Recent Submissions

  • Journal Article

    Stem and soil nitrous oxide fluxes from rainforest and cacao agroforest on highly weathered soils in the Congo Basin 

    Iddris, Najeeb Al-Amin; Corre, Marife D.; Yemefack, Martin; van Straaten, Oliver; Veldkamp, Edzo
    Biogeosciences 2020; 17(21) p.5377-5397
    Although tree stems act as conduits for greenhouse gases (GHGs) produced in the soil, the magnitudes of tree contributions to total (soil + stem) nitrous oxide (N$_2$O) emissions from tropical rainforests on heavily weathered soils remain unknown. Moreover, soil GHG fluxes are largely understudied in African rainforests, and the effects of land-use change on these gases are identified as an important research gap in the global GHG budget. In this study, we quantified the changes in stem and soil N$_2$O fluxes with forest conversion to cacao agroforestry. Stem and soil N$_2$O fluxes were measured monthly for a year (2017–2018) in four replicate plots per land use at three sites across central and southern Cameroon. Tree stems consistently emitted N$_2$O throughout the measurement period and were positively correlated with soil N$_2$O fluxes. $^{15}$N-isotope tracing from soil mineral N to stem-emitted $^{15}$N$_2$O and correlations between temporal patterns of stem N$_2$O emissions, soil–air N$_2$O concentration, soil N$_2$O emissions and vapour pressure deficit suggest that N$_2$O emitted by the stems originated predominantly from N$_2$O produced in the soil. Forest conversion to extensively managed, mature (>20 years old) cacao agroforestry had no effect on stem and soil N$_2$O fluxes. The annual total N$_2$O emissions were 1.55 ± 0.20 kg N ha$^{−1}$ yr$^{−1}$ from the forest and 1.15 ± 0.10 kg N ha$^{−1}$ yr$^{−1}$ from cacao agroforestry, with tree N$_2$O emissions contributing 11 % to 38 % for forests and 8 % to 15 % for cacao agroforestry. These substantial contributions of tree stems to total N$_2$O emissions highlight the importance of including tree-mediated fluxes in ecosystem GHG budgets. Taking into account that our study sites' biophysical characteristics represented two-thirds of the humid rainforests in the Congo Basin, we estimated a total N$_2$O source strength for this region of 0.18 ± 0.05 Tg N$_2$O-N yr$^{−1}$.
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  • Journal Article

    Herbicide weed control increases nutrient leaching compared to mechanical weeding in a large-scale oil palm plantation 

    Formaglio, Greta; Veldkamp, Edzo; Duan, Xiaohong; Tjoa, Aiyen; Corre, Marife D.
    Biogeosciences 2020; 17(21) p.5243-5262
    Nutrient leaching in intensively managed oil palm plantations can diminish soil fertility and water quality. There is a need to reduce this environmental footprint without sacrificing yield. In a large-scale oil palm plantation in Acrisol soil, we quantified nutrient leaching using a full factorial experiment with two fertilization rates (260 kg N, 50 kg P, and 220 kg K ha$^{−1}$ yr$^{−1}$ as conventional practice and 136 kg N, 17 kg P, and 187 kg K ha$^{−1}$ yr$^{−1}$, equal to harvest export, as reduced management) and two weeding methods (conventional herbicide application and mechanical weeding as reduced management) replicated in four blocks. Over the course of 1 year, we collected monthly soil pore water at 1.5 m depth in three distinct management zones: palm circle, inter-row, and frond-stacked area. Nutrient leaching in the palm circle was low due to low solute concentrations and small drainage fluxes, probably resulting from large plant uptake. In contrast, nitrate and aluminum leaching losses were high in the inter-row due to the high concentrations and large drainage fluxes, possibly resulting from low plant uptake and low pH. In the frond-stacked area, base cation leaching was high, presumably from frond litter decomposition, but N leaching was low. Mechanical weeding reduced leaching losses of base cations compared to the conventional herbicide weeding probably because herbicides decreased ground vegetation and thus reduced soil nutrient retention. Reduced fertilization rates diminished the nitrate leaching losses. Leaching of total nitrogen in the mechanical weeding with reduced fertilization treatment (32±6 kg N ha$^{−1}$ yr$^{−1}$) was less than half of the conventional management (74±20 kg N ha$^{−1}$ yr$^{−1}$), whereas yields were not affected by these treatments. Our findings suggest that mechanical weeding and reduced fertilization should be included in the program by the Indonesian Ministry of Agriculture for precision farming (e.g., variable rates with plantation age), particularly for large-scale oil palm plantations. We further suggest including mechanical weeding and reduced fertilization in science-based policy recommendations, such as those endorsed by the Roundtable for Sustainable Palm Oil association.
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  • Journal Article

    Evapotranspiration over agroforestry sites in Germany 

    Markwitz, Christian; Knohl, Alexander; Siebicke, Lukas
    Biogeosciences 2020; 17(20) p.5183-5208
    In the past few years, the interest in growing crops and trees for bioenergy production has increased. One agricultural practice is the mixed cultivation of fast-growing trees and annual crops or perennial grasslands on the same piece of land, which is referred to as one type of agroforestry (AF). The inclusion of tree strips into the agricultural landscape has been shown – on the one hand – to lead to reduced wind speeds and higher carbon sequestration above ground and in the soil. On the other hand, concerns have been raised about increased water losses to the atmosphere via evapotranspiration (ET). Therefore, we hypothesise that short rotation coppice agroforestry systems have higher water losses to the atmosphere via ET compared to monoculture (MC) agriculture without trees. In order to test the hypothesis, the main objective was to measure the actual evapotranspiration of five AF systems in Germany and compare those to five monoculture systems in the close vicinity of the AF systems. We measured actual ET at five AF sites in direct comparison to five monoculture sites in northern Germany in 2016 and 2017. We used an eddy covariance energy balance (ECEB) set-up and a low-cost eddy covariance (EC-LC) set-up to measure actual ET over each AF and each MC system. We conducted direct eddy covariance (EC) measurement campaigns with approximately 4 weeks' duration for method validation. Results from the short-term measurement campaigns showed a high agreement between ETEC-LC and ETEC, indicated by slopes of a linear regression analysis between 0.86 and 1.3 ($R^2$ between 0.7 and 0.94) across sites. Root mean square errors of $LE_{EC-LC}$ vs. $LE_{EC}$ (where LE is the latent heat flux) were half as small as $LE_{ECEB}$ vs. $LE_{EC}$, indicating a superior agreement of the EC-LC set-up with the EC set-up compared to the ECEB set-up. With respect to the annual sums of ET over AF and MC, we observed small differences between the two land uses. We interpret this as being an effect of compensating the small-scale differences in ET next to and in between the tree strips for ET measurements on the system scale. Most likely, the differences in ET rates next to and in between the tree strips are of the same order of magnitude, but of the opposite sign, and compensate each other throughout the year. Differences between annual sums of ET from the two methods were of the same order of magnitude as differences between the two land uses. Compared to the effect of land use and different methods on ET, we found larger mean evapotranspiration indices (∑ET/∑P ) across sites for a drier than normal year (2016) compared to a wet year (2017). This indicates that we were able to detect differences in ET due to different ambient conditions with the applied methods, rather than the potentially small effect of AF on ET. We conclude that agroforestry has not resulted in an increased water loss to the atmosphere, indicating that agroforestry in Germany can be a land-use alternative to monoculture agriculture without trees.
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  • Journal Article

    In-depth studies on the modifying effects of natural ageing on the chemical structure of European spruce (Picea abies) and silver fir (Abies alba) woods 

    Ghavidel, Amir; Scheglov, Anna; Karius, Volker; Mai, Carsten; Tarmian, Asghar; Vioel, Wolfgang; Vasilache, Viorica; Sandu, Ion
    Journal of Wood Science 2020; 66(1) p.1-11: Art. 77
    Abstract Wood is usually stable under relatively dry conditions but may still undergo slow deterioration. The type of deterioration and how these processes affect the wood are important questions that need consideration if old wooden structures are to be studied and properly preserved. The aim of this paper is to establish the main structural and morphological differences between new and naturally aged European spruce (~ 150–200 years) and silver fir wood (~ 150 years). Naturally aged European spruce (a) was sourced from an outdoor part of a building constructed in the seventeenth century and naturally aged European spruce (b) were obtained from a furniture item located in a historical building from the eighteenth century. The principal age-induced changes in fir are the degradation of C–O and C=O groups in hemicellulose, according to the FTIR analysis. Degradation of cellulose and hemicelluloses was observed for spruce, with a greater effect seen in the indoor aged sample. X-ray photoelectron spectroscopy (XPS) showed that after aging C–C/C–H peaks were smaller in the spruce and fir samples, while C–O and O–C–O peaks were larger. The crystallinity index (CrI) obtained by X-ray diffraction showed that due to weathering the CrI of naturally aged spruce (a) increased compared to the new wood. The CrI of the aged spruce (b) and aged fir was lower than in the new woods. The ratios for the spruce sample, which aged indoors, were higher than those for the one aged outdoors. According to the observations made in this study, hemicellulose and cellulose are easily degraded under environmental conditions.
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  • Journal Article

    Surface Activation of Polylactic Acid-Based Wood-Plastic Composite by Atmospheric Pressure Plasma Treatment 

    Sauerbier, Philipp; Köhler, Robert; Renner, Gerrit; Militz, Holger
    Materials 2020; 13(20) p.1-13: Art. 4673
    Wood-plastic composite (WPC) based on a polylactic acid (PLA) matrix is a promising material since it is biobased, degradable, sustainable, and 3D printable. However, due to its coloring, visible layers after 3D-printing, and small build volumes of these printers, a coating or gluing of parts might be required. This study investigates the influence of a dielectric barrier discharge (DBD) plasma treatment of PLA-based WPC to activate the surface and improve, e.g., coating capabilities. X-ray photoelectron spectroscopy (XPS) measurements showed the oxidation of the surface due to the formation of carbonyl and carboxyl groups. Laser scanning microscopy revealed a surface roughening after the treatment. Contact angles of water and diiodomethane decreased significantly after the plasma treatment and the consecutively calculated surface free energy increased. Finally, two practical adhesion tests revealed an improvement of the applied acrylic dispersion coating’s adhesion to the WPC surface: The assigned cross-cut class improved, and the pull-off strength increased from 1.4 to 2.3 N/mm$^2$.
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  • Journal Article

    Legacy Effects Overshadow Tree Diversity Effects on Soil Fungal Communities in Oil Palm-Enrichment Plantations 

    Ballauff, Johannes; Zemp, Delphine Clara; Schneider, Dominik; Irawan, Bambang; Daniel, Rolf; Polle, Andrea
    Microorganisms 2020; 8(10) p.1-17: Art. 1577
    Financially profitable large-scale cultivation of oil palm monocultures in previously diverse tropical rain forest areas constitutes a major ecological crisis today. Not only is a large proportion of the aboveground diversity lost, but the belowground soil microbiome, which is important for the sustainability of soil function, is massively altered. Intermixing oil palms with native tree species promotes vegetation biodiversity and stand structural complexity in plantations, but the impact on soil fungi remains unknown. Here, we analyzed the diversity and community composition of soil fungi three years after tree diversity enrichment in an oil palm plantation in Sumatra (Indonesia). We tested the effects of tree diversity, stand structural complexity indices, and soil abiotic conditions on the diversity and community composition of soil fungi. We hypothesized that the enrichment experiment alters the taxonomic and functional community composition, promoting soil fungal diversity. Fungal community composition was affected by soil abiotic conditions (pH, N, and P), but not by tree diversity and stand structural complexity indices. These results suggest that intensive land use and abiotic filters are a legacy to fungal communities, overshadowing the structuring effects of the vegetation, at least in the initial years after enrichment plantings.
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  • Journal Article

    Implications of Development Cooperation and State Bureaucracy on Climate Change Adaptation Policy in Bangladesh 

    Rahman, Md Saifur; Sarker, Pradip Kumar; Hirono, Ryokichi; Giessen, Lukas
    Climate 2020; 8(10) p.1-24: Art. 118
    Policy action is visible in national and international climate governance. However, policy-making and its implementation often fail to generate the desired outcomes that aim to adapt to the adverse impact of climate change in a developing nation, such as Bangladesh—a country highly vulnerable to the impact of climate change. Against this backdrop, the study aims to analyze the implication of development cooperation and bureaucratic politics on the policy-making and implementation of climate change adaptation policy in Bangladesh. In doing so, the research uses national and international climate adaptation funds and the existing state administrative framework of the climate adaptation regime. Methodologically, it follows a mixed qualitative–quantitative research approach. The study discusses the following key findings: (1) the general cross-sectoral nature and thrusts of domestic and external climate adaptation funding; (2) how Bangladesh technical departments, such as that for water management, have reacted successfully to ensure the utilization of the funds is for implementing adaptation policy; (3) simultaneously, how Bangladesh bureaucracy, made of the elite, together with politics, have maintained their traditional values, practices, and structures in responding to the administrative requirements of climate adaptation funders, especially bilateral and multilateral development agencies, and (4) what changes should be brought to the bureaucratic cadre and added to the administrative setup in Bangladesh to provide a better overall impact of the adaptation policy and funding.
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  • Journal Article

    Improving precision of field inventory estimation of aboveground biomass through an alternative view on plot biomass 

    Kleinn, Christoph; Magnussen, Steen; Nölke, Nils; Magdon, Paul; Álvarez-González, Juan G; Fehrmann, Lutz; Pérez-Cruzado, César
    Forest Ecosystems. 2020 Oct 23;7(1):57
    Abstract We contrast a new continuous approach (CA) for estimating plot-level above-ground biomass (AGB) in forest inventories with the current approach of estimating AGB exclusively from the tree-level AGB predicted for each tree in a plot, henceforth called DA (discrete approach). With the CA, the AGB in a forest is modelled as a continuous surface and the AGB estimate for a fixed-area plot is computed as the integral of the AGB surface taken over the plot area. Hence with the CA, the portion of the biomass of in-plot trees that extends across the plot perimeter is ignored while the biomass from trees outside of the plot reaching inside the plot is added. We use a sampling simulation with data from a fully mapped two hectare area to illustrate that important differences in plot-level AGB estimates can emerge. Ideally CA-based estimates of mean AGB should be less variable than those derived from the DA. If realized, this difference translates to a higher precision from field sampling, or a lower required sample size. In our case study with a target precision of 5% (i.e. relative standard error of the estimated mean AGB), the CA required a 27.1% lower sample size for small plots of 100 m2 and a 10.4% lower sample size for larger plots of 1700 m2. We examined sampling induced errors only and did not yet consider model errors. We discuss practical issues in implementing the CA in field inventories and the potential in applications that model biomass with remote sensing data. The CA is a variation on a plot design for above-ground forest biomass; as such it can be applied in combination with any forest inventory sampling design.
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  • Journal Article

    Revisiting wind speed measurements using actively heated fiber optics: a wind tunnel study 

    van Ramshorst, Justus G. V.; Coenders-Gerrits, Miriam; Schilperoort, Bart; van de Wiel, Bas J. H.; Izett, Jonathan G.; Selker, John S.; Higgins, Chad W.; Savenije, Hubert H. G.; van de Giesen, Nick C.
    Atmospheric Measurement Techniques 2020; 13(10) p.5423-5439
    Near-surface wind speed is typically only measured by point observations. The actively heated fiber-optic (AHFO) technique, however, has the potential to provide high-resolution distributed observations of wind speeds, allowing for better spatial characterization of fine-scale processes. Before AHFO can be widely used, its performance needs to be tested in a range of settings. In this work, experimental results on this novel observational wind-probing technique are presented. We utilized a controlled wind tunnel setup to assess both the accuracy and the precision of AHFO under a range of operational conditions (wind speed, angles of attack and temperature difference). The technique allows for wind speed characterization with a spatial resolution of 0.3 m on a 1 s timescale. The flow in the wind tunnel was varied in a controlled manner such that the mean wind ranged between 1 and 17 m s$^{−1}$. The AHFO measurements are compared to sonic anemometer measurements and show a high coefficient of determination (0.92–0.96) for all individual angles, after correcting the AHFO measurements for the angle of attack. Both the precision and accuracy of the AHFO measurements were also greater than 95 % for all conditions. We conclude that AHFO has the potential to measure wind speed, and we present a method to help choose the heating settings of AHFO. AHFO allows for the characterization of spatially varying fields of mean wind. In the future, the technique could potentially be combined with conventional distributed temperature sensing (DTS) for sensible heat flux estimation in micrometeorological and hydrological applications.
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  • Journal Article

    Selection markers for transformation of the sequenced reference monokaryon Okayama 7/#130 and homokaryon AmutBmut of Coprinopsis cinerea 

    Dörnte, Bastian; Peng, Can; Fang, Zemin; Kamran, Aysha; Yulvizar, Cut; Kües, Ursula
    Fungal Biology and Biotechnology. 2020 Oct 12;7(1):15
    Abstract Background Two reference strains have been sequenced from the mushroom Coprinopsis cinerea, monokaryon Okayama 7/#130 (OK130) and the self-compatible homokaryon AmutBmut. An adenine-auxotrophy in OK130 (ade8-1) and a para-aminobenzoic acid (PABA)-auxotrophy in AmutBmut (pab1-1) offer selection markers for transformations. Of these two strains, homokaryon AmutBmut had been transformed before to PABA-prototrophy and with the bacterial hygromycin resistance marker hph, respectively. Results Gene ade8 encodes a bifunctional enzyme with an N-terminal glycinamide ribonucleotide synthase (GARS) and a C-terminal aminoimidazole ribonucleotide synthase (AIRS) domain required for steps 2 and 5 in the de novo biosynthesis of purines, respectively. In OK130, a missense mutation in ade8-1 rendered residue N231 for ribose recognition by the A loop of the GARS domain into D231. The new ade8+ vector pCcAde8 complements the auxotrophy of OK130 in transformations. Transformation rates with pCcAde8 in single-vector and co-transformations with ade8+-selection were similarly high, unlike for trp1+ plasmids which exhibit suicidal feedback-effects in single-vector transformations with complementation of tryptophan synthase defects. As various other plasmids, unselected pCcAde8 helped in co-transformations of trp1 strains with a trp1+-selection vector to overcome suicidal effects by transferred trp1+. Co-transformation rates of pCcAde8 in OK130 under adenine selection with nuclear integration of unselected DNA were as high as 80% of clones. Co-transformation rates of expressed genes reached 26–42% for various laccase genes and up to 67% with lcc9 silencing vectors. The bacterial gene hph can also be used as another, albeit less efficient, selection marker for OK130 transformants, but with similarly high co-transformation rates. We further show that the pab1-1 defect in AmutBmut is due to a missense mutation which changed the conserved PIKGT motif for chorismate binding in the C-terminal PabB domain to PIEGT in the mutated 4-amino-4-deoxychorismate synthase. Conclusions ade8-1 and pab1-1 auxotrophic defects in C. cinerea reference strains OK130 and AmutBmut for complementation in transformation are described. pCcAde8 is a new transformation vector useful for selection in single and co-transformations of the sequenced monokaryon OK130 which was transformed for the first time. The bacterial gene hph can also be used as an additional selection marker in OK130, making in combination with ade8+ successive rounds of transformation possible.
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  • Journal Article

    Chloroplast Haplotypes of Northern Red Oak (Quercus rubra L.) Stands in Germany Suggest Their Origin from Northeastern Canada 

    Götz, Jeremias; Krutovsky, Konstantin V.; Leinemann, Ludger; Müller, Markus; Rajora, Om P.; Gailing, Oliver
    Forests 2020; 11(9) p.1-15: Art. 1025
    Northern red oak (Quercus rubra L.) is one of the most important foreign tree species in Germany and considered as a major candidate for prospective sustainable forestry in the face of climate change. Therefore, Q. rubra was subject of many previous studies on its growth traits and attempts to infer the origin of various populations of this species using nuclear and chloroplast DNA markers. However, the exact geographic origin of German red oak stands has still not been identified. Its native range widely extends over North America, and the species can tolerate a broad range of environmental conditions. We genotyped individual trees in 85 populations distributed in Germany and North America using five chloroplast microsatellite and three novel chloroplast CAPS markers, resulting in the identification of 29 haplotypes. The new marker set enabled the identification of several new red oak haplotypes with restricted geographic origin. Some very rare haplotypes helped us narrow down the origin of Q. rubra stands in Germany, especially some stands from North Rhine-Westphalia, to the northern part of the species’ natural distribution area including the Peninsula of Nova Scotia, where the most similar haplotype composition was observed, compared to distinct German stands.
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  • Journal Article

    Siberian larch (Larix sibirica Ledeb.) mitochondrial genome assembled using both short and long nucleotide sequence reads is currently the largest known mitogenome 

    Putintseva, Yuliya A; Bondar, Eugeniya I; Simonov, Evgeniy P; Sharov, Vadim V; Oreshkova, Natalya V; Kuzmin, Dmitry A; Konstantinov, Yuri M; Shmakov, Vladimir N; Belkov, Vadim I; Sadovsky, Michael G; et al.
    Keech, OlivierKrutovsky, Konstantin V
    BMC Genomics. 2020 Sep 23;21(1):654
    Abstract Background Plant mitochondrial genomes (mitogenomes) can be structurally complex while their size can vary from ~ 222 Kbp in Brassica napus to 11.3 Mbp in Silene conica. To date, in comparison with the number of plant species, only a few plant mitogenomes have been sequenced and released, particularly for conifers (the Pinaceae family). Conifers cover an ancient group of land plants that includes about 600 species, and which are of great ecological and economical value. Among them, Siberian larch (Larix sibirica Ledeb.) represents one of the keystone species in Siberian boreal forests. Yet, despite its importance for evolutionary and population studies, the mitogenome of Siberian larch has not yet been assembled and studied. Results Two sources of DNA sequences were used to search for mitochondrial DNA (mtDNA) sequences: mtDNA enriched samples and nucleotide reads generated in the de novo whole genome sequencing project, respectively. The assembly of the Siberian larch mitogenome contained nine contigs, with the shortest and the largest contigs being 24,767 bp and 4,008,762 bp, respectively. The total size of the genome was estimated at 11.7 Mbp. In total, 40 protein-coding, 34 tRNA, and 3 rRNA genes and numerous repetitive elements (REs) were annotated in this mitogenome. In total, 864 C-to-U RNA editing sites were found for 38 out of 40 protein-coding genes. The immense size of this genome, currently the largest reported, can be partly explained by variable numbers of mobile genetic elements, and introns, but unlikely by plasmid-related sequences. We found few plasmid-like insertions representing only 0.11% of the entire Siberian larch mitogenome. Conclusions Our study showed that the size of the Siberian larch mitogenome is much larger than in other so far studied Gymnosperms, and in the same range as for the annual flowering plant Silene conica (11.3 Mbp). Similar to other species, the Siberian larch mitogenome contains relatively few genes, and despite its huge size, the repeated and low complexity regions cover only 14.46% of the mitogenome sequence.
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  • Journal Article

    A new dataset on plant occurrences on smallislands, including species abundances andfunctional traits across different spatial scales 

    Schrader, Julian; Moeljono, Soetjipto; Tambing, Junus; Sattler, Cornelia; Kreft, Holger
    Biodiversity Data Journal 2020; 8 p.1-16: Art. e55275
    Background We introduce a new dataset of woody plants on 60 small tropical islands located in the Raja Ampat archipelago in Indonesia. The dataset includes incidence, abundance and functional trait data for 57 species. All islands were sampled using a standardised transect and plot design providing detailed information on plant occurrences at different spatial scales ranging from the local (plot and transect scale) to the island scale. In addition, the dataset includes information on key plant functional traits linked to species dispersal, resource acquisition and competitive strategies. The dataset can be used to address ecological questions connected to the species-area relationship and community assembly processes on small islands and in isolated habitats. New information The dataset yields detailed information on plant community structure and links incidence, abundance and functional trait data at different spatial scales. Furthermore, this is the first plant-island dataset for the Raja Ampat archipelago, a remote and poorly studied region, and provides important new information on species occurrences.
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  • Journal Article

    De novo sequencing, assembly and functional annotation of Armillaria borealis genome 

    Akulova, Vasilina S; Sharov, Vadim V; Aksyonova, Anastasiya I; Putintseva, Yuliya A; Oreshkova, Natalya V; Feranchuk, Sergey I; Kuzmin, Dmitry A; Pavlov, Igor N; Litovka, Yulia A; Krutovsky, Konstantin V
    BMC Genomics. 2020 Sep 10;21(Suppl 7):534
    Abstract Background Massive forest decline has been observed almost everywhere as a result of negative anthropogenic and climatic effects, which can interact with pests, fungi and other phytopathogens and aggravate their effects. Climatic changes can weaken trees and make fungi, such as Armillaria more destructive. Armillaria borealis (Marxm. & Korhonen) is a fungus from the Physalacriaceae family (Basidiomycota) widely distributed in Eurasia, including Siberia and the Far East. Species from this genus cause the root white rot disease that weakens and often kills woody plants. However, little is known about ecological behavior and genetics of A. borealis. According to field research data, A. borealis is less pathogenic than A. ostoyae, and its aggressive behavior is quite rare. Mainly A. borealis behaves as a secondary pathogen killing trees already weakened by other factors. However, changing environment might cause unpredictable effects in fungus behavior. Results The de novo genome assembly and annotation were performed for the A. borealis species for the first time and presented in this study. The A. borealis genome assembly contained ~ 68 Mbp and was comparable with ~ 60 and ~ 79.5 Mbp for the A. ostoyae and A. mellea genomes, respectively. The N50 for contigs equaled 50,544 bp. Functional annotation analysis revealed 21,969 protein coding genes and provided data for further comparative analysis. Repetitive sequences were also identified. The main focus for further study and comparative analysis will be on the enzymes and regulatory factors associated with pathogenicity. Conclusions Pathogenic fungi such as Armillaria are currently one of the main problems in forest conservation. A comprehensive study of these species and their pathogenicity is of great importance and needs good genomic resources. The assembled genome of A. borealis presented in this study is of sufficiently good quality for further detailed comparative study on the composition of enzymes in other Armillaria species. There is also a fundamental problem with the identification and classification of species of the Armillaria genus, where the study of repetitive sequences in the genomes of basidiomycetes and their comparative analysis will help us identify more accurately taxonomy of these species and reveal their evolutionary relationships.
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  • Journal Article

    Plasma Treatment of Polypropylene-Based Wood–Plastic Composites (WPC): Influences of Working Gas 

    Sauerbier, Philipp; Köhler, Robert; Renner, Gerrit; Militz, Holger
    Polymers 2020; 12(9) p.1-15: Art. 1933
    In this study, a polypropylene (PP)-based wood–plastic composite with maleic anhydride-grafted polypropylene (MAPP) as a coupling agent and a wood content of 60% was extruded and specimens were injection molded. The samples were plasma treated utilizing a dielectric barrier discharge (DBD) setup with three different working gases: Ar/O$_2$ (90%/10%), Ar/N$_2$ (90%/10%), and synthetic air. This process aims to improve the coating and gluing properties of the otherwise challenging apolar surface of PP based wood–plastic composites (WPC). Chemical analysis with X-ray photoelectron spectroscopy (XPS) and Fourier-transform infrared spectroscopy (FTIR) showed the formation of oxygen-based functional groups on the surface, independently from the working gas used for the treatment. Laser scanning microscopy (LSM) examined the surface roughness and revealed that the two argon-containing working gases roughened the surface more than synthetic air. However, the contact angle for water was reduced significantly after treatment, revealing measurement artifacts for water and diiodomethane due to the severe changes in surface morphology. The adhesion of acrylic dispersion coating was significantly increased, resulting in a pull-off strength of approximately 4 N/mm$^2$, and cross-cut tests assigned the best adhesion class (0), on a scale from 0 to 5, after plasma treatment with any working gas.
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  • Journal Article

    Plant species richness increases with light availability, but not variability, in temperate forests understorey 

    Dormann, Carsten F; Bagnara, Maurizio; Boch, Steffen; Hinderling, Judith; Janeiro-Otero, Andrea; Schäfer, Deborah; Schall, Peter; Hartig, Florian
    BMC Ecology. 2020 Jul 29;20(1):43
    Abstract Background Temperate forest understorey vegetation poses an excellent study system to investigate whether increases in resource availability lead to an increase in plant species richness. Most sunlight is absorbed by the species-poor tree canopy, making the much more species-rich understorey species inhabit a severely resource-limited habitat. Additionally, the heterogeneity of light availability, resulting from management-moderated tree composition and age structure, may contribute to species coexistence. One would therefore expect that the diversity in the herb layer correlates positively with either the overall light availability, or the light heterogeneity, depending on whether resource availability or heterogeneity are more important drivers of diversity. To test this idea, we assessed variability of light conditions in 75 forest plots across three ecoregions with four different methods. Results We correlated these data with vegetation relevés and found light availability to be strongly positively correlated with understorey plant species richness, as well as with understorey cover. Light variability (assessed with two approaches) within plots was positively correlated with transmittance, but did not improve the relationship further, suggesting that the main driver of species richness in this system is the overall resource availability. Two of the three beech-dominated regions exhibited near-identical effects of light transmittance, while the third, featuring pine alongside beech and thus with the longest gradient of transmittance and lowest species richness, displayed a weaker light response. Conclusions While site conditions are certainly responsible for the trees selected by foresters, for the resulting forest structure, and for the differences in plant species pools, our results suggest that light transmittance is a strong mediating factor of understorey plant species richness.
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  • Journal Article

    Mating System in a Native Norway Spruce (Picea abies [L.] KARST.) Stand-Relatedness and Effective Pollen Population Size Show an Association with the Germination Percentage of Single Tree Progenies 

    Caré, Oliver; Gailing, Oliver; Müller, Markus; Krutovsky, Konstantin V.; Leinemann, Ludger
    Diversity 2020; 12(7) p.1-18: Art. 266
    Norway spruce differs little in neutral genetic markers among populations and provenances often reported, but in terms of putative adaptive traits and their candidate genes, some clear differences have been observed. This has previously been shown for crown morphotypes. Stands with mostly narrow crown shapes are adapted to high elevation conditions, but these stands are scattered, and the forest area is often occupied by planted stands with predominantly broad crowned morphotypes. This raises questions on whether this differentiation can remain despite gene flow, and on the level of gene flow between natural and planted stands growing in close neighbourhood. The locally adapted stands are a valuable seed source, the progeny of which is expected to have high genetic quality and germination ability. The presented case study is useful for spruce plantation by demonstrating evaluation of these expectations. Immigrant pollen and seeds from planted trees could be maladaptive and may alter the genetic composition of the progeny. This motivated us to study single tree progenies in a locally adapted stand with narrow crowned trees in a partial mast year at nuclear genomic simple sequence repeat (SSR) markers. Spruce is a typical open-pollinated conifer tree species with very low selfing rates, which were also observed in our study (s = 0.3–2.1%) and could be explained by efficient cross-pollination and postzygotic early embryo abortion, common in conifers. The estimated high amount of immigrant pollen found in the pooled seed lot (70.2–91.5%) is likely to influence the genetic composition of the seedlings. Notably, for individual mother trees located in the centre of the stand, up to 50% of the pollen was characterised as local. Seeds from these trees are therefore considered to retain most of the adaptive variance of the stand. Germination percentage varied greatly between half-sib families (3.6–61.9%) and was negatively correlated with relatedness and positively with effective pollen population size of the respective families. As pollen mostly originated from outside the stand and no family structures in the stand itself were found, germination differences can likely be explained by diversity differences in the individual pollen cloud.
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  • Journal Article

    Towards Tree Green Crown Volume: A Methodological Approach Using Terrestrial Laser Scanning 

    Zhu, Zihui; Kleinn, Christoph; Nölke, Nils
    Remote Sensing 2020; 12(11) p.1-12: Art. 1841
    Crown volume is a tree attribute relevant in a number of contexts, including photosynthesis and matter production, storm resistance, shadowing of lower layers, habitat for various taxa. While commonly the total crown volume is being determined, for example by wrapping a convex hull around the crown, we present here a methodological approach towards assessing the tree green crown volume (TGCVol), the crown volume with a high density of foliage, which we derive by terrestrial laser scanning in a case study of solitary urban trees. Using the RGB information, we removed the hits on stem and branches within the tree crown and used the remaining leaf hits to determine TGCVol from k-means clustering and convex hulls for the resulting green 3D clusters. We derived a tree green crown volume index (TGCVI) relating the green crown volume to the total crown volume. This TGCVI is a measure of how much a crown is “filled with green” and scale-dependent (a function of specifications of the k-means clustering). Our study is a step towards a standardized assessment of tree green crown volume. We do also address a number of remaining methodological challenges.
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  • Journal Article

    De novo transcriptome assembly of cold stressed clones of the hexaploid Sequoia sempervirens (D. Don) Endl. 

    Breidenbach, Natalie; Sharov, Vadim V.; Gailing, Oliver; Krutovsky, Konstantin V.
    Scientific Data 2020; 7(1) p.1-8: Art. 239
    Coast redwood is a very important endemic conifer timber species in Southern Oregon and Northern California in the USA. Due to its good wood properties and fast growth rate it can be considered as a prospective timber species also in other countries with similar or changing toward similar climatic conditions due to global climate warming, such as Germany. In general, it is frost sensitive and suffers from freezing temperatures. To study genetic mechanisms of frost resistance in this species and to select the most frost tolerant trees we tested 17 clones in climate control chamber experiments and generated two de novo assemblies of the coast redwood transcriptome from a pooled RNA sample using Trinity and CLC Genomic Workbench software, respectively. The hexaploid nature of the coast redwood genome makes it very challenging to successfully assemble and annotate the coast redwood transcriptome. The de novo transcriptome assembly generated by Trinity and CLC considering only reads with a minimum length of 180 bp and contigs no less than 200 bp long resulted in 634,772 and 788,464 unigenes (unique contigs), respectively.
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  • Journal Article

    Initial Survival and Development of Planted European Beech (Fagus sylvatica L.) and Small-Leaved Lime (Tilia cordata Mill.) Seedlings Competing with Black Cherry (Prunus serotina Ehrh.) 

    Hasstedt, Sarah L.; Annighöfer, Peter
    Plants 2020; 9(6) p.1-17: Art. 677
    Black cherry (Prunus serotina Ehrh.) is considered one of the most invasive tree species in central Europe and causes problems for both nature conservation and silviculture. Besides mechanical control treatments, a suggested control method to prevent its ongoing spread is to underplant shade-tolerant native tree species. Therefore, we combined two mechanical treatments, with underplanting of European beech (Fagus sylvatica L.) or small-leaved lime (Tilia cordata Mill.) on fenced and unfenced plots. After the first growing season, survival rates were evaluated, and selected seedlings were destructively harvested to analyze their growth performance and leaf morphology in association with the different light regimes resulting from mechanical treatments Survival rates for both seedlings were very high (>95%). Survival rates were higher on fenced plots than on unfenced plots, most likely as result of browsing. The mortality of F. sylvatica decreased with increasing light availability on fenced plots. The mortality of T. cordata did not change along the light gradient. After one vegetation period no differences with respect to biomass allocation could be detected along the light gradient. However, the specific leaf areas of both species responded similarly, decreasing with increasing light availability. In summary, both species were able to establish and survive in the dense P. serotina understory and might have the potential to outcompete the invasive alien species in the long run.
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