genetics and hormonal factors involved in Quercus robur root growth regulation in different cultivation system.

Understanding the molecular processes and hormonal signals that govern root growth is of paramount importance for effective forest management. While Arabidopsis studies have shed light on the role of the primary root in root system development, the structure of root systems in trees is considerably more intricate, posing challenges to comprehend taproot growth in acorn-sown and nursery-cultivated seedlings. In this study, we investigated Quercus robur seedlings using rhizotrons, containers, and transplanted containers to rhizotrons, aiming to unravel the impact of forest nursery practices on processes governing taproot growth and root system development. Root samples were subjected to RNA-seq analysis to identify gene expression patterns and perform differential gene expression and phytohormone analysis. Among studied cultivation systems, differentially expressed genes (DEGs) exhibited significant diversity, where the number of co-occurring DEGs among cultivation systems was significantly smaller than the number of unique DEGs in different cultivation systems. Moreover, the results imply that container cultivation triggers the activation of several genes associated with linolenic acid and peptide synthesis in root growth. Upon transplantation from containers to rhizotrons, rapid enhancement in gene expression occurs, followed by gradual reduction as root growth progresses, ultimately reaching a similar expression pattern as observed in the taproot of rhizotron-cultivated seedlings. Phytohormone analysis revealed that taproot growth patterns under different cultivation systems are regulated by the interplay between auxin and cytokinin concentrations. Moreover, the diversification of hormone levels within the root zone and cultivation systems allows for taproot growth inhibition and prompt recovery in transplanted seedlings. Our study highlights the crucial role of hormone interactions during the early stages of taproot elongation, influencing root system formation across.

Ensemble species distribution modeling and multilocus phylogeography provide insight into the spatial genetic patterns and distribution dynamics of a keystone forest species, Quercus glauca.

BACKGROUND: Forests are essential for maintaining species diversity, stabilizing local and global climate, and providing ecosystem services. Exploring the impact of paleogeographic events and climate change on the genetic structure and distribution dynamics of forest keystone species could help predict responses to future climate change. In this study, we combined an ensemble species distribution model (eSDM) and multilocus phylogeography to investigate the spatial genetic patterns and distribution change of Quercus glauca Thunb, a keystone of East Asian subtropical evergreen broad-leaved forest. RESULTS: A total of 781 samples were collected from 77 populations, largely covering the natural distribution of Q. glauca. The eSDM showed that the suitable habitat experienced a significant expansion after the last glacial maximum (LGM) but will recede in the future under a general climate warming scenario. The distribution centroid will migrate toward the northeast as the climate warms. Using nuclear SSR data, two distinct lineages split between east and west were detected. Within-group genetic differentiation was higher in the West than in the East. Based on the identified 58 haplotypes, no clear phylogeographic structure was found. Populations in the Nanling Mountains, Wuyi Mountains, and the southwest region were found to have high genetic diversity. CONCLUSIONS: A significant negative correlation between habitat stability and heterozygosity might be explained by the mixing of different lineages in the expansion region after LGM and/or hybridization between Q. glauca and closely related species. The Nanling Mountains may be important for organisms as a dispersal corridor in the west-east direction and as a refugium during the glacial period. This study provided new insights into spatial genetic patterns and distribution dynamics of Q. glauca.

Unravelling DNA methylation dynamics during developmental stages in Quercus ilex subsp. ballota [Desf.] Samp.

BACKGROUND: DNA methylation is a critical factor influencing plant growth, adaptability, and phenotypic plasticity. While extensively studied in model and crop species, it remains relatively unexplored in holm oak and other non-domesticated forest trees. This study conducts a comprehensive in-silico mining of DNA methyltransferase and demethylase genes within the holm oak genome to enhance our understanding of this essential process in these understudied species. The expression levels of these genes in adult and seedling leaves, as well as embryos, were analysed using quantitative real-time PCR (qRT-PCR). Global DNA methylation patterns were assessed through methylation-sensitive amplified polymorphism (MSAP) techniques. Furthermore, specific methylated genomic sequences were identified via MSAP sequencing (MSAP-Seq). RESULT: A total of 13 DNA methyltransferase and three demethylase genes were revealed in the holm oak genome. Expression levels of these genes varied significantly between organs and developmental stages. MSAP analyses revealed a predominance of epigenetic over genetic variation among organs and developmental stages, with significantly higher global DNA methylation levels observed in adult leaves. Embryos exhibited frequent demethylation events, while de novo methylation was prevalent in seedling leaves. Approximately 35% of the genomic sequences identified by MSAP-Seq were methylated, predominantly affecting nuclear genes and intergenic regions, as opposed to repetitive sequences and chloroplast genes. Methylation was found to be more pronounced in the exonic regions of nuclear genes compared to their promoter and intronic regions. The methylated genes were predominantly associated with crucial biological processes such as photosynthesis, ATP synthesis-coupled electron transport, and defence response. CONCLUSION: This study opens a new research direction in analysing variability in holm oak by evaluating the epigenetic events and mechanisms based on DNA methylation. It sheds light on the enzymatic machinery governing DNA (de)methylation, and the changes in the expression levels of methylases and demethylases in different organs along the developmental stages. The expression level was correlated with the DNA methylation pattern observed, showing the prevalence of de novo methylation and demethylation events in seedlings and embryos, respectively. Several methylated genes involved in the regulation of transposable element silencing, lipid biosynthesis, growth and development, and response to biotic and abiotic stresses are highlighted. MSAP-seq integrated with whole genome bisulphite sequencing and advanced sequencing technologies, such as PacBio or Nanopore, will bring light on epigenetic mechanisms regulating the expression of specific genes and its correlation with the phenotypic variability and the differences in the response to environmental cues, especially those related to climate change.

Mass spectrometry in the study of wood compounds released in the barrel-aged wine and spirits.

Aging of wines and spirits in wooden barrels is an industrial process used to stabilize the color, to improve the limpidity and to enrich the sensorial characteristics of the products. In red wines, the oxygen that permeates through the wood staves promotes the oxidization of polyphenols and the formation of new pigments with consequent stabilization of the wine color. Barrel aging of spirits, such as brandy, whisky, rum, and grappa is finalized to enrich their aroma and improve their sensorial characteristics by the contribute of the compounds released by the wood. Oak is the wood type mostly used in making barrels; however, an increasing interest in the use of chestnut, cherry, acacia, and in less extent, ash and mulberry, has been observed in the recent years. Gas chromatography-mass spectrometry and liquid chromatography-mass spectrometry are the main techniques used to characterize respectively the volatile and polar metabolites released by the wood barrels in the products. In this article are reported the recent advancements in this field.

Genomic basis of the distinct biosynthesis of ß-glucogallin, a biochemical marker for hydrolyzable tannin production, in three oak species.

Hydrolyzable tannins (HTs), predominant polyphenols in oaks, are widely used in grape wine aging, feed additives, and human healthcare. However, the limited availability of a high-quality reference genome of oaks greatly hampered the recognition of the mechanism of HT biosynthesis. Here, high-quality reference genomes of three Asian oak species (Quercus variabilis, Quercus aliena, and Quercus dentata) that have different HT contents were generated. Multi-omics studies were carried out to identify key genes regulating HT biosynthesis. In vitro enzyme activity assay was also conducted. Dual-luciferase and yeast one-hybrid assays were used to reveal the transcriptional regulation. Our results revealed that ß-glucogallin was a biochemical marker for HT production in the cupules of the three Asian oaks. UGT84A13 was confirmed as the key enzyme for ß-glucogallin biosynthesis. The differential expression of UGT84A13, rather than enzyme activity, was the main reason for different ß-glucogallin and HT accumulation. Notably, sequence variations in UGT84A13 promoters led to different trans-activating activities of WRKY32/59, explaining the different expression patterns of UGT84A13 among the three species. Our findings provide three high-quality new reference genomes for oak trees and give new insights into different transcriptional regulation for understanding ß-glucogallin and HT biosynthesis in closely related oak species.

Restricted internal diffusion weakens transpiration-photosynthesis coupling during heatwaves: Evidence from leaf carbonyl sulphide exchange.

Increasingly frequent and intense heatwaves threaten ecosystem health in a warming climate. However, plant responses to heatwaves are poorly understood. A key uncertainty concerns the intensification of transpiration when heatwaves suppress photosynthesis, known as transpiration-photosynthesis decoupling. Field observations of such decoupling are scarce, and the underlying physiological mechanisms remain elusive. Here, we use carbonyl sulphide (COS) as a leaf gas exchange tracer to examine potential mechanisms leading to transpiration-photosynthesis decoupling on a coast live oak in a southern California woodland in spring 2013. We found that heatwaves suppressed both photosynthesis and leaf COS uptake but increased transpiration or sustained it at non-heatwave levels throughout the day. Despite statistically significant decoupling between transpiration and photosynthesis, stomatal sensitivity to environmental factors did not change during heatwaves. Instead, midday photosynthesis during heatwaves was restricted by internal diffusion, as indicated by the lower internal conductance to COS. Thus, increased evaporative demand and nonstomatal limitation to photosynthesis act jointly to decouple transpiration from photosynthesis without altering stomatal sensitivity. Decoupling offered limited potential cooling benefits, questioning its effectiveness for leaf thermoregulation in xeric ecosystems. We suggest that adding COS to leaf and ecosystem flux measurements helps elucidate diverse physiological mechanisms underlying transpiration-photosynthesis decoupling.

A strategy for studying epigenetic diversity in natural populations: proof of concept in poplar and oak.

In the last 20 years, several techniques have been developed for quantifying DNA methylation, the most studied epigenetic marks in eukaryotes, including the gold standard method, whole-genome bisulfite sequencing (WGBS). WGBS quantifies genome-wide DNA methylation but has several inconveniences rendering it less suitable for population-scale epigenetic studies. The high cost of deep sequencing and the large amounts of data generated prompted us to seek an alternative approach. Restricting studies to parts of the genome would be a satisfactory alternative had there not been a major limitation: the need to select upstream targets corresponding to differentially methylated regions as targets. Given the need to study large numbers of samples, we propose a strategy for investigating DNA methylation variation in natural populations, taking into account the structural complexity of genomes, their size, and their content in unique coding regions versus repeated regions as transposable elements. We first identified regions of highly variable DNA methylation in a subset of genotypes representative of the biological diversity in the population by WGBS. We then analysed the variations of DNA methylation in these targeted regions at the population level by sequencing capture bisulfite (SeqCapBis). The entire strategy was then validated by applying it to another species. Our strategy was developed as a proof of concept on natural populations of two forest species: Populus nigra and Quercus petraea.

Rapid migration of Mongolian oak into the southern Asian boreal forest.

The migration of trees induced by climatic warming has been observed at many alpine treelines and boreal-tundra ecotones, but the migration of temperate trees into southern boreal forest remains less well documented. We conducted a field investigation across an ecotone of temperate and boreal forests in northern Greater Khingan Mountains of northeast China. Our analysis demonstrates that Mongolian oak (Quercus mongolica), an important temperate tree species, has migrated rapidly into southern boreal forest in synchrony with significant climatic warming over the past century. The average rate of migration is estimated to be 12.0 ± 1.0 km decade-1 , being slightly slower than the movement of isotherms (14.7 ± 6.4 km decade-1 ). The migration rate of Mongolian oak is the highest observed among migratory temperate trees (average rate 4.0 ± 1.0 km decade-1 ) and significantly higher than the rates of tree migration at boreal-tundra ecotones (0.9 ± 0.4 km decade-1 ) and alpine treelines (0.004 ± 0.003 km decade-1 ). Compared with the coexisting dominant boreal tree species, Dahurian larch (Larix gmelinii), temperate Mongolian oak is observed to have significantly lower capacity for light acquisition, comparable water-use efficiency but stronger capacity to utilize nutrients especially the most limiting nutrient, nitrogen. In the context of climatic warming, and in addition to a high seed dispersal capacity and potential thermal niche differences, the advantage of nutrient utilization, reflected by foliar elementomes and stable nitrogen isotope ratios, is also likely a key mechanism for Mongolian oak to coexist with Dahurian larch and facilitate its migration toward boreal forest. These findings highlight a rapid deborealization of southern Asian boreal forest in response to climatic warming.

High heat tolerance, evaporative cooling, and stomatal decoupling regulate canopy temperature and their safety margins in three European oak species.

Heatwaves and soil droughts are increasing in frequency and intensity, leading many tree species to exceed their thermal thresholds, and driving wide-scale forest mortality. Therefore, investigating heat tolerance and canopy temperature regulation mechanisms is essential to understanding and predicting tree vulnerability to hot droughts. We measured the diurnal and seasonal variation in leaf water potential (Ψ), gas exchange (photosynthesis Anet and stomatal conductance gs), canopy temperature (Tcan), and heat tolerance (leaf critical temperature Tcrit and thermal safety margins TSM, i.e., the difference between maximum Tcan and Tcrit) in three oak species in forests along a latitudinal gradient (Quercus petraea in Switzerland, Quercus ilex in France, and Quercus coccifera in Spain) throughout the growing season. Gas exchange and Ψ of all species were strongly reduced by increased air temperature (Tair) and soil drying, resulting in stomatal closure and inhibition of photosynthesis in Q. ilex and Q. coccifera when Tair surpassed 30°C and soil moisture dropped below 14%. Across all seasons, Tcan was mainly above Tair but increased strongly (up to 10°C > Tair) when Anet was null or negative. Although trees endured extreme Tair (up to 42°C), positive TSM were maintained during the growing season due to high Tcrit in all species (average Tcrit of 54.7°C) and possibly stomatal decoupling (i.e., Anet ≤0 while gs >0). Indeed, Q. ilex and Q. coccifera trees maintained low but positive gs (despite null Anet), decreasing Ψ passed embolism thresholds. This may have prevented Tcan from rising above Tcrit during extreme heat. Overall, our work highlighted that the mechanisms behind heat tolerance and leaf temperature regulation in oak trees include a combination of high evaporative cooling, large heat tolerance limits, and stomatal decoupling. These processes must be considered to accurately predict plant damages, survival, and mortality during extreme heatwaves.

Volatile phenols in wine: overview of origin, formation, analysis, and sensory expression.

Volatile phenols impart particular aromas to wine. Due to their distinctive aroma characteristics and low sensory thresholds, volatile phenols can easily influence and modify the aroma of wine. Since these compounds can be formed in wines in various ways, it is necessary to clarify the possible sources of each volatile phenol to achieve management during the winemaking process. The sources of volatile phenols in wine are divided into berry-derived, fermentation-derived, and oak-derived. The pathways and factors influencing the formation of volatile phenols from each source are then reviewed respectively. In addition, an overview of the sensory impact of volatile phenols is given, both in terms of the aroma these volatile phenols directly bring to the wine and their contribution through aroma interactions. Finally, as an essential basis for exploring the scientific problems of volatile phenols in wine, approaches to quantitation of volatile phenols and their precursors are discussed in detail. With the advancement of analytical techniques, more details on volatile phenols have been discovered. Further exploration is worthwhile to achieve more detailed monitoring and targeted management of volatile phenols in wine.

Responses of oak seedlings to increased herbivory and drought: a possible trade-off?

BACKGROUND AND AIMS: Anthropogenic disturbances are causing a co-occurring increase in biotic (ungulate herbivory) and abiotic (drought) stressors, threatening plant reproduction in oak-dominated ecosystems. However, we wonder whether herbivory could compensate for the adverse impact of drought by reducing evapotranspiration. Thus, we investigate the isolated and joint effects of herbivory and drought on oak seedlings of two contrasting Mediterranean species that differ in leaf habit and drought resistance. METHODS: California oak seedlings from the evergreen, and more drought-resistant, Quercus agrifolia and the deciduous Q. lobata (n=387) were assigned to a fully crossed factorial design with herbivory and drought as stress factors. Seedlings were assigned in a greenhouse to 3-4 clipping levels simulating herbivory and 3-4 watering levels, depending on the species. We measured survival, growth, and leaf attributes (chlorophyll, secondary metabolites, leaf area and weight) once a month (May-Sep) and harvested above- and below-ground biomass at the end of the growing season. KEY RESULTS: For both oak species, simulated herbivory enhanced seedling survival during severe drought or delayed its adverse effects, probably due to reduced transpiration resulting from herbivory-induced leaf area reduction and compensatory root growth. Seedlings from the deciduous, and less drought-resistant species, benefitted from herbivory at lower levels of water stress, suggesting different response across species. We also found complex interactions between herbivory and drought on their impact on leaf attributes. In contrast to chlorophyll content which was not affected by herbivory, anthocyanins increased with herbivory - although water stress reduced differences in anthocyanins due to herbivory. CONCLUSIONS: Herbivory seems to facilitate Mediterranean oak seedlings to withstand summer drought, potentially alleviating a key bottleneck in the oak recruitment process. Our study highlights the need to consider ontogenetic stages and species-specific traits in understanding complex relationships between herbivory and drought stressors for the persistence and restoration of multi-species oak savannas.

Introgression and incomplete lineage sorting blurred phylogenetic relationships across the genomes of sclerophyllous oaks from southwest China.

Resolving evolutionary relationships among closely related species with interspecific gene flow is challenging. Genome-scale data provide opportunities to clarify complex evolutionary relationships in closely related species and to observe variations in species relationships across the genomes of such species. The Himalayan-Hengduan subalpine oaks have a nearly completely sympatric distribution in southwest China and probably constitute a syngameon. In this study, we mapped resequencing data from different species in this group to the Quercus aquifolioides reference genome to obtain a high-quality filtered single nucleotide polymorphism (SNP) dataset. We also assembled their plastomes. We reconstructed their phylogenetic relationships, explored the level and pattern of introgression among these species and investigated gene tree variation in the genomes of these species using sliding windows. The same or closely related plastomes were found to be shared extensively among different species within a specific geographical area. Phylogenomic analyses of genome-wide SNP data found that most oaks in the Himalayan-Hengduan subalpine clade showed genetic coherence, but several species were found to be connected by introgression. The gene trees obtained using sliding windows showed that the phylogenetic relationships in the genomes of oaks are highly heterogeneous and therefore highly obscured. Our study found that all the oaks of the Himalayan-Hengduan subalpine clade from southwest China form a syngameon. The obscured phylogenetic relationships observed empirically across the genome are best explained by interspecific gene flow in conjunction with incomplete lineage sorting.

Urbanization exacerbates climate sensitivity of eastern United States broadleaf trees.

Tree growth is a key mechanism driving carbon sequestration in forest ecosystems. Environmental conditions are important regulators of tree growth that can vary considerably between nearby urban and rural forests. For example, trees growing in cities often experience hotter and drier conditions than their rural counterparts while also being exposed to higher levels of light, pollution, and nutrient inputs. However, the extent to which these intrinsic differences in the growing conditions of trees in urban versus rural forests influence tree growth response to climate is not well known. In this study, we tested for differences in the climate sensitivity of tree growth between urban and rural forests along a latitudinal transect in the eastern United States that included Boston, Massachusetts, New York City, New York, and Baltimore, Maryland. Using dendrochronology analyses of tree cores from 55 white oak trees (Quercus alba), 55 red maple trees (Acer rubrum), and 41 red oak trees (Quercus rubra) we investigated the impacts of heat stress and water stress on the radial growth of individual trees. Across our three-city study, we found that tree growth was more closely correlated with climate stress in the cooler climate cities of Boston and New York than in Baltimore. Furthermore, heat stress was a significant hindrance to tree growth in higher latitudes while the impacts of water stress appeared to be more evenly distributed across latitudes. We also found that the growth of oak trees, but not red maple trees, in the urban sites of Boston and New York City was more adversely impacted by heat stress than their rural counterparts, but we did not see these urban-rural differences in Maryland. Trees provide a wide range of important ecosystem services and increasing tree canopy cover was typically an important component of urban sustainability strategies. In light of our findings that urbanization can influence how tree growth responds to a warming climate, we suggest that municipalities consider these interactions when developing their tree-planting palettes and when estimating the capacity of urban forests to contribute to broader sustainability goals in the future.

Naturally diverse plant communities do not resist invasion by the strong competitor, Microstegium vimineum.

PREMISE: Theory predicts and empirical studies have shown that ecologically manipulated communities with high species diversity are resistant to invasion, but do these predictions and results hold true when applied to highly competitive invaders in natural communities? Few studies of diversity-mediated invasion resistance have measured both invasion resistance and invader impact in the same study. METHODS: We used a two-year field experiment to test: (1) diversity-mediated competitive resistance to patch expansion by the grass, Microstegium vimineum; and (2) the competitive effect of M. vimineum on resident plant diversity. We examined responses of M. vimineum to two native plant density-reduction treatments that had opposite effects on species diversity: (1) reducing species richness via the removal of rare species; and (2) reducing dominance by reducing the density of the dominant resident species. We examined the effects of M. vimineum reduction by pre-emergent herbicide on resident diversity in the second year of the study. RESULTS: Neither rare species removal nor dominant species reduction significantly increased M. vimineum density (relative growth rate). The pre-emergent herbicide dramatically reduced M. vimineum in year 2 of the study, but not most resident plants, which were perennials and indirectly benefited from the herbicide at a more productive site, presumably due to reduced competition from M. vimineum. CONCLUSIONS: Diversity-mediated resistance did not effectively deter invasion by a highly competitive invader. In the case of M. vimineum and at more productive sites, it would appear that nearly complete removal of this invader is necessary to preserve plant species diversity.

Long-term Dynamics of Fungal Communities Inhabiting Decaying Stumps of Quercus robur.

We studied the diversity, composition, and long-term dynamics of wood-inhabiting fungi in Quercus robur stumps left after commercial tree harvesting in Lithuania. Sampling of wood was carried out at three sites and from stumps, which were 10-, 20-, 30-, 40-, and 50-year-old. DNA was isolated from wood samples and fungal communities analyzed using high-throughput sequencing. Results showed that stump age had a limited effect on fungal diversity. The development of fungal communities in oak stums was found to be a slow process as fungal communities remained similar for decades, while larger changes were only detected in older stumps. The most common fungi were Eupezizella sp. (18.4%), Hyphodontia pallidula (12.9%), Mycena galericulata (8.3%), and Lenzites betulinus (7.1%). Fistulina hepatica, which is a red-listed wood-decay oak fungus, was also detected at a low relative abundance in stump wood. In the shortage of suitable substrate, oak stumps may provide habitats for long-term survival of different fungal species, including red-listed and oak-related fungi.

Sustainable Lignin Extraction Using a Mild Acidic γ-Valerolactone Process for the Identification of White and Red Oaks.

Current wood identification struggles to differentiate white and red oak (Quercus alba and Quercus rubra) due to highly similar microstructures, as demonstrated by morphological microscope analysis. The present research explores lignin composition as a potential discriminating factor. Here, a rapid and sustainable method for extracting high-quality lignin from oak samples using acidic γ-valerolactone (GVL) under mild conditions is described. As-extracted lignin is thoroughly characterized using various analytical methods, and results reveal a distinct structural difference between the lignin from the two species. White oak lignin possesses a unique "Hibbert ketone" unit detectable by nuclear magnetic resonance spectroscopy (NMR), which is absent in red oak lignin. In addition, infrared spectroscopy differentiates the species based on specific carbonyl groups present in their lignin. These findings suggest that identifying the presence of the Hibbert ketone unit in lignin may offer a highly efficient and reliable method for differentiating white and red oak, opening new avenues for wood identification.

The genome assembly of Island Oak (Quercus tomentella), a relictual island tree species.

Island oak (Quercus tomentella) is a rare relictual island tree species that exists only on six islands off the coast of California and Mexico, but was once widespread throughout mainland California. Currently, this species is endangered by threats such as non-native plants, grazing animals, and human removal. Efforts for conservation and restoration of island oak currently underway could benefit from information about its range-wide genetic structure and evolutionary history. Here we present a high-quality genome assembly for Q. tomentella, assembled using PacBio HiFi and Omni-C sequencing, developed as part of the California Conservation Genomics Project (CCGP). The resulting assembly has a length of 781 Mb, with a contig N50 of 22.0 Mb and a scaffold N50 of 63.4 Mb. This genome assembly will provide a resource for genomics-informed conservation of this rare oak species. Additionally, this reference genome will be the first one available for a species in Quercus section Protobalanus, a unique oak clade present only in western North America.