Maatalous- metsätieteellinen tiedekunta
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(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.
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(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.
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(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.
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(Helsingin yliopisto, 2017)The objective of this thesis was threefold: 1) to compare alternative growth functions fitted to pig live-weight data, with particular emphasis on the ability of the growth function to predict live-weight; 2) to estimate genetic (co)variances for the parameters of the previously determined most appropriate growth function using alternative modelling approaches; 3) to estimate genetic (co)variance parameters pertaining to live-weight, feed intake and two other efficiency traits using Legendre polynomial equations. The final dataset used included 51,893 live-weight and 903,436 feed intake records from 10,201 pigs obtained from the Finnish pig breeding company Figen Oy. Fixed effects and mixed models were applied to three different growth functions, namely von Bertalanffy, Gompertz, and Richards; fixed and mixed model polynomial equations were also considered. Each growth function’s ability to predict future live-weight was determined by excluding a selection of animal live-weight records post 160 days of age, and comparing the predicted live-weight to actual live-weight. The accuracy of fit for each model was determined as the square of the correlation between the actual and predicted weights. The root mean square error (RMSE) values for each model scenario were also estimated. The Gompertz growth function achieved the greatest accuracy squared of modelling pig live-weight (0.997) and lowest RMSE (1.60 kg). When used in a mixed model framework the Gompertz growth function also achieved the greatest accuracy squared of predicting future live-weight records (0.846) with the lowest corresponding RMSE (5.35 kg). Based on the results from the first study the Gompertz growth function was used to estimate the genetic (co)variance of the function’s parameters asymptotic mature weight (A), the logarithm of the ratio of mature weight to birth weight (B) and rate of maturation (k). Three alternative approaches were utilised to estimate the variances; a two-step fixed effects approach, a two-step mixed model approach and a one-step mixed model approach. The two-step approach initially used growth function parameter estimates from the first study (paragraph above) and subsequently estimated the variance component parameters for A, B and k, using a linear mixed model; whereas, the one-step approach used an iterative method to calculate the variance component estimates for the growth function parameters, in a mixed model framework. Results from this genetic analysis highlighted that ample genetic variation exists for all three Gompertz growth function parameters; greater heritability estimates for the Gompertz growth function parameters were obtained from the one-step mixed model approach. Genetic (co)variances for live-weight, feed intake and two efficiency measures, namely residual feed intake and residual daily gain, were estimated using random regression Legendre polynomial models. Results using the random regression Legendre polynomial models showed heritability of live-weight, feed intake, residual feed intake and residual daily gain increased in the early growing phase, peaked and subsequently decreased as the age of the animal increased. Ample genetic variation existed for all four traits, indicating the potential to alter curve profiles to meet specific breeding objectives. Results from this thesis can be implemented into genetic evaluations for pigs, providing comprehensive information on the profile of growth and efficiency throughout the growing period of the animal’s life, thus helping breeders identify genetically superior animals.
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(Helsingin yliopisto, 2017)Leuconostocs are lactic acid bacteria used as starters in food fermentations. They can also be spoilage bacteria, especially in vacuum packed meat products. Many Leuconostocs produce antimicrobial peptides, also known as bacteriocins. Leuconostoc bacteriocins are usually small, less than 10 kDa non-modified peptides, which are secreted by dedicated transporters. These bacteriocins kill many different bacteria, including strains of Enterococcus, Listeria, and Staphylococcus genera. Sensitivity to bacteriocins is usually dependent on a specific receptor on the target cell membrane. On Listeria cell membrane, mannose-phosphotransferase system Man-PTS has been shown to be the target for bacteriocins leucocins A and C from Leuconostoc. These class IIa bacteriocins bind to the subunit IIC (MptC) of Man-PTS and open the transporter, which leads to cell leakage and eventually cell death. Bacteriocin producers express specific immunity proteins, which protect the producer cells by blocking the transporter pore. In this doctoral dissertation, the bacteriocins produced by Leuconostoc carnosum 4010 were studied. The strain 4010 is a commercial protective culture for vacuum packaged meat products. The strain produces two antilisterial bacteriocins, leucocins A and C. In this study, the strain was found to produce a third bacteriocin, leucocin B, which is active against some Leuconostoc and Weissella strains. Genes required for the production of the three leucocins were characterised. The leucocin genes were arranged in operons on two native plasmids. A single ABC-transporter was found in the strain 4010 and was believed to carry out the bacteriocin secretion for all three leucocins. Immediately downstream of the leucocin genes lcnA, lebB, and lecC, putative immunity genes lcnB, lebI, and lecI were found. The immunity mechanisms of leucocin C was studied by expressing the lecI gene in L. monocytogenes. LecI producing Listeria was less sensitive to the leucocin C, showing the immunity function of LecI. By cloning the leucocin genes in plasmid vectors, active bacteriocins were produced in heterologous hosts Escherichia coli and Lactococcus lactis. Finally, leucocins A and C were used in a Lc. lactis genome editing method developed in this study. It has been shown that expression of Listerial mptC gene in Lc. lactis renders the host sensitive to class IIa bacteriocins. In this doctoral study, a counterselection method based on bacteriocin sensitivity was developed to select the loss of a plasmid. Listerial mptC gene was cloned in an integration vector aiming at a chromosomal deletion, and the plasmid was transferred into Lc. lactis. When the bacteriocin sensitive integrants were cultured with leucocin A or C, only the cells which had lost the mptC-plasmid through a second homologous recombination could survive. The second recombination may also cause the desired deletion. With this bacteriocin counterselection method, fragments up to 35 kb were deleted from Lc. lactis chromosome. The results obtained from this doctoral study provide further knowledge of Leuconostoc bacteriocins and their scientific use.
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(Helsingin yliopisto, 2017)The concentrations of heavy metal chromium (Cr) and vanadium (V) in soils have increased due to loading from anthropogenic sources, e.g. combustion of fossil fuels, leachates from mine tailings, chemical industry and as impurities in fertilizers and soil amendments. Chromium exists as Cr(III) and Cr(VI) species. The trivalent species (CrIII) is an essential nutrient, whereas the Cr(VI) is highly toxic. The stable V species under environmental conditions are V(IV)and V(V), with V(V) considered more harmful. The environmental impacts of Cr and V species rely on their availability for biological uptake, i.e. on their chemical bioavailability. Soluble species are easily taken up by biota and transferred to natural waters by leaching. This research demonstrated that the pH-dependent reactions occurring in soil dictate the chemical bioavailability of Cr and V species. Fine sand soils were incubated with added V(IV) and V(V) species (0 500 mg V kg-1) over a pH range of 4.0 6.9. Chemical bioavailability of both V species was lowered by organic matter (OM). Soil OM was able to reduce V(V) to V(IV) and bind both V species. At higher pH, the reduction of V(V) by OM diminished, whereas the oxidation of V(IV) to V(V) increased. Due to the predominance of V(V) species, the chemical bioavailability of V increased in response to elevated soil pH, irrespective of the initial V speciation. Field soil samples were incubated over a pH range of 3.9 6.3 with or without synthetic MnO2. Net-oxidation of Cr(III) to Cr(VI) (i.e. the oxidation of Cr(III) minus subsequent reduction of produced Cr(VI)) in soil suspended in a 1 mM CrCl3 solution occurred only in samples incubated with added MnO2. The amount of Cr(VI) formed in oxic soil conditions was regulated by the balance between: 1) oxidation of Cr(III) to Cr(VI) by MnO2 and 2) the subsequent reduction of Cr(VI) to Cr(III) by organic matter. The production of CrVI was lowest under acidic soil conditions. At low pH, net-oxidation of Cr(III) diminished due to the enhanced reduction of Cr(VI) back to Cr(III). At higher pH, the Cr(III) oxidation was limited by greater precipitation (or adsorption) of Cr(III), which lowered the overall amount of Cr(III) available for oxidation. At elevated pH the chemical availability of added Cr(III) decreased, whereas that of newly produced Cr(VI) increased. Moreover, the oxidation reactions were found to be inhibited by formation of Cr(OH)3 on the surface of MnO2. In addition, the risks of the utilization of alkaline steel industry slags as liming materials (at dosages equivalent to 10 and 100 t ha-1), was assessed in terms of their Cr and V content chemically bioaccessible in soil. During an incubation period of 3 months, the release of Cr(III) or Cr(VI) species from BOFS (Blast Oxygen Furnace slag) to soil was insignificant. Because of the low solubility of Cr(III), its oxidation on the oxidative surfaces of soil MnO2 can be expected to be negligible. Instead, up to 8 12% of the total V in blast oxygen furnace slag (BOFS, 14 000 mg V kg-1) and high vanadium slag (HVS, 26 000 mg V kg-1) was in the water-soluble form. However, release of V from granulated blast furnace slag (GBFS) to soil was negligible.
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(Helsingin yliopisto, 2017)A diet rich in fruits and vegetables has been suggested to decrease the risk of colorectal cancer and the protective effects of these foods could probably be at least partly mediated by their polyphenolic compounds. The number of different polyphenols is huge and their effects on cells and tissues may differ. The promising results on chemopreventive effects of ellagitannin-rich pomegranate suggest that the other dietary sources of ellagitannins may also be effective in cancer prevention. The overall aim of the research reported in this thesis was to study the effects of cloudberry (Rubus chamaemorus), which is rich in ellagitannins, on all phases of intestinal tumour development. Specifically, the effects of cloudberry on the first two phases of carcinogenesis, initiation and promotion, were studied using the ApcMin mouse model. In addition, the effects of cloudberry extract on the indicators of the last phase of cancer development, progression and metastasis, and particularly cancer cell migration that is essential for this phase, were studied using scattering and wound healing assays in hepatocyte growth factor-induced HT29 and HCA7 human colon adenocarcinoma cell lines. A whole-cloudberry diet containing 10% (w/w) freeze-dried cloudberries significantly decreased the number and size of intestinal adenomas in ApcMin mice. In contrast, cloudberry seeds, cloudberry pulp, or pure ellagic acid, when incorporated into the diets in concentrations that corresponded to the whole-cloudberry diet, had no apparent effect. The effects of cloudberry on the development of adenomas were also compared with the effects of bilberry (Vaccinium myrtillus), which is rich in anthocyanins. Both berries decreased the number of adenomas, but their effects of adenoma size were different: thus, the adenoma size was decreased by cloudberry and increased by bilberry in comparison to the control diet. The opposite effects of the berries on tumour growth were associated with the changes in the gut microbiota, intestinal immunity, and the expression of energy metabolism-related genes. The activation of Met, which is also known as hepatocyte growth factor receptor induces cell migration and is considered to play an important role in tumour metastasis. Cloudberry extract inhibited cell migration by inhibiting the activation of Met in hepatocyte growth factor-induced human HT29 and HCA7 colon adenocarcinoma cells, and thus Met signalling and consequent activation of the phosphatidylinositol 3-kinase/AKT pathway. The activation of Met signalling in the tumours of cloudberry-fed ApcMin mice was also inhibited. The results of the research presented in this thesis suggest that consumption of cloudberry or cloudberry preparations may reduce the risk of colon cancer, slow down the growth of colon adenomas, and have therapeutic value in reducing cancer progression and metastasis. Long-term studies in human subjects are needed to confirm these results.
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(Helsingin yliopisto, 2017)The demand for mechanized tree planting is expected to increase in the future. This dissertation assessed mechanized tree planting in Finland and suggests ways to improve its current productivity. The work on which this thesis is based was described in five peer-reviewed articles (I V) addressing four specific research questions (SQs) that focus on productivity and cost-competitiveness, automation, capacity utilization, and the quality of planting work. While productivity of mechanized planting is higher than manual methods, it is not yet cost-competitive. However, increasing efficiency by skilled operators and worksite selection make it possible for mechanized planting costs to remain lower than those of excavator spot mounding followed by manual planting. Increasing productivity and reducing operating costs are possible with an effective automatic seedling feeding system, although the Risutec APC is not yet sufficiently developed to reach that goal. Planting machine capacity is underutilized and could be utilized more effective to enhance productivity and cost-efficiency. Technical availability of planting machines in Finland is good, and the quality of mechanized planting work is high. Optimization and integration of the entire mechanized planting chain from the nursery to outplanting is important to minimize total cost. In summary, for mechanized planting to be effective the following criteria must be satisfied: machine reliability; highly-skilled machine operator; suitable worksite; seedling quality, availability, and supply to worksite. In the future, it is important to continue developing new and existing machines to enhance productivity, e.g., by continuously working planting machines.
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(Helsingin yliopisto, 2017)The peatlands in Southeast Asia have been impacted and turned to vast carbon dioxide sources (CO2) by land management often involving drainage and deforestation. The amount of released CO2 in decomposition is related to management intensity likely resulting from altered conditions for decomposition. However, the link between decomposition processes and land-use change are poorly understood. To provide insight to the effects of land-use change intensities to decomposition processes in Central Kalimantan, Indonesia, we examined physical (dry bulk density, total pore space, particle size) and chemical properties (pH, loss-on-ignition; total concentrations of N, P, K, C, Ca, Mg, Mn, Zn, Al, Fe, S, Si, DOC and DON; organic matter quality characterized by infrared spectroscopy and on compound level), which together were used to determine the decomposition stage and decomposability (i.e., substrate quality) of peat. The peat biological properties (microbial biomass and enzyme activity) were used to provide insight to the decomposition activity at various land-use types and as a response to known peat properties. The study sites were: near-pristine swamp (i) and drained (ii) forest, deforested and drained degraded (iii), agricultural (iv) and reforested (v) sites. At the most intensively altered deforested sites the peat was denser, finer and enriched with recalcitrant compounds. The highest enzyme activity and microbial biomass were in the surface peat of swamp forest, where the amount of labile carbohydrates was highest. The six years ago reforested site did not yet show signs of recovery in peat properties, which was likely due the limited litter production capacity of the young plantation and microbial activity limited by chemical weeding. The main conclusion is that the litter input, or rather the lack of it after land-use change, and intensive management practices forms the main factors affecting to decomposition processes and leading to poorer substrate quality and reduced biological activity.
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(Helsingin yliopisto, 2017)This thesis focused on the bioreactive pools of silicon (Si) in sediments and phenomena affecting Si release from sediments. There are several potentially mobile pools of Si in sediment, e.g. biogenic Si (BSi), dissolved Si, and adsorbed Si (AdSi). These various Si pools make the investigation of a single pool challenging because of the interference caused by other Si pools. To evaluate the impact different Si pools have on the Si cycle of water ecosystems, it is important to have reliable estimates of the pool sizes. In this thesis, a Bayesian probability model was successfully created to separate two pools of Si, AdSi, and BSi in a catchment area in Southern Finland. The potential correlation between AdSi and BSi was studied to determine whether the size of the AdSi pool could be inferred from the total Si pool (AdSi + BSi). Bayesian inference was also successfully utilized for the explicit separation of different sources of variation caused by measurement imprecision and inter-sample variation. Clear differences were observed between the studied AdSi and BSi pools. The potential error caused by simultaneous extraction of AdSi in BSi determinations was also quantified. The role of land use and vegetation on the Si speciation was also taken into account and seen to affect the amounts of different Si species in sediments. Erosion and nutrient leaching can have large effects on the BSi speciation in water and sediments. The role of phytoliths, amorphous silica originating from plants, was seen as an important Si species to be taken into account in future research and modeling. The effects of anoxia on Si release from sediments were also studied. Because of the chemical similarities with phosphorus (P), the same well-known processes that affect adsorbed P and its release could therefore affect Si and its release. This assumption and the effects of anoxia on AdSi dynamics in surface sediments were addressed by two separate experiments: a sequential extraction for the effects of anoxia on different AdSi fractions and a longer-term release dynamics experiment. The study areas were a small catchment area in Siuntio and the Vantaa River estuary in Southern Finland. Our study showed that anoxia does affect the release of Si. It did not however enhance the release of Si, contrary to the a priori assumption. Silicon also appeared to be released more slowly under anoxic than oxic conditions in most of the studied sediments. The results indicated that anoxia can both increase and decrease Si mobilization. The results were, however, far from clear-cut and more studies are clearly needed to unravel the behavior of Si under anoxic conditions.
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(Helsingin yliopisto, 2017)The purpose of the study was to evaluate technical efficiency in smallholder rice production and how it relates to the production system and participation in agricultural microcredit in Northern Ghana. Smallholder farmers play an important role in agricultural production in Ghana and account for about 80 percent of domestic food production. However, smallholders continue to face challenges concerning access to and utilization of production resources thus constraining their productivity and efficiency. Research has shown that raising the productivity and efficiency of smallholder farmers requires an improvement in access to and utilization of agricultural inputs particularly microcredit, fertilizer and irrigation. Available statistics show that while global food production is on the increase, many developing countries particularly in Sub-Saharan Africa continue to face the challenge of inadequate food production. The critical factors limiting agricultural production in most of these countries include resource constraints, over-reliance on rainfall, low uptake of improved technologies, weak and poorly developed input and output markets, weak extension service and inadequate government support for agriculture. This thesis, based on four articles, used data from a farm household survey conducted in 2014 involving 300 smallholder rice-producing households in Northern Ghana. The empirical analysis used both parametric and non-parametric frontier approaches to estimate efficiency. The study also used propensity score matching to account for self-selection arising from non-randomness in assignment of participants into irrigation and microcredit. Probit analysis was used as the selection model to estimate participation in microcredit and irrigation. In article I, the study estimated technical efficiency and its determinants using an extended Cobb-Douglas stochastic frontier production function. Mean technical efficiency was 63.8 percent, indicating considerable scope for improving the efficiency of production at the current level of technology and input use. Irrigation technology and double-cropping were associated with higher productivity. The study also revealed regional variation in productivity among the producers. In article II, the study evaluated technical efficiency of microcredit users and non-users using a Cobb-Douglas stochastic frontier production function. The study addressed self-selection into microcredit using propensity score matching. The empirical results showed a non-significant association between microcredit and technical efficiency. The result may be due to the small loan sizes. The study also revealed regional variation in farmers participation in microcredit. In article III, the study compared the technical efficiency of irrigators and non-irrigators using a Cobb-Douglas stochastic frontier production function which incorporated an inefficiency effects model. Self-selection into irrigation was addressed using propensity score matching. Based on a heterogeneous production technology assumption, irrigators were found to be 9.2 percentage points more efficient than rain-fed producers. The difference in efficiency was however larger when selection bias was ignored and the wrong technology type was assumed. In article IV, the study investigated scale efficiency of smallholder rice farmers in northern Ghana using a two-stage data envelopment analysis (DEA). The DEA scores from the first stage were regressed on farm and farmer characteristics using truncated regression with bootstrap to overcome the limitations associated with the standard Tobit model in two-stage DEA models. Smallholder farmers in the study area had a scale efficiency of 69.5 percent. Larger farms were found to be more scale efficient justifying the need for smaller farms to expand their scale of operation. The study also identified socio-economic factors associated with the scale efficiency of smallholder rice production in the study area. The results of the study highlight considerable inefficiency in production implying that there is scope for enhancing farmers level of efficiency. The use of agricultural microcredit by smallholders remains a critical challenge in the study area. Irrigation technology had a positively significant relationship with efficiency and productivity of the farmers while participation in farmer-based organizations was positively related to efficiency of production. Farmer groups are important to smallholder producers because they are effective conduits for extension delivery, access to inputs, agricultural microcredit, among others. Incentivizing these farmer groups will therefore enable them to continue to offer such services to their members. Keywords: Technical efficiency, irrigation, microcredit, smallholder farmers, Northern Ghana, stochastic frontier analysis, propensity score matching, probit model, selection bias.
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Low apoplastic water potential in trees - dehydration stress on living cells and embolism in xylem (Helsingin yliopisto, 2017)Low apoplastic water potentials can affect trees by decreasing the hydraulic conductivity of xylem due to embolism and by causing dehydration stress in living cells. Low apoplastic water potentials regularly occur in trees during summer and winter. These can either be caused by loss of water due to transpiration or by freezing due to the chemical properties of ice. In this thesis the effects of low apoplastic water potential on trees were studied by causing low water potentials with three different methods: desiccation, freezing and by adjusting the osmotic concentration of xylem sap. Tree responses in this thesis were measured with stem diameter changes, leaf gas exchange, tree temperature and xylem water potential. Living parenchyma cells are thought to have negligible effect on xylem diameter changes but this thesis shows that the role of parenchyma can, in fact, be much more significant. Evidence for the major role of parenchyma cells in the diameter changes of frozen xylem also supported the theory of extracellular freezing. Furthermore, mesophyll cells were shown to react to freezing with a rapid depression of photosynthesis. It was also studied how a pressure increase in the xylem conduits, resulting from low water potentials, affects tree water relations during embolism formation and ice propagation. A gas burst was detected emerging from the tree stem during freezing. A decrease in the amount of gases in the xylem conduit can benefit trees in avoiding winter embolism. It was also experimentally confirmed that the formation of embolism in trees can temporarily even help relieve water stress due to the so called ´capacitive effect´. Low apoplastic water potential affects both the xylem and living cells in trees, and the interconnectedness of these responses are also shown in this thesis.
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(Helsingin yliopisto, 2017)Most cropping systems in the Boreal Nemoral region of Europe are characterized by intensified cereal production, which has resulted in a heavy dependence on foreign vegetable protein imports for feed supplementation and high consumption of synthetic fertilizer. This in turn have caused numerous critical environmental impacts such as copious greenhouse gas emissions from fertilizer production and use, heavy reliance on a narrow range of crop protection methods, leading to risks of resistance to agrochemicals, nutrient runoff and losses in soil health locally, and in land-use change abroad. Hence, crop diversification is needed, and this work focuses on the potential to use grain legumes to help meet the demand for the local vegetable protein and to mitigate the environmental impacts resulting from the current narrow diversity on crop rotations and from the feed and fertilizer trade. In this dissertation, three grain legume crops, namely faba bean (Vicia faba L.), narrow-leafed (NL) lupin (Lupinus angustifolius L.) and lentil (Lens culinaris Medik.) were grown in field trials in order to assess their potential adaptation to the Boreal Nemoral region of Europe and to find their best place in the cereal-based crop rotations that are conventional in the region. The research focused on 1) the protein yield potential of each crop and their nutritive quality particularities, 2) the pre-crop effect of cereals on grain legumes, and 3) the exploration of flowering time in faba bean as a key component of adaptation to high latitudes. The results show, that faba bean was the crop with highest protein yield stability, and with higher protein concentration than is achieved at lower latitudes, whereas lentil and narrow-leafed lupin had comparable protein concentration as those achieved in other locations. Nutritive quality of all three crops was within the normal range, and amino-acid and DIAAS scores suggested that cultivar selection is important, since major variations in the content of lysine, cysteine and tryptophan influence the feed and food value. The screening trials revealed that among the available lentil and NL lupin cultivars, earliness is sufficient with some reaching maturity in about 100 days, whereas significant improvement on the earliness of Kontu faba bean is needed in order for the crop to be grown in the northern most part of the Boreal Nemoral region. The crop rotation trial showed that NL lupin produced equally high yields after turnip rape and oat, while faba bean gave higher yields after turnip rape and then after barley. Overall, the pre-crop effect on nutrient composition of NL lupin was less evident than on that of faba bean, the latter having 19, while the former 7 significant differences out of the 88 nutrient uptake variables measured. Among these 26 significant measures, barley was the best pre-crop in 9 variables, and oat in 5. The pre-crop effect was present on both the shoot and seed composition, and it was apparent that the pre-crop effect was able to influence soil nutrient availability and thus uptake. This study shows some insight about best pre-crop for grain legumes, but the effects need to be tested further to elucidate the mechanisms and to verify the reproducibility of such effect on crop sequences. The upgraded flowering model showed that flowering control in faba bean in addition to photoperiod and temperature sum, depends on solar radiation (as measured by PAR or sunshine duration, the former providing a better model fit), and water deficit (as measured by the Sielianinow hydrothermal index K ). Understanding the effect of these two new variables in flowering makes it possible to seek more types of variation in earliness be used to identify sources of variation that can serve as material for the selection and development of new cultivars for high latitudes or short seasons. Overall, this study shows that faba bean and NL lupin have great potential for diversifying crop rotations in the Boreal Nemoral region of Europe, whereas the susceptibility of lentil to the wet autumns typical of the region will make its management challenging. Each of the crops has different advantages, so they complement each other in terms of optimum soil type, nutrient uptake and nutrient composition. It is recommended that their cultivation should be promoted not only to solve the vegetable protein deficit, but also to improve the sustainability of cropping systems in the region.
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Modelling intra- and inter-annual growth dynamics of Scots pine in the whole-tree carbon framework (Helsingin yliopisto, 2017)Environmental factors have a dual effect on growth as they affect both the momentary growth rate (direct effect) and the rate of ontogenetic development (indirect effect). Photosynthesis on the other hand is the source of carbon that is needed for growth, respiration and other purposes. There are two opposite theories about the factor determining growth rate: 1) the availability of carbon for growth (source limitation) and 2) limitation that environmental factors cause on tissue ability to grow (sink limitation). Understanding the responses of the growth of tree organs (wood, needles, roots) to environmental and other factors is important to be able to understand the changes in tree growth and carbon balance in changing climatic conditions. The purpose of this study was to define the effects of temperature on Scots pine growth at different temporal scales and to estimate the relative importances of the source and sink effects on growth. For that, a dynamic growth model CASSIA (Carbon Allocation Sink Source InterAction) was constructed. CASSIA was able to predict daily primary and secondary wood and needle growth rate variation with indirect and direct effects of temperature. In addition, the temperature of warm previous late summer was observed to lead to enhanced length of the growth period (in temperature accumulation units) of shoots in the following year. Growth onset during spring was observed to be a continuous process determined by temperature accumulation, instead of momentary temperatures. Short-term growth variations in normal conditions were concluded to be sink limited because CASSIA was able to predict the within year growth with temperature and without direct effect of photosynthesis or stored carbon. On the other hand carbon source effect (gross primary production) was needed to produce the between year variation in growth. According to the results of this study, growth is limited by a complex combination of sink and source effects. Furthermore, environmental factors affect growth at different time scales varying from instantaneous effects to delayed effects from previous year(s). More research is needed to identify the factors determining the carbon flows to different processes.
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(Helsingin yliopisto, 2017)Soils that are contaminated with organic aromatic compounds such as polyaromatic hydrocarbons (PAHs), polychlorinated dibenzo-p-dioxins and dibenzofurans (PCDD/Fs) and 2,4,6-trinitrotoluene (TNT) have previously been treated by combustion at elevated temperatures. Although, combustion is effective, it is expensive due to high energy and equipment requirements. However, innovative technologies such as the use of fungi and/or biochar can offer an alternative option that is friendly to the environment in treating such soils. This thesis evaluates three treatment options to treat these contaminants in soil: 1) the use of fungi growing on pine bark, 2) the use of fungal enzymes, and 3) treatment with both fungi and wood derived biochar. Fungal treatment of TNT-contaminated soil was applied in both laboratory and in pilot scale experiments. In the laboratory experiments, fungi were tested for their capability to grow in soil contaminated with the explosive 2,4,6-trinitrotoluene (TNT) and to accelerate its degradation. TNT concentration in the soil was 1000 mg kg-1. White-rot fungi, Gymnopilus luteofolius, Kuehneromyces mutabilis, and Phanerochaete velutina grew in the contaminated soil and produced a significant amount of manganese peroxidase (MnP) in TNT contaminated soil during that incubation, but no laccase. The most efficient fungus, P. velutina, degraded 80% of TNT in 2.5 months. The soil treatment process was scaled-up in a 0.56 m3 reactor with 0.3 t of TNT-contaminated soil and P. velutina grown on pine bark. TNT concentration in the soil was 1000 mg kg-1 and the soil:fungal inoculum ratio was 30:1. P. velutina degraded 70% of TNT in 49 days, and no further degradation occurred during the next 58 days of incubation. TNT metabolites, namely 4-amino-2,6-diaminotoluene and 2-amino-4,6-diaminotoluene, accounted for less than 0.5% of the original TNT concentration at the end of the incubation. For PCDD/F-contaminated soil, the approach was to treat the soil with either fungal inoculum or crude MnP. Treatment with fungal inoculum proved to be an effective treatment option as PCDD/Fs were degraded 62% and 64% of the WHO-TEQ (World Health Organisation Total Equivalent) value by Stropharia rugosoannulata and P. velutina, respectively, compared to a control where no degradation was observed. However, when PCDD/F-contaminated soil was treated with crude MnP, no degradation was observed even though significant levels of MnP activity were detected in the soil. Treatment of PAH-contaminated soils (humus-poor soil named sloam and humus-rich forest soil) were studied. Pyrene-contaminated soil was amended with wood-derived biochar, and the ability of fungi to grow in the amended soil was tested. Agrocybe praecox and P. velutina survived well in the amended soil and were selected for further studies. In addition, the role of fungi in pyrene sorption to amended soil was investigated. Fungal treatment of pyrene-contaminated soil amended with biochar increased the sorption of pyrene up to 47 56% to biochar amended forest soils compared to the controls (13 25%) incubated without fungi. Strong fungal/biochar synergistic effects were observed in cases of the sorption of pyrene in the amended soils. In non-sterile contaminated forest soil amended with biochar and incubated with one fungus, higher levels of pyrene (50%) was sorbed to the soil compared with a mere 13% in a similar soil without the fungus. In humus-poor sloam amended with biochar and incubated with fungus, only 9 12% pyrene was sorbed to amended soil. Similar results were obtained for both fungi used in the study. They had significant impact on forest soil with a higher organic matter content compared with sloam. Fungal treatment provides a viable treatment option and an alternative to traditional treatment options such as combustion of soils that are contaminated with organic aromatic contaminants. Fungi have shown strong potential to degrade these contaminants in soil. The addition of biochar and fungi to PAH- contaminated soil may help to reduce the risk of leaching of contaminants to ground water and above all to promote remediation of contaminated soils.
