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The role of mycorrhizal networks in forest dynamics is poorly understood because of the elusiveness of their spatial structure. We mapped the belowground distribution of the fungi Rhizopogon vesiculosus and Rhizopogon vinicolor and interior Douglas-fir trees (Pseudotsuga menziesii var. glauca) to determine the architecture of a mycorrhizal network in a multi-aged old-growth forest. Rhizopogon spp. mycorrhizas were collected within a 30 x 30 m plot. Trees and fungal genets were identified using multi-locus microsatellite DNA analysis. Tree genotypes from mycorrhizas were matched to reference trees aboveground. Two trees were considered linked if they shared the same fungal genet(s). The two Rhizopogon species each formed 13-14 genets, each colonizing up to 19 trees in the plot. Rhizopogon vesiculosus genets were larger, occurred at greater depths, and linked more trees than genets of R. vinicolor. Multiple tree cohorts were linked, with young saplings established within the mycorrhizal network of Douglas-fir veterans. A strong positive relationship was found between tree size and connectivity, resulting in a scale-free network architecture with small-world properties. This mycorrhizal network architecture suggests an efficient and robust network, where large trees play a foundational role in facilitating conspecific regeneration and stabilizing the ecosystem.

Separating edaphic impacts on tree distributions from those of climate and geography is notoriously difficult. Aboveground and belowground factors play important roles, and determining their relative contribution to tree success will greatly assist in refining predictive models and forestry strategies in a changing climate. In a common glasshouse, seedlings of interior Douglas-fir (Pseudotsuga menziesii var. glauca) from multiple populations were grown in multiple forest soils. Fungicide was applied to half of the seedlings to separate soil fungal and nonfungal impacts on seedling performance. Soils of varying geographic and climatic distance from seed origin were compared, using a transfer function approach. Seedling height and biomass were optimized following seed transfer into drier soils, whereas survival was optimized when elevation transfer was minimised. Fungicide application reduced ectomycorrhizal root colonization by c. 50%, with treated seedlings exhibiting greater survival but reduced biomass. Local adaptation of Douglas-fir populations to soils was mediated by soil fungi to some extent in 56% of soil origin by response variable combinations. Mediation by edaphic factors in general occurred in 81% of combinations. Soil biota, hitherto unaccounted for in climate models, interacts with biogeography to influence plant ranges in a changing climate.

Land managers use hazard (susceptibility) and risk rating systems to guide the application of forest management treatments that aim to reduce future damages to forests. Rating systems are typically designed for individual damage agents, but tree mortality often results from multiple agents without a clear proximate cause. In interior Douglas‐fir (DF, Pseudotsuga menziesii var. glauca) forests in the Northern Rocky Mountains, USA, multiple damage agents are commonly associated with DF tree mortality, such as insects, disease, weather, and fire. We investigated how recent DF tree mortality from insects and diseases (excluding fire and harvest) shifted stand structure and composition in DF forests and was influenced by susceptibility (e.g., stand structure and composition, topography, and spatial variability in climate) and risk (biotic agent pressure). Our multi‐scale analysis used 884 plots remeasured after 10 years from the USDA Forest Inventory and Analysis program with support from spatial datasets. Across a large, forested landscape, 60% of the plots had no new DF mortality, and most plots (80%) experienced mortality <10% of DF basal area. However, severe tree mortality, defined as >25% loss of DF basal area, occurred in 6% of plots. Most of the dead DF trees (68%) were smaller diameter (12.7–29 cm at breast height) and mortality rates of smaller trees were significantly greater than those of larger diameter trees (>29 cm), a finding consistent with natural stand development processes. During the remeasurement period, average DF tree size increased in most plots (80%) and <4% of DF‐dominated plots with severe mortality shifted in dominance from DF to another tree species. Greater DF mortality (percentage of initial DF basal area) was associated with lower tree growth rates, larger average tree sizes, greater availability of DF tree hosts for biotic agents, cooler and wetter topo‐climatic locations, and higher Douglas‐fir beetle population pressure. The relative importance of each variable differed west and east of the Continental Divide. By identifying thresholds in susceptibility and risk variables associated with higher DF tree mortality, our results support adaptive forest management for multiple damage agents, when the goal is to reduce tree mortality of a widespread and abundant conifer.

Twentieth-century land management has altered the structure and composition of mixed-conifer forests and decreased their resilience to fire, drought, and insects in many parts of the Interior West. These forests occur across a wide range of environmental settings and historical disturbance regimes, so their response to land management is likely to vary across landscapes and among ecoregions. However, this variation has not been well characterized and hampers the development of appropriate management and restoration plans. We identified mixed-conifer types in central Oregon based on historical structure and composition, and successional trajectories following recent changes in land use, and evaluated how these types were distributed across environmental gradients. We used field data from 171 sites sampled across a range of environmental settings in two subregions: the eastern Cascades and the Ochoco Mountains. We identified four forest types in the eastern Cascades and four analogous types with lower densities in the Ochoco Mountains. All types historically contained ponderosa pine, but differed in the historical and modern proportions of shade-tolerant vs. shade-intolerant tree species. The Persistent Ponderosa Pine and Recent Douglas-fir types occupied relatively hot-dry environments compared to Recent Grand Fir and Persistent Shade Tolerant sites, which occupied warm-moist and cold-wet environments, respectively. Twentieth-century selective harvesting halved the density of large trees, with some variation among forest types. In contrast, the density of small trees doubled or tripled early in the 20th century, probably due to land-use change and a relatively cool, wet climate. Contrary to the common perception that dry ponderosa pine forests are the most highly departed from historical conditions, we found a greater departure in the modern composition of small trees in warm-moist environments than in either hot-dry or cold-wet environments. Furthermore, shade-tolerant trees began infilling earlier in cold-wet than in hot-dry environments and also in topographically shaded sites in the Ochoco Mountains. Our new classification could be used to prioritize management that seeks to restore structure and composition or create resilience in mixed-conifer forests of the region.

Forests near the lower limit of montane tree cover are expected to be particularly vulnerable to warming climate, potentially converting to non‐forest for prolonged periods if affected by canopy‐removing disturbances. Such disturbance‐catalyzed shifts are by nature stochastic, offering few opportunities to test these predictions. We capitalized on a landmark event exemplary of recent large disturbances—the 1988 wildfires in Yellowstone National Park (USA)—to investigate long‐term (24‐yr) regeneration dynamics in Douglas‐fir (Pseudotsuga menziesii var. glauca) forests, which compose the lower treeline yet have received little study. We tested the hypothesis that, under current conditions (warmest decades in last 6000 yr), dry lower‐margin stands are less apt to attain self‐replacement than adjacent, but more mesic, stands farther from the ecotone. Mesic sites characterized by dense forests prefire regenerated robustly regardless of burn severity, even in large high‐severity patches, whereas dry sites did so only if nearby seed sources survived (i.e., small patch size or moderate burn severity). Regeneration continued over two decades, peaking between ~5 and 15 yr, with mesic stands continuing regenerating beyond 15 yr to a greater degree than dry stands. Self‐replacement of stands by 24 yr postfire was nearly universal in mesic stands, variable but common in dry stands not adjacent to the lower ecotone, and uncommon in dry stands near the ecotone—particularly if burned at high severity. Whether the lack of regeneration in ecotonal stands is categorically directional with warming climate or part of a long‐term cycle is unresolved, but we estimate that the 1988 fires converted > 4000 ha of lower‐montane forest to grass/sage steppe for at least several decades, possibly indefinitely given current trends in climate. These data support the notion that climate‐driven shifts in vegetation cover are likely to occur in punctuated fashion with disturbances, with relatively abrupt implications for montane forest cover, biogeography, and ecosystem function.

1. From the phytocentric perspective, a mycorrhizal network (MN) is formed when the roots of two or more plants are colonized by the same fungal genet. MNs can be modelled as interaction networks with plants as nodes and fungal genets as links. The potential effects of MNs on facilitation or competition between plants are increasingly recognized, but their network topologies remain largely unknown. This information is needed to understand the ecological significance of MN functional traits. 2. The objectives of this study were to describe the interaction network topologies of MNs formed between two ectomycorrhizal fungal species, Rhizopogon vesiculosus and R. vinicolor, and interior Douglas-fir trees at the forest stand scale, identify factors leading to this structure and to contrast MN structures between forest plots with xeric versus mesic soil moisture regimes. 3. Tuberculate mycorrhizas were sampled in six 10 × 10 m plots with either xeric or mesic soil moisture regimes. Microsatellite DNA markers were used to identify tree and fungal genotypes isolated from mycorrhizas and for comparison with reference tree boles above-ground. 4. In all six plots, trees and fungal genets were highly interconnected. Size asymmetries between different tree cohorts led to non-random MN topologies, while differences in size and connectivity between Rhizopogon species-specific subnetwork components contributed towards MN nestedness. Large mature trees acted as network hubs with a significantly higher node degree compared to smaller trees. MNs representing trees linked by R. vinicolor genets were mostly nested within larger, more highly connected R. vesiculosus-linked MNs. 5. Attributes of network nodes showed that hub trees were more important to MN topology on xeric than mesic sites, but the emergent structures of MNs were similar in the two soil moisture regimes. 6. Synthesis. This study suggests MNs formed between interior Douglas-fir trees and R. vesiculosus and R. vinicolor genets are resilient to the random loss of participants, and to soil water stress, but may be susceptible to the loss of large trees or fungal genets. Our results regarding the topology of MNs contribute to the understanding of forest stand dynamics and the resilience of forests to stress or disturbance.

Douglas-fir (Pseudotsuga menziesii) is native to western North America. It grows in a wide range of environmental conditions and is an important timber tree. Although there are several studies on the gene expression responses of Douglas-fir to abiotic cues, the absence of high-quality transcriptome and genome data is a barrier to further investigation. Like for most conifers, the available transcriptome and genome reference dataset for Douglas-fir remains fragmented and requires refinement. We aimed to generate a highly accurate, and complete reference transcriptome and genome annotation. We deep-sequenced the transcriptome of Douglas-fir needles from seedlings that were grown under nonstress control conditions or a combination of heat and drought stress conditions using long-read (LR) and short-read (SR) sequencing platforms. We used 2 computational approaches, namely de novo and genome-guided LR transcriptome assembly. Using the LR de novo assembly, we identified 1.3X more high-quality transcripts, 1.85X more “complete” genes, and 2.7X more functionally annotated genes compared to the genome-guided assembly approach. We predicted 666 long noncoding RNAs and 12,778 unique protein-coding transcripts including 2,016 putative transcription factors. We leveraged the LR de novo assembled transcriptome with paired-end SR and a published single-end SR transcriptome to generate an improved genome annotation. This was conducted with BRAKER2 and refined based on functional annotation, repetitive content, and transcriptome alignment. This high-quality genome annotation has 51,419 unique gene models derived from 322,631 initial predictions. Overall, our informatics approach provides a new reference Douglas-fir transcriptome assembly and genome annotation with considerably improved completeness and functional annotation.

Douglas-fir (Pseudotsuga menziesii var. menziesii) is an important species in the Pacific Northwest including California forests. Due to the increasing need for reforestation in this region after widespread disturbances related to changes in climate (i.e., drought, megafires, beetle mortality), it is necessary to examine the factors that contribute to performance and survival of planted seedlings in reforestation projects. While most conifer planting in northern California is done in spring, fall planting is also an alternative practice used. With the recent increase in demand of seedlings for reforestation projects beyond which the current infrastructure is capable of, particularly in spring, expanding the fall planting season has potential to mitigate this and constraints to the spring labor force. Here, we studied the first-year performance of both spring and fall planted Douglas-fir seedlings for different seed sources and nursery cultural timings at a single site in northern California. We found that the fall planting can be successful in October or November, while planting earlier requires immediately favorable temperature and soil moisture conditions. Later sowing and blackout regimes also resulted in increases in height growth and bud development while also reducing damage due to spring freezes. For spring planting, early sow and blackout resulted in earlier bud break, while later sow, blackout, and lift dates benefited the first-year growth of height and diameter.

Understanding the genomic and environmental basis of cold adaptation is key to understand how plants survive and adapt to different environmental conditions across their natural range. Univariate and multivariate genome-wide association (GWAS) and genotype-environment association (GEA) analyses were used to test associations among genome-wide SNPs obtained from whole-genome resequencing, measures of growth, phenology, emergence, cold hardiness, and range-wide environmental variation in coastal Douglas-fir (Pseudotsuga menziesii). Results suggest a complex genomic architecture of cold adaptation, in which traits are either highly polygenic or controlled by both large and small effect genes. Newly discovered associations for cold adaptation in Douglas-fir included 130 genes involved in many important biological functions such as primary and secondary metabolism, growth and reproductive development, transcription regulation, stress and signaling, and DNA processes. These genes were related to growth, phenology and cold hardiness and strongly depend on variation in environmental variables such degree days below 0c, precipitation, elevation and distance from the coast. This study is a step forward in our understanding of the complex interconnection between environment and genomics and their role in cold-associated trait variation in boreal tree species, providing a baseline for the species’ predictions under climate change.

Mycorrhizal networks (MNs) are fungal hyphae that connect roots of at least two plants. It has been suggested that these networks are ecologically relevant because they may facilitate interplant resource transfer and improve regeneration dynamics. This study investigated the effects of MNs on seedling survival, growth and physiological responses, interplant resource (carbon and nitrogen) transfer, and ectomycorrhizal (EM) fungal colonization of seedlings by trees in dry interior Douglas-fir (Pseudotsuga menziesii var. glauca) forests. On a large, recently harvested site that retained some older trees, we established 160 isolated plots containing pairs of older Douglas-fir \"donor\" trees and either manually sown seed or planted Douglas-fir \"receiver\" seedlings. Seed- and greenhouse-grown seedlings were sown and planted into four mesh treatments that served to restrict MN access (i.e., planted into mesh bags with 0.5-, 35-, 250-μm pores, or without mesh). Older trees were pulse labeled with carbon (¹³CO₂) and nitrogen (¹⁵NH₄¹⁵NO₃) to quantify resource transfer. After two years, seedlings grown from seed in the field had the greatest survival and received the greatest amounts of transferred carbon (0.0063% of donor photo-assimilates) and nitrogen (0.0018%) where they were grown without mesh; however, planted seedlings were not affected by access to tree roots and hyphae. Size of \"donor\" trees was inversely related to the amount of carbon transferred to seedlings. The potential for MNs to form was high (based on high similarity of EM communities between hosts), and MN-mediated colonization appeared only to be important for seedlings grown from seed in the field. These results demonstrate that MNs and mycorrhizal roots of trees may be ecologically important for natural regeneration in dry forests, but it is still uncertain whether resource transfer is an important mechanism underlying seedling establishment.