Analysis of EST-SSRs in silver birch (<Emphasis Type="Italic">Betula pendula</Emphasis> Roth.)

Simple sequence repeats (SSRs) defined as sequence repeat units between 1 and 6 bp occur abundantly in both coding and non-coding regions in eukaryotic genomes and these repeats can affect gene expression. In this study, ESTs (expressed sequence tags) of Betula pendula (silver birch) were analyzed for in silico mining of EST-SSRs, protein annotation, open reading frames (ORFs), designing primers, and identifying codon repetitions. In B. pendula, the frequency of ESTs containing SSRs was 7.8 % with an average of 1SSR/4. 78 kb of EST sequences. A total of 188 SSRs was identified by using MISA software and di-nucleotide SSR motifs (65.9 %) were found to be the most abundant type of repeat motif followed by tri- (27.1 %), tetra- (4.8 %), and penta- (2.2 %) motifs. Based on ORF analysis, 175 of 178 sequences were predicted as ORFs and the most frequent SSRs were detected in 5′ UTR (58.43 %), followed by in ORF (31.46 %) and in 3′ UTR (8.43 %). 102 of 178 ESTs were annotated as ribosomal protein, transport protein, membrane protein, carrier protein, binding protein, and transferase protein. For a total of 102 SSRs (57.3 %) with significant matches, a set of 102 primers (100 %) with forward and reverse strands was designed by using Primer3 software. Serine (Ser, 19.6 %) was predominant in putative encoded amino acids and most of amino acids showed nonpolar (35.3 %) nature. Our data provide resources for B. pendula and can be useful for in silico comparative analyses of Betulaceae species, including SSR mining.     

Early growth and development of silver birch (<Emphasis Type="Italic">Betula pendula</Emphasis> Roth.) plantations on abandoned agricultural land

Eight-year-old plantations (11) of silver birch were studied on abandoned agricultural land in Estonia. Trees were planted on uncovered soil and on polyethylene. After eight growing seasons, the height and diameter at breast height of the trees grown on polyethylene were significantly (P < 0.001) larger than corresponding parameters of the trees grown on uncovered soil. The annual height increment of the birches grown on the polyethylene was significantly (P < 0.05) larger during six growing seasons after planting compared to that of the trees grown on uncovered soil. However, annual height increments were not significantly different in the 7th and the 8th growing seasons. The use of polyethylene mulching had a statistically significant effect (P < 0.001) on the height of the beginning of the live crown in 8-year-old plantations. The differences between the values of live crown ratio of the trees grown on polyethylene and the values of live crown ratio of the trees grown on uncovered soil decreased during six growing seasons. However, by the 7th and 8th growing seasons, there was no significant difference (P > 0.05) between the values of the live crown ratio. The height growth of silver birch grown without mulching as well as with mulching was found to be more intensive on Glossic Podzoluvisol, Calcaric Cambisol, Calcaric Luvisol and Dystric Gleysol; however, the height growth was more intensive on mulched soil. The height growth of the birches was modelled on the single-tree and stand levels for five soil types.     

Effects of log storage and drying on birch (<Emphasis Type="Italic">Betula pendula</Emphasis>) wood proanthocyanidin concentration and discoloration

In conventional drying, sawn birch (Betula sp.) timber darkens and reddens from the inside while the layer a few millimetres under the yellowish surface remains light in color. Lack of information concerning the chemical basis of the discoloration hinders the development of a reliable solution for this problem. In this study, the role of soluble proanthocyanidins in discoloration of birch wood was investigated because the polymerization and oxidation of these compounds are known to yield insoluble reddish compounds. Different periods of log storage affected the synthesis of soluble proanthocyanidins during conventional drying. Concentration of proanthocyanidins also correlated with changes in the color of birch wood. Discoloration appeared differently in conventionally dried and vacuum-dried wood, which indicates that the discoloration mechanism in these drying methods may differ chemically, and/or the compounds that take part in discoloration may be different at different drying temperatures.     

Fine-root rhizosphere and morphological adaptations to site conditions in interaction with tree mineral nutrition in young silver birch (<Emphasis Type="Italic">Betula pendula</Emphasis> Roth.) stands

Limited nutrient acquisition from soil is a key process limiting productivity in boreal forest. We investigated short-root morphological adaptations and rhizosphere effect in relation to site conditions in interaction with tree mineral nutrition. We studied seven young (8- to 14-year-old) silver birch (Betula pendula Roth.) stands on abandoned agricultural land in Estonia. Soil pH varied from 3.8 to 7.0, and soil N % from 0.07 to 0.26%. Tree nutrient (NPK) status was expressed by leaf nutrient concentrations. Leaf N correlated negatively with short-root specific length and area. Summed activity (SA) and metabolic diversity of bacteria (by BIOLOG Ecoplate™), bacterial community diversity (by DGGE) and pH_KCl were determined for rhizosphere (R) and bulk soil (S) to reveal the extent of the rhizosphere effect. Bacterial activity in rhizosphere was 1.4–4.7 times higher than in bulk soil. Ratio SA_R/SA_S indicating root support to the rhizosphere bacterial communities decreased with increasing bulk soil pH; however, when bulk soil pH was ≥5, the decrease in SA_R/SA_S was insignificant, i.e. the rhizosphere effect stayed at a stable level. Diversity of bacterial community was 6% higher in bulk soil than in rhizosphere. Rhizosphere acidification occurred in studied stands when bulk soil pH_KCl ≥ 5. Short-root N % correlated positively with SA_R/SA_S. We concluded that tree N-nutritional status was related to short-root morphological parameters but not to studied microbiological characteristics in the soil of young silver birch stands.     

Identification of SSR loci in <Emphasis Type="Italic">Betula luminifera</Emphasis> using birch EST data

Expressed sequence tags(ESTs) are generated from single-pass sequencing of randomly picked cDNA clones and can be used for development of simple sequence repeat(SSR) markers or microsatellites.However,EST databases have been developed for only a small number of species.This paper provides a case study of the utility of freely available birch EST resources for the development of markers necessary for the genetic analysis of Betula luminifera.Based on birch EST data,primers for 80 EST-SSR candidate loci were ...     

Successful <Emphasis Type="Italic">Agrobacterium</Emphasis>-mediated transformation of <Emphasis Type="Italic">Populus tomentosa</Emphasis> with apple <Emphasis Type="Italic">SPDS</Emphasis> gene

The problem of salinized soils has become one of the most serious constraints to agricultural and forest productivity. With the purpose of enhancing salt stress tolerance of Populus tomentosa, we transformed this tree species with spermidine synthase （SPDS） genes derived from an apple by an Agrobacterium-mediated method. Four transgenic clones were confu＇med by PCR and Southern blot analysis. As well, the expression of introduced SPDS genes was analyzed by real-time quantitative PCR.     

Insecticidal properties of <Emphasis Type="Italic">Thymus persicus</Emphasis> essential oil against <Emphasis Type="Italic">Tribolium castaneum</Emphasis> and <Emphasis Type="Italic">Sitophilus oryzae</Emphasis>

Red flour beetle Tribolium castaneum (Herbst) and rice weevil Sitophilus oryzae (L.) are considered to be the major insect pests in storage. Essential oils from aromatic plants are recognized as proper alternatives to fumigants. Thymus persicus (Ronniger ex Rech. f.) is one of these plants that have medicinal properties and is indigenous to Iran. The essential oil was obtained from aerial parts of the plant and analyzed by GC and GC–MS. Carvacrol (44.69%) and thymol (11.05%) were the major constituents of the oil extracted. In this experiment, fumigant toxicity of the essential oil was studied against T. castaneum, S. oryzae at 27 ± 1°C and 60 ± 5% RH in dark condition. The adult insects were exposed to the concentrations of 51.9, 111.1, 207.4 and 370.4 μl/l air to estimate median lethal time (LT₅₀) values. The fumigant toxicity was increased in response to increased essential oil concentrations. The LT₅₀ values at the lowest and the highest concentrations tested were ranged from 28.09 to 13.47 h for T. castaneum, and 3.86 to 2.30 h for S. oryzae. It was found that S. oryzae adults were much more susceptible to the oil than T. castaneum. After 24 h of exposure, the LC₅₀ values (95% fiducial limit) for T. castaneum and S. oryzae were estimated to be 236.9 (186.27–292.81) and 3.34 (2.62–4.28) μl/l air, respectively. These results suggest that T. persicus essential oil merits further study as potential fumigant for the management of these stored-product insects.     

<Emphasis Type="Italic">Bursaphelenchus mucronatus</Emphasis> (Nematoda: Aphelenchoididae) vectored by <Emphasis Type="Italic">Monochamus </Emphasis><Emphasis Type="Italic">urussovi</Emphasis> (Coleoptera: Cerambycidae) in Hokkaido,Japan

Bursaphelenchus mucronatus Mamiya et Enda has been recovered for the first time from adults of the cerambycid beetle, Monochamus urussovi (Fischer), in Hokkaido, Japan. The nematode was also recovered from the inner bark of Picea jezoensis (Siebold et Zuccarini) Carrière and Abies sachalinensis (Fr Schmidt) Masters infested with M. urussovi larvae. PCR–RFLP analysis indicated that B. mucronatus in Hokkaido is the European type.     

Effectiveness of Neem (<Emphasis Type="Italic">Azadirachta indica</Emphasis>) insecticides against Brassica pod midge (<Emphasis Type="Italic">Dasineura brassicae</Emphasis> Winn<Emphasis Type="Italic">.</Emphasis>)

The efficiency of the botanical insecticide (BI) NeemAzal T/S (containing 1% Azadirachtin A), on the basis of azadirachtin applied in a dose of 20 g a.i. ha⁻¹ against Brassica pod midge (Dasineura brassicae), has been monitored for 4 years. The biological efficiency of BI was compared with the efficiency of some synthetic insecticides. It was ascertained that BI was very efficient in decreasing the number of damaged oilseed rape pods (ranging from 56.5 to 85.9% compared to untreated plants) and its efficiency was comparable with synthetic insecticides based on Chloronicotinyl (Thiacloprid) and Neonicotinoid (Acetamiprid). BI’s efficiency was, in some years, even significantly higher compared to pyrethroid (λ-cyhalothrin). The high biological efficiency of azadirachtin that we ascertained was significantly reflected in increasing potential crop yields. The yield increase of azadirachtin ranged between 9.3 and 19.4% compared to the control sample. Azadirachtin showed the highest yield for the whole time of experimentation, and in some years the yield increase was significantly higher compared to some synthetic agents.     

<Emphasis Type="Italic">Quercus suber</Emphasis> forest and <Emphasis Type="Italic">Pinus</Emphasis> plantations show different post-fire resilience in Mediterranean north-western Africa

Key message

In the African rim of the Western Mediterranean Basin, cork oak forests and pine plantations coexist. Under similar fire regimes, cork oak forest is more resilient in terms of habitat structure (canopy, understory, and complexity of vegetation strata) than pine plantation. By contrast, both woodland types show similar resilience in plant species composition. Resilience in habitat structure varies between the two woodland types because of the resprouting and seeding strategies of cork oak and pine species, respectively. These differences can be relevant for the conservation of biodiversity of forested ecosystems in a future scenario of increased fire frequency and scale in the Mediterranean basin.

Context

Wildfires have major impacts on ecosystems globally. In fire-prone regions, plant species have developed adaptive traits (resprouting and seeding) to survive and persist due to long evolutionary coexistence with fire. In the African rim of the Western Mediterranean Basin, cork oak forest and pine plantation are the most frequently burnt woodlands. Both species have different strategies to respond fire: cork oak is a resprouter while pines are mostly seeders.

Aims

We have examined the hypothesis that pine plantations are less resilient in habitat structure (canopy, understory, diversity of vegetation strata) and plant composition than cork oak woodlands.

Methods

The habitat structure and plant species composition were measured in 30 burnt and 30 unburnt 700-m transects at 12 burnt sites from north-western Africa, where the two forest types can coexist. Habitat structure and plant species composition were compared between burnt and unburnt transects from cork oak and pine plantation woodlands with generalized linear mixed models and general linear models.

Results

The results showed significant interaction effect of fire and forest type, since cork oak forest was more resilient to fire than was pine plantation in habitat structure. By contrast, both forest types were resilient to fire in the composition of the plant communities, i.e., plant composition prior to fire did not change afterwards.

Conclusion

The higher structural resilience of cork oak forest compared to pine plantation is related to the resprouting and seeding strategies, respectively, of the dominant tree species. Differences in the responses to fire need to be considered in conservation planning for the maintenance of the Mediterranean biodiversity in a future scenario of changes in fire regime.

     

Bioremediation of CCA-treated wood by brown-rot fungi <Emphasis Type="Italic">Fomitopsis palustris</Emphasis>, <Emphasis Type="Italic">Coniophora puteana</Emphasis>, and <Emphasis Type="Italic">Laetiporus sulphureus</Emphasis>

This study evaluated oxalic acid accumulation and bioremediation of chromated copper arsenate (CCA)-treated wood by three brown-rot fungi Fomitopsis palustris, Coniophora puteana, and Laetiporus sulphureus. The fungi were first cultivated in a fermentation broth to accumulate oxalic acid. Bioremediation of CCA-treated wood was then carried out by leaching of heavy metals with oxalic acid over a 10-day fermentation period. Higher amounts of oxalic acid were produced by F. palustris and L. sulphureus compared with C. puteana. After 10-day fermentation, oxalic acid accumulation reached 4.2 g/l and 3.2 g/l for these fungi, respectively. Fomitopsis palustris and L. sulphureus exposed to CCA-treated sawdust for 10 days showed a decrease in arsenic of 100% and 85%, respectively; however, C. puteana remediation removed only 18% arsenic from CCA-treated sawdust. Likewise, chromium removal in F. palustris and L. sulphureus remediation processes was higher than those for C. puteana. This was attributed to low oxalic acid accumulation. These results suggest that F. palustris and L. sulphureus remediation processes can remove inorganic metal compounds via oxalic acid production by increasing the acidity of the substrate and increasing the solubility of the metals.An erratum to this article can be found at     

Aboveground biomass equations for individual trees of <Emphasis Type="Italic">Cryptomeria japonica</Emphasis>, <Emphasis Type="Italic">Chamaecyparis obtusa</Emphasis> and <Emphasis Type="Italic">Larix kaempferi</Emphasis> in Japan

Generic equations are proposed for stem, branch and foliage biomass of individual trees in even-aged pure stands of Cryptomeria japonica, Chamaecyparis obtusa and Larix kaempferi. Biomass data was collected from a total of 1,016 individual trees from 247 stands throughout Japan, and five regression models were assessed by root mean square error, mean bias, fit index (FI), and AIC. The results show that a power equation using diameter at breast height (dbh) and height is the most suitable for all species and components. This equation is more accurate than the familiar power equation that uses ‘dbh² height’, and it expresses the greater volume of branch and foliage mass of trees with a lower height/diameter ratio. A power equation using dbh is more reasonable for models with dbh as the only independent variable and more accurate than a power equation using ‘dbh² height’ for estimating branch and foliage mass. Estimating error for branch and foliage mass is larger than that for stem mass, but the entire aboveground biomass can be estimated with an error of less than 19%, except in the case of small trees with dbh less than 10 cm.     

Modelling <Emphasis Type="Italic">Phytophthora</Emphasis> disease risk in <Emphasis Type="Italic">Austrocedrus chilensis</Emphasis> forests of Patagonia

Austrocedrus chilensis forests suffer from a disease caused by Phytophthora austrocedrae, which is found often in wet soils. We applied three widely used modelling techniques, with different data requirements, to model disease potential distribution under current environmental conditions: Mahalanobis distance, Maxent and Logistic regression. Each model was built using field data of health condition and landscape layers of environmental conditions (distance to streams, slope, aspect, elevation, mean annual precipitation and soil pH NaF). We compared model predictions by area under the receiver operating characteristic curve and Kappa statistics. A reasonable ability to predict observed disease distribution was found for each of the three modelling techniques. However, Maxent and Logistic regression presented the best predictive performance, with significant differences with respect to the Mahalanobis distance model. Our results suggested that if good absence data are available, Logistic regression should be used in order to better discriminate sites with high risk of disease. On the other hand, if absence data are not available or doubtful, Maxent could be a very good option. The three models predicted that around 50% (49–56%) of the currently asymptomatic forests are located on sites at risk of disease according to abiotic factors. Most of these asymptomatic forests surround the current diseased patches, at distances lower than 100 m from diseased patches. Management considerations and the scope of future studies were discussed in this article.     

Enzymatic saccharification and ethanol production of <Emphasis Type="Italic">Acacia mangium</Emphasis> and <Emphasis Type="Italic">Paraserianthes falcataria</Emphasis> wood,and <Emphasis Type="Italic">Elaeis guineensis</Emphasis> trunk

We examined the saccharification and fermentation of meals from Acacia mangium wood, Paraserianthes falcataria wood, and Elaeis guineensis trunk. The levels of enzymatic hydrolysis of cellulose and ethanol production were highest for P. falcataria wood and lowest for A. mangium wood. Ultrasonication pretreatment of meal further increased the rates of hydrolysis and ethanol production in meal from P. falcataria wood. Through this pretreatment, hemicelluloses (xylan and xyloglucan) and cellulose were released in the meal from P. falcataria wood. Loosening of hemicellulose associations can be expected to make P. falcataria wood more useful for bioethanol production.     

<Emphasis Type="Italic">In vitro</Emphasis> morphogenic response of leaf sheath of <Emphasis Type="Italic">Phyllostachys bambusoides</Emphasis>

Nodal segments from secondary branches of saplings of Phyllostachys bambusoides were inoculated in MS medium to assess the in vitro morphogenic response of leaf sheath through the induction to callogenesis by Picloram(4-amino-3,5,6-trichloropicolinic acid) at different concentrations of carbohydrate under the same conditions with presence or absence of luminosity.In our experiment,secondary explants were kept in MS medium containing 8.0 mg·L-1 of Picloram for the callus formation.Calluses were transferred in MS medium supplemented with sucrose,fructose and glucose(control,2%,4% and 6%).Results show that Picloram induced the callogenesis in leaf sheath.The secondary embryogenesis was formed in yellow-globular callus.The sucrose as carbohydrate source in the absence of light was more efficient to induce rhizogenesis.Glucose was more efficiency in the presence of light.Callogenic induction and further embryogenesis evidenced the competence and determination of leaf sheath cells.     

Fertility variation in endemic populations of Ehrami black pine (<Emphasis Type="Italic">Pinus nigra</Emphasis> Arnold. subsp. <Emphasis Type="Italic">pallasiana</Emphasis> var. <Emphasis Type="Italic">pyramidata</Emphasis>)

Fertility variation and effective number of parents were estimated in the 100 individuals from each of three plantation populations (P1, P2 and P3) of the endangered Pinus nigra. subsp. pallasiana var. pyramidata established in the Isparta–Golcuk district in southern Turkey in 1990. Potential relations between cone yield and growth characters (height, diameter at breast height, diameter at base and crown diameter) were also investigated. Large differences were found among populations and within populations for cone production and growth characters. Mean cone production was eight (ranging from 6.5 in P2 to 9.1 in P1) for the three populations. The 10 most productive individuals for cones produced 32% of the total cones in P1, 39% in P2 and 34% in P3; 21, 16 and 6 individuals, respectively did not produce any cones in the populations. According to the correlation analyses, the relation between cone yield and growth characters changed for the populations, while height, diameter at breast height and crown diameter were positively significantly correlated (r = 0.182, 0.135 and 0.209; p ≤ 0.05) with cone production for the three populations. Fertility variation was 1.81 in total of three populations, ranging from 1.72 in P3 to 3.45 in P1). Effective number of parents was 142 (55.2 of number of parents censused; 29%, P1; 49.8%, P2; 58.3%, P3).     

Cultivation of <Emphasis Type="Italic">Pleurotus eryngii</Emphasis> on umbrella plant (<Emphasis Type="Italic">Cyperus alternifolius</Emphasis>) substrate

Mycelial growth and mushroom yields of three strains of Pleurotus eryngii produced on wheat bran-supplemented umbrella plant (Cyperus alternifolius) substrate were assessed using surface brightness, bromophenol blue color reactions, ergosterol and glucosamine contents, and water potential as indicators of strain performance. Mycelial growth was 31%–46% greater, depending on strain, on the umbrella plant substrate compared with the mushroom industry standard sugi (Cryptomeria japonica) substrate. Mushroom yields on the first flush were 20%–23% higher, depending on strain, on the plastic bottle-contained umbrella plant substrate. However, yields on the second break were lower from the umbrella plant substrate. Because many growers in Japan only harvest one flush, production of P. eryngii on umbrella plant substrate may offer commercial producers an alternative basal ingredient to diminishing supplies of sugi sawdust.Part of this report was presented at the 52nd Annual Meeting of the Japan Wood Research Society, Gifu, April 2002.     

Comparison of postfire mortality in endemic Corsican black pine (<Emphasis Type="Italic">Pinus nigra</Emphasis> ssp. <Emphasis Type="Italic">laricio</Emphasis>) and its direct competitor (<Emphasis Type="Italic">Pinus pinaster</Emphasis>)

• Introduction   

Laricio pine (Pinus nigra J.F. Arn. ssp. laricio (Poiret) Maire var Corsicana Hyl.) is a form of black pine endemic to Corsica, that may now be under threat due to current fire regimes and competition with maritime pine (Pinus pinaster Aiton).