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Background Microorganisms serve important functions within numerous eukaryotic host organisms. An understanding of the variation in the plant niche-level microbiome, from rhizosphere soils to plant canopies, is imperative to gain a better understanding of how both the structural and functional processes of microbiomes impact the health of the overall plant holobiome. Using Populus trees as a model ecosystem, we characterized the archaeal/bacterial and fungal microbiome across 30 different tissue-level niches within replicated Populus deltoides and hybrid Populus trichocarpa × deltoides individuals using 16S and ITS2 rRNA gene analyses. Results Our analyses indicate that archaeal/bacterial and fungal microbiomes varied primarily across broader plant habitat classes (leaves, stems, roots, soils) regardless of plant genotype, except for fungal communities within leaf niches, which were greatly impacted by the host genotype. Differences between tree genotypes are evident in the elevated presence of two potential fungal pathogens, Marssonina brunnea and Septoria sp., on hybrid P. trichocarpa × deltoides trees which may in turn be contributing to divergence in overall microbiome composition. Archaeal/bacterial diversity increased from leaves, to stem, to root, and to soil habitats, whereas fungal diversity was the greatest in stems and soils. Conclusions This study provides a holistic understanding of microbiome structure within a bioenergy relevant plant host, one of the most complete niche-level analyses of any plant. As such, it constitutes a detailed atlas or map for further hypothesis testing on the significance of individual microbial taxa within specific niches and habitats of Populus and a baseline for comparisons to other plant species.

Upward transport of CO2 via the transpiration stream from belowground to aboveground tissues occurs in tree stems. Despite potentially important implications for our understanding of plant physiology, the fate of internally transported CO2 derived from autotrophic respiratory processes remains unclear. We infused a 13CO2-labeled aqueous solution into the base of 7-yr-old field-grown eastern cottonwood (Populus deltoides) trees to investigate the effect of xylem-transported CO2 derived from the root system on aboveground carbon assimilation and CO2 efflux. The 13C label was transported internally and detected throughout the tree. Up to 17% of the infused label was assimilated, while the remainder diffused to the atmosphere via stem and branch efflux. The largest amount of assimilated 13C was found in branch woody tissues, while only a small quantity was assimilated in the foliage. Petioles were more highly enriched in 13C than other leaf tissues. Our results confirm a recycling pathway for respired CO2 and indicate that internal transport of CO2 from the root system may confound the interpretation of efflux-based estimates of woody tissue respiration and patterns of carbohydrate allocation.

In order to progress in the understanding of mechanical stress generation, the mesoporosity of the cell wall and its changes during maturation of poplar (Populus deltoides x P. nigra) tension wood (TW) and opposite wood (OW) were measured by nitrogen adsorption–desorption. Variations in the thickness of the gelatinous layer (G-layer) were also measured to clarify whether the mesoporosity change simultaneously with the deposition of the G-layer in TW. Results show that mesoporous structures of TW and OW were very similar in early development stages before the deposition of G-layers. With the formation of the S2 layer in OW and the G-layer in TW, the mesopore volume decreased steeply before lignification. However, in TW only, the decrease in mesopore volume occurred together with the pore shape change and a progressive increase in pore size. The different patterns observed in TW revealed that pores from G-layers appear with a different shape compared to those of the compound middle lamella, and their size increases duringthe maturation process until stabilising in mature wood. This observation strongly supports the hypothesis of the swelling of the G-layer matrix during maturation as the origin of maturation stress in poplar tension wood.

Background Nitrogen (N) is one of the main factors limiting the wood yield in poplar cultivation. Understanding the molecular mechanism of N utilization could play a guiding role in improving the nitrogen use efficiency (NUE) of poplar. Results In this study, three N-efficient genotypes (A1-A3) and three N-inefficient genotypes (C1-C3) of Populus deltoides were cultured under low N stress (5 μM NH 4 NO 3 ) and normal N supply (750 μM NH 4 NO 3 ). The dry matter mass, leaf morphology, and chlorophyll content of both genotypes decreased under N starvation. The low nitrogen adaptation coefficients of the leaves and stems biomass of group A were significantly higher than those of group C ( p  < 0.05). Interestingly, N starvation induced fine root growth in group A, but not in group C. Next, a detailed time-course analysis of enzyme activities and gene expression in leaves identified 2062 specifically differentially expressed genes (DEGs) in group A and 1118 in group C. Moreover, the sensitivity to N starvation of group A was weak, and DEGs related to hormone signal transduction and stimulus response played an important role in the low N response this group. Weighted gene co-expression network analysis identified genes related to membranes, catalytic activity, enzymatic activity, and response to stresses that might be critical for poplar’s adaption to N starvation and these genes participated in the negative regulation of various biological processes. Finally, ten influential hub genes and twelve transcription factors were identified in the response to N starvation. Among them, four hub genes were related to programmed cell death and the defense response, and PodelWRKY18 , with high connectivity, was involved in plant signal transduction. The expression of hub genes increased gradually with the extension of low N stress time, and the expression changes in group A were more obvious than those in group C. Conclusions Under N starvation, group A showed stronger adaptability and better NUE than group C in terms of morphology and physiology. The discovery of hub genes and transcription factors might provide new information for the analysis of the molecular mechanism of NUE and its improvement in poplar.

Leaf chlorophyll content (LCC) is a key indicator in representing the photosynthetic capacity of Populus deltoides (Populus deltoides Marshall). Unmanned aerial vehicle (UAV) hyperspectral imagery provides an effective approach for LCC estimation, but the issue of band redundancy significantly impacts model accuracy and computational efficiency. Commonly used single feature selection algorithms not only fail to balance computational efficiency with optimal set search but also struggle to combine different regression algorithms under dynamic set conditions. This study proposes an ensemble feature selection framework to enhance LCC estimation accuracy using UAV hyperspectral data. Firstly, the embedded algorithm was improved by introducing the SHapley Additive exPlanations (SHAP) algorithm into the ranking system. A dynamic ranking strategy was then employed to remove bands in steps of 10, with LCC models developed at each step to identify the initial band subset based on estimation accuracy. Finally, the wrapper algorithm was applied using the initial band subset to search for the optimal band subset and develop the corresponding model. Three regression algorithms including gradient boosting regression trees (GBRT), support vector regression (SVR), and gaussian process regression (GPR) were combined with this framework for LCC estimation. The results indicated that the GBRT-Optimal model developed using 28 bands achieved the best performance with R2 of 0.848, RMSE of 1.454 μg/cm2 and MAE of 1.121 μg/cm2. Compared with a model performance that used all bands as inputs, this optimal model reduced the RMSE value by 24.37%. In addition to estimating biophysical and biochemical parameters, this method is also applicable to other hyperspectral imaging tasks.

While using sap-flow sensor measurements is a well-established technique for quantifying leaf water transpiration in tree species, installing and maintaining a large number of sensors and data loggers in large-scale plantations to obtain accurate measurements is both costly and time-consuming. We developed a copula-based approach to predict sap flows based on readily available vapor pressure deficits (VPDs) and found that the Normal copula was the best among five commonly used copulas. The Normal-copula approach was validated using our field-measured eastern cottonwood (Populus deltoides (Bartr. ex Marsh.)) sap flow data, yielding solid statistical measures, including Mann–Kendall’s τ = 0.59, R2 = 0.81, and p-value < 0.01. The approach was applied to predict sap flows of eastern cottonwood during the growing period from 1 March to 31 October 2015 as well as the 5-year growing period from 2019 to 2023. It successfully replicated the characteristic diurnal sap flow pattern, with rates increasing during the day and decreasing at night, as well as the typical seasonal pattern, with rates rising from winter to summer and decreasing from summer to next winter. Our study suggests that the copula-based approach is a reliable tool for estimating sap flows based on VPD data.

The fast-growing tree, eastern cottonwood (Populus deltoides), currently is being planted to catalyze native forest restoration on degraded agricultural sites in the southeastern United States. Many of these restoration sites are appropriate for short rotation woody crop (SRWC) culture that addresses climate mitigation objectives, but information needed to optimize climate mitigation objectives through such plantings is limited. Therefore, we established a 10-year experiment on degraded agricultural land located in the Mississippi Alluvial Valley, USA, aiming to quantify the dynamics of aboveground carbon (AGC) accumulation in a cottonwood planting of four replicated spacing levels (3.7 × 3.7 m, 2.7 × 1.8 m, 2.1 × 0.8 m, and (0.8 + 1.8) × 0.8 m) aligned with SRWC systems targeting various ecosystem services. Annual sampling revealed a substantial range in increments of AGC and year 10 carbon stocks among stands of different densities. Mean annual increments for AGC (MAIAGC) were similar for the two tightest spacing levels, peaking higher than for the other two spacings at about 7.5 Mg ha−1 y−1 in year 7. Year 10 AGC ranged between 22.3 Mg ha−1 for stands spaced 3.7 × 3.7 m and 70.1 Mg ha−1 for stands of the two tightest spacings, leading us to conclude that a spacing between 2.1 × 0.8 m and 2.7 × 1.8 m would maximize aboveground carbon stocks through year 10 on sites of similar agricultural degradation. Increments and accumulation of AGC on the degraded site trended lower than values reported from more productive sites but illustrate that quick and substantial transformation of the carbon stock status of degraded agricultural sites can be achieved with the application of SRWCs to restore forests for climate mitigation and other compatible ecosystem services.

Freshwater ecosystems across the planet continue to be invaded by the New Zealand mudsnail (NZMS) (Potamopyrgus antipodarum), but factors that control their individual growth rates—a key predictor of a species’ invasion success—have yet to be fully elucidated. NZMS are often categorized as herbivore-detritivores; there is a lack of empirical evidence, however, regarding their consumption of detritus and related processes, such as rates of organic-matter decomposition. To help fill this gap, we reared individual NZMS on leaves of four species (eastern cottonwood, Populus deltoides; green ash, Fraxinus pennsylvanica; red maple, Acer saccharum; and red oak, Quercus rubra) that are changing in their abundance due to anthropogenic factors. We assigned replicate microcosms containing one live juvenile NZMS to each litter species, as well as microcosms that contained no leaves as a control, and determined NZMS growth rates. To evaluate the effect of snail presence on leaf decomposition, we established control microcosms with no snails for each litter species. We found a significant difference in individual NZMS growth rates among litter species, with snails reared on cottonwood and ash leaves having higher growth rates than snails reared on maple and oak leaves. Decomposition rates differed among leaf species, and there was a significant interaction between NZMS presence and leaf decomposition, indicating the effect of NZMS on decomposition rates depended on leaf species. Snails had the greatest effect on ash leaves, increasing decomposition rates by 200% relative to controls without snails, followed by a 100% increase in the decomposition rate of cottonwood leaves. These results, to our knowledge, are the first evidence that NZMS consume leaf litter (either intentionally, or incidentally while scraping/grazing) and that the litter species on which they feed can influence their growth rates, with potential consequences for their success as invaders. Moreover, these results highlight the potential for NZMS to impact detrital pathways in stream ecosystems.

Plants produce two phosphorylated enzymes: pyrophosphate-dependent fructose-6-phosphate phosphotransferase (PFP) and ATP-dependent phosphofructokinase (PFK). However, the characterization of phosphofructokinase (PFK) family members and their functions remains unexplored in Eastern Cottonwood (Populus deltoides). This study comprehensively analyzed 17 phosphofructokinase genes in the P. deltoides genome, including their gene structure, conserved domains, evolutionary relationships, and expression patterns. Genome-wide analysis of the poplar genome identified 11 genes belonging to PdPFK and 6 genes belonging to PdPFP. Phylogenetic, gene structure, and motif analyses revealed two main categories of PFK genes: PFK with eleven genes and PFP with six genes. Quantitative PCR (qPCR) analysis demonstrated that all 17 phosphofructokinase genes were induced in various tissues and developmental stages of P. deltoides. PFPs were strongly expressed throughout P. deltoides’ growth and development, notably in the roots, according to the transcript analysis. This genome-wide analysis provides insights into PFK and PFP genes and establishes a foundation for future investigations into the role of genes in P. deltoids.

The North American beaver (Castor canadensis Kuhl) and cottonwoods (Populus spp.) are foundation species, the interactions of which define a much larger community and affect a threatened riparian habitat type. Few studies have tested the effect of these interactions on plant chemistry and a diverse arthropod community. We experimentally examined the impact of beaver foraging on riparian communities by first investigating beaver food preferences for one cottonwood species, Fremont cottonwood (P. fremontii S. Watson), compared to other locally available woody species. We next examined the impact of beaver foraging on twig chemistry and arthropod communities in paired samples of felled and unfelled cottonwood species in northern Arizona (P. fremontii) and southwestern Colorado (narrowleaf cottonwood, P. angustifolia James, and Eastern cottonwood, P. deltoides W. Bartram ex Marshall). Four major patterns emerged: (1) In a cafeteria experiment, beavers chose P. fremontii six times more often than other woody native and exotic species. (2) With two cottonwood species, we found that the nitrogen and salicortin concentrations were up to 45% greater and lignin concentration 14% lower in the juvenile resprout growth of felled trees than the juvenile growth on unfelled trees (six of seven analyses were significant for P. fremontii and four of six were significant for P. angustifolia). (3) With two cottonwood species, arthropod community composition on juvenile branches differed significantly between felled and unfelled trees, with up to 38% greater species richness, 114% greater relative abundance and 1282% greater species diversity on felled trees (six of seven analyses with P. fremontii and four of six analyses with P. angustifolia were significant). The above findings indicate that the highest arthropod diversity is achieved in the heterogenous stands of mixed felled and unfelled trees than in stands of cottonwoods, where beavers are not present. These results also indicate that beaver herbivory changes the chemical composition in 10 out of 13 chemical traits in the juvenile growth of two of the three cottonwood species to potentially allow better defense against future beaver herbivory. (4) With P. deltoides, only one of five analyses in chemistry was significant, and none of the four arthropod community analyses were significant, suggesting that this species and its arthropod community responds differently to beaver. Potential reasons for these differences are unknown. Overall, our findings suggest that in addition to their impact on riparian vegetation, other mammals, birds, and aquatic organisms, beavers also may define the arthropod communities of two of three foundation tree species in these riparian ecosystems.