Hasil untuk "Forestry"

M. Herrero, B. Henderson, P. Havlík et al.

J. Canadell, M. Raupach

R. Blackman, V. Eastop

Sanjay Sharma, I. Henriques

R. Schmid

T. Tokiwa, Y. Yin, R. Onishi

Trees are key roughness elements in urban environments, shaping airflow, microclimates, and pollutant dispersion. Yet the aerodynamic drag of complex tree-like structures at high Reynolds numbers remains poorly characterized compared with the well-studied drag crisis of simple bluff bodies. We combine large-scale lattice Boltzmann simulations with an analytical branch-wise drag model to examine fractal trees over a wide range of height-based Reynolds numbers, $Re_H$. Direct numerical simulations using a cumulant lattice Boltzmann method with adaptive mesh refinement cover $2.5\times10^3 \le Re_H \le 1.2\times10^5$, and the analytical model extends predictions to $Re_H \sim 10^9$. Under uniform inflow, the analysis indicates a drag-crisis transition near $Re_H \approx 3\times10^6$, with increasing structural complexity smoothing this transition because smaller branches remain subcritical. Introducing inflow turbulence with streamwise intensity $I_u \approx 8\%$, representative of atmospheric-boundary-layer winds, shifts the apparent onset to $Re_H \approx 1.5\times10^5$ and further moderates the drag reduction. Interpreted at full scale, this suggests that urban trees of order $10$--$30$ m exposed to winds of $1$--$10~\mathrm{m/s}$ generally operate in the crisis or post-crisis regime. In both uniform and turbulent inflow, the framework predicts a reversal in drag-coefficient ordering across geometries: simplified trees show lower drag in the subcritical regime but may exhibit higher drag in the supercritical regime, whereas more complex trees undergo a smoother, moderated crisis. These results challenge the common assumption that pruning always reduces aerodynamic loading and highlight the need to reassess vegetation-drag parameterizations and pruning strategies in high-$Re_H$ conditions.

Adrian Straker, Paul Magdon, Marco Zullich et al.

Aiming to advance research in the field of interpretability of deep learning models for tree species classification using TLS 3D point clouds we present insights in the classification abilities of YOLOv8 through a new framework which enables systematic analysis of saliency maps derived from CAM (Class Activation Mapping). To investigate the contribution of structural tree features to the classification decisions of the models, we link regions with high saliency derived from the application of Finer-CAM to segments of 2D side-view images that correspond to structural tree features. Using TLS 3D point clouds from 2445 trees across seven European tree species, we trained five YOLOv8 models with cross-validation, reaching a mean accuracy of 96% (SD = 0.24%) when applied to the test data. Our results demonstrate that Finer-CAM can be considered faithful in identifying discriminative regions that discriminate target tree species. This renders Finer-CAM suitable for enhancing the interpretability of the tree species classification models. Analysis of 630 saliency maps indicate that the models primarily rely on image regions associated with tree crowns for species classification. While this result is pronounced in Silver Birch, European Beech, English oak, and Norway Spruce, image regions associated with stems contribute more frequently to the differentiation of European ash, Scots pine, and Douglas-fir. We demonstrate that the visibility of detailed structural tree features in the 2D side-view images enhances the discriminative performances of the models, indicating YOLOv8`s abilities to leverage detailed point cloud representations. Our results represent a first step toward enhancing the understanding of the classification decision processes of tree species classification models, aiding in the identification of data set and model limitations, and building confidence in model predictions.

Jiantang Xu, Jiantang Xu, Tianjin Liu et al.

Caffeic acid O-methyltransferase (COMT) catalyzes the penultimate methylation in monolignol biosynthesis, controlling lignin composition and abiotic-stress tolerance. Kenaf (Hibiscus cannabinus L.), a fast bast-fiber crop rich in lignin, is valued for its mechanical strength and resilience to salinity. However, the COMT gene family has not yet been systematically characterized in this species. Here, we integrated phylogenetics, synteny, promoter and transcriptome analyses to create a comprehensive profile of kenaf COMT genes. Genome-wide screening identified 81 HcCOMT genes. Phylogenetic reconstruction with COMTs from Arabidopsis thaliana and Gossypium hirsutum resolved 10 distinct clades. Synteny analysis revealed 2 collinear blocks with Arabidopsis and 14 with cotton, whereas intraspecific duplication events indicated recent lineage-specific expansion. Promoter analysis identified numerous cis-elements responsive to light, phytohormones and abiotic stress, suggesting complex transcriptional regulation. Transcriptome mining uncovered 6 candidate genes with pronounced tissue specificity and salt responsiveness; qRT-PCR confirmed these patterns in root, stem and leaf tissues under 200 mM NaCl: HcCOMT28 and HcCOMT29 were repressed in the leaf, whereas HcCOMT11, HcCOMT12, HcCOMT13, and HcCOMT17 were up-regulated, consistent with altered lignin deposition patterns. Our findings provide a comprehensive genomic resource delineating the structure, evolution, and salt-responsive expression of the kenaf COMT family, and establish a foundation for elucidating the molecular mechanisms underlying lignin-mediated salt tolerance and for breeding elite kenaf cultivars with tailored fiber properties.

Houjun Zhou, Xueqin Song, Meng-Zhu Lu

IntroductionHybrid poplars are industrial trees in China. An understanding of the molecular mechanism underlying wood formation in hybrid poplars is necessary for molecular breeding. Although the division and differentiation of vascular cambial cells is important for secondary growth and wood formation, the regulation of this process is largely unclear.MethodsIn this study, mPagGRF15 OE and PagGRF15-SRDX transgenic poplars were generated to investigate the function of PagGRF15. RNA-seq and qRT-PCR were conducted to analyze genome-wide gene expression, while ChIP‒seq and ChIP-PCR were used to identified the downstream genes regulated by PagGRF15.Results and discussionWe report that PagGRF15 from hybrid poplar (Populus alba × P. glandulosa), a growth-regulating factor, plays a critical role in the regulation of vascular cambium activity. PagGRF15 was expressed predominantly in the cambial zone of vascular tissue. Overexpression of mPagGRF15 (the mutated version of GRF15 in the miR396 target sequence) in Populus led to decreased plant height and internode number. Further stem cross sections showed that the mPagGRF15 OE plants exhibited significant changes in vascular pattern with an increase in xylem and a reduction in phloem. In addition, cambium cell files were decreased in the mPagGRF15 OE plants. However, dominant suppression of the downstream genes of PagGRF15 using PagGRF15-SRDX showed an opposite phenotype. Based on the RNA-seq and ChIP-seq results, combining qRT-PCR and ChIP-PCR analysis, candidate genes, such as WOX4b, PXY and GID1.3, were obtained and found to be mainly involved in cambial activity and xylem differentiation. Accordingly, we speculated that PagGRF15 functions as a positive regulator mediating xylem differentiation by repressing the expression of the WOX4a and PXY genes to set the pace of cambial activity. In contrast, PagGRF15 mediated the GA signaling pathway by upregulating GID1.3 expression to stimulate xylem differentiation. This study provides valuable information for further studies on vascular cambium differentiation mechanisms and genetic improvement of the specific gravity of wood in hybrid poplars.

Klaus von Gadow

Wei Wang, Yuhan Feng, Ruotong Wu et al.

With the development of agriculture and industry, the increase in nitrogen (N) deposition has caused widespread concern among scientists. Although emission reduction policies have slowed N releases in Europe and North America, the threat to biodiversity cannot be ignored. Arbuscular mycorrhizal (AM) fungi play an important role in the establishment and maintenance of plant communities in forest ecosystems, and both their distribution and diversity have vital ecological functions. Therefore, we analyzed the effects of long-term N addition on AM fungi and understory herbaceous plants in a Korean pine plantation in northern China. The soil properties, community structure, and diversity of AM fungi and understory herbaceous plants were detected at different concentrations of NH4NO3 (0, 20, 40, 80 kg N ha−1 year−1) after 7 years. The results showed that long-term N deposition decreased soil pH, increased soil ammonium content, and caused significant fluctuations in P elements. N deposition improved the stability of soil aggregates by increasing the content of glomalin-related soil protein (GRSP) and changed the AM fungal community composition. The Glomus genus was more adaptable to the acidic soil treated with the highest N concentration. The species of AM fungi, understory herbaceous plants, and the biomass of fine roots were decreased under long-term N deposition. The fine root biomass was reduced by 78.6% in the highest N concentration treatment. In summary, we concluded that long-term N deposition could alter soil pH, the distribution of N, P elements, and the soil aggregate fractions, and reduce AM fungal and understory herb diversity. The importance of AM fungi in maintaining forest ecosystem diversity was verified under long-term N deposition.

Jiao-Jiao Chen, Zhang Zhang, Yi Wang et al.

AbstractAntrodia cinnamomea, an edible and medicinal fungus with significant economic value and application prospects, is rich in terpenoids, benzenoids, lignans, polysaccharides, and benzoquinone, succinic and maleic derivatives. In this study, the transcriptome of A. cinnamomea cultured on the wood substrates of Cinnamomum glanduliferum (YZM), C. camphora (XZM), and C. kanehirae (NZM) was sequenced using the high-throughput sequencing technology Illumina HiSeq 2000, and the data were assembled by de novo strategy to obtain 78,729 Unigenes with an N50 of 4,463 bp. Compared with public databases, about 11,435, 6,947, and 5,994 Unigenes were annotated to the Non-Redundant (NR), Gene Ontology (GO), and Kyoto Encyclopedia of Genes and Genome (KEGG), respectively. The comprehensive analysis of the mycelium terpene biosynthesis-related genes in A. cinnamomea revealed that the expression of acetyl-CoA acetyltransferase (AACT), acyl-CoA dehydrogenase (MCAD), 3-hydroxy-3-methylglutaryl-coenzyme A (HMG-CoA), mevalonate pyrophosphate decarboxylase (MVD), and isopentenyl diphosphate isomerase (IDI) was significantly higher on NZM compared to the other two wood substrates. Similarly, the expression of geranylgeranyltransferase (GGT) was significantly higher on YZM compared to NZM and XZM, and the expression of farnesyl transferase (FTase) was significantly higher on XZM. Furthermore, the expressions of 2,3-oxidized squalene cyclase (OCS), squalene synthase (SQS), and squalene epoxidase (SE) were significantly higher on NZM. Overall, this study provides a potential approach to explore the molecular regulation mechanism of terpenoid biosynthesis in A. cinnamomea.

Haijie Ma, Xinyue Meng, Kai Xu et al.

Highly efficient genetic transformation technology is greatly beneficial for crop gene function analysis and precision breeding. However, the most commonly used genetic transformation technology for woody plants, mediated by Agrobacterium tumefaciens, is time-consuming and inefficient, which limits its utility for gene function analysis. In this study, a simple, universal, and highly efficient genetic transformation technology mediated by A. rhizogenes K599 is described. This technology can be applied to multiple citrus genotypes, and only 2–8 weeks were required for the entire workflow. Genome-editing experiments were simultaneously conducted using 11 plasmids targeting different genomic positions and all corresponding transformants with the target knocked out were obtained, indicating that A. rhizogenes-mediated genome editing was highly efficient. In addition, the technology is advantageous for investigation of specific genes (such as ACD2) for obtaining “hard-to-get” transgenic root tissue. Furthermore, A. rhizogenes can be used for direct viral vector inoculation on citrus bypassing the requirement for virion enrichment in tobacco, which facilitates virus-induced gene silencing and virus-mediated gene expression. In summary, we established a highly efficient genetic transformation technology bypassing tissue culture in citrus that can be used for genome editing, gene overexpression, and virus-mediated gene function analysis. We anticipate that by reducing the cost, required workload, experimental period, and other technical obstacles, this genetic transformation technology will be a valuable tool for routine investigation of endogenous and exogenous genes in citrus.

Guangming Shao, Tianliang He, Yinnan Mu et al.

Summary: How organisms cope with coldness and high pressure in the hadal zone remains poorly understood. Here, we sequenced and assembled the genome of hadal sea cucumber Paelopatides sp. Yap with high quality and explored its potential mechanisms for deep-sea adaptation. First, the expansion of ACOX1 for rate-limiting enzyme in the DHA synthesis pathway, increased DHA content in the phospholipid bilayer, and positive selection of EPT1 may maintain cell membrane fluidity. Second, three genes for translation initiation factors and two for ribosomal proteins underwent expansion, and three ribosomal protein genes were positively selected, which may ameliorate the protein synthesis inhibition or ribosome dissociation in the hadal zone. Third, expansion and positive selection of genes associated with stalled replication fork recovery and DNA repair suggest improvements in DNA protection. This is the first genome sequence of a hadal invertebrate. Our results provide insights into the genetic adaptations used by invertebrate in deep oceans.

Hari Prasad Pandey, Narayan Prasad Pokhrel

The community forests of Nepal are a showcase of participatory forest management models to the global communities. However, the scenario of formation trend and their future formation potential is unknown. This paper presents 40 years of community forests (CF) formation trend in Nepal and discusses its potential formation scenario. The researchers have used updated data (mid-July, 2020) for trend analysis using Mann-Kendall and Sen's slope coefficient test. The policy provision of women participation and their actual involvement in the executive committee (EC) of community forests users' group (CFUG) has also been compared. The analysis showed 22,519 CF with an area of 2,312,545 hectares of national forests being managed by 3,088,259 households (HH). This constitutes 15.67% of the total land area, 34.98% of total forested area, 56.90% of total HH, and 62.68% of the total population of Nepal being involved in CF. Though the formation trend of CF and their respective area, HH involvement, EC members, and participation of women in EC was in increasing trend in the late 1990s to early 2000s, these variables are now decreasing. Although not statistically significant (p>0.05), the overall annual growth shows a negative trend, indicating the CF formation near the saturation point. Result reveals efforts and time to be invested in the management of CF rather than investing in a new formation. Moreover, results evident that CF ensures and obtains more than 50% women involvement both in policy and practice in the decision-making process for participatory common resource management in Nepal. Results would be a reference to policy guidance related to sustainable CF management and gender-inclusive participatory common resource management. This, again, would be a good example of a gender-inclusive natural resource management model to the other sectors in Nepal and to the global community.

Irwan Mahakam Lesmono Aji, Raden Sutriono, Arna Diansyah

This study aims to find out the effect of submersion by using 1% acetic acid, 100% palm juice, and 100% coconut water to break the dormancy of palm seeds at different maturity levels. The research was conducted in the Green House of Forestry Study Program, University of Mataram, using the experimental method with Complet Random Design (CRD) three factors. The first factor is the maturity level consists of 3 levels, the second factor is the submersion liquid substance consist of 3 levels, and the third factor is the period of submersion consist of 4 levels.The results of this study indicate that maturity rate gives significant influence on the following parameter i.e: percentage potency of seed germination, rotten seed, seed weight, seed moisture content, and embryo lenght, while seed dormancy parameter is not significant. The submersion factor significantly influenced on the following parameter i.e: seed weight, and seed water content, while the other parameters are not significant. The submersion period factor is significant only on seed moisture content and the embryo lenght, while the other parameters have no significant effect. While in all interactions between factors show no significant result on all parameters.

Erik J. Boren, Luigi Boschetti, Dan M. Johnson

Radiative transfer model (RTM) inversion allows for the quantitative estimation of vegetation biochemical composition from satellite sensor data, but large uncertainties associated with inversion make accurate estimation difficult. The leaf structure parameter (<i>N_s</i>) is one of the largest sources of uncertainty in inversion of the widely used leaf-level PROSPECT model, since it is the only parameter that cannot be directly measured. In this study, we characterize <i>N_s</i> as a function of phenology by collecting an extensive dataset of leaf measurements from samples of three dicotyledon species (hard red wheat, soft white wheat, and upland rice) and one monocotyledon (soy), grown under controlled conditions over two full growth seasons. A total of 230 samples were collected: measured leaf reflectance and transmittance were used to estimate <i>N_s</i> from each sample. These experimental data were used to investigate whether <i>N_s</i> depends on phenological stages (early/mid/late), and/or irrigation regime (irrigation at 85%, 75%, 60% of the initial saturated tray weight, and pre-/post-irrigation). The results, supported by the extensive experimental data set, indicate a significant difference between <i>N_s</i> estimated on monocotyledon and dicotyledon plants, and a significant difference between <i>N_s</i> estimated at different phenological stages. Different irrigation regimes did not result in significant <i>N_s</i> differences for either monocotyledon or dicotyledon plant types. To our knowledge, this study provides the first systematic record of <i>N_s</i> as a function of phenology for common crop species.

Y. Bergeron, S. Gauthier, Victor Kafka et al.

Nadine Eickenscheidt, Nicole H. Augustin, Nicole Wellbrock

Spatio-temporal modelling of tree defoliation data of German forest condition survey is presented. In the present study generalized additive mixed models were used to estimate the spatio-temporal trends of defoliation of the main tree species from 1989 to 2015 and to examine the suitability of different monitoring grid resolutions. Although data has been collected since 1989, this is the first time the spatio-temporal modelling for entire Germany has been carried out. Besides the space-time component, stand age showed a significant effect on defoliation. The mean age and the species-specific relation between defoliation and age determined the general level of defoliation whereas fluctuations of defoliation were primarily related to weather conditions. The study indicates a strong association between drought stress and defoliation of all four main tree species. Besides direct effects of weather conditions, indirect effects seem to play a further role. Defoliation of the comparably drought-tolerant species pine and oak was primarily affected by insect infestations following drought whereas considerable time for regeneration was required by beech following drought stress and recurring substantial fructification. South-eastern Germany has emerged as the region with the highest defoliation since the drought year 2003. This region was characterized by the strongest water deficits in 2003 compared to the long-term reference period. The present study gives evidence that the focus has moved from air pollution to climate change. Furthermore, the spatio-temporal model was used to carry out a simulation study to compare different survey grid resolutions. This grid examination indicated that an 8 x 8 km grid instead of the standard 16 x 16 km grid is necessary for spatio-temporal trend estimation and for detecting hot-spots in defoliation in space and time, especially regarding oak.

Henrike Häbel, András Balázs, Mari Myllymäki

With recent developments in remote sensing technologies, plot-level forest resources can be predicted utilizing airborne laser scanning (ALS). The prediction is often assisted by mostly vertical summaries of the ALS point clouds. We present a spatial analysis of the point cloud by studying the horizontal distribution of the pulse returns through canopy height models thresholded at different height levels. The resulting patterns of patches of vegetation and gabs on each layer are summarized to spatial ALS features. We propose new features based on the Euler number, which is the number of patches minus the number of gaps, and the empty-space function, which is a spatial summary function of the gab space. The empty-space function is also used to describe differences in the gab structure between two different layers. We illustrate usefulness of the proposed spatial features for predicting different forest variables that summarize the spatial structure of forests or their breast height diameter distribution. We employ the proposed spatial features, in addition to commonly used features from literature, in the well-known k-nn estimation method to predict the forest variables. We present the methodology on the example of a study site in Central Finland.