A high resolution green area index for modelling the seasonal dynamics of CO<Subscript>2</Subscript> exchange in peatland vascular plant communities

We studied vegetation dynamics at peatlands, differing in their climate, land use management history and vegetation community in Ireland and Finland over a two-year period. Our aim was to develop a species-specific method to be used to (1) describe the seasonal dynamics of green (photosynthetic) area (GA) of the vegetation and (2) incorporate these changes into CO₂ exchange models. The extent of temporal and spatial variation between and within communities indicated the need for a two-step calculation approach for each community. Firstly, at biweekly to monthly intervals, GA of all species within a range of vascular plant communities was estimated by non-destructive field measurements. Gaussian or log-normal models were fitted to describe the seasonal dynamics of each species. Secondly, an estimate of community vascular green area (VGA) was obtained by summing the modelled daily GA of all species within the community. The highest values of VGA (2.1–6.0 m² m⁻²) occurred within the reed communities at the rewetted cutaway peatland in Ireland and the lowest at the ombrotrophic lawn communities in Finland (0.5–1.0 m² m⁻²). The relationship between light saturated gross photosynthesis (P _G) and VGA was either linear or hyperbolic depending on the degree of self-shading that occurred within each community. The addition of the VGA term into P _G models improved the explaining power of the model by 57.6, 24.5 and 23% within the Typha latifolia, Phalaris arundinacea and Eriophorum angustifolium/Carex rostrata communities, respectively. VGA proved useful in recording the seasonal development of a wide range of peatland vascular plant communities over geographically and climatically different regions.     

Epirrita autumnata induced VOC emission of silver birch differ from emission induced by leaf fungal pathogen

The production of volatile organic compounds (VOCs) through the activation of different signal-transduction pathways may be induced in various biotic and abiotic stress situations having importance e.g. in insect and disease resistance. We compared the emission of VOCs emitted from silver birch Betula pendula Roth (clones 4 and 80) twigs damaged either by larvae of Epirrita autumnata, or infected with pathogenic leaf spot causing fungus Marssonina betulae. We also analysed whether local herbivore damage can systemically induce the release of VOCs from the undamaged top of same sapling. The emissions of methylsalicylate (MeSA), (Z)-ocimene, (E)-β-ocimene, (E)-4,8-dimethyl-1,3,7-nonatriene (DMNT) and linalool were induced from the twigs after 72 h feeding damage by E. autumnata larvae. However, 48 h feeding damage did not induce rapid systemic release of VOCs from undamaged top leaves of the same twigs. Pathogen-infected birch twigs had significantly greater emission of (Z)-ocimene and (E)-β-ocimene than intact control twigs. The emission of DMNT was not significantly induced and MeSA was not found at all after pathogen infection, both being significantly different from herbivore damaged twigs. According to our results leaf fungal pathogen induces VOC emission profile differs from that of arthropod herbivore-damaged leaves, suggesting that birch is able to transmit parasite-specific information via VOC emissions to conspecifics and natural enemies of herbivores. Handling editor: Yvan Rahbé     

Increased Production of Xylanase by Expression of a Truncated Version of the xyn11A Gene from Nonomuraea flexuosa in Trichoderma reesei

We have previously shown that the Nonomuraea flexuosa Xyn11A polypeptides devoid of the carbohydrate binding module (CBM) have better thermostability than the full-length xylanase and are effective in bleaching of pulp. To produce an enzyme preparation useful for industrial applications requiring high temperature, the region encoding the CBM was deleted from the N. flexuosa xyn11A gene and the truncated gene was expressed in Trichoderma reesei. The xylanase sequence was fused to the T. reesei mannanase I (Man5A) signal sequence or 3′ to a T. reesei carrier polypeptide, either the Man5A core/hinge or the cellulose binding domain (CBD) of cellobiohydrolase II (Cel6A, CBHII). The gene and fusion genes were expressed using the cellobiohydrolase 1 (cel7A, cbh1) promoter. Single-copy isogenic transformants in which the expression cassette replaced the cel7A gene were cultivated and analyzed. The transformants expressing the truncated N. flexuosa xyn11A produced clearly increased amounts of both the xylanase/fusion mRNA and xylanase activity compared to the corresponding strains expressing the full-length N. flexuosa xyn11A. The transformant expressing the cel6A CBD-truncated N. flexuosa xyn11A produced about 1.9 g liter⁻¹ of the xylanase in laboratory-scale fermentations. The xylanase constituted about 25% of the secreted proteins. The production of the truncated xylanase did not induce the unfolded protein response (UPR) pathway. However, the UPR was induced when the full-length N. flexuosa xyn11A with an exact fusion to the cel7A terminator was expressed. We suggest that the T. reesei folding/secretion machinery is not able to cope properly with the bacterial CBM when the mRNA of the full-length N. flexuosa xyn11A is efficiently translated.     

Fuzzy supervisory control of fed-batch baker's yeast process

Summary A fuzzy supervisory system for bioprocess control was developed, and applied to baker's yeast fermentation. The system was based on hierarchical bioprocess control with fuzzy phase recognition and separate fuzzy control of each process phase. A two-level knowledge base included rules both for the phase recognition and control. The system was tested by using experimental data of fed-batch baker's yeast cultivations and by process simulations.     

Radial and vertical variation of wood nutrients in Bornean tropical forest trees

Nitrogen, phosphorus, potassium, calcium, and magnesium concentrations in woody tissue are poorly documented, but are necessary for understanding whole-tree nutrient use and storage. Here, we report how wood macronutrient concentrations vary radially and along the length of a tree for 10 tropical tree species in Sabah, Malaysia. Bark nutrient concentrations were consistently high: 2.9–13.7 times greater than heartwood depending on the nutrient. In contrast, within the wood both the radial (sapwood vs. heartwood) and vertical (trunk bottom vs. trunk middle) variation was modest. Higher concentrations in sapwood relative to heartwood provide empirical support for wood nutrient resorption during sapwood senescence. Dipterocarp species showed resorption rates of 25.3 ± 7.1% (nitrogen), 62.7 ± 11.9% (phosphorus), and 56.2 ± 12.5% (potassium), respectively, while non-dipterocarp species showed no evidence of nutrient resorption in wood. This suggests that while dipterocarps have lower wood nutrient concentrations, this family is able to compensate for this by using wood nutrient resorption as an efficient nutrient conservation mechanism. In contrast to other nutrients, calcium and magnesium tended to accumulate in heartwood. Wood density (WD) showed little vertical variation along the trunk. Across the species (WD range of 0.33 to 0.94 mg/cm³), WD was negatively correlated with wood P and K concentration and positively correlated with wood Ca concentration. As our study showed exceptionally high nutrient concentrations in the bark, debarking and leaving the bark of the harvested trees on site during logging operations could substantially contribute to maintaining nutrients within forest ecosystems.     

Threat spots and environmental determinants of red-listed plant,butterfly and bird species in boreal agricultural environments

The aims of this study were (1) to examine the geographic distribution of red-listed species of agricultural environments and identify their national threat spots (areas with high diversity of threatened species) in Finland and (2) to determine the main environmental variables related to the richness and occurrence patterns of red-listed species. Atlas data of 21 plant, 17 butterfly and 11 bird species recorded using 10 km grid squares were employed in the study. Generalized additive models (GAMs) were constructed separately for species richness and occurrence of individual species of the three species groups using climate and land cover predictor variables. The predictive accuracy of models, as measured using correlation between the observed and predicted values and AUC statistics, was generally good. Temperature-related variables were the most important determinants of species richness and occurrence of all three taxa. In addition, land cover variables had a strong effect on the distribution of species. Plants and butterflies were positively related to the cover of grasslands and birds to small-scale agricultural mosaic as well as to arable land. Spatial coincidence of threat spots of plants, butterflies and birds was limited, which emphasizes the importance of considering the potentially contrasting environmental requirements of different taxa in conservation planning. Further, it is obvious that the maintenance of various non-crop habitats and heterogeneous agricultural landscapes has an essential role in the preservation of red-listed species of boreal rural environments.     

Expression of Six Peptidases from Lactobacillus helveticus in Lactococcus lactis

For development of novel starter strains with improved proteolytic properties, the ability of Lactococcus lactis to produce Lactobacillus helveticus aminopeptidase N (PepN), aminopeptidase C (PepC), X-prolyl dipeptidyl aminopeptidase (PepX), proline iminopeptidase (PepI), prolinase (PepR), and dipeptidase (PepD) was studied by introducing the genes encoding these enzymes into L. lactis MG1363 and its derivatives. According to Northern analyses and enzyme activity measurements, the L. helveticus aminopeptidase genes pepN, pepC, and pepX are expressed under the control of their own promoters in L. lactis. The highest expression level, using a low-copy-number vector, was obtained with the L. helveticus pepN gene, which resulted in a 25-fold increase in PepN activity compared to that of wild-type L. lactis. The L. helveticus pepI gene, residing as a third gene in an operon in its host, was expressed in L. lactis under the control of the L. helveticus pepX promoter. The genetic background of the L. lactis derivatives tested did not affect the expression level of any of the L. helveticus peptidases studied. However, the growth medium used affected both the recombinant peptidase profiles in transformant strains and the resident peptidase activities. The levels of expression of the L. helveticus pepD and pepR clones under the control of their own promoters were below the detection limit in L. lactis. However, substantial amounts of recombinant pepD and PepR activities were obtained in L. lactis when pepD and pepR were expressed under the control of the inducible lactococcal nisA promoter at an optimized nisin concentration.     

Structure-activity relationship of sphingomyelin analogs with sphingomyelinase from Bacillus cereus

The aim of this study was to examine how structural properties of different sphingomyelin (SM) analogs affected their substrate properties with sphingomyelinase (SMase) from Bacillus cereus. Using molecular docking and dynamics simulations (for SMase-SM complex), we then attempted to explain the relationship between SM structure and enzyme activity. With both micellar and monolayer substrates, 3O-methylated SM was found not to be degraded by the SMase. 2N-methylated SM was a substrate, but was degraded at about half the rate of its 2NH-SM control. PhytoPSM was readily hydrolyzed by the enzyme. PSM lacking one methyl in the phosphocholine head group was a good substrate, but PSM lacking two or three methyls failed to act as substrates for SMase. Based on literature data, and our docking and MD simulations, we conclude that the 3O-methylated PSM fails to interact with Mg(2+) and Glu53 in the active site, thus preventing hydrolysis. Methylation of 2NH was not crucial for binding to the active site, but appeared to interfere with an induced fit activation of the SMase via interaction with Asp156. An OH on carbon 4 in the long-chain base of phytoPSM appeared not to interfere with the 3OH interacting with Mg(2+) and Glu53 in the active site, and thus did not interfere with catalysis. Removing two or three methyls from the PSM head group apparently increased the positive charge on the terminal N significantly, which most likely led to ionic interactions with Glu250 and Glu155 adjacent to the active site. This likely interaction could have misaligned the SM substrate and hindered proper catalysis.     

Interacting effects of leaf litter species and macrofauna on decomposition in different litter environments

The leaf litter environment (single species versus mixed species), and interactions between litter diversity and macrofauna are thought to be important in influencing decomposition rates. However, the role of soil macrofauna in the breakdown of different species of leaf litter is poorly understood. In this study we examine the multiple biotic controls of decomposition – litter quality, soil macrofauna and litter environment and their interactions. The influence of soil macrofauna and litter environment on the decomposition of six deciduous tree species (Fraxinus excelsior L., Acer pseudoplatanus L., Acer campestre L., Corylus avellana L., Quercus robur L., Fagus sylvatica L.) was investigated in a temperate forest, Wytham Woods, Southern England. We used litterbags that selectively excluded macrofauna to assess the relative importance of macrofauna versus microbial, micro and mesofauna decomposition, and placed single species bags in either conspecific single species or mixed species litter environments. The study was designed to separate plant species composition effects on litter decomposition rates, allowing us to evaluate whether mixed species litter environments affect decomposition rates compared to single species litter environments, and if so whether the effects vary among litter species, over time, and with regard to the presence of soil macrofauna. All species had faster rates of decomposition when macrofauna were present, with 22–41% of the total mass loss attributed to macrofauna. Macrofauna were most important for easily decomposable species as soon as the leaves were placed on the ground, but were most important for recalcitrant species after nine months in the field. The mass loss rates did not differ between mixed and single species litter environments, indicating that observed differences between single species and mixed species litterbags in previous field studies are due to the direct contact of neighbouring species inside the litterbag rather than the litter environment in which they are placed.