Browsing by Subject "SCOTS PINE"

Sort by: Order: Results:

Now showing items 1-20 of 121
  • Virjamo, Virpi; Fyhrquist, Pia; Koskinen, Akseli; Lavola, Anu; Nissinen, Katri; Julkunen-Tiitto, Riitta (2020)
    Knowledge about the defensive chemistry of coniferous trees has increased in recent years regarding a number of alkaloid compounds; in addition to phenolics and terpenes. Here, we show that Norway spruce (Picea abies (L.) H. Karst.), an important boreal zone tree species; accumulates 1,6-dehydropinidine (2-methyl-6-(2-propenyl)-1,6-piperideine) in its needles and bark. We reanalyzed previously published GC-MS data to obtain a full picture of 1,6-dehydropinidine in P. abies. 1,6-dehydropinidine appeared to especially accumulate in developing spring shoots. We used solid-phase partitioning to collect the alkaloid fraction of the sprouts and thin-layer chromatography to purify 1,6-dehydropinidine. The antibacterial properties of the 1,6-dehydropinidine fraction were tested using a broth microdilution method; with Streptococcus equi subsp. equi as a model organism. Based on our results 1,6-dehydropinidine is common in alkaloid extractions from P. abies (0.4 +/- 0.03 mg g(-1) dw in mature needles) and it is especially abundant in young spruce shoots (2.7 +/- 0.5 mg g(-1) dw). Moreover; 1,6-dehydropinidine extracted from P. abies sprouts showed mild antibacterial potential against Streptococcus equi subsp. equi (MIC 55 mu g mL(-1)). The antibacterial activity of a plant compound thought of as an intermediate rather than an end-product of biosynthesis calls for more detailed studies regarding the biological function of these coniferous alkaloids
  • Neefjes, Ivo; Laapas, Mikko; Liu, Yang; Medus, Erika; Miettunen, Elina; Ahonen, Lauri; Quelever, Lauriane; Aalto, Juho; Bäck, Jaana; Kerminen, Veli-Matti; Lampilahti, Janne; Luoma, Krista; Mäki, Mari; Mammarella, Ivan; Petäjä, Tuukka; Räty, Meri; Sarnela, Nina; Ylivinkka, Ilona; Hakala, Simo; Kulmala, Markku; Nieminen, Tuomo; Lintunen, Anna (2022)
    Boreal forests are an important source of trace gases and atmospheric aerosols, as well as a crucial carbon sink. As such, they form a strongly interconnected coupled system with the atmosphere. The SMEAR II station is located in a boreal Scots pine forest in Hyytiala, Finland, and has over 25 years of continuous measurements of atmospheric and ecosystem variables. In this study, we analyse the seasonal variations of trace gases, atmospheric aerosols, greenhouse gases, and meteorological variables, measured at the SMEAR II sta-tion during the past two and a half decades. Several ecosystem and atmospheric variables show seasonal correlations with each other, which suggests seasonal interactions within the climate system that links together ecosystem processes, greenhouse gases, trace gases and atmospheric aerosols. For instance, increased global radiation in summer increases air temperature and consequently affects the plant phenology, which promotes the ecosystem carbon exchange and biogenic volatile organic compound (biogenic VOC) release. This further affects the ambient concentrations of highly oxygenated organic molecules (HOMs) as well as the formation and growth of atmospheric organic aerosols. Organic aerosols subsequently influence aerosol optical properties and, through increased scattering, have the potential to cool the climate. We also discuss the impacts of the warm and dry summers of 2010 and 2018 on the studied variables. For these years, we find a higher-than-average ecosystem primary production especially in June, leading to an increased VOC flux from the forest. The increased VOC flux in turn leads to higher HOM and secondary aerosol concentration in the atmosphere. The latter increases light scattering by atmospheric aero-sol particles and thus leads to climate cooling. The results obtained in this study improve our understanding of how boreal forests respond to climate change.
  • Helama, Samuli; Arppe, Laura; Timonen, Mauri; Mielikäinen, Kari; Oinonen, Markku (2018)
    Tree-ring stable isotope chronologies provide very high-resolution palaeoclimatic data, and the number of records is increasing rapidly worldwide. To extend the chronologies back in time, before the period covered by the old living trees, the use of subfossil wood samples is required. Typically, the longest continuous subfossil chronologies consist of regionally collected tree-ring materials, rather than tree rings from a single site, and are likely more sensitive to data heterogeneity. Yet, the characteristics of such datasets remain hitherto unexplored. Here we produce a continuous, decadally resolved chronology of C-13/C-12 ratio (delta C-13) from Finnish Lapland over the past 7.5 ka (5500 BCE to 2010 CE) for which there is replication of at least five Pinus sylvestris trees. Less negative delta C-13 values were observed as trees age and for western sites (higher in elevation and further from the cold oceanic air flow). The age -related trends in living tree delta C-13 data were expressed mainly over the first fifty years mimicking the "juvenile effect" whereas the subfossil data showed trend over the trees' lifespan. These findings demonstrated the need to detrend the individual delta C-13 series before averaging them into the mean chronology. The corresponding biases were removed from the isotopic data using the methods frequently applied for tree-ring width and density proxies, the Regional Curve Standardization (RCS) combined with signal-free approach. While the RCS procedures commonly preserve the long-term variations in the resulting chronology, not all types of them did so as demonstrated for chronologies produced using separate RCS models for the delta C-13 series with relatively high and low isotopic level (offset from the grand mean). It was shown that these delta C-13 levels (i.e. the relative isotopic enrichment) result both from the low-frequency climate signal and biogeographical aspects (the site longitude/altitudes). The non-climatic biases were removed from the delta C-13 series by using separate RCS models for the subsets (western and eastern) of isotopic series. Similar to previous investigations using annually resolved delta C-13 data from Lapland, our chronology had strong negative correlations to variations in cloud cover. Here, a bootstrapping experiment was used to verify this dendroclimatic association. The resulting palaeo-cloud reconstruction portrayed decadal to multi-millennial variations with centennial anomalies coinciding with the mid and late Holocene events of climate transitions, highlighting the value of subfossil isotope chronologies from tree rings in synthesising climate dynamics from several proxy sources over the present interglacial.
  • Härkönen, S.; Neumann, M.; Mues, V.; Berninger, F.; Bronisz, K.; Cardellini, G.; Chirici, G.; Hasenauer, H.; Koehl, M.; Lang, M.; Merganicova, K.; Mohren, F.; Moiseyev, A.; Moreno, A.; Mura, M.; Muys, B.; Olschofsky, K.; Del Perugia, B.; Rorstad, P. K.; Solberg, B.; Thivolle-Cazat, A.; Trotsiuk, V.; Mäkelä, A. (2019)
    FORMIT-M is a widely applicable, open-access, simple and flexible, climate-sensitive forest management simulator requiring only standard forest inventory data as input. It combines a process-based carbon balance approach with a strong inventory-based empirical component. The model has been linked to the global forest sector model EFI-GTM to secure consistency between timber cutting and demand, although prescribed harvest scenarios can also be used. Here we introduce the structure of the model and demonstrate its use with example simulations until the end of the 21st century in Europe, comparing different management scenarios in different regions under climate change. The model was consistent with country-level statistics of growing stock volumes (R-2=0.938) and its projections of climate impact on growth agreed with other studies. The management changes had a greater impact on growing stocks, harvest potential and carbon balance than projected climate change, at least in the absence of increased disturbance rates.
  • Hu, Man; Pitkanen, Timo P.; Minunno, Francesco; Tian, Xianglin; Lehtonen, Aleksi; Makela, Annikki (2021)
    Background and Aims Branch biomass and other attributes are important for estimating the carbon budget of forest stands and characterizing crown structure. As destructive measuring is time-consuming and labour-intensive, terrestrial laser scanning (TLS) as a solution has been used to estimate branch biomass quickly and non-destructively. However, branch information extraction from TLS data alone is challenging due to occlusion and other defects, especially for estimating individual branch attributes in coniferous trees. Methods This study presents a method, entitled TSMtls, to estimate individual branch biomass non-destructively and accurately by combining tree structure models and TLS data. The TSMtls method constructs the stem-taper curve from TLS data, then uses tree structure models to determine the number, basal area and biomass of individual branches at whorl level. We estimated the tree structural model parameters from 122 destructively measured Scots pine (Pinus sylvestris) trees and tested the method on six Scots pine trees that were first TLS-scanned and later destructively measured. Additionally, we estimated the branch biomass using other TLS-based approaches for comparison. Key Results Tree-level branch biomass estimates derived from TSMtls showed the best agreement with the destructive measurements [coefficient of variation of root mean square error (CV-RMSE) = 9.66 % and concordance correlation coefficient (CCC) = 0.99], outperforming the other TLS-based approaches (CV-RMSE 12.97-57.45 % and CCC 0.43-0.98 ). Whorl-level individual branch attributes estimates produced from TSMtls showed more accurate results than those produced from TLS data directly. Conclusions The results showed that the TSMtls method proposed in this study holds promise for extension to more species and larger areas.
  • Lappalainen, Hanna K.; Sevanto, Sanna; Dal Maso, Miikka; Taipale, Risto; Kajos, Maija; Kolari, Pasi; Back, Jaana (2013)
  • Sievänen, Risto; Raumonen, Pasi; Perttunen, Jari; Nikinmaa, Eero Heikki; Kaitaniemi, Pekka Juhani (2018)
    Background and Aims: Functional-structural plant models (FSPMs) allow simulation of tree crown development as the sum of modular (e.g. shoot-level) responses triggered by the local environmental conditions. The actual process of space filling by the crowns can be studied. Although the FSPM simulations are at organ scale, the data for their validation have usually been at more aggregated levels (whole-crown or whole-tree). Measurements made by terrestrial laser scanning (TLS) that have been segmented into elementary units (internodes) offer a phenotyping tool to validate the FSPM predictions at levels comparable with their detail. We demonstrate the testing of different formulations of crown development of Scots pine trees in the LIGNUM model using segmented TLS data. Methods: We made TLS measurements from four sample trees growing in a forest on a relatively poor soil from sapling size to mature stage. The TLS data were segmented into intenodes. The segmentation also produced information on whether needles were present in the internode. We applied different formulations of crown development (flushing of buds and length of growth of new internodes) in LIGNUM. We optimized the parameter values of each formulation using genetic algorithms to observe the best fit of LIGNUM simulations to the measured trees. The fitness function in the estimation combined both tree-level characteristics (e.g. tree height and crown length) and measures of crown shape (e.g. spatial distribution of needle area). Key Results: Comparison of different formulations against the data indicates that the Extended Borchert- Honda model for shoot elongation works best within LIGNUM. Control of growth by local density in the crown was important for all shoot elongation formulations. Modifying the number of lateral buds as a function of local density in the crown was the best way to accomplish density control. Conclusions: It was demonstrated how segmented TLS data can be used in the context of a shoot-based model to select model components.
  • Halmeenmäki, Elisa; Heinonsalo, Jussi; Putkinen, Anuliina; Santalahti, Minna; Fritze, Hannu; Pihlatie, Mari (2017)
    The contribution of boreal forest plants to the methane (CH4) cycle is still uncertain. We studied the above and belowground CH4 fluxes of common boreal plants, and assessed the possible contribution of CH4 producing and oxidizing microbes (methanogens and methanotrophs, respectively) to the fluxes. We measured the CH4 fluxes and the amounts of methanogens and methanotrophs in the above- and belowground parts of Vaccinium myrtillus, Vaccinium vitis-idaea, Calluna vulgaris and Pinus sylvestris seedlings and in non-planted soil in a microcosm experiment. The shoots of C. vulgaris and P. sylvestris showed on average emissions of CH4, while the shoots of the Vaccinium species indicated small CH4 uptake. All the root-soil-compartments consumed CH4, however, the non-rooted soils showed on average small CH4 emission. We found methanotrophs from all the rooted and non-rooted soils. Methanogens were not detected in the plant or soil materials. The presence of plant roots seem to increase the amount of methanotrophs and thus CH4 uptake in the soil. The CH4 emissions from the shoots of C. vulgaris and P. sylvestris demonstrate that the plants have an important contribution to the CH4 exchange dynamics in the plant-soil systems.
  • Alberto Ramirez-Valiente, Jose; Sole-Medina, Aida; Pyhajarvi, Tanja; Savolainen, Outi; Heer, Katrin; Opgenoorth, Lars; Danusevicius, Darius; Jose Robledo-Arnuncio, Juan (2021)
    Early-stage fitness variation has been seldom evaluated at broad scales in forest tree species, despite the long tradition of studying climate-driven intraspecific genetic variation. In this study, we evaluated the role of climate in driving patterns of population differentiation at early-life stages in Pinus sylvestris and explored the fitness and growth consequences of seed transfer within the species range. We monitored seedling emergence, survival and growth over a 2-yr period in a multi-site common garden experiment which included 18 European populations and spanned 25 degrees in latitude and 1700 m in elevation. Climate-fitness functions showed that populations exhibited higher seedling survival and growth at temperatures similar to their home environment, which is consistent with local adaptation. Northern populations experienced lower survival and growth at warmer sites, contrary to previous studies on later life stages. Seed mass was higher in populations from warmer areas and was positively associated with survival and growth at more southern sites. Finally, we did not detect a survival-growth trade-off; on the contrary, bigger seedlings exhibited higher survival probabilities under most climatic conditions. In conclusion, our results reveal that contrasting temperature regimes have played an important role in driving the divergent evolution of P. sylvestris populations at early-life stages.
  • Zhang-Turpeinen, Huizhong; Kivimäenpää, Minna; Berninger, Frank; Köster, Kajar; Zhao, Peng; Zhou, Xuan; Pumpanen, Jukka (2021)
    The amplification of global warming in the Northern regions results in a higher probability of wildfires in boreal forests. On the forest floor, wildfires have long-term effects on vegetation composition as well as soil and its microbial communities. A large variety of biogenic volatile organic compounds (BVOCs) such as isoprene, monoterpenes, sesquiterpenes have been observed to be emitted from soil and understory vegetation of boreal forest floor. Ultimately, the fire-induced changes in the forest floor affect its BVOC fluxes, and the recovery of the forest floor determines the quantity and quality of BVOC fluxes. However, the effects of wildfires on forest floor BVOC fluxes are rarely studied. Here we conducted a study of the impacts of post-fire succession on forest floor BVOC fluxes along a 158-year fire chronosequence in boreal Scots pine stands near the northern timberline in north-eastern Finland throughout a growing season. We determined the forest floor BVOC fluxes and investigated how the environmental and ground vegetation characteristics, soil respiration rates, and soil microbial and fungal biomass are associated with the BVOC fluxes during the post-fire succession. The forest floor was a source of diverse BVOCs. Monoterpenes (MTs) were the largest group of emitted BVOCs. We observed forest age-related differences in the forest floor BVOC fluxes along the fire chronosequence. The forest floor BVOC fluxes decreased with the reduction in ground vegetation coverage resulted from wildfire, and the decreased fluxes were also connected to a decrease in microbial activity as a result of the loss of plant roots and soil organic matter. The increase in BVOC fluxes was associated with the recovery of aboveground plant coverage and soils. Our results suggested taking into consideration the implications of BVOC flux variations on the atmospheric chemistry and climate feedbacks.
  • Mencuccini, Maurizio; Salmon, Yann; Mitchell, Patrick; Hölttä, Teemu; Choat, Brendan; Meir, Patrick; O'Grady, Anthony; Tissue, David; Zweifel, Roman; Sevanto, Sanna; Pfautsch, Sebastian (2017)
    Substantial uncertainty surrounds our knowledge of tree stem growth, with some of the most basic questions, such as when stem radial growth occurs through the daily cycle, still unanswered. We employed high-resolution point dendrometers, sap flow sensors, and developed theory and statistical approaches, to devise a novel method separating irreversible radial growth from elastic tension-driven and elastic osmotically driven changes in bark water content. We tested this method using data from five case study species. Experimental manipulations, namely a field irrigation experiment on Scots pine and a stem girdling experiment on red forest gum trees, were used to validate the theory. Time courses of stem radial growth following irrigation and stem girdling were consistent with a-priori predictions. Patterns of stem radial growth varied across case studies, with growth occurring during the day and/or night, consistent with the available literature. Importantly, our approach provides a valuable alternative to existing methods, as it can be approximated by a simple empirical interpolation routine that derives irreversible radial growth using standard regression techniques. Our novel method provides an improved understanding of the relative source-sink carbon dynamics of tree stems at a sub-daily time scale.
  • Rantala, P.; Aalto, J.; Taipale, R.; Ruuskanen, T. M.; Rinne, J. (2015)
    Long-term flux measurements of volatile organic compounds (VOC) over boreal forests are rare, although the forests are known to emit considerable amounts of VOCs into the atmosphere. Thus, we measured fluxes of several VOCs and oxygenated VOCs over a Scots-pine-dominated boreal forest semi-continuously between May 2010 and December 2013. The VOC profiles were obtained with a proton transfer reaction mass spectrometry, and the fluxes were calculated using vertical concentration profiles and the surface layer profile method connected to the Monin-Obukhov similarity theory. In total fluxes that differed significantly from zero on a monthly basis were observed for 13 out of 27 measured masses. Monoterpenes had the highest net emission in all seasons and statistically significant positive fluxes were detected from March until October. Other important compounds emitted were methanol, ethanol+ formic acid, acetone and isoprene+ methylbutenol. Oxygenated VOCs showed also deposition fluxes that were statistically different from zero. Isoprene+ methylbutenol and monoterpene fluxes followed well the traditional isoprene algorithm and the hybrid algorithm, respectively. Emission potentials of monoterpenes were largest in late spring and autumn which was possibly driven by growth processes and decaying of soil litter, respectively. Conversely, largest emission potentials of isoprene+ methylbutenol were found in July. Thus, we concluded that most of the emissions of m/z 69 at the site consisted of isoprene that originated from broadleaved trees. Methanol had deposition fluxes especially before sunrise. This can be connected to water films on surfaces. Based on this assumption, we were able to build an empirical algorithm for bi-directional methanol exchange that described both emission term and deposition term. Methanol emissions were highest in May and June and deposition level increased towards autumn, probably as a result of increasing relative humidity levels leading to predominance of deposition.
  • Rinta-Kanto, J. M.; Pehkonen, K.; Sinkko, H.; Tamminen, M. V.; Timonen, S. (2018)
    In this study, the abundance and composition of prokaryotic communities associated with the inner tissue of fruiting bodies of Suillus bovinus, Boletus pinophilus, Cantharellus cibarius, Agaricus arvensis, Lycoperdon perlatum, and Piptoporus betulinus were analyzed using culture-independent methods. Our findings indicate that archaea and bacteria colonize the internal tissues of all investigated specimens and that archaea are prominent members of the prokaryotic community. The ratio of archaeal 16S rRNA gene copy numbers to those of bacteria was >1 in the fruiting bodies of four out of six fungal species included in the study. The largest proportion of archaeal 16S rRNA gene sequences belonged to thaumarchaeotal classes Terrestrial group, Miscellaneous Crenar-chaeotic Group (MCG), and Thermoplasmata. Bacterial communities showed characteristic compositions in each fungal species. Bacterial classes Gammaproteobacteria, Actinobacteria, Bacilli, and Clostridia were prominent among communities in fruiting body tissues. Bacterial populations in each fungal species had different characteristics. The results of this study imply that fruiting body tissues are an important habitat for abundant and diverse populations of archaea and bacteria.
  • Pyorala, Jiri; Liang, Xinlian; Saarinen, Ninni; Kankare, Ville; Wang, Yunsheng; Holopainen, Markus; Hyyppa, Juha; Vastaranta, Mikko (2018)
    Terrestrial laser scanning (TLS) accompanied by quantitative tree-modeling algorithms can potentially acquire branching data non-destructively from a forest environment and aid the development and calibration of allometric crown biomass and wood quality equations for species and geographical regions with inadequate models. However, TLS's coverage in capturing individual branches still lacks evaluation. We acquired TLS data from 158 Scots pine (Pinus sylvestris L.) trees and investigated the performance of a quantitative branch detection and modeling approach for extracting key branching parameters, namely the number of branches, branch diameter (b(d)) and branch insertion angle (b) in various crown sections. We used manual point cloud measurements as references. The accuracy of quantitative branch detections decreased significantly above the live crown base height, principally due to the increasing scanner distance as opposed to occlusion effects caused by the foliage. b(d) was generally underestimated, when comparing to the manual reference, while b was estimated accurately: tree-specific biases were 0.89cm and 1.98 degrees, respectively. Our results indicate that full branching structure remains challenging to capture by TLS alone. Nevertheless, the retrievable branching parameters are potential inputs into allometric biomass and wood quality equations.
  • 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.
  • Nadal-Sala, Daniel; Grote, Ruediger; Birami, Benjamin; Lintunen, Anna; Mammarella, Ivan; Preisler, Yakir; Rotenberg, Eyal; Salmon, Yann; Tatarinov, Fedor; Yakir, Dan; Ruehr, Nadine K. (2021)
    Climate change will impact forest productivity worldwide. Forecasting the magnitude of such impact, with multiple environmental stressors changing simultaneously, is only possible with the help of process-based models. In order to assess their performance, such models require careful evaluation against measurements. However, direct comparison of model outputs against observational data is often not reliable, as models may provide the right answers due to the wrong reasons. This would severely hinder forecasting abilities under unprecedented climate conditions. Here, we present a methodology for model assessment, which supplements the traditional output-to-observation model validation. It evaluates model performance through its ability to reproduce observed seasonal changes of the most limiting environmental driver (MLED) for a given process, here daily gross primary productivity (GPP). We analyzed seasonal changes of the MLED for GPP in two contrasting pine forests, the Mediterranean Pinus halepensis Mill. Yatir (Israel) and the boreal Pinus sylvestris L. Hyytiala (Finland) from three years of eddy-covariance flux data. Then, we simulated the same period with a state-of-the-art process-based simulation model (LandscapeDNDC). Finally, we assessed if the model was able to reproduce both GPP observations and MLED seasonality. We found that the model reproduced the seasonality of GPP in both stands, but it was slightly overestimated without site-specific fine-tuning. Interestingly, although LandscapeDNDC properly captured the main MLED in Hyytiala (temperature) and in Yatir (soil water availability), it failed to reproduce high-temperature and high-vapor pressure limitations of GPP in Yatir during spring and summer. We deduced that the most likely reason for this divergence is an incomplete description of stomatal behavior. In summary, this study validates the MLED approach as a model evaluation tool, and opens up new possibilities for model improvement.
  • Saarinen, Ninni; Kankare, Ville; Pyorala, Jiri; Yrttimaa, Tuomas; Liang, Xinlian; Wulder, Michael A.; Holopainen, Markus; Hyyppa, Juha; Vastaranta, Mikko (2019)
    Large and comprehensive datasets, traditionally based on destructive stem analysis or other labor-intensive approaches, are commonly considered as a necessity in developing stem-volume equations. The aim here was to investigate how a decreasing number of sample trees affects parametrizing an existing taper curve equation and resultant stem-volume estimates. Furthermore, the potential of terrestrial laser scanning (TLS) in producing taper curves was examined. A TLS-based taper curve was derived for 246 Scots pines (Pinus sylvestris L.) from southern Finland to parametrize an existing taper curve equation. To assess sensitivity of the parametrization regarding sample size, the number of Scots pines included in the parametrization varied between full census and 1 Scots pine at a time. Root mean square error of stem-volume estimates remained = 46 Scots pines. Thus, it can be concluded that, with a rather small sample size, a taper curve equation can be re-parametrized for local conditions using point clouds from TLS to produce consistent stem-volume estimates.
  • Cervantes, Sandra; Vuosku, Jaana; Pyhajarvi, Tanja (2021)
    Despite their ecological and economical importance, conifers genomic resources are limited, mainly due to the large size and complexity of their genomes. Additionally, the available genomic resources lack complete structural and functional annotation. Transcriptomic resources have been commonly used to compensate for these deficiencies, though for most conifer species they are limited to a small number of tissues, or capture only a fraction of the genes present in the genome. Here we provide an atlas of gene expression patterns for conifer Pinus sylvestris across five tissues: embryo, megagametophyte, needle, phloem and vegetative bud. We used a wide range of tissues and focused our analyses on the expression profiles of genes at tissue level. We provide comprehensive information of the per-tissue normalized expression level, indication of tissue preferential upregulation and tissue-specificity of expression. We identified a total of 48,001 tissue preferentially upregulated and tissue specifically expressed genes, of which 28% have annotation in the Swiss-Prot database. Even though most of the putative genes identified do not have functional information in current biological databases, the tissue-specific patterns discovered provide valuable information about their potential functions for further studies, as for example in the areas of plant physiology, population genetics and genomics in general. As we provide information on tissue specificity at both diploid and haploid life stages, our data will also contribute to the understanding of evolutionary rates of different tissue types and ploidy levels.
  • Ren, Wenzi; Penttilä, Reijo; Kasanen, Risto; Asiegbu, Fred (2022)
    The microbiome of Heterobasidion-induced wood decay of living trees has been previously studied; however, less is known about the bacteria biota of its perennial fruiting body and the adhering wood tissue. In this study, we investigated the bacteria biota of the Heterobasidion fruiting body and its adhering deadwood. Out of 7,462 operational taxonomic units (OTUs), about 5,918 OTUs were obtained from the fruiting body and 5,469 OTUs were obtained from the associated dead wood. Interestingly, an average of 52.6% of bacteria biota in the fruiting body was shared with the associated dead wood. The overall and unique OTUs had trends of decreasing from decay classes 1 to 3 but increasing in decay class 4. The fruiting body had the highest overall and unique OTUs number in the fourth decay class, whereas wood had the highest OTU in decay class 1. Sphingomonas spp. was significantly higher in the fruiting body, and phylum Firmicutes was more dominant in wood tissue. The FAPROTAX functional structure analysis revealed nutrition, energy, degradation, and plant-pathogen-related functions of the communities. Our results also showed that bacteria communities in both substrates experienced a process of a new community reconstruction through the various decay stages. The process was not synchronic in the two substrates, but the community structures and functions were well-differentiated in the final decay class. The bacteria community was highly dynamic; the microbiota activeness, community stability, and functions changed with the decay process. The third decay class was an important turning point for community restructuring. Host properties, environmental factors, and microbial interactions jointly influenced the final community structure. Bacteria community in the fruiting body attached to the living standing tree was suppressed compared with those associated with dead wood. Bacteria appear to spread from wood tissue of the standing living tree to the fruiting body, but after the tree is killed, bacteria moved from fruiting body to wood. It is most likely that some of the resident endophytic bacteria within the fruiting body are either parasitic, depending on it for their nutrition, or are mutualistic symbionts.