Maatalous- metsätieteellinen tiedekunta

 

Recent Submissions

  • Mäkelä, Noora (Helsingin yliopisto, 2017)
    Cereal (1→3)(1→4)-β-D-glucan, known as β-glucan, has both technological and physiological functionality related to its ability to increase viscosity in solutions. The viscosity is dependent on the molar mass, concentration and solubility of β-glucan, and thus any degradation during processing and storage may diminish its functionality. Quite recently, chemical oxidation was shown to be one factor leading to the degradation of β-glucan. The present study aimed to investigate the hydroxyl radical-mediated oxidation of cereal β-glucan, including the pathways and reaction products. Additionally, oxidised lipids were tested as a source of radicals in β-glucan oxidation. Finally, the physicochemical properties (e.g. aggregation and gelation) were studied in order to understand the influence of oxidation on functionality. Hydrogen peroxide was shown to be the strongest oxidant, leading to both oxidative degradation and the formation of oxidised groups (e.g. carbonyl groups) within the chain. Additionally, oxidation of reducing end glucose units led to the formation of arabinose and formic acid. With ascorbic acid the oxidation was milder and mostly scission of β-glucan occurred. This difference was also seen in the aggregation behaviour, with very large but densely packed aggregates being formed when oxidising β-glucan with hydrogen peroxide. With ascorbic acid, fewer aggregates were formed and they could not be separated from single oxidised molecules during field-flow fractionation. This finding suggests the formation of cross-links via the oxidised groups in the molecules. The study showed for the first time that cereal β-glucan can be degraded by radicals from lipid oxidation although the oxidative degradation was significantly milder than with hydrogen peroxide. The gelation of cereal β-glucan has been shown to be affected by the molar mass and structure (e.g. the ratio of DP3 and DP4 units) of β-glucan. However, former studies show gelation only at relatively high concentrations. In this study, gelation of barley and oat β-glucans (both native and oxidised) was shown with 1% and 1.5% solutions, respectively, when using optimised dissolution temperatures that resulted in partial solubilisation of β-glucan molecules. The partial dissolution was proposed to enable formation of nucleation cites for gelation. In this study, changes in the structure and physicochemical properties of barley and oat β-glucans due to oxidation were demonstrated. Additionally, gelation of both non-oxidised and oxidised β-glucan was shown at concentrations relevant for food products. The results of this study provide an understanding of the role of oxidation for the stability of β-glucan in processing and storage of foods. The study suggests that gelation of β-glucan could overcome the negative effects of oxidation-related viscosity loss.
  • Savelieva, Kateryna (Helsingin yliopisto, 2017)
    The transmission of family characteristics across generations is a well-established phenomenon. Both advantages (e.g., a higher socioeconomic position), and disadvantages (e.g., child maltreatment) are likely to “run in families”. However, the pathways underlying the transmission of the family environment are poorly understood, as their health consequences. The aim of this study is to examine a) the extent to what characteristics of the family environment are transmitted across generations, b) the mediating and moderating factors that account for this transmission, and c) the role transmission plays in cardiovascular health of offspring. The family environment is conceptualized in the study in terms of two characteristics: qualities of the parent–child relationship and socioeconomic position (SEP). Three subsamples were derived from the population-based Young Finns Study (YFS; N = 3,596), which is a cohort study representative of the Finnish population. The parents of the original YFS participants represented Generation 1 (G1; mean age = 38 years in 1980). They were measured for two dimensions of parent–child relationship qualities (emotional warmth and acceptance) and four dimensions of SEP (education, occupation, income, and employment stability) at the baseline of the study in 1980. Their offspring (original YFS participants) represented Generation 2 (G2), who were 10 years old on average in 1980. When participants in G2 had become adults, they were examined in 2007 and 2012 for the same family characteristics that were measured from their parents. The G2 participants were also subjected to personality testing in 2001, and assessed for ideal cardiovascular health in 2007 and 2012 according to the American Heart Association’s guidelines. The findings revealed that qualities of the parent–child relationship were transmitted from one generation to another in a domain-specific way. Intergenerational transmission of emotional warmth was stronger in the mother–son than in the mother–daughter dyads. G2 character traits such as Self-directedness and Cooperativeness partly mediated (16%) the transmission of emotional warmth from one generation to another. SEP was also transmitted across generations. Offspring SEP in adulthood partly mediated (33%) the positive impact of higher parental SEP on offspring cardiovascular health in adulthood. In addition, the G2 participants who achieved higher SEP than their parents had better cardiovascular health in adulthood than those who stayed in their SEP of origin. These findings indicate that the family environment in terms of parent–child relationship qualities and SEP is likely to be transmitted from one generation to another. The transmission was modest in magnitude, but significant even after controlling for various demographic and family characteristics in both generations and taking the exceptionally long duration of the follow-up period into account. To some extent, the child’s personality development and continuity of socioeconomic position seemed to explain pathways linking parental and child characteristics. These results shed light on the factors that account for the transmission, and may be useful in early prevention efforts involving the targeting of interventions to families and children at risk. Given the observational nature of this study, there is a need for randomized experimental trials to assess the extent to which interventions directed at early-life or later-life circumstances will mitigate the intergenerational transmission of psychosocial risks.
  • Mansouri, Sadegh (Helsingin yliopisto, 2017)
    Plant biomass contains complex polysaccharides that can be divided into structural and storage polysaccharides. Plant biomass is a major carbon source utilized by chemoheterotrophic microorganisms, such as filamentous fungi to grow and produce energy. Plant biomass-degrading fungi secrete a wide range of extracellular enzymes to convert complex plant biomass into metabolizable compounds. As a result, they are able to colonize and degrade a wide range of organic materials. The industrially and biotechnologically important fungal genera Penicillium and Aspergillus are among the best-studied decomposers of plant biomass polysaccharides. The focus of this study was on two ascomycete fungi, Penicillium subrubescens (FBCC 1632) and Aspergillus niger N402 (ATCC 64947), and their potential for producing extracellular enzymes for the decomposition of plant biomass polysaccharides. Here, a new species, native Finnish isolate, P. subrubescens sp. nov. was described. It belongs to the section Lanata-Divaricata subgenus Aspergilloides. P. subrubescens was selected amongst 200 fungal strains screened for their ability to produce polyfructan inulin-degrading enzymes. Inulin is a storage polysaccharide located in the roots and tubers of flowering plants. P. subrubescens was identified based on the combined analysis of phenotype together with molecular phylogenetic analysis and extrolite data. P. subrubescens produced inulinase more efficiently than it did invertase. Only fructose, not fructo-oligosaccharides was detected as the endproduct of inulin hydrolysis indicating exo-type inulinase activity. The ability of P. subrubescens and A. niger to produce plant structural polysaccharide-degrading enzymes was studied by growth profiling and in plant biomass-containing liquid cultures. These data indicated similar (hemi-)cellulolytic capacities for these fungi. The extracellular enzyme mixtures of P. subrubescens and A. niger were used in the hydrolysis of wheat bran, sugar beet pulp and a mixture of these. Its favourable ability to hydrolyse complex plant-derived biomasses indicated that P. subrubescens has the potential to produce biotechnologically important enzyme mixtures. A new feruloyl esterase, FaeC of A. niger was cloned and heterologously produced from the plant biomass-acting enzymes. The biochemical properties of recombinant FaeC (rFaeC) were characterized, and the hydrolysis of wheat arabinoxylan and sugar beet pectin by rFaeC released both ferulic and p-coumaric acid. The synergistic activity of rFaeC and xylanase was detected in hydrolysis of plant biomass-derived substrates. The induction of faeA, faeB and faeC gene expression in the presence of various phenolic compounds and complex polysaccharides was examined. The differing expression levels of the three fae genes suggests that the corresponding enzymes can act cooperatively, leading to improvement in the efficiency of plant biomass decomposition.
  • Laakso, Johanna (Helsingin yliopisto, 2017)
    Phosphorus (P) losses from agricultural soils impair the quality of receiving surface waters by enhancing eutrophication. Most of the P carried by surface runoff and field drainage waters from clay soils in SW Finland is in particulate form, but more than half of the total P is potentially bioavailable. Thus, decreasing the load of suspended particles is important in controlling eutrophication. Constructed wetlands and ponds (CWs) have become a popular means for trapping suspended material and particulate P in agricultural runoff. Efficient CWs can collect a large amount of particulate matter through sedimentation, and this needs to be removed regularly. Dredged sediment is often advised to be recycled back to the surrounding fields. However, the material ending up in CWs is subjected to several processes, which affect its P fractions and sorption-desorption characteristics. Changes in sediment characteristics occur 1) during erosion, 2) in the (anoxic) bottom of CW and 3) after dredging when the sediment is re-exposed to air. This thesis examines P speciation and P sorption properties of sediments collected from five agricultural CWs established on clay soils, and compares the differences between the sediments and the source field soils in the catchments. Dredged, air-dried sediments were characterised separately from fresh sediments to assess the drying-induced changes in the P sorption-desorption properties. Phosphorus availability to Italian ryegrass (Lolium multiflorum L.) was tested by mixing CW sediment with soil in different ratios. Furthermore, the potential of using dredged sediment to immobilise soil P was assessed by exposing sediment-amended soil to simulated rainfall. Overall, the soils and sediments were analysed to predict the likely environmental consequences of applying CW sediments to fields. The soils and CW sediments had similar total P contents, but clearly different P speciation when fresh sediments, air-dried sediments and the source soils were compared. In general, the sediment content of aluminium (Al)-associated P was significantly lower, and iron (Fe)-associated P significantly higher, than in the source soils. Reduced conditions, conducive to mobilisation of Fe-associated P and suggestive to Fe sulphide formation, were observed in all CWs. As a consequence of high clay and Al and Fe (hydr)oxide concentrations, possibly accentuated by Fe sulphide oxidation, dredged (re-oxidised) sediments showed a high affinity for P in sorption-desorption tests. In these tests a substantial decline in the equilibrium P concentration (EPC0) was observed already at 2% to 5% (by fresh volume) sediment addition rates. The high affinity for P by sediment matter was also supported by observations in a growth experiment and simulated rainfall test. The lower the P plant availability for ryegrass and dissolved reactive P (DRP) concentration in percolating water, the more sediment was mixed into the soils. The results suggest that the plant availability of P in CW sediments is very low due to the high concentrations of clay, and Al and Fe (hydr)oxides in sediments. Returning CW sediments to fields in large quantities is therefore likely to decrease the amount of P readily available for crop uptake. However, application of sediments dredged from CWs can be expected to immobilise soil P and decrease nonpoint source P loads when applied to critical source area soils with environmentally problematic P saturation. A practical rate of sediment addition to the surface soil layer could be approximately 5% (by fresh volume).
  • Muurinen, Johanna (Helsingin yliopisto, 2017)
    Agricultural antibiotic use is considered to foster the development and spread of resistant pathogens threatening human health and thus it is suggested that the use of antibiotics in production animals should be limited. Unlike in many big countries in the world, Finnish animal production uses antibiotics predominantly for treating bacterial infections. Nonetheless, the circulation of antibiotic resistance genes through intersecting ecosystems, such as production animal farms, might have a considerable role in transferring resistance genes from environmental bacteria to human or animal associated bacteria. Agroecosystems are unique settings where bacteria originating from animals and the environment are constantly mixed due to land application of manure and ingestion of harvested forage by production animals. In this work it was clarified if genes related to antibiotic resistance and transfer disseminate from farms to the environment due to manure fertilization, if the abundance of these genes is affected by winter storage of manure and if resistance gene abundances are elevated in soils at crop harvesting time, and thus potentially cycled into the animal gut via forage. A field-compatible protocol for detecting antibiotic concentrations sensed by bacteria in different samples was also established. Manure had the highest abundance of genes related to antibiotic resistance and transfer, and the abundance increased during storage. The genes abundant in manure disseminated to soil when manure was applied; however, at the harvesting time the soil resistome resembled the resistome of unfertilized soil. Antibiotic resistance genes were also detected in ditch water but most of them were undetected in manure, suggesting that genes in manure were not spreading to receiving waters. The results propose that manure fertilization does not inevitably generate a risk of disseminating antibiotic resistance and that agricultural practices largely determine whether or not the use of antibiotics in production animals contaminates the agricultural environment with resistance determinants. The presented field-use suitable assay can be used for samples with minor matrix-effects, e.g. surface waters. With further method development, the protocol could help in progressing from detection of antibiotics to the evaluation of their ecological effects in the studied environment.
  • Ingutia, Rose (UNIGRAFIA, 2017)
    A majority of Africa’s disadvantaged children have one or more characteristics. They are – rural, malnourished, orphans, invisible, out of school, child brides or child labourers, have illiterate mothers who were denied access to productive resources, have mothers who watch helplessly as their children waste away and die of easily treatable illnesses. Our objective is to analyse factors affecting child poverty, factors like women’s low status because the wellbeing of children cannot be separated from that of their mothers; child poverty is inseparable from mothers’ poverty. The analysis has been done through the investigation of questions like: which are the most important variables affecting child poverty; does the lack of access to education cause child poverty or does child poverty cause the lack of access to education; to what extent can the low status of rural women be considered as a contributing factor to child poverty and Africa’s progress in child poverty issues, and differences in progress between lower and lower middle income countries; under-five mortality rate (U5MR) above and below 10% countries and region wise differences. An investigation of 30 African countries between1990-2010 has been undertaken. Due to the nature of multiple interdependencies among factors affecting child poverty, the principal component analysis statistical technique (PCA) was applied to eliminate redundant variables and to retain those that explained most of the variations in the dataset. The findings suggest that although causes of child poverty are multidimensional and call for simultaneous solutions, estimated elasticities indicate that FAG has the greatest effect on U5MR, while CPI has the greatest effect on both PSE and CU. These findings tend to point to agriculture as the solution to child poverty issues in Africa. This is by providing an enabling environment for women in agriculture to access productive resources which will contribute to better crop production that will both increase PSE, decreases CU and in the process, reduce child poverty (U5MR). Elasticity ranking shows that what is at issue is not the effect of education on reducing child poverty or the effect of child poverty on reducing education, but the improvement of women’s status particularly in the agricultural sector. Policies for long lasting solutions should highlight institutional quality as a prerequisite in child poverty reduction, it presents children and women with equal opportunities to access basic needs. Education investment should shift focus from higher investments in primary school to preschool with feeding programs to cater for underweight children because the early years of life are crucial for cognitive development.
  • Rantanen, Marja (2017)
    Plants adjust their development by responding to temperature, photoperiod and light quality as indicators of season and the prevailing environment. Seasonal flowering strawberries (Fragaria sp.) and red raspberry (Rubus idaeus) are temperate species that are typically induced to flower under the short days (SD) that occur in the autumn. Temperature strongly influences the SD effects. Woodland strawberry (Fragaria vesca) is a model plant for the garden strawberry (F.× ananassa) and woody Rosaceae plants. The floral repressor FvTERMINAL FLOWER1 (FvTFL1) in the woodland strawberry causes seasonal flowering. Under non-inductive long day (LD) activation of FvFLOWERING LOCUS T1 (FvFT1) >FvSUPPRESSOR OF OVEREXPRESSION OF CONSTANS1 (FvSOC1) > FvTFL1-pathway suppresses flowering. The objective was to study how temperature regulates flowering in the woodland strawberry. In addition, the effects of light quality in the woodland strawberry and the tunnel-grown red raspberry were studied. Expression studies and transgenic plant approaches showed that FvTFL1 protein integrates the photoperiod and temperature signals in the woodland strawberry. At non-inductive high temperature FvTFL1 is highly activated to suppress flowering. Other regulators than FvSOC1 are involved in the up-regulation of the FvTFL1 gene: especially under SD conditions. The FvSOC1 dependent photoperiodic regulation of FvTFL1 has a major role but only at intermediate temperatures. The down-regulation of the FvTFL1 gene allows for flower induction at cool temperatures. FvFT1 was observed to mediate the light quality signal. Far-red and red wavelengths had opposite effect on flowering of the SD and LD flowering genotypes indicating that floral response depends on the presence of FvTFL1. Furthermore, in the absence of functional FvTFL1 protein, the FvFT1 was found to function as an LD dependent floral activator. Light quality also affected flowering in the raspberry in a cultivar dependent manner. The use of an FR absorbing photoselective film led to increased number of flowers in primocane fruiting cultivars (LD plants) and decreased number of flowers in floricane fruiting cultivars (SD plants). The results suggest that the modification of a combination of temperature, photoperiod and light quality is a potential approach to use in controlling vegetative and generative growth in strawberry and raspberry.
  • Birge, Traci (Helsingin yliopisto, 2017)
    Farming has indelibly shaped the landscapes and cultures of Europe. Agriculturally marginal areas tend to host the highest amount of endangered species and are also the most at risk of abandonment as traditional agriculture is replaced by intensive high yield production. Farmlands with particularly strong habitat function, especially for species of European conservation concern, are priorities in European agri-environmental policy, and farmers are eligible for payments in exchange for management of such farmlands. Farmers are the key actors in agro-ecosystems and are motivated by a range of factors. Research increasingly supports calls for improving farmland conservation through better engagement with farmers to engender long-term attitudinal change and improve efficiency of agri-environmental payments. The aims of this thesis are to 1) examine farmers’ behaviour and decision-making as it applies to farmland conservation targets in Finland, and 2) explore how an approach addressing both social and ecological dimensions of conservation on farmland could be used to (potentially) improve outcomes. I examine farm-level decision-making using two cases: i) management of semi-natural grazed woodlands and meadows, collectively known as traditional rural biotopes, and ii) potential for a results-based approach to paying farmers for achieving biodiversity targets. Research was carried out in southern Finland. For traditional rural biotopes, I focus on farmer motivations and the benefits farmers receive from management of the sites. In the second case, I use a hypothetical results-based measure based on an existing, low threshold measure called nature management grassland. The cases represent two contrasting modes of policy delivery, where traditional rural biotopes are governed through demanding schemes by a small number of farmers (‘narrow and deep’), while long-term nature management grasslands are managed via low-threshold supports with high level of uptake (‘broad and shallow’). The study is grounded in agroecology, a multidisciplinary field. I use approaches and tools from the social sciences (interviews and questionnaires, thematic analysis) and ecology (species survey), and I approach the research from the position of wanting to understand the views and strategies that go into farmer participation (or not) for nature conservation on farmlands. The studies revealed high heterogeneity within the populations studied (e.g. in behaviour, farming styles, and farm structure). A variety of reasons were found for managing traditional rural biotopes (II). Farmers participated in the existing grassland fallow scheme mainly for convenience as a low-threshold subsidy type for fallows, and are not used to thinking about achieving biodiversity or other results through the scheme (III, IV). The ‘tidy landscape’ narrative was evident in both studies and impacted management decisions (II, IV). Farmers with a disposition toward managing for nature values were found in both studies (II, IV), and a particular farming style, ‘traditional rural biotope entrepreneur’ was also identified (II). Evidence was found for ecological and cultural feasibility for the results-based approach.
  • Forssell, Sini (Helsingin yliopisto, 2017)
    This doctoral dissertation examines the phenomenon of alternative food networks (AFNs) from the perspective of food system sustainability. AFNs are seen as a promising response to the sustainability issues associated with the conventional food system, but have also attracted criticism. Criticisms include uncertainty over AFNs’ actual sustainability impacts; arguments that many AFNs are hybrid rather than purely alternative; and that their impact on food system sustainability is limited, due to their marginal position. In this dissertation, comprising three original research articles and an introductory section, I explore the above-mentioned criticisms to advance understanding of AFNs' sustainability. I seek to i) understand what sustainability claims we can make for AFNs based on their characteristics, ii) to develop understanding of AFNs' hybrid nature and their complex relationship to the conventional food system through empirically examining the negotiation of acceptable practice in AFNs; and iii) understand how this negotiation can be understood to drive wider food system sustainability transitions by shaping norms. The main theoretical framework used is convention theory. This theory examines the deployment of different notions of worth in coordinating economic activity, as actors navigate in different situations, and shape these situations through their negotiation of acceptable practices. I also apply convention theory to the framework of sustainability transitions, to frame the examination of norm-shaping within the niche of AFNs. The empirical focus of this study is on an often-overlooked AFN actor, alternative food retailers, involving a qualitative, multiple case study research covering nine cases of alternative food retail in Finland and the UK. My findings suggest that AFNs may potentially contribute to sustainability, but their sustainability should be critically assessed on a case-by-case basis. The findings also suggest a plurality of shared ideals in the domain of AFNs and several areas of tension in AFN practice that AFN actors must navigate. In doing this, the actors may also shape the norms and ideals in the sector. The conceptual examination contributes a clarified overview of AFNs’ potential sustainability impacts and limitations, and provides a practical framework to assess different food networks’ sustainability. The empirical analysis challenges certain underlying assumptions in the previous literature, and contributes a new understanding of AFNs’ hybridity, its causes and consequences, and the challenges involved in adopting sustainable practices. The analysis can help practitioners understand consumer considerations, and opportunities and obstacles to more sustainable practices. It also deepens the understanding of how new norms are negotiated in the sector, and suggests an alternative view of AFNs’ potential to drive change, besides scaling up and gaining a larger share of the food market. It uncovers the deeper ideals that the alternative food retailers promote, and how these are different from or similar to conventional food system norms and ideals. This understanding can also help practitioners in their norm-shaping work. Theoretically, the study contributes a more dynamic application of convention theory to agri-food studies. The use of convention theory contributes a new understanding of the human and cultural aspect of sustainability transitions. AFNs are ultimately both more and less than their promise. They are not automatically sustainable, or always purely alternative, but can challenge the conventional food system. Their indirect impact on the wider food system may be greater than suggested by their small size and reach. AFNs operate in a dialogue between different parties, and the general direction of this dialogue is instrumental in shaping what AFNs might be or become, and the achievement of sustainability in AFNs.
  • Fahmi, Mustafa (Helsingin yliopisto, 2017)
    ABSTRACT Livelihoods are precarious in arid and semi-arid regions, such as Sudan, as the main food crops are often grown in production systems that heavily depend on climatic conditions and appear to be threatened by several factors. Over 70% of Sudanese are farmers who rely mainly on rain-fed agriculture to secure their livelihoods. Their crop cultivation is constrained by such factors as climate change and variability, as well as low soil fertility, which is aggravated by limited agricultural inputs. Indigenous legume trees, such as acacias, can potentially alleviate the vulnerability of these systems. In practice this is possible by integrating trees with agricultural crops on the same piece of land, thus forming an agroforestry system. Nevertheless, the adoption of agroforestry also remains constrained by several factors, including unclear tree tenure and small farm size. The main objectives of this research were: (I) To classify and compare various land-use systems so as to facilitate an analysis of the socio-economic impacts of farming practices in the semi-arid zone of Sudan; (II) To define the determinants and constraints for agroforestry based on the integration of natural acacia trees with agricultural crops, thus forming the agroforestry parkland system in Sudan; (III) To identify and analyse the main factors underlying the variability of crop yields during the period 2001–2010; and (IV) To characterize the impact of land-use changes between 1972 and 2010 on natural forests and land productivity. The research was conducted at two distinct sites, El Dali and El Mazmum in Sennar state, Sudan (latitudes 12° 5ʹ and 14° 7ʹ N and longitudes 32° 58ʹ and 34° 42ʹ E, respectively). Principal data on households and crop yields were collected from 281 randomly selected households in face-to-face interviews using a pre-structured questionnaire. Soil and rainfall data along with satellite images were obtained from associated institutions in Sudan. Qualitative and quantitative methods were used to analyse crop and household data, and the Excel template MAKESENS was used to study the rainfall data. GIS software applications and economic analysis were used in clarifying land-use changes and crop profitability with various land-use systems, respectively. Agroforestry parklands that consist of the integration of acacia trees with agricultural crops were found to financially be the most profitable system, offering higher crop yields than monoculture systems. The number of people in a household, agro-ecological location, incentives from agricultural associations, and land holding size were the main drivers for farmers to combine acacia trees with agricultural crops, forming an agroforestry parkland system. Constraints for practicing agroforestry included insecurity of tree ownership, poor interaction between farmers and extension agents, lack of tree planting materials (in cases where a farmer would have adopted tree planting as a method to increase the tree cover), uncontrollable livestock movements on farms, and land owners’ preference to rent their entire holding to landless farmers. The yields of most of the studied crops (sorghum, pearl millet and sesame) were affected by interannual variability in rainfall rather than agricultural practices. Land use and land cover have remarkably changed over time, resulting in a negative impact on soil properties and crop performance. This research concludes for the region now studied in Sudan that climatic variability, low soil fertility and inadequate agricultural inputs contribute to a decline in crop yields. The lack of an appropriate tree tenure regime constitutes the strongest disincentive factor inhibiting farmers from practicing agroforestry, obviously the best available land-use option for sustainable crop cultivation and securing rural livelihoods. Key words: Sudan, livelihoods, rain-fed agriculture, agroforestry parklands, crop yields, climate change and variability, tree tenure, acacia trees
  • Lim, Kean-Jin (Helsingin yliopisto, 2017)
    Scots pine is an ecologically and economically important tree species in Finland because of its heartwood (HW) quality traits that contributed by the pine HW extractives, which is mainly attributed to stilbenes. Pine stilbenes, pinosylvin (PS) and its monomethyl ether, are development and stress inducible metabolites. During HW formation, biosynthesis of pine stilbene takes place in a narrow zone between the HW and the sapwood (SW), namely the transition zone (TZ). Pine stilbenes can also be induced in SW or needles in response to stressors. Despite the importance of pine HW, studies on the molecular development of HW formation from its TZ are scarce. Besides, the timing and type of HW formation in Scots pine has not been satisfactorily described. Scots pine HW extractive content varies between individuals and is highly heritable, thus breeding for high extractives in pine is possible. However, traditional forest tree breeding is time-consuming, particularly for a trait that can only be assessed in mature trees. A solution for early selection in forest tree breeding could be with a genomic approach coupled with bioinformatics analysis. In this work, the transcriptome changes during HW formation were studied in the TZ compared to the SW of mature pine trees. In addition, the stress response transcriptome changes were studied by wounding the stems of pine seedlings. The timing of Scots pine HW formation was investigated by studying the year-round expression profile of selected transcripts using quantitative RT-PCR. HW formation was initiated in spring and ceased in late autumn. The process was marked by programmed cell death. During HW formation, sucrose was metabolised for stilbene biosynthesis, indicating that pine stilbenes are biosynthesised in situ in the TZ. The pine stilbene biosynthetic pathway is upregulated both during HW formation and in response to stress. Interestingly, distinct transcripts encoding two enzymes acting at the beginning of the pathway were induced during development and stress. This work also showed that the previously characterised PS O-methyltransferase, PMT1, is probably not part of the stilbene pathway. A newly characterised O-methyltransferase, PMT2, turned out to be PS specific, and is strictly coexpressed with stilbene synthase. Unexpectedly, the resin acid biosynthetic transcripts were not induced in concert with stilbene biosynthesis. The year-round expression study showed that the expression of resin acid biosynthetic transcripts was induced in early spring and ceased later in spring. Resin acid biosynthesis was not induced in response to wounding. Single members of the MYB and NAC transcription factor families were upregulated in the TZ compared to SW, and closely followed the expression of stilbene biosynthesis and its upstream pathways. However, other members of the MYB and NAC families were transiently induced in response to wounding. Similarly, distinct transcripts associated with cell wall modification, water deficit stress and plant defence were induced during development and stress. This work demonstrated that only little similarity occurred in the transcriptome changes between HW formation and wounding response in pine. Despite stilbene synthase and PMT2 being commonly induced in both conditions, different sets of transcripts were induced, suggesting their physiological roles may be development and stress specific in Scots pine.
  • Mäkinen, Hanna (Helsingin yliopisto, 2017)
    Climate change is characterized by uncertainty in climate and increasing variability in weather. In addition to traditional ‘predict and adapt’ approaches of preparing for projected average long-term change in climate, approaches addressing adaptive capacity and system resilience are required. Diversity is associated with enhanced stability and resilience in the face of climate change. However, any kind of diversity does not necessarily enhance resilience, but the diversity of responses is critical to resilience. Such response diversity means that the ability to react to changes and variability differs within a functional group. In this thesis, response diversity was empirically assessed using forage crops, a response diversity index (RD-index) was constructed and the practical significance of the RD-index was demonstrated. Forage crops were chosen for the studies because they are a cornerstone of Finnish dairy and beef farming. The following species and their cultivars were included: timothy (Phleum pratense L.), meadow fescue (Festuca pratensis Huds.), tall fescue (Festuca arundinacea Schreb. syn. Lolium arundinaceum Schreb.), festulolium (Festulolium pabulare), Italian ryegrass (Lolium multiflorum L.) and red clover (Trifolium pratense L.). The analyses started with testing the effect of the hypothetically critical agro-climatic variables on forage crop yield performance using plant data from the Official Variety Trials of Natural Resources Institute Finland (126 cultivars) and the weather data of the Finnish Meteorological Institute from 1979 to 2012 that was matched to the phenology of the crops. A linear mixed model was used to determine the effect of the site, year and weather on crop yields (I, II). In the second round of analyses, the three-way interaction of cultivars, soil types and weather were analysed using mixed models (III). Within-species diversity of responses to individual weather variables was firstly investigated for the modern set of forage crop cultivars. The results revealed that in these, within-species diversity in response to weather was generally low, particularly within the modern set of timothy and meadow fescue cultivars. On the other hand, the set of modern festulolium cultivars showed higher levels of differences in responses, which indicates their greater capacity to cope with climate change (II). Principal component analysis was used to determine common weather patterns, and forage crops and their cultivars were clustered based on the scores of the principal component analysis (I, III). Response diversity to the critical weather patterns within the set of forage crop species and cultivars was found. The value of the RD-index, measured as numbers of identifiable functional groups of species and cultivars with similar yield responses, was 10 across the soil types. An increase in RD-index decreased the yield response variation. The practical significance of complementarity of yield 10 responses of forage crops and their cultivars represents an option for the enhancement of climate resilience of feed production. The RD-index of forage crops and their cultivars varied from one climate–soil type pattern to another, with the following RD-index values: coarse mineral soils = 4, clay = 9, organic soils = 8 (III). Due to the demonstrated dependency of crop responses to climate change on soil type, attention should be given to the plausible shifts in soil–climate combinations when planning adaptation.
  • Deptula, Paulina (Helsingin yliopisto, 2017)
    Vitamin B12 is the most complex vitamin in existence and one of the most complex non-polymeric molecules occurring in nature. It is predominantly present in animal-derived products, which places vegetarians and people with limited access to animal-derived foods at risk for developing vitamin B12 deficiency. With the current trend of limiting the consumption of foods of animal origin, the deficiency may also affect other populations. In situ fortification of foods through microbial fermentation with food-grade bacteria is a viable method for the introduction of vitamin B12 into foods, if the microorganism is capable of synthesising the active vitamin form. Here, the capability of Propionibacterium freudenreichii to produce active vitamin B12 was explored with the use of a combination of microbiological and molecular approaches. First, the activity of the heterogolously expressed and purified enzyme BluB/CobT2 was investigated. The results showed that the novel fusion enzyme was responsible for biosynthesis of 5,6-dimethylbenzimidazole (DMBI) base and its activation for attachment as the lower ligand of vitamin B12. The enzyme’s inability to activate adenine, the lower ligand of pseudovitamin B12, revealed a mechanism favouring production of active vitamin B12 in P. freudenreichii. The in vivo study showed that formation of DMBI is oxygen dependent as no vitamin B12 was produced under strictly anaerobic atmosphere. Exogenous DMBI was incorporated into the vitamin molecule under both microaerobic and anaerobic conditions, with a clear preference over incorporation of adenine. In the following study, the capability of 27 P. freudenreichii and 3 Acidipropionibacterium acidipropionici strains to produce active vitamin B12 was examined by UHPLC. The yields obtained from growth in whey-based medium enriched in cobalt and supplemented with either DMBI, with the precursors of DMBI- riboflavin and nicotinamide, or without supplementation. A. acidipropionici strains required supplementation of DMBI to produce small amounts of active vitamin B12 (<0.2 µg/mL), while all of the P. freudenreichii strains were able to produce active vitamin B12 in all conditions tested. The yields of active vitamin B12 produced by P. freudenreichii and responses to supplementation were strain dependent and ranged from 0.2 to 5.3 µg/mL. Subsequently, the active vitamin B12 production by the strain P. freudenreichii 2067 without addition of cobalt or DMBI was tested. The experiments were performed in a medium mimicking cheese environment as well as in the whey-based medium. The production of other key metabolites was examined by HPLC, while the global protein production was compared by gel-based proteomics. The results showed that regardless of different effects of the media on the metabolic state of the cells, which was reflected by distinct metabolite and protein production patterns, P. freudenreichii produced nutritionally relevant levels of active vitamin B12. Finally, whole genome sequencing was employed to better characterise the species through a comparative genomics study. The use of PacBio sequencing platform, a PCR-free method producing long reads, resulted in discovery of additional circular elements: two novel, putative conjugative plasmids and three active, lysogenic bacteriophages. The long reads also permitted characterisation and classification of two distinct types of CRISPR-Cas systems. In addition, the use of PacBio sequencing platform allowed for identification of DNA modifications, which led to characterisation of Restriction-Modification systems together with their recognition motifs, many of which were reported for the first time. Genome mining suggested surface piliation in the strain P. freudenreichii JS18, which was confirmed by transmission electron microscopy and assessment of specific mucus binding.
  • Rajala, Pauliina (Helsingin yliopisto, 2017)
    Low- and intermediate-level radioactive waste (LLW/ILW) is produced during the operation and decommission of nuclear power plants. At the Olkiluoto power plant, LLW/ILW is disposed of in an underground repository excavated into the bedrock 60–100 m below sea level. The metallic portion of this waste is typically made of carbon steel and stainless steels. In anoxic conditions, such as the groundwater at the Olkiluoto repository site, carbon steel corrosion rate is very slow unless the groundwater is highly acidic or microbial activity is high, altering local conditions to corrosion inducing direction. Microorganisms are able to accelerate general corrosion as well as induce localized corrosion forms and stress corrosion cracking as conditions under the biofilm can differ markedly from those in the adjacent environment. Critically, corrosion of metallic waste can release radioactive nuclides into the groundwater and threaten the long-term integrity of the storage site. The objective of this research was to determine the importance of microbially- induced corrosion (MIC) of carbon steel placed in deep geological repository containing LLW/ILW. The structure and function of microbial communities in the deep biosphere are still poorly understood but could have important consequences for the long-term storage of radioactive waste in underground repositories. MIC of carbon steel in anoxic groundwater was studied in the laboratory and in situ in experiments with exposure time ranging from 3 months to 15 years. MIC was examined using gravimetric and electrochemical techniques complemented by molecular biology and surface characterization methods. It was shown that conditions beneath the microbial biofilm accelerated corrosion rate of carbon steel, especially localized corrosion, and that microbial activity in deep groundwater is enhanced by the presence of carbon steel. Naturally- occurring microorganisms in deep groundwater environments have a great affinity for the surface of carbon steel and rapidly form a biofilm. Phylum proteobacteria, beta- or deltaproteobacteria depending on the experiment, were in the majority in the biofilm forming bacterial community. Archaeal biofilm was formed by phylas Euryarchaeota (DHVE) and Thaumarcheota (MBGB). However, corrosion was inhibited in concrete-encased environments, due to high alkalinity and calcium carbonate concentration in the environment. In many cases, LLW/ILW repositories contain concrete materials, which according to the present results hinders the corrosion at least in the beginning of repository time scale.
  • Honkaniemi, Juha (Finnish Society of Forest Science, Faculty of Agriculture and Forestry of the University of Helsinki, School of Forest Sciences of the University of Eastern Finland, 2017)
    Disturbances, caused by abiotic and biotic agents, are discrete events in time disrupting the ecosystem and resulting in the reduction of plant biomass. They play a key role in forest ecosystems, but in the managed forests pose a risk to forest productivity. The projected climate change is expected to increase the risk of various disturbances in the boreal forests. In Europe, the major risks threatening the Norway spruce (Picea abies) dominated stands are caused by Heterobasidion root rot, wind storms, and European spruce bark beetle (Ips typographus). Heterobasidion root rot causes growth losses, mortality and decreases the timber quality. It also decreases the mechanical stability of the tree against wind load and increases the stand vulnerability for wind damages. Bark beetles benefit from the low resistance breeding material, i.e., wind damaged trees, when the population is low and can emerge as outbreaks in the right conditions. This thesis presents a simulation framework WINDROT to simulate the interactive dynamics of these disturbance agents. WINDROT consists of four simulation models, each responsible for either the dynamics of the host or one of the disturbance agents. A stand level decision support system, MOTTI, simulates the growth and dynamics of tree stands as affected by forest management, and provides inputs for mechanistic models Hmodel, HWIND and BBDYN simulating the dynamics and effects of disturbance agents. The model performance analyses in tree and stand scale showed that; i) the Heterobasidion dynamics are driven by primary and secondary infections on large stumps; ii) increasing intensity of Heterobasidion root rot damages increases the risk for wind damages; and iii) the increasing wind damages increased the subsequent bark beetle damages. The simulation framework can be used to analyze the sensitivity of different forest management regimes to the risks posed by these damages alone and in various combinations.