Browsing by Subject "SPRUCE"

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  • Pyorala, Jiri; Kankare, Ville; Liang, Xinlian; Saarinen, Ninni; Rikala, Juha; Kivinen, Veli-Pekka; Sipi, Marketta; Holopainen, Markus; Hyyppa, Juha; Vastaranta, Mikko (2019)
    Wood procurement in sawmills could be improved by resolving detailed three-dimensional stem geometry references from standing timber. This could be achieved, using the increasingly available terrestrial point clouds from various sources. Here, we collected terrestrial laser-scanning (TLS) data from 52 Scots pines (Pinus sylvestris L.) with the purpose of evaluating the accuracy of the log geometry and analysing its relationship with wood quality. For reference, the log-specific top-end diameter, volume, tapering, sweep, basic density and knottiness were measured in a sawmill. We produced stem models from the TLS data and bucked them into logs similar to those measured in the sawmill. In comparison to the sawmill data, the log-specific TLS-based top-end diameter, volume, taper and sweep estimates showed relative mean differences of 1.6, -2.4, -3.0 and 78 per cent, respectively. The correlation coefficients between increasing taper and decreasing wood density and whorl-to-whorl distances were 0.49 and -0.51, respectively. Although the stem-model geometry was resolved from the point clouds with similar accuracy to that at the sawmills, the remaining uncertainty in defining the sweep and linking the wood quality with stem geometry may currently limit the method's feasibilities. Instead of static TLS, mobile platforms would likely be more suitable for operational point cloud data acquisition.
  • Peuhu, Elina; Thomssen, Pia-Maria; Siitonen, Juha (2019)
    Hollow trees are an important habitat for a large number of saproxylic invertebrates, many of which are rare or threatened. Large old trees occur frequently in cities, but the saproxylic fauna inhabiting these trees has been poorly studied. Sampling in urban areas includes the risk of trap failure due to human interference, which needs to be considered when designing sampling. The aim of our study was to find an efficient trap type for sampling saproxylic beetles in hollow urban trees. We compared the species richness and species composition of saproxylic beetle assemblages between trunk window, aluminium foil tray and pitfall traps placed inside hollow trees in the Helsinki metropolitan area, Finland. A total of 30 traps of each trap type were set in 15 trees. The traps caught a total of 4004 saproxylic beetle individuals belonging to 131 species. Trunk window and aluminium foil traps had similar assemblage and trapping efficiency, and were significantly more efficient than pitfall traps. However, pitfall traps caught certain species more efficiently than the other two trap types. Time spent separating insects from samples was the most laborious work stage. The time increased with increasing sample weight, i.e. the amount of wood mould in the trap. Trunk windows were the most efficient trap type also in terms of saproxylic species and individuals per handling time. We conclude that saproxylic beetle fauna living in hollow urban trees can be efficiently sampled with small trunk window traps or containers placed on the inner walls of hollows.
  • Morais de Carvalho, Danila; Lahtinen, Maarit; Lawoko, Martin; Mikkonen, Kirsi S. (2020)
    Lignin-carbohydrate complexes (LCCs) are hybrid structures containing covalently linked moieties of lignin and carbohydrates. The structure and behavior of LCCs affect both industrial processes and practical applications of lignocellulosic biomass. However, the identification of phenylglycoside, benzylether, and gamma (gamma)-ester LCC bonds in lignocellulosic biomass is limited due to their relatively low abundance compared to plain carbohydrate and lignin structures. Herein, we enriched the LCC bonds in softwood galactoglucomannan (GGM)-rich extract fractionated by (1) a solvent (ethanol), (2) enzymes, and (3) physical techniques. Two-dimensional nuclear magnetic resonance (NMR) spectroscopy analysis was used to identify the LCC bonds. Phenylglycoside and benzylether bonds were concentrated in the ethanol-soluble GGM fractions. A benzylether bond was concentrated into GGM fractions containing larger molecules (>500 Da) through physical techniques. The gamma-ester bond was identified in all studied GGM fractions, which is explained by its stability and possible presence in residual xylan. In summary, we demonstrated the potential of the suggested techniques to enrich LCC bonds in softwood extract and improve LCC identification. Such techniques may also enable further studies on the structure and functionality of LCC bonds and open new prospects in the engineering of biomolecules.
  • Kulha, Niko; Pasanen, Leena; Aakala, Tuomas (2018)
    Time series of repeat aerial photographs currently span decades in many regions. However, the lack of calibration data limits their use in forest change analysis. We propose an approach where we combine repeat aerial photography, tree-ring reconstructions, and Bayesian inference to study changes in forests. Using stereopairs of aerial photographs from five boreal forest landscapes, we visually interpreted canopy cover in contiguous 0.1-ha cells at three time points during 1959-2011. We used tree-ring measurements to produce calibration data for the interpretation, and to quantify the bias and error associated with the interpretation. Then, we discerned credible canopy cover changes from the interpretation error noise using Bayesian inference. We underestimated canopy cover using the historical low-quality photographs, and overestimated it using the recent high-quality photographs. Further, due to differences in tree species composition and canopy cover in the cells, the interpretation bias varied between the landscapes. In addition, the random interpretation error varied between and within the landscapes. Due to the varying bias and error, the magnitude of credibly detectable canopy cover change in the 0.1-ha cells depended on the studied time interval and landscape, ranging from -10 to -18 percentage points (decrease), and from +10 to +19 percentage points (increase). Hence, changes occurring at stand scales were detectable, but smaller scale changes could not be separated from the error noise. Besides the abrupt changes, also slow continuous canopy cover changes could be detected with the proposed approach. Given the wide availability of historical aerial photographs, the proposed approach can be applied for forest change analysis in biomes where tree-rings form, while accounting for the bias and error in aerial photo interpretation.
  • Bock, Peter; Nousiainen, Paula; Elder, Thomas; Blaukopf, Markus; Amer, Hassan; Zirbs, Ronald; Potthast, Antje; Gierlinger, Notburga (2020)
    Vibrational spectroscopy is a very suitable tool for investigating the plant cell wall in situ with almost no sample preparation. The structural information of all different constituents is contained in a single spectrum. Interpretation therefore heavily relies on reference spectra and understanding of the vibrational behavior of the components under study. For the first time, we show infrared (IR) and Raman spectra of dibenzodioxocin (DBDO), an important lignin substructure. A detailed vibrational assignment of the molecule, based on quantum chemical computations, is given in the Supporting Information; the main results are found in the paper. Furthermore, we show IR and Raman spectra of synthetic guaiacyl lignin (dehydrogenation polymer-G-DHP). Raman spectra of DBDO and G-DHP both differ with respect to the excitation wavelength and therefore reveal different features of the substructure/polymer. This study confirms the idea previously put forward that Raman at 532 nm selectively probes end groups of lignin, whereas Raman at 785 nm and IR seem to represent the majority of lignin substructures.
  • Purhonen, Jenna; Ovaskainen, Otso; Halme, Panu; Komonen, Atte; Huhtinen, Seppo; Kotiranta, Heikki; Laessoe, Thomas; Abrego, Nerea (2020)
    Tree species is one of the most important determinants of wood-inhabiting fungal community composition, yet its relationship with fungal reproductive and dispersal traits remains poorly understood. We studied fungal communities (total of 657 species) inhabiting broadleaved and coniferous dead wood (total of 192 logs) in 12 semi-natural boreal forests. We utilized a trait-based hierarchical joint species distribution model to examine how the relationship between dead wood quality and species occurrence correlates with reproductive and dispersal morphological traits. Broadleaved trees had higher species richness than conifers, due to discomycetoids and pyrenomycetoids specializing in them. Resupinate and pileate species were generally specialized in coniferous dead wood. Fungi inhabiting broadleaved trees had larger and more elongated spores than fungi in conifers. Spore size was larger and spore shape more spherical in species occupying large dead wood units. These results indicate the selective effect of dead wood quality, visible not only in species diversity, but also in reproductive and dispersal traits. (C) 2019 Elsevier Ltd and British Mycological Society. All rights reserved.
  • Blokhina, Olga; Laitinen, Teresa; Hatakeyama, Yuto; Delhomme, Nicolas; Paasela, Tanja; Zhao, Lei; Street, Nathaniel R.; Wada, Hiroshi; Karkonen, Anna; Fagerstedt, Kurt (2019)
    A comparative transcriptomic study and a single-cell metabolome analysis were combined to determine whether parenchymal ray cells contribute to the biosynthesis of monolignols in the lignifying xylem of Norway spruce (Picea abies). Ray parenchymal cells may function in the lignification of upright tracheids by supplying monolignols. To test this hypothesis, parenchymal ray cells and upright tracheids were dissected with laser-capture microdissection from tangential cryosections of developing xylem of spruce trees. The transcriptome analysis revealed that among the genes involved in processes typical for vascular tissues, genes encoding cell wall biogenesis-related enzymes were highly expressed in both developing tracheids and ray cells. Interestingly, most of the shikimate and monolignol biosynthesis pathway-related genes were equally expressed in both cell types. Nonetheless, 1,073 differentially expressed genes were detected between developing ray cells and tracheids, among which a set of genes expressed only in ray cells was identified. In situ single cell metabolomics of semi-intact plants by picoliter pressure probe-electrospray ionization-mass spectrometry detected monolignols and their glycoconjugates in both cell types, indicating that the biosynthetic route for monolignols is active in both upright tracheids and parenchymal ray cells. The data strongly support the hypothesis that in developing xylem, ray cells produce monolignols that contribute to lignification of tracheid cell walls. Transcriptomics combined with single-cell metabolomics give new information on the role of rays in lignification of developing xylem in Norway spruce.
  • Hakola, H; Tarvainen, V; Bäck, Jaana; Ranta, H; Bonn, Boris; Rinne, Janne; Kulmala, Markku (2006)
  • Lyczakowski, Jan J.; Bourdon, Matthieu; Terrett, Oliver M.; Helariutta, Ykä; Wightman, Raymond; Dupree, Paul (2019)
    The woody secondary cell walls of plants are the largest repository of renewable carbon biopolymers on the planet. These walls are made principally from cellulose and hemicelluloses and are impregnated with lignin. Despite their importance as the main load bearing structure for plant growth, as well as their industrial importance as both a material and energy source, the precise arrangement of these constituents within the cell wall is not yet fully understood. We have adapted low temperature scanning electron microscopy (cryo-SEM) for imaging the nanoscale architecture of angiosperm and gymnosperm cell walls in their native hydrated state. Our work confirms that cell wall macrofibrils, cylindrical structures with a diameter exceeding 10 nm, are a common feature of the native hardwood and softwood samples. We have observed these same structures in Arabidopsis thaliana secondary cell walls, enabling macrofibrils to be compared between mutant lines that are perturbed in cellulose, hemicellulose, and lignin formation. Our analysis indicates that the macrofibrils in Arabidopsis cell walls are dependent upon the proper biosynthesis, or composed, of cellulose, xylan, and lignin. This study establishes that cryo-SEM is a useful additional approach for investigating the native nanoscale architecture and composition of hardwood and softwood secondary cell walls and demonstrates the applicability of Arabidopsis genetic resources to relate fibril structure with wall composition and biosynthesis.
  • Ojeda, Dario I.; Mattila, Tiina M.; Ruttink, Tom; Kujala, Sonja T.; Kärkkäinen, Katri; Verta, Jukka-Pekka; Pyhäjärvi, Tanja (2019)
    Compared to angiosperms, gymnosperms lag behind in the availability of assembled and annotated genomes. Most genomic analyses in gymnosperms, especially conifer tree species, rely on the use of de novo assembled transcriptomes. However, the level of allelic redundancy and transcript fragmentation in these assembled transcriptomes, and their effect on downstream applications have not been fully investigated. Here, we assessed three assembly strategies for short-reads data, including the utility of haploid megagametophyte tissue during de novo assembly as single-allele guides, for six individuals and five different tissues in Pinus sylvestris. We then contrasted haploid and diploid tissue genotype calls obtained from the assembled transcriptomes to evaluate the extent of paralog mapping. The use of the haploid tissue during assembly increased its completeness without reducing the number of assembled transcripts. Our results suggest that current strategies that rely on available genomic resources as guidance to minimize allelic redundancy are less effective than the application of strategies that cluster redundant assembled transcripts. The strategy yielding the lowest levels of allelic redundancy among the assembled transcriptomes assessed here was the generation of SuperTranscripts with Lace followed by CD-HIT clustering. However, we still observed some levels of heterozygosity (multiple gene fragments per transcript reflecting allelic redundancy) in this assembled transcriptome on the haploid tissue, indicating that further filtering is required before using these assemblies for downstream applications. We discuss the influence of allelic redundancy when these reference transcriptomes are used to select regions for probe design of exome capture baits and for estimation of population genetic diversity.
  • Jenna, Purhonen; Nerea, Abrego; Atte, Komonen; Seppo, Huhtinen; Heikki, Kotiranta; Thomas, Laessoe; Panu, Halme (2021)
    The general negative impact of forestry on wood-inhabiting fungal diversity is well recognized, yet the effect of forest naturalness is poorly disentangled among different fungal groups inhabiting dead wood of different tree species. We studied the relationship between forest naturalness, log characteristics and diversity of different fungal morpho-groups inhabiting large decaying logs of similar quality in spruce dominated boreal forests. We sampled all non-lichenized fruitbodies from birch, spruce, pine and aspen in 12 semi-natural forest sites of varying level of naturalness. The overall fungal community composition was mostly determined by host tree species. However, when assessing the relevance of the environmental variables separately for each tree species, the most important variable varied, naturalness being the most important explanatory variable for fungi inhabiting pine and aspen. More strikingly, the overall species richness increased as the forest naturalness increased, both at the site and log levels. At the site scale, the pattern was mostly driven by the discoid and pyrenoid morpho-groups inhabiting pine, whereas at the log scale, it was driven by pileate and resupinate morpho-groups inhabiting spruce. Although our study demonstrates that formerly managed protected forests serve as effective conservation areas for most wood-inhabiting fungal groups, it also shows that conservation planning and management should account for group- or host tree -specific responses.