Lignin biosynthesis in Norway spruce: from a model system to the tree

Lignin is a hydrophobic polymer that is synthesised in the secondary cell walls of all vascular plants. It enables water conduction through the stem, supports the upright growth habit and protects against invading pathogens. In addition, lignin hinders the utilisation of the cellulosic cell walls of plants in pulp and paper industry and as forage. Lignin precursors are synthesised in the cytoplasm through the phenylpropanoid pathway, transported into the cell wall and oxidised by peroxidases or laccases to phenoxy radicals that couple to form the lignin polymer. This study was conducted to characterise the lignin biosynthetic pathway in Norway spruce (Picea abies (L.) Karst.). We focused on the less well-known polymerisation stage, to identify the enzymes and the regulatory mechanisms that are involved. Available data for lignin biosynthesis in gymnosperms is scarce and, for example, the latest improvements in precursor biosynthesis have only been verified in herbaceous plants. Therefore, we also wanted to study in detail the roles of individual gene family members during developmental and stress-induced lignification, using EST sequencing and real-time RT-PCR. We used, as a model, a Norway spruce tissue culture line that produces extracellular lignin into the culture medium, and showed that lignin polymerisation in the tissue culture depends on peroxidase activity. We identified in the culture medium a significant NADH oxidase activity that could generate H2O2 for peroxidases. Two basic culture medium peroxidases were shown to have high affinity to coniferyl alcohol. Conservation of the putative substrate-binding amino acids was observed when the spruce peroxidase sequences were compared with other peroxidases with high affinity to coniferyl alcohol. We also used different peroxidase fractions to produce synthetic in vitro lignins from coniferyl alcohol; however, the linkage pattern of the suspension culture lignin could not be reproduced in vitro with the purified peroxidases, nor with the full complement of culture medium proteins. This emphasised the importance of the precursor radical concentration in the reaction zone, which is controlled by the cells through the secretion of both the lignin precursors and the oxidative enzymes to the apoplast. In addition, we identified basic peroxidases that were reversibly bound to the lignin precipitate. They could be involved, for example, in the oxidation of polymeric lignin, which is required for polymer growth. The dibenzodioxocin substructure was used as a marker for polymer oxidation in the in vitro polymerisation studies, as it is a typical substructure in wood lignin and in the suspension culture lignin. Using immunolocalisation, we found the structure mainly in the S2+S3 layers of the secondary cell walls of Norway spruce tracheids. The structure was primarily formed during the late phases of lignification. Contrary to the earlier assumptions, it appears to be a terminal structure in the lignin macromolecule. Most lignin biosynthetic enzymes are encoded for by several genes, all of which may not participate in lignin biosynthesis. In order to identify the gene family members that are responsible for developmental lignification, ESTs were sequenced from the lignin-forming tissue culture and developing xylem of spruce. Expression of the identified lignin biosynthetic genes was studied using real-time RT-PCR. Candidate genes for developmental lignification were identified by a coordinated, high expression of certain genes within the gene families in all lignin-forming tissues. However, such coordinated expression was not found for peroxidase genes. We also studied stress-induced lignification either during compression wood formation by bending the stems or after Heterobasidion annosum infection. Based on gene expression profiles, stress-induced monolignol biosynthesis appeared similar to the developmental process, and only single PAL and C3H genes were specifically up-regulated by stress. On the contrary, the up-regulated peroxidase genes differed between developmental and stress-induced lignification, indicating specific responses.

Revision of the family Alycidae (Acariformes, Acari), with special reference to European species

The thesis provides a proposal to divide Alycidae G. Canestrini & Fanzago into two subfamilies and four tribes. This new hierarchy is based on a reassessment and reranking of new and previously known synapomorphies of the clusters concerned by cladistic analysis, using 60 morphological characters for 48 ingroup species. The basic characters of the taxa are illustrated either by SEM micrographs (Scanning Electron Microscopy) or by outline drawings. The presented classification includes the definitions of Alycini G. Canestrini & Fanzago new rank; Bimichaeliini Womersley new rank; Petralycini new rank; and the (re)descriptions of Alycus C.L. Koch, Pachygnathus Dugès, Amphialycus Zachvatkin, Bimichaelia Thor and Laminamichaelia gen. nov. The species described or redescribed are: Pachygnathus wasastjernae sp. nov. from Kvarken (Merenkurkku), Finland; Pachygnathus villosus Dugès (in Oken); Alycus roseus C.L. Koch; Alycus denasutus (Grandjean) comb. and stat. nov.; Alycus trichotus (Grandjean) comb. nov.; Alycus marinus (Schuster) comb. nov.; Amphialycus (Amphialycus) pentophthalmus Zachvatkin; Amphialycus (Amphialycus) leucogaster (Grandjean); and Amphialycus (Orthacarus) oblongus (Halbert) comb. nov.; Bimichaelia augustana (Berlese); Bimichaelia sarekensis Trägårdh; Laminamichaelia setigera (Berlese) comb. nov.; Laminamichelia arbusculosa (Grandjean) comb. nov.; Laminamichelia subnuda (Berlese) comb. nov. and Petralycus unicornis Grandjean. Fourteen nominal species were found to be junior synonymies. The importance of sensory organs in taxonomy is well recognized, but inclusion of the elaborate skin pattern seemed to improve essentially the usefulness of the prodorsal sensory area. The detailed pictures of the prodorsa of the European alycids could be used like passport photographs for the species. A database like this of prodorsa of other mite taxa as well might be an answer to future needs of species identification in soil zoology, ecology and conservation.

Spectral Tuning and Adaptation to Different Light Environments of Mysid Visual Pigments

In the present thesis, questions of spectral tuning, the relation of spectral and thermal properties of visual pigments, and evolutionary adaptation to different light environments were addressed using a group of small crustaceans of the genus Mysis as a model. The study was based on microspectrophotometric measurements of visual pigment absorbance spectra, electrophysiological measurements of spectral sensitivities of dark-adapted eyes, and sequencing of the opsin gene retrieved through PCR. The spectral properties were related to the spectral transmission of the respective light environments, as well as to the phylogentic histories of the species. The photoactivation energy (Ea) was estimated from temperature effects on spectral sensitivity in the long-wavelength range, and calculations were made for optimal quantum catch and optimal signal-to-noise ratio in the different light environments. The opsin amino acid sequences of spectrally characterized individuals were compared to find candidate residues for spectral tuning. The general purpose was to clarify to what extent and on what time scale adaptive evolution has driven the functional properties of (mysid) visual pigments towards optimal performance in different light environments. An ultimate goal was to find the molecular mechanisms underlying the spectral tuning and to understand the balance between evolutionary adaptation and molecular constraints. The totally consistent segregation of absorption maxima (λmax) into (shorter-wavelength) marine and (longer-wavelength) freshwater populations suggests that truly adaptive evolution is involved in tuning the visual pigment for optimal performance, driven by selection for high absolute visual sensitivity. On the other hand, the similarity in λmax and opsin sequence between several populations of freshwater M. relicta in spectrally different lakes highlights the limits to adaptation set by evolutionary history and time. A strong inverse correlation between Ea and λmax was found among all visual pigments studied in these respects, including those of M. relicta and 10 species of vertebrate pigments, and this was used to infer thermal noise. The conceptual signal-to-noise ratios thus calculated for pigments with different λmax in the Baltic Sea and Lake Pääjärvi light environments supported the notion that spectral adaptation works towards maximizing the signal-to-noise ratio rather than quantum catch as such. Judged by the shape of absorbance spectra, the visual pigments of all populations of M. relicta and M. salemaai used exclusively the A2 chromophore (3, 4-dehydroretinal). A comparison of amino acid substitutions between M. relicta and M. salemaai indicated that mysid shrimps have a small number of readily available tuning sites to shift between a shorter - and a longer -wavelength opsin. However, phylogenetic history seems to have prevented marine M. relicta from converting back to the (presumably) ancestral opsin form, and thus the more recent reinvention of marine spectral sensitivity has been accomplished by some other novel mechanism, yet to be found

Dynamics of Finnish starlings in 1951-2005 : from monitoring to population modelling

Farmland bird species have been declining in Europe. Many declines have coincided with general intensification of farming practices. In Finland, replacement of mixed farming, including rotational pastures, with specialized cultivation has been one of the most drastic changes from the 1960s to the 1990s. This kind of habitat deterioration limits the persistence of populations, as has been previously indicated from local populations. Integrated population monitoring, which gathers species-specific information of population size and demography, can be used to assess the response of a population to environment changes also at a large spatial scale. I targeted my analysis at the Finnish starling (Sturnus vulgaris). Starlings are common breeders in farmland habitats, but severe declines of local populations have been reported from Finland in the 1970s and 1980s and later from other parts of Europe. Habitat deterioration (replacement of pasture and grassland habitats with specialized cultivation areas) limits reproductive success of the species. I analysed regional population data in order to exemplify the importance of agricultural change to bird population dynamics. I used nestling ringing and nest-card data from 1951 to 2005 in order to quantify population trends and per capita reproductive success within several geographical regions (south/north and west/east aspects). I used matrix modelling, acknowledging age-specific survival and fecundity parameters and density-dependence, to model population dynamics. Finnish starlings declined by 80% from the end of the 1960s up to the end of the 1980s. The observed patterns and the model indicated that the population decline was due to the decline of the carrying capacity of farmland habitats. The decline was most severe in north Finland where populations largely become extinct. However, habitat deterioration was most severe in the southern breeding areas. The deteriorations in habitat quality decreased reproduction, which finally caused the decline. I suggest that poorly-productive northern populations have been partly maintained by immigration from the highly-productive southern populations. As the southern populations declined, ceasing emigration caused the population extinction in north. This phenomenon was explained with source sink population dynamics, which I structured and verified on the basis of a spatially explicit simulation model. I found that southern Finnish starling population exhibits ten-year cyclic regularity, a phenomenon that can be explained with delayed density-dependence in reproduction.

Export of organic matter, sulphate and base cations from boreal headwater catchments downstream to the coast: impacts of land use and climate

The terrestrial export of dissolved organic matter (DOM) is associated with climate, vegetation and land use, and thus is under the influence of climatic variability and human interference with terrestrial ecosystems, their soils and hydrological cycles. The present study provides an assessment of spatial variation of DOM concentrations and export, and interactions between DOM, catchment characteristics, land use and climatic factors in boreal catchments. The influence of catchment characteristics, land use and climatic drivers on the concentrations and export of total organic carbon (TOC), total organic nitrogen (TON) and dissolved organic phosphorus (DOP) was estimated using stream water quality, forest inventory and climatic data from 42 Finnish pristine forested headwater catchments, and water quality monitoring, GIS land use, forest inventory and climatic data from the 36 main Finnish rivers (and their sub-catchments) flowing to the Baltic Sea. Moreover, the export of DOM in relation to land use along a European climatic gradient was studied using river water quality and land use data from four European areas. Additionally, the role of organic and minerogenic acidity in controlling pH levels in Finnish rivers and pristine streams was studied by measuring organic anion, sulphate (SO4) and base cation (Ca, Mg, K and Na) concentrations. In all study catchments, TOC was a major fraction of DOM, with much lower proportions of TON and DOP. Moreover, most of TOC and TON was in a dissolved form. The correlation between TOC and TON concentrations was strong and TOC concentrations explained 78% of the variation in TON concentrations in pristine headwater streams. In a subgroup of 20 headwater catchments with similar climatic conditions and low N deposition in eastern Finland, the proportion of peatlands in the catchment and the proportion of Norway spruce (Picea abies Karsten) of the tree stand had the strongest correlation with the TOC and TON concentrations and export. In Finnish river basins, TOC export increased with the increasing proportion of peatland in the catchment, whereas TON export increased with increasing extent of agricultural land. The highest DOP concentrations and export were recorded in river basins with a high extent of agricultural land and urban areas, reflecting the influence of human impact on DOP loads. However, the most important predictor for TOC, TON and DOP export in Finnish rivers was the proportion of upstream lakes in the catchment. The higher the upstream lake percentage, the lower the export indicating organic matter retention in lakes. Molar TOC:TON ratio decreased from headwater catchments covered by forests and peatlands to the large river basins with mixed land use, emphasising the effect of the land use gradient on the stoichiometry of rivers. This study also demonstrated that the land use of the catchments is related to both organic and minerogenic acidity in rivers and pristine headwater streams. Organic anion dominated in rivers and streams situated in northern Finland, reflecting the higher extent of peatlands in these areas, whereas SO4 dominated in southern Finland and on western coastal areas, where the extent of fertile areas, agricultural land, urban areas, acid sulphate soils, and sulphate deposition is highest. High TOC concentrations decreased pH values in the stream and river water, whereas no correlation between SO4 concentrations and pH was observed. This underlines the importance of organic acids in controlling pH levels in Finnish pristine headwater streams and main rivers. High SO4 concentrations were associated with high base cation concentrations and fertile areas, which buffered the effects of SO4 on pH.