Leaf gene expression trajectories during the growing season are consistent between sites and years in American beech.

Transcriptomics provides a versatile tool for ecological monitoring. Here, through genome-guided profiling of transcripts mapping to 33 042 gene models, expression differences can be discerned among multi-year and seasonal leaf samples collected from American beech trees at two latitudinally separated sites. Despite a bottleneck due to post-Columbian deforestation, the single nucleotide polymorphism-based population genetic background analysis has yielded sufficient variation to account for differences between populations and among individuals. Our expression analyses during spring-summer and summer-autumn transitions for two consecutive years involved 4197 differentially expressed protein coding genes. Using Populus orthologues we reconstructed a protein-protein interactome representing leaf physiological states of trees during the seasonal transitions. Gene set enrichment analysis revealed gene ontology terms that highlight molecular functions and biological processes possibly influenced by abiotic forcings such as recovery from drought and response to excess precipitation. Further, based on 324 co-regulated transcripts, we focused on a subset of GO terms that could be putatively attributed to late spring phenological shifts. Our conservative results indicate that extended transcriptome-based monitoring of forests can capture diverse ranges of responses including air quality, chronic disease, as well as herbivore outbreaks that require activation and/or downregulation of genes collectively tuning reaction norms maintaining the survival of long living trees such as the American beech.

Effects of the nematode Litylenchus crenatae subsp. mccannii and beech leaf disease on leaf fungal and bacterial communities on Fagus grandifolia (American beech).

Beech leaf disease (BLD) is a newly emerging disease in North America that affects American beech (Fagus grandifolia). It is increasingly recognized that BLD is caused by a subspecies of the anguinid nematode Litylenchus crenatae subsp. mccannii (hereafter L. crenatae), which is likely native to East Asia. How nematode infestation of leaves affects the leaf microbiome and whether changes in the microbiome could contribute to BLD symptoms remain uncertain. In this study, we examined bacterial and fungal communities associated with the leaves of F. grandifolia across nine sites in Ohio and Pennsylvania that were either symptomatic or asymptomatic for BLD and used qPCR to measure relative nematode infestation levels. We found significantly higher levels of infestation at sites visibly symptomatic for BLD. Low levels of nematode infestation were also observed at asymptomatic sites, which suggests that nematodes can be present without visible symptoms evident. Bacterial and fungal communities were significantly affected by sampling site and symptomology, but only fungal communities were affected by nematode presence alone. We found many significant indicators of both bacteria and fungi related to symptoms of BLD, with taxa generally occurring in both asymptomatic and symptomatic leaves, suggesting that microbes are not responsible for BLD but could act as opportunistic pathogens. Of particular interest was the fungal genus Erysiphe, which is common in the Fagaceae and is reported to overwinter in buds-a strategy consistent with L. crenatae. The specific role microbes play in opportunistic infection of leaves affected by L. crenatae will require additional study. IMPORTANCE: Beech leaf disease (BLD) is an emerging threat to American beech (Fagus grandifolia) and has spread quickly throughout the northeastern United States and into southern Canada. This disease leads to disfigurement of leaves and is marked by characteristic dark, interveinal banding, followed by leaf curling and drop in more advanced stages. BLD tends to especially affect understory leaves, which can lead to substantial thinning of the forest understory where F. grandifolia is a dominant tree species. Understanding the cause of BLD is necessary to employ management strategies that protect F. grandifolia and the forests where it is a foundation tree species. Current research has confirmed that the foliar nematode Litylenchus crenatae subsp. mccannii is required for BLD, but whether other organisms are involved is currently unknown. Here, we present a study that investigated leaf-associated fungi and bacteria of F. grandifolia to understand more about how microorganisms may contribute to BLD.

Development of Primers Specific for Detection of Litylenchus crenatae, the Causal Agent of Beech Leaf Disease, in Plant Tissue.

Beech leaf disease (BLD), an emerging threat to American beech (Fagus grandifolia) in the northern United States and Canada, was recently confirmed to be caused by the nematode Litylenchus crenatae subsp. mccannii (hereafter L. crenatae). Consequently, there is a need for a rapid, sensitive, and accurate method for detecting L. crenatae for both diagnostic as well as control purposes. This research developed a new set of DNA primers that specifically amplify L. crenatae and allow for accurate detection of the nematode in plant tissue. These primers have also been used in quantitative PCR (qPCR) to determine relative differences in gene copy number between samples. This primer set provides an improved, effective tool for monitoring and detecting L. crenatae in temperate tree leaf tissue which is necessary to understand the spread of this emerging forest pest and to develop management strategies.

Temperate Forests Dominated by Arbuscular or Ectomycorrhizal Fungi Are Characterized by Strong Shifts from Saprotrophic to Mycorrhizal Fungi with Increasing Soil Depth.

In temperate and boreal forests, competition for soil resources between free-living saprotrophs and ectomycorrhizal (EcM) fungi has been suggested to restrict saprotrophic fungal dominance to the most superficial organic soil horizons in forests dominated by EcM trees. By contrast, lower niche overlap with arbuscular mycorrhizal (AM) fungi could allow fungal saprotrophs to maintain this dominance into deeper soil horizons in AM-dominated forests. Here we used a natural gradient of adjacent forest patches that were dominated by either AM or EcM trees, or a mixture of both to determine how fungal communities characterized with high-throughput amplicon sequencing change across organic and mineral soil horizons. We found a general shift from saprotrophic to mycorrhizal fungal dominance with increasing soil depth in all forest mycorrhizal types, especially in organic horizons. Vertical changes in soil chemistry, including pH, organic matter, exchangeable cations, and extractable phosphorus, coincided with shifts in fungal community composition. Although fungal communities and soil chemistry differed among adjacent forest mycorrhizal types, variations were stronger within a given soil profile, pointing to the importance of considering horizons when characterizing soil fungal communities. Our results also suggest that in temperate forests, vertical shifts from saprotrophic to mycorrhizal fungi within organic and mineral horizons occur similarly in both ectomycorrhizal and arbuscular mycorrhizal forests.

Consumption of red maple in anticipation of beech mast-seeding drives reproduction in eastern chipmunks.

Understanding the determinants of reproduction is a central question in evolutionary ecology. In pulsed-resource environments, the reproduction and population dynamics of seed consumers are driven by pulsed production of seeds by trees or mast-seeding. In Southern Québec, eastern chipmunks Tamias striatus exclusively reproduce during the summer before and the spring after a mast-seeding event of American beech. They thus seem to anticipate beech mast by reproducing during early summer, so that juveniles can emerge at the time of maximum beechnut abundance during late summer. However, the cues allowing chipmunks to anticipate beech mast remain unknown, and the existence of the anticipation process itself has been questioned. To tackle those issues, we investigated the links between the nutritional ecology and reproduction of adult chipmunks and compared their spring diet in mast- versus post-mast years. We monitored female reproductive status (N = 446), analysed cheek pouch contents at capture (n = 3,761 captures) and recorded seed production by deciduous trees on three different sites in Mont-Sutton from 2006 to 2018. Results revealed a systematic shift in chipmunk diet towards red maple seeds in springs preceding a beech mast, with red maple seeds composing more than 77% of chipmunk diet. However, red maple consumption was unrelated to red maple production, but was related to beech seed production in the upcoming fall. We also found that red maple consumption best predicted the proportion of females in summer oestrus. Our results confirm that chipmunks anticipate beech mast-seeding and highlight a key role of red maple consumption in that anticipation. Results also suggest that red maple seeds may contain nutrients or secondary plant components essential to sustain or trigger the summer reproduction in chipmunks, which allow them to remain synchronized with pulsed productions of both red maple and beech and improve their fitness.

The functional implications of tracheary connections across growth rings in four northern hardwood trees.

BACKGROUND AND AIMS: Deciduous angiosperm trees transport xylem sap through trunks and branches in vessels within annual growth rings. Utilizing previous growth rings for sap transport could increase vessel network size and redundancy but may expose new xylem to residual air embolisms in the network. Despite the important role of vessel networks in sap transport and drought resistance, our understanding of cross-ring connections within and between species is limited. METHODS: We studied cross-ring connections in four temperate deciduous trees using dye staining and X-ray microcomputed tomography (microCT) to detect xylem connectivity across growth rings and quantify their impact on hydraulic conductivity. KEY RESULTS: Acer rubrum and Fraxinus americana had cross-ring connections visible in microCT but only A. rubrum used previous growth rings for axial sap flow. Fagus grandifolia and Quercus rubra, however, did not have cross-ring connections. Accounting for the number of growth rings that function for axial transport improved hydraulic conductivity estimates. CONCLUSIONS: These data suggest that the presence of cross-ring connections may help explain aspects of whole-tree xylem sap transport and should be considered for plant hydraulics measurements in these species and others with similar anatomy.

Hydraulic safety margins and air-seeding thresholds in roots, trunks, branches and petioles of four northern hardwood trees.

During drought, xylem sap pressures can approach or exceed critical thresholds where gas embolisms form and propagate through the xylem network, leading to systemic hydraulic dysfunction. The vulnerability segmentation hypothesis (VSH) predicts that low-investment organs (e.g. leaf petioles) should be more vulnerable to embolism spread compared to high-investment, perennial organs (e.g. trunks, stems), as a means of mitigating embolism spread and excessive negative pressures in the perennial organs. We tested this hypothesis by measuring air-seeding thresholds using the single-vessel air-injection method and calculating hydraulic safety margins in four northern hardwood tree species of the northeastern United States, in both saplings and canopy height trees, and at five points along the soil-plant-atmosphere continuum. Acer rubrum was the most resistant to air-seeding and generally supported the VSH. However, Fagus grandifolia, Fraxinus americana and Quercus rubra showed little to no variation in air-seeding thresholds across organ types within each species. Leaf-petiole xylem operated at water potentials close to or exceeding their hydraulic safety margins in all species, whereas roots, trunks and stems of A. rubrum, F. grandifolia and Q. rubra operated within their safety margins, even during the third-driest summer in the last 100 yr.

Habitat differences influence genetic impacts of human land use on the American beech (Fagus grandifolia).

Natural reforestation after regional forest clearance is a globally common land-use sequence. The genetic recovery of tree populations in these recolonized forests may depend on the biogeographic setting of the landscape, for instance whether they are in the core or in the marginal part of the species' range. Using data from 501 individuals genotyped across 7 microsatellites, we investigated whether regional differences in habitat quality affected the recovery of genetic variation in a wind-pollinated tree species, American beech (Fagus grandifolia) in Massachusetts. We compared populations in forests that were recolonized following agricultural abandonment to those in remnant forests that have only been logged in both central inland and marginal coastal regions. Across all populations in our entire study region, recolonized forests showed limited reduction of genetic diversity as only observed heterozygosity was significantly reduced in these forests (H(O) = 0.520 and 0.590, respectively). Within inland region, this pattern was observed, whereas in the coast, recolonized populations exhibited no reduction in all genetic diversity estimates. However, genetic differentiation among recolonized populations in marginal coastal habitat increased (F(st) logged = 0.072; F(st) secondary = 0.249), with populations showing strong genetic structure, in contrast to inland region. These results indicate that the magnitude of recovery of genetic variation in recolonized populations can vary at different habitats.

Comparative genome analyses suggest a hemibiotrophic lifestyle and virulence differences for the beech bark disease fungal pathogens Neonectria faginata and Neonectria coccinea.

Neonectria faginata and Neonectria coccinea are the causal agents of the insect-fungus disease complex known as beech bark disease (BBD), known to cause mortality in beech forest stands in North America and Europe. These fungal species have been the focus of extensive ecological and disease management studies, yet less progress has been made toward generating genomic resources for both micro- and macro-evolutionary studies. Here, we report a 42.1 and 42.7 mb highly contiguous genome assemblies of N. faginata and N. coccinea, respectively, obtained using Illumina technology. These species share similar gene number counts (12,941 and 12,991) and percentages of predicted genes with assigned functional categories (64 and 65%). Approximately 32% of the predicted proteomes of both species are homologous to proteins involved in pathogenicity, yet N. coccinea shows a higher number of predicted mitogen-activated protein kinase genes, virulence determinants possibly contributing to differences in disease severity between N. faginata and N. coccinea. A wide range of genes encoding for carbohydrate-active enzymes capable of degradation of complex plant polysaccharides and a small number of predicted secretory effector proteins, secondary metabolite biosynthesis clusters and cytochrome oxidase P450 genes were also found. This arsenal of enzymes and effectors correlates with, and reflects, the hemibiotrophic lifestyle of these two fungal pathogens. Phylogenomic analysis and timetree estimations indicated that the N. faginata and N. coccinea species divergence may have occurred at ∼4.1 million years ago. Differences were also observed in the annotated mitochondrial genomes as they were found to be 81.7 kb (N. faginata) and 43.2 kb (N. coccinea) in size. The mitochondrial DNA expansion observed in N. faginata is attributed to the invasion of introns into diverse intra- and intergenic locations. These first draft genomes of N. faginata and N. coccinea serve as valuable tools to increase our understanding of basic genetics, evolutionary mechanisms and molecular physiology of these two nectriaceous plant pathogenic species.

Canopy gradients in leaf functional traits for species that differ in growth strategies and shade tolerance.

In temperate deciduous forests, vertical gradients in leaf mass per area (LMA) and area-based leaf nitrogen (Narea) are strongly controlled by gradients in light availability. While there is evidence that hydrostatic constraints on leaf development may diminish LMA and Narea responses to light, inherent differences among tree species may also influence leaf developmental and morphological response to light. We investigated vertical gradients in LMA, Narea and leaf carbon isotope composition (δ13C) for three temperate deciduous species (Carpinus caroliniana Walter, Fagus grandifolia Ehrh., Liriodendron tulipifera L.) that differed in growth strategy (e.g., indeterminate and determinate growth), shade tolerance and leaf area to sapwood ratio (Al:As). Leaves were sampled across a broad range of light conditions within three vertical layers of tree crowns to maximize variation in light availability at each height and to minimize collinearity between light and height. All species displayed similar responses to light with respect to Narea and δ13C, but not for LMA. Light was more important for gradients in LMA for the shade-tolerant (C. caroliniana) and -intolerant (L. tulipifera) species with indeterminate growth, and height (e.g., hydrostatic gradients) and light were equally important for the shade-tolerant (F. grandifolia) species with determinate growth. Fagus grandifolia had a higher morphological plasticity in response to light, which may offer a competitive advantage in occupying a broader range of light conditions throughout the canopy. Differences in responses to light and height for the taller tree species, L. tulipifera and F. grandifolia, may be attributed to differences in growth strategy or Al:As, which may alter morphological and functional responses to light availability. While height was important in F. grandifolia, height was no more robust in predicting LMA than light in any of the species, confirming the strong role of light availability in determining LMA for temperate deciduous species.

The fate of 15N-labelled nitrate additions to a northern hardwood forest in eastern Maine, USA.

We followed the movements of 15N-labelled nitrate additions into biomass and soil pools of experimental plots (15×15 m each) in a mid-successional beech-maple-birch-spruce forest in order to identify sinks for nitrate inputs to a forest ecosystem. Replicate plots (n=3) were spray-irrigated with either 28 or 56 kg N ha-1 year-1 using 15N-labelled nitric acid solutions (δ15N = 344‰ ) during four successive growing seasons (April-October). The 15N contents of foliage, bolewood, forests floor and mineral soil (0-5 cm) increased during the course of treatments. Mass balance calculations showed that one-fourth to one-third of the nitrate applied to forest plots was assimilated into and retained by above ground plant tissues and surface soil horizons at both rates of nitrate application. Plant and microbial assimilation were of approximately equal importance in retaining nitrate additions to this forest. Nitrate use among tree species varied, however, with red spruce showing lower rates of nitrate assimilation into foliage and bolewood than American beech and other deciduous species.

Criconema proclivus n. sp. (Nematoda: Criconematinae) from Woodlands.

Criconema proclivis n. sp. from soil around roots of woodland trees in the northeastern USA is described and illustrated. It is characterized by a total of 67-74 annules, two naked offset head annules, a stylet length of 68.7 -80.7 mu, a sculpted vulval flap, and forward-projecting body annules. The annules at midbody are covered with a continuous fringe of 60-70 spines.

Cascading effects of a highly specialized beech-aphid-fungus interaction on forest regeneration.

Specialist herbivores are thought to often enhance or maintain plant diversity within ecosystems, because they prevent their host species from becoming competitively dominant. In contrast, specialist herbivores are not generally expected to have negative impacts on non-hosts. However, we describe a cascade of indirect interactions whereby a specialist sooty mold (Scorias spongiosa) colonizes the honeydew from a specialist beech aphid (Grylloprociphilus imbricator), ultimately decreasing the survival of seedlings beneath American beech trees (Fagus grandifolia). A common garden experiment indicated that this mortality resulted from moldy honeydew impairing leaf function rather than from chemical or microbial changes to the soil. In addition, aphids consistently and repeatedly colonized the same large beech trees, suggesting that seedling-depauperate islands may form beneath these trees. Thus this highly specialized three-way beech-aphid-fungus interaction has the potential to negatively impact local forest regeneration via a cascade of indirect effects.