Maatalous- metsätieteellinen tiedekunta


Recent Submissions

  • Kymäläinen, Maija (Helsingin yliopisto, 2015)
    The need to replace fossil fuels with renewable energy sources has become an increasingly important field of research and development in order to combat the global climate change. Wood is a well utilised and much studied source of energy that has some inherent problematic characteristics common to all lignocellulosic biomass. Moisture affects the entire supply chain of wood fuels negatively by complicating transport, handling, storage, and combustion. During storage, the wood takes up moisture, which leads to fungal deterioration and consequently losses of heating value. The problem has been addressed by reducing the hygroscopicity of wood through the thermal pre-treatment process of torrefaction. In addition to hydrophobicity, torrefaction leads to other beneficial characteristics that are expected to improve the performance of lignocellulosic biomass in logistics and combustion. Due to hydrophobicity the material is said to be resistant to fungal degradation and subsequent dry matter losses. The combustion would be efficient without the need to evaporate water that can form up to 60% of untreated woody biomass. However, only few studies exist, and the material s performance in storage has been pointed out as an important research area. To tackle this challenge, this thesis aimed to provide much needed answers related to the storage properties of torrefied wood and charcoal, most importantly the effect of moisture. This thesis is made up of four studies, in which the sorption properties and fungal degradation of torrefied spruce and birch, as well as charcoal produced from the same feedstock, were investigated. In one experiment torrefied pellets and steam explosion pellets were compared with the undensified material. It was found that the pyrolysed material adsorbed only minor amounts of water vapour both in laboratory experiments as well as in an outside storage trial. The hydroxyl group accessibility and the particle size of the material were also reduced. However, although the capillary absorption was slower, the capacity for water uptake was increased. This led to high moisture contents during the storage trials. It was also shown that the material can serve as the sole carbon source and is therefore subjected to fungal degradation. The degradation was slow, but significant dry matter losses were recorded from certain samples in laboratory conditions. Furthermore, the fungal activity increased the material s moisture content. The torrefied material hosted abundant fungal flora following outside storage trials, and many of the identified genera were known allergens. Also it was shown that torrefied pellets do not tolerate contact with water. Many of the properties of torrefied wood are favourable in terms of easier handling and improved combustion behaviour. However, the results presented in this thesis show that the storage of the material may not be as easy as speculated. The torrefied wood, whether as chips or pellets, should be stored in covered areas and direct contact with water should be avoided. The working safety issues should be carefully addressed to avoid unnecessary exposure and accidents when handling the pre-treated material.
  • Zou, Ling (Helsingin yliopisto, 2015)
    Factors limiting barley yield have been reduced since the Green Revolution globally. Nevertheless, higher yields are pursued with the pressure to feed the increasing human population and domestic animals. However, sustainability can be impaired by the cereal monocultures, in particular, cereal-specific pathogen inocula can increase at the cost of diversity of soil microfauna. Use of pesticides has selected for resistance in weeds and pathogens. Use of mineral fertilizers has resulted in waste of resources and pollution. In Finland, about half of the arable land is used for continuous cereal production, and barley (Hordeum vulgare), as an important source for food and feed, is the most cultivated cereal crop. In this dissertation, research focused on evaluating the effects of various rotation crops on weeds, pathogenic fungi, soil fertility and yield of subsequent barley. The competitive ability of six crops, namely buckwheat (Fagopyrum esculentum), caraway (Carum carvi), faba bean (Vicia faba), hemp (Cannabis sativa), common vetch (Vicia sativa) and white lupin (Lupinus albus) with weeds was evaluated in glasshouse and field experiments. In the glasshouse experiment, couch grass (Elymus repens) grown with buckwheat accumulated the least dry matter. Activated charcoal was used to exclude the effect of root exudates from donor crops. The results indicated that activated charcoal incorporated in the soil deactivated buckwheat root exudates that apparently inhibited the growth of couch grass. In the field experiment, buckwheat s fast growth and formation of effective leaf area inhibited growth of weeds most effectively among the crops tested. The effect of turnip rape [Brassica rapa L. ssp. oleifera (DC.) Metzg.] on several soil pathogenic fungi was evaluated in a field trial in two growing seasons involving five different cultivation regimes: mixed culture of barley and turnip rape, turnip rape sown after barley, and turnip rape incorporated as green manure either in autumn or in spring, with continuous barley monoculture as a control. Soil fungal community structure was monitored with capillary-based LH PCR of the ITS region using primers ITS1F/ITS4. The mixed culture and sowing turnip rape after barley did not significantly decrease the relative abundance of Fusarium spp. Incorporation of turnip rape plants into the soil, as a source of organic matter and nutrients, was associated with a low relative abundance of Fusarium spp. Fungal diversity was the lowest and the relative abundance of Fusarium spp. the highest in continuous barley. Higher fertilizer application and organic matter incorporation, leading to high fungal diversity, seemed more important in affecting Fusarium spp. than the allelochemicals of turnip rape, as turnip rape extracts did not detectably inhibit the growth of F. culmorum in an in vitro test. In growth media of different nutrient levels, 10 g soil were suspended in 100 mL sterile water, then 400 μL of the suspended solution was spread on the media of each nutrient level with four replicates. The number of fungal colonies was counted. The soil Fusarium CFU count was higher on nutrient-poor growth medium than on rich medium, supporting the results of field experiments. Results of sequencing indicated that Penicillium spp. might also tolerate low nutrient availability. In two experiments that ran 2010-2012 and 2011-2013, faba bean, turnip rape and barley were sown as first crops and their residues were tilled into the soil after harvest in blocks in the first year. In the following year, barley, buckwheat, caraway, faba bean, hemp and white lupin were sown in each block and incorporated either at flowering stage (except barley) or after harvest. Barley yield and grain protein concentration were determined. Mineral N concentrations in the plough layer two months after incorporation of crops and before sowing barley in the following spring were determined. In the third year, all the plots were sown with barley. The beneficial effect of faba bean and turnip rape, as first crops, on yields and grain protein concentration of barley was still detectable in the third year. Barley yields after white lupin, faba bean and hemp, as second crops, were higher than in continuous barley. Barley grain protein concentration was increased after faba bean. In contrast, barley yield and grain protein concentration were not improved after buckwheat and caraway. Incorporation of plants at flowering stage posed a risk of increased N leaching, suggesting that incorporation of plants should be delayed or catch crops should be used during winter to reduce N leaching. The response of barley yields to increased mineralized N from green manure or residues after harvest of rotation crops was significant only in the first experiment conducted in 2010-2012 suggesting that increased mineral N in the plough layer has minor influence on barley yield. Thus, rotation with faba bean, white lupin and hemp was beneficial to barley grain yield. In addition, barley grain protein concentration was increased after rotation with faba bean. Weed growth was most strongly suppressed by buckwheat as a complement to current weed management regime, but, rotation with buckwheat and incorporation of its residues did not improve the yield of the successive barley. The effect of glucosinolates of turnip rape on soil-borne pathogens was outweighed by high fungal bio-diversity suggesting that allelochemicals released from plants sown at a realizable density in the field are unlikely to control pathogens. Maintaining high microbial diversity through sufficient nutrient input is crucial to control pathogenic Fusarium spp. populations.
  • Zhang, Yanlei (Helsingin yliopisto, 2015)
    Type 2 diabetes occurs as a consequence of aging, family history, physical inactivity, unhealthy diet and obesity and it is an increasing public health problem worldwide. The condition is associated with high rates of mortality from co-morbid cardiovascular diseases and poor health-related quality of life (HRQoL). A large proportion of individuals with type 2 diabetes are not diagnosed for up to a decade after onset unless a screening programme has been implemented. The estimated prevalence of undiagnosed diabetes in China accounts for about 60-70% of the diabetes population. Diabetes education that is targeted at the general population is the key to increase public knowledge and awareness and is a fundamental building block for addressing the diabetes epidemic. Screening for identifying undiagnosed diabetes could lead to earlier identification and intervention, and postpone or prevent the onset of diabetes and its complications. However, there is a paucity of study on the impact of education and screening programmes on HRQoL, lifestyle modification of the targeted population, and the cost-effectiveness of such programmes. The objectives of this study were to investigate 1) the cost and effectiveness of a population-based education programme to increase public knowledge and awareness of diabetes; 2) the cost-effectiveness of two different screening tools for undiagnosed diabetes; 3) impact of type 2 diabetes and its complications on individuals HRQoL; 4) impact of a screening programme on individuals overall HRQoL, depression dimension and lifestyle modification. This study was based on data analyses of two population-based diabetes surveys conducted in 2006 (Survey A) and 2009 (Survey C), and a dataset of diabetes high-risk population identified through the Qingdao Diabetes Prevention Program (QD-DPP) between 2007 and 2010 in Qingdao, China (Survey B). The same stratified, random cluster sampling method was used in Surveys A and C to recruit a representative sample of the general population who had lived in Qingdao city for at least five years. A total of 5355 individuals in Survey A and 5110 in Survey C aged 35-74 years participated in the surveys. A total of 3108 rural participants who did not have diabetes at baseline in 2009 were invited for a re-examination and 1782 individuals attended the follow-up survey. A standard 2h 75g oral glucose tolerance test was administrated to all participants in both surveys. Diabetes education and health promotion information and activities under the framework of QD-DPP were given via printed and audio-visual media, the internet, free distribution of information booklets and diabetes risk score (DRS) flyers that targeted the entire population of 1.94 million who lived in the intervention areas. An adult with a DRS more or as much as 14 was considered at high-risk for diabetes and invited to a nearby community clinic for a free capillary blood glucose test. The proportions of participants who correctly marked obesity, physical inactivity and positive family history of diabetes as the risk factors of diabetes were doubled in both urban and rural populations, irrespective of age and gender during the QD-DPP education campaign period. The cheapest way to inform 1000 individuals about type 2 diabetes was to distribute DRS flyers (¥54, ¥ = Chinese yuan), followed by the newspapers articles (¥77), booklets (¥313) and by radio programmes (¥375) (1 ≈7¥, for the year 2015). The fasting capillary glucose (FCG) test and Chinese DRS questionnaire were used as the first-line screening tools and these were evaluated for detecting undiagnosed diabetes in primary care settings. The sensitivity of FCG and DRS was 65.1% and 65.8%, whereas their respective specificity was 72.4% and 55.2%. The costs per undiagnosed diabetes identified at the optimal cut-off values of 6.1 mmol/l for FCG and 14 for DRS were ¥674 and ¥844, respectively. The area under curve (AUC) was higher for FCG than for DRS (75.3% vs. 63.7%, p less than 0.001). People with previously known type 2 diabetes reported that the symptomatic comorbidities had a strong negative impact on HRQoL; no significant difference was detected between people without diabetes and with newly diagnosed diabetes. The screening and labelling as pre-diabetes or normoglycaemia had no adverse impact on the participants overall HRQoL and depression. An improvement in lifestyle as measured by the frequency of physical activity and vegetable intake was observed at 3 years post screening in both groups. In conclusion, the QD-DPP education campaign efficiently increased public knowledge and awareness of diabetes. The DRS questionnaire is a simple, non-invasive and reliable first-line screening tool to identify undiagnosed diabetes at primary care settings. The diabetes screening programme in Qingdao generated positive changes towards a healthy lifestyle and did not result in any harm to the participants.
  • Détry, Nicolas (Helsingin yliopisto, 2015)
    Oxidoreductases are found in all living organisms and play essential roles in housekeeping, perception of environmental stress, plant-pathogen interactions, defense reactions, and pathogenicity. In particular, laccase, peroxidases and NADPH oxidase, have been implicated in virulence of phytopathogenic fungi in pathogenicity. Despite its relevance towards plant microbe interaction, the identification and comparative analysis of fungal peroxidase-encoding genes at the genomic level have been limited by the lack of a bioinformatics platform as well as paucity of information on transcript profiling of potential candidate oxidoreductase genes. In this project, one of the primary tasks addressed was the construction and development of a new fungal peroxidase database (fPoxDB). The availability of fPoxDB platform facilitated comparative and evolutionary studies of fungal peroxidases at the genomic level. The database contains 6,113 peroxidase genes of 25 gene families from 331 genomes. The archived genes were subjected to pre-computational analyses using eight different bioinformatic tools: SignalP 3.0, SecretomeP 1.0f, TargetP 1.1b, predictNLS, ChloroP 1.1, TMHMM 2.0c, PSortII, and InterPro Scan. Similarity search tools including HMMER, ClustalW, Blast, and BlastMatrix are provided on the platform. A web interface enables researchers to browse the database via either species or class . Graphics support the work and enhance user-friendliness. Retrieved data can be exported to other family web-systems including the comparative fungal genomics platform (CFGP). In parallel to the above study, the second project was focused on in silico comparative analysis fungal NADPH oxidase (Nox) genes sequences. Nox proteins are transmembrane enzymes found in most eukaryotic organisms and influence many biological processes by generating reactive oxygen species (ROS). In fungi, Nox enzymes play roles in pathogenicity, such as the weakening of plant cell walls by ROS. The enzymes exhibit high sequence similarities to the ferric-reductases (Fre) and ferric-chelate reductases (FRO) proteins, which are involved in reduction of Fe3+ to Fe2+ for iron uptake. A total of 34 eukaryotic genomes, covering 28 fungal, one Oomycota, three animal and two plant species, were subjected to bioinformatic analysis. The results indicate that the properties of fungal Nox genes differ from those of the human and plants, providing novel insights that will enable more accurate identification and characterization of the fungal genes. In the third project, as not much is known is about precise role of oxidoreductase encoding genes in pathogenesis, we explored expression profiling of a typical oxidoreductase gene, laccase, in Heterobasidion conifer pathosystem. Laccases are multi-copper oxidoreductases catalyzing the oxidation of phenolic substrates, and they play diverse roles in plants and fungi. In fungi, laccase have been shown to be involved in pathogenicity, as well as in lignin degradation. To understand the potential roles of laccases of the forest pathogen Heterobasidion annosum, a total of 18 laccase genes was identified in this fungus and phylogenetically analyzed. The expression levels of the genes, and laccase activities, during growth of H. annosum on its host in the presence or absence of additional carbon source, such as glucose and sucrose, were investigated. Based on increased transcript expression levels eight laccases were considered to be potentially involved in H. annosum virulence. In summary, we provide the research community with a database dedicated to fungal peroxidases, and our in silico analysis affords new insights in the structure of fungal NADPH oxidases. Lastly, we present experimental evidence that some H. annosum laccases might be involved in virulence during infection of non-suberized Scots pine seedlings.
  • Lienemann, Taru (Helsingin yliopisto, 2015)
    Salmonella is one of the most commonly reported foodborne pathogens and enterohaemorrhagic Escherichia coli (EHEC) is one of the most dangerous. They both spread by zoonotic and person-to-person transmission routes. Most Salmonella infections are characterized by mild-to-moderate self-limited diarrhea but also serious disease resulting in death has been reported.Bloody diarrhea is a common symptom of human EHEC infection and the infection may lead to severe post-infection disease such as hemolytic uremic syndrome (HUS), thrombotic thrombocytopenic purpura (TTP) and even death. The purpose of this thesis was to investigate the diversity of Salmonella and EHEC strains isolated from domestically acquired infections using several pheno- and genotyping methods for surveillance and outbreak investigation purposes as well as evaluate certain epidemiological typing methods in Finland. All Salmonella and EHEC isolates of domestic origin during 2007-2014 in Finland were studied. Serotyping, phage typing, antimicrobial susceptibility testing, phenotype microarray, pulsed-field gel electrophoresis (PFGE) and multilocus variable-number tandem repeat analysis (MLVA) were applied as epidemiological typing tools for Salmonella isolates. EHEC isolates were analyzed using serotyping, phage typing, antimicrobial susceptibility testing, virulence gene detection (stx1, stx2, eae, hlyA and saa) and PFGE. During the study period, the number of domestically acquired Salmonella infections has decreased about one fifth compared to the previous decade whereas the number of domestic EHEC infections have increased about one third.Th e incidence of Salmonella infections was highest in 2012 (7.5/100,000 population) and lowest in 2014 (5.4/100,000 population). The incidence of EHEC infections was highest in 2013 (0.33/100,000 population) and lowest in 2008 (0.07/100,000 population). 15% of all Salmonella strains and 70% of all EHEC strains were considered domestically acquired. A total of 131 different Salmonella serovars were detected. The most common serovars were Typhimurium (32%), Enteritidis (15%) and group B (6%). Among Typhimurium strains, phage types DT1 (37%), RDNC (18%) and DT104 (9%) were the most common ones. The most frequently detected phage types among the domestically acquired S. Enteritidis infections were PT8 (17%), PT1B (14%) and PT4 (13%). Th e majority of domestic Typhimurium and Enteritidis (60%) strains were susceptible to tested antimicrobials. During the study period, a total of 188 infections caused by EHEC were detected. Most of them were caused by serotype O157:H7 (60%). The majority of O157 strains (63%) were unable to ferment sorbitol. PT8 was the most common phage type among the sorbitol-negative and PT88 among sorbitol positive O157 strains. Among non-O157, 22 distinct O:H serotypes were detected. The most common ones were O26:H11, O103:H2 and O145:H-. The majority of domestic EHEC strains (81%) were susceptible to all tested antimicrobials: 96% of O157:H7/H- and 60% of non-O157 strains. All O157 strains carried stx2 (40% in combination with stx1), eae and hlyA genes. In contrast, 55% of non-O157 stains had stx1 gene and 76% carried eae and hlyA genes. The MLVA method was found to be a powerful epidemiological tool for S. Typhimurium with discriminatory power similar to PFGE. In addition, MLVA was faster, cheaper and the results were easier to compare between laboratories. The domestic S. Typhimurium strains were divided into 170 distinct MLVA types (diversity index 0.891). In MLVA, the three most common profiles (3-16-NA-NA-0311, 3-15-NA-NA-0311 and 3-17-NA-NA-0311) counted for 47% of the strains showing that the lack of locus STTR6 and locus STTR10p was characteristic for domestic S. Typhimurium. However, XbaI-PFGE remains a useful genotyping method for investigations of other Salmonella serovars and EHEC strains. The interpretation of XbaI-PFGE profiles can be challenging as demonstrated by a Finnish nationwide outbreak caused by S. Newport and S. Reading -contaminated iceberg lettuce. The S. Reading strains had four diff erent XbaI-PFGE profiles. Based on epidemiological information, all these different variants of the outbreak causing strains were considered as outbreak-related. The sources of the most EHEC outbreaks remained undetermined. In one out four EHEC O157 outbreaks, unpasteurized milk was found as the source of the infections. Although 40% of the domestic EHEC strains were non-O157, only strains of serogroup O157 caused outbreaks in Finland. However, non-O157 strains caused several family clusters and were linked with HUS. In 2009, a sorbitol-fermenting EHEC O78:H-:stx1c:hlyA was detected in blood and fecal samples of a neonate. This EHEC serotype had not been seen in Finland prior to this family-related outbreak and bacteremia caused by EHEC is exceptionally rare. Taken together, Salmonella and EHEC infections are a major public health concern. This thesis provides new information about the characteristics of Salmonella and EHEC strains isolated from domestically acquired infections in Finland and evidence that effective surveillance is needed for early detection and prevention of the spread of Salmonella and EHEC infections. In particular, typing methods used should be internationally harmonized and the results made comparable.
  • Suurnäkki, Suvi (Helsingin yliopisto, 2015)
    Cyanobacteria produce variety of secondary metabolites that may be toxic or cause odor problems in water environments. Taste and odor problems occur worldwide in freshwater, drinking water, and in the fish industry. Cyanobacterial mass occurrences pose a threat to users of water due to hepatotoxic or neurotoxic strains. Toxins are also a risk to recreational water use and have caused number of animal poisonings. Anatoxin-a and homoanatoxin-a are alkaloid neurotoxins produced by strains of several cyanobacterial genera. Cyanobacteria also produce strong odorous metabolites that cause musty and/or earthy odor and taste in water. The best known of these odorous metabolites are geosmin and 2-methylisoborneol (MIB). These odorous metabolites cause problems in extremely low concentrations due to the very low odor threshold of humans. Producers of bioactive metabolites and non-producing strains can occur in the same species and thus cannot be distinguished morphologically by microscopy techniques. The aims of this study were: I) to identify the ana gene cluster responsible for the biosynthesis of anatoxin-a from the strain Anabaena sp. 37; II) to develop molecular detection methods (PCR, quantitative PCR, restriction fragment length polymorphism RFLP) for the detection of potential anatoxin-a and homoanatoxin-a producers, and apply methods to environmental samples; and III) to develop a PCR-based molecular method for the detection of the producers of geosmin and MIB in cyanobacteria. Of the genomic sequence of Anabaena sp. 37, the gene cluster responsible for anatoxin-a biosynthesis (ana) was identified based on the comparison to the gene cluster from cyanobacteria Oscillatoria sp. PCC 6506. While the organization of the genes differed, the anatoxin-a synthetase genes were highly similar with Oscillatoria sp. PCC 6506 genes. PCR and qPCR detection methods were developed for anatoxin-a producing cyanobacteria. General primers were used to identify all the producer genera at the same time and genus-specific primers for Anabaena or Oscillatoria producers. Primers were designed to recognize the anaC gene and tested with anatoxin-a and/or homoanatoxin-a producing strains in PCR and qPCR. In addition, RFLP analysis of the anaC amplicons was used to simultaneously identify three anatoxin-a producer genera Anabaena, Oscillatoria, and Aphanizomenon. Molecular methods for anatoxin-a producers were also applied to environmental samples. With developed PCR and RFLP methods, the presence of Anabaena and Oscillatoria as potential anatoxin-a producers in Finnish freshwaters and the Baltic Sea was observed. The developed qPCR method was used to quantify the anaC gene copy numbers in Lake Garda during February-November 2013. The gene copy numbers correlated positively with the anatoxin-a concentration measured in lake samples. Thus, the developed method could be used for the detection of potential anatoxin-a and homoanatoxin-a producers in cyanobacterial strains and to predict the amount of anatoxin-a producers from lake water samples. A hundred cyanobacterial strains were studied with solid-phase microextraction coupled with gas chromatography/mass spectrometry (SPME GC-MS) in order to identify the producers of geosmin and MIB. Geosmin was found in 21 strains out of the 100 studied, representing Nostoc, Oscillatoria, Calothrix, Planktothrix, Aphanizomenon, and Cylindrospermum genera. MIB was found in two strains, Planktothrix and Oscillatoria, both also producing geosmin. Cyanobacteria-specific primers were designed to detect biosynthetic genes of geosmin (geoA) and MIB (MIB synthase) and tested with the odorous metabolite-producing strains. Molecular detection by PCR was consistent with chemical detection by SPME GC-MS. Molecular detection methods developed in this study to detect anatoxin-a or odorous metabolites producing strains could be used in surveys to identify possible producers among cyanobacterial strains and in environmental samples.
  • Virtanen, Seija (Helsingin yliopisto, 2015)
    Acid loading from cultivated acid sulphate soils (AS) deteriorates the quality of the recipient waters, especially on the coast of the Gulf of Bothnia. These fields reclaimed in the past without knowing their deleterious consequences still cause long-lasting hazards. The aim of this thesis was to explore redox processes in AS soils in relation to their water management aiming at mitigation the water quality. Redox processes and the quality of pore and discharge water were investigated for 2 ½ years in waterlogged cropped and bare lysimeters as well as in effectively drained cropped lysimeters. This methodology has not been previously used in studies on boreal AS soils. In addition, the level and quality of groundwater was monitored for three years in an AS field. Physical properties of the soil were determined to unravel the ripening processes under different water management systems. The results obtained at the lysimeter and field scales were compared using the similarity approach, a new methodology in soil science. Upon waterlogging, the reduction-induced elevation of pH immobilized Al but concomitantly increased the Fe2+ concentration in pore and discharge water. This reaction pattern maintained the acidity of discharge water. This finding contrasts with the results obtained in warmer environments. The main reasons for the discrepancy were: 1) acidic conditions favour iron reducers before sulphate reducers, 2) the AS soils rich in poorly ordered Fe oxides, 3) low temperature, 4) freshwater used in waterlogging and 5) low labile organic matter in horizons poor in root material. However, intensified drainage caused the oxidation of sulphidic material in subsoils. The oxidation proceeded rapidly, although the most reactive sulphides constituted only 1% of the total sulphides. Ripening processes enhanced the oxidation of sulphides by promoting the diffusion/convection of oxygen and nitrate into the sulphidic horizon. The findings suggest that nitrate may also oxidize sulphides in boreal AS soils. These results highlight the importance of preventing soil ripening in order to keep sulphidic horizons waterlogged and impermeable. The findings reveal that to mitigate environmental hazards it is not rational to waterlog cultivated boreal AS fields close to the plough layer. Otherwise there is a risk that Fe2+ will leach to watercourses, where it will cause acidity as well as oxygen depletion as a result of oxidation and hydrolysis. The study revealed that the acidity retained in the form of secondary minerals retards neutralization and thus counteracts the mitigation measures. Waterlogging of only the transition and sulphidic horizons appears to be the most efficient water management option to improve discharge water quality. This practice can especially be recommended on the coast of the Gulf of Bothnia, where AS soils are abundant in reactive sulphides and may oxidized by nitrate, leading also to increased nitrous oxide emissions.
  • Garlant, Linda (Helsingin yliopisto, 2015)
    This dissertation is aimed at studying the emergence and invasiveness of a new soft rot bacterium: Dickeya solani. Members of the Dickeya genus cause soft rot and blackleg in potato, which is one of the world s most important food crops. D. solani was first isolated in Finland in 2004; since then, it has been identified in many European countries. It most likely emerged in the Netherlands and spread elsewhere in Europe and beyond via the potato seed trade, and it has rapidly became a major threat for potato production, along with the other commonly known soft rot bacteria D. dianthicola and Pectobacterium species. In this study, the ecological aspects and genomics of D. solani were investigated to elucidate the mechanisms underlying its fast spread and high aggressiveness. A real-time PCR test was developed to analyze plant samples containing Dickeya species. This test ensures the fast determination of the amount of Dickeya cells present in symptomatic plant tissue and avoids lengthy and labored procedures for bacterial cell isolation, thereby representing an advantageous diagnostic tool. Biovar 3 Dickeya isolates were biochemically characterized and found to differ from the other known Dickeya species isolated from potatoes and ornamentals in Europe. Taxonomic analysis indicated that these strains belonged to a new species within the genus Dickeya, which was consequently named D. solani. The genome of a Finnish D. solani strain was sequenced to study the invasive character of this new species. Comparative genomic analysis indicated the presence of a set of specific genes involved in the production of toxic secondary metabolites, which triggered the investigation of the ability of D. solani to outcompete other bacterial species present in the potato environment. A newly identified bacteriocin-like molecule produced by D. solani promoted the growth inhibition of some Pectobacterium species, thus partly explaining the rapid colonization and dominance of the potato environment by this novel soft rot pathogen. This study provides novel information about the ecology, taxonomic status and genomics of the new potato pathogen D. solani. This information is likely to contribute to applied studies to improve potato production and plant health in general in the future.
  • Saarela, Svetlana (Helsingin yliopisto, 2015)
    Over the past decades it has been shown that remotely sensed auxiliary data have a potential to increase the precision of key estimators in sample-based forest surveys. This thesis was motivated by the increasing availability of remotely sensed data, and the objectives were to investigate how this type of auxiliary data can be used for improving both the design and the estimators in sample-based surveys. Two different modes of inference were studied: model-based inference and design-based inference. Empirical data for the studies were acquired from a boreal forest area in the Kuortane region of western Finland. The data comprised a combination of auxiliary information derived from airborne LiDAR and Landsat data, and field sample plot data collected using a modification of the 10th Finnish National Forest Inventory. The studied forest attribute was growing stock volume. In Paper I, remotely sensed data were applied at the design stage, using a newly developed design which spreads the sample efficiently in the space of auxiliary data. The analysis was carried out through Monte Carlo sampling simulation using a simulated population developed by way of a copula technique utilizing empirical data from Kuortane. The results of the study showed that the new design resulted in a higher precision when compared to a traditional design where the samples were spread only in the space of geographical data. In Paper II, remotely sensed auxiliary data were applied in connection with model-assisted estimation. The auxiliary data were used mainly in the estimation stage, but also in the design stage through probability-proportional-to-size sampling utilizing Landsat data. The results showed that LiDAR auxiliary data considerably improved the precision compared to estimation based only on field samples. Additionally, in spite of their low correlation with growing stock volume, adding Landsat data as auxiliary data further improved the precision of the estimators. In Paper III, the focus was set on model-based inference and the influence of the use of different models on the precision of estimators. For this study, a second simulated population was developed utilizing the empirical data, including only non-zero growing stock volume observations. The results revealed that the choice of model form in model-based inference had minor to moderate effects on the precision of the estimators. Furthermore, as expected, it was found that model-based prediction and model-assisted estimation performed almost equally well. In Paper IV, the precision of model-based prediction and model-assisted estimation was compared in a case where field and remotely sensed data were geographically mismatched. The same simulated population as used in Paper III was employed in this study. The results showed that the precision in most cases decreased considerably, and more so when LiDAR auxiliary data were applied, compared to when Landsat auxiliary data were used. As for the choice of inferential framework, it was revealed that model-based inference in this case had some advantages compared to design-based inference through model-assisted estimators. The results of this thesis are important for the development of forest inventories to meet the requirements which stem from an increasing number of international commitments and agreements related to forests. Keywords: design-based, Landsat, LiDAR, model-based, multivariate probability distribution, sampling.
  • Hovi, Aarne (Helsingin yliopisto, 2015)
    This thesis presents basic research on how airborne LiDAR measurements of forest vegetation are influenced by the interplay of the geometric-optical properties of vegetation, sensor function and acquisition settings. Within the work, examining the potential of waveform (WF) recording sensors was of particular interest. Study I focused upon discrete return LiDAR measurements of understory trees. It showed that transmission losses influenced the intensity of observations and echo triggering probabilities, and also skewed the distribution of echoes towards those triggered by highly reflective or dense targets. The intensity data were of low value for species identification, but the abundance of understory trees could be predicted based on echo height distributions. In study II, a method of close-range terrestrial photogrammetry was developed. Images were shown as being useful for visualizations and even the geometric quality control of LiDAR data. The strength of backscattering was shown to correlate with the projected area extracted from the images. In study III, a LiDAR simulation model was developed and validated against real measurements. The model was able to be used for sensitivity analyses to illustrate how plant structure or different pulse properties influence the WF data. Both simulated and real data showed that WF data were able to capture small-scale variations in the structural and optical properties of juvenile forest vegetation. Study IV illustrated the potential of WF data in the species classification of larger trees. The WF features that separated tree species were also dependent on other variables such as tree size and phenology. Inherent between-tree differences in structure were quantified and the effects of pulse density on the features were examined. Overall, the thesis provides basic findings on how LiDAR pulses interact with forest vegetation, and serves to link theory with real observations. The results contribute to an improved understanding of LiDAR measurements and their limitations, and thus provide support for further improvements in both data interpretation methods and specific sensor design.
  • Ma, Hairan (VTT Technical Research Centre of Finland Ltd, 2015)
    Milk proteins, sodium caseinate (CN) and whey protein isolate (WPI) are used in food industries as emulsifiers. The stability of an O/W emulsion is dependent on the electrostatic and steric repulsion provided by the interfacial proteins against droplet aggregation or lipid oxidation. Therefore, modifications of the surface charge or the interfacial conformation of protein emulsifiers are expected to enhance their emulsifying properties and emulsion stability. In this present work, sodium caseinate and whey protein isolate were modified by different chemical and enzymatic approaches. The modified proteins were characterized using multiple techniques, and the effect of these modifications on emulsifying properties of proteins and emulsion stability was investigated. Succinylation converts the positively charged amino groups into negatively charged carboxyl groups, lowering the isoelectric point (pI) of protein. The ethylene diamine (EDA) modification worked in the opposite way, leading to an increased pI. The extent of these two modifications was studied using SDS-PAGE and MALDI-TOF mass spectrometry. The pI of succinylated and EDA modified milk proteins was studied using zeta-potential measurement. As a result, the succinylation to full extent altered the pI of CN from 4.2 to 2.7, and the EDA modification shifted the pI of CN and WPI from 4.2 to 9.4 and from 4.9 to 9.5 respectively. The pH stability of emulsion made with the modified milk proteins was monitored by following the increase of particle size during storage. The results suggested that succinylation and EDA modification could enhance the emulsion stability at pH 4 7 by increasing the electrostatic repulsion between droplets. Regarding the enzymatic modification of milk proteins, the laccase and transglutaminase (Tgase) catalyzed cross-linking were applied on WPI and CN respectively. In order to improve the reactivity of WPI towards the laccase, a vanillic acid modification was carried out to incorporate additional methoxyphenol groups into the protein surface. The cross-linking of vanillic acid modified WPI (Van-WPI) by laccase was studied using SDS-PAGE. The extent of cross-linking of Van-WPI was found to be significantly higher compared to the unmodified WPI and the combination of WPI and free phenolic compound as a mediator. The effect of laccase catalyzed cross-linking on storage stability of emulsions was investigated by visual observation and confocal microscopy. The post-emulsification cross-linking was proven to enhance the stability of the emulsions prepared with Van-WPI during the storage. The reduced droplet coalescence could be most likely attributed to an extended interfacial protein layer formed via the interaction between the adsorbed proteins and non-adsorbed proteins in the water phase. In contrast with the limited extent of cross-linking of WPI by laccase, CN was extensively cross-linked by Tgase. The physical stability of emulsions was studied by measuring the increase of particle size during storage, and the oxidative stability was evaluated by following the formation of fatty acid hydroperoxides and volatile compounds in different stages of the lipid oxidation. The pre-emulsification cross-linking showed no obvious influence on the physical stability of CN emulsion but significantly improved its stability against lipid oxidation. The improvement of oxidative stability of emulsions could be contributed to a thicker and denser interfacial protein layer, which thus increases the amount of anti-oxidative groups located at the interface and provides a stronger barrier against competitive adsorption by oil oxidation products.
  • Karkman, Antti (Helsingin yliopisto, 2015)
    Increasing microbial resistance against antibiotics is threatening their efficiency in the future and we might be heading back to pre-antibiotic era. Infectious diseases still treatable with antibiotics might soon become life threatening. There is a strong correlation between antibiotic use and antibiotic resistance occurrence. Hotspots for antibiotic resistance are mainly man made such as wastewater treatment plants, animal farms and aquaculture. Aquaculture is the fastest growing food industry in the world and uses antibiotics to treat and prevent fish diseases. The use of antibiotics is linked to increase in antibiotic resistance at the farms. At urban wastewater treatment plants microbes from various sources can mix and exchange genetic material. In addition wastewaters contain antibiotics that can further select for resistant microbes. In this work hundreds of antibiotic resistance genes were quantified with cutting-edge molecular methods. The global patterns of antibiotic resistance gene movement were determined using publicly available metagenomic data. In addition, the famous Baas-Becking hypothesis everything is everywhere, but the environment selects was tested on gene level. Aquaculture increases the amount of antibiotic resistance genes in the farms. The resistance genes persist in the aquaculture sites without a clear selection pressure, however the impact is only local. Urban wastewater treatment plants efficiently removed antibiotic resistance genes from wastewaters. The release of wastewater had only a limited impact on the sediment resistome near the release site. When looking at the metagenomic data, antibiotic resistance genes were found to have different dispersal pattern compared to other genes in the metagenomes. Antibiotic resistance genes can cross taxonomical and geographical barriers with ease, possibly explaining their wide dispersal in the environment and the clinic. These results show that antibiotic resistance is ubiquitous in the environment and the anthropogenic activities affect the incidence of antibiotic resistance.
  • Mattila, Osmo (Helsingin yliopisto, 2015)
    Forests offer various, sometimes contradictory utilities to their owners and all other users on the global societal and ecological levels. In Finland, meeting the industrial requirements for a stable roundwood supply has defined the forestry service market, as it has been widely supported by the forest owners, the industrial buyers, and the national forest policy. Along with the changes among the owners themselves, demand for forestry services has fragmented. Recently, by introducing the new Forest Act, which gives more freedom for forest owners to choose between management practices, Finnish government has triggered a change that aims at the creation of more market-oriented distribution of forestry services. Based on the concepts of institutional transition at the market level, service-orientation as value-creation logic change, and business model thinking as the unit-level logic, the theoretical objective of the thesis is to define the ongoing renewal of the forestry service market. Using public and private owners as customers and the current forestry service organizations as service providers, the practical aim of this dissertation is to identify potential opportunities and barriers with respect to creating new services in the forestry service market. Methodologically both qualitative interview studies on forestry service organizations (n=22 and n=17) and quantitative multivariate analysis based on survey data with private (n=557) and public (n=139) forest owners are used. According to the results, there is a growing tension in the market environment accelerated by institutional transition: private forest owners are fragmented into multifaceted groups with various needs, while public owners (such as municipalities) are facing versatile user pressures on their publicly owned forests. Therefore, it seems that the traditional roundwood supply approach may no longer match the needs of versatile customer groups. From structural perspective, the established service market dominated by a small number of players is limiting the successful entry of new enterprises. The lack of dynamic middle-sized companies in the Finnish forest sector coupled with difficulties in adopting a more cooperative mind set is proving to be hindrance for renewal of the forestry service market despite the development of information technology, which can facilitate the use of participative methods in forest management and service marketing.
  • Terhonen, Eeva-Liisa (Helsingin yliopisto, 2015)
    Scots pine (Pinus sylvestris) and Norway spruce (Picea abies) cover large areas in boreal regions with significant economic importance to Finnish forest industry. Approximately 15% of the spruce trees felled in Finland are rotten and thus commercially less valuable. The majority of this conifer wood decay is due to the root and butt rot pathogen Heterobasidion annosum sensu lato. Extensive logging of conifer forests has changed the environment into favouring this pathogen in stands where it originally has been rare. The saprotrophic fungus Phlebiopsis gigantea has for several years been used as a biocontrol agent against H. annosum s.l. in spruce and pine stumps. A major problem is that, although the effectiveness of P. gigantea as a biocontrol agent has empirically been shown, the long-term biological effect of this fungus on other decomposing wood microbiota has not been proven. The first objective of this thesis is to evaluate the impact of the only biocontrol agent used against root and butt rot fungus (H. annosum s.l.) on other resident microflora of Norway spruce stumps. An additional objective is to screen and identify other potentially novel bioagents that can be deployed for the biocontrol of the conifer pathogen. To find out whether the P. gigantea treatment impacts the overall diversity of other non-target stump microbes we used the 454- pyrosequencing approach. Samples were collected from forest sites previously pre-treated with P. gigantea either one, six or 13 years ago. Similarly samples were collected from untreated stumps within the same forest site over the same period of time. The results revealed that initial application of the biocontrol agent influenced the fungal species composition, but the overall fungal diversity was not affected and no statistical differences were observed between treated and non-treated stumps in the mycobiota. The biocontrol treatment significantly decreased the initial bacterial richness in the stumps, but the bacterial community gradually recovered and the negative effect of P. gigantea was attenuated. In parallel to the above studies, I further explored the potential of finding other novel biocontrol agents for use in managing the disease caused by the root rot pathogen Heterobasidion parviporum. This necessitated isolation studies of fungal root endophytes from forestry sites such as pristine mires and drained peatlands where the spread of H. annosum s.l. species have not been commonly reported. A total of 113 isolates of fungal root endophytes were obtained from non-mycorrhizal P. abies roots, which were assigned to 15 different operational taxonomic units (OTUs). Nineteen of the isolates (17%) inhibited the growth of the conifer root rot pathogen in vitro. From these, two isolates were further used to test the potential inhibitory effects during interaction, in vitro, with H. parviporum. Additionally, the metabolites secreted by the selected root endophytes were extracted and the inhibitory effects on these pathogenic fungi were assayed. The secreted metabolites were further chemically analysed using ultra-performance liquid chromatography/quadrupole time-of-flight mass spectrometry (UPLC-QTOF/MS). These results give new information from the new possibilities to protect the valuable seedling roots from root rot. The results of the thesis provide new information to facilitate better management and protection of these forest sites from H. annosum s.l. as well as support the continued used of P. gigantea for stump pre-treatment in Finnish forests.
  • Selim, Shaimaa (Helsingin yliopisto, 2015)
    The objective of the research described in this thesis was to increase the understanding of the transcriptional adaptations of genes encoding proteins, which have key roles in lipid and glucose metabolism, insulin signalling and inflammation, in situations of overfeeding energy during the dry period in dairy cows and summer grazing season in mares. Emphasis was placed on the potential to decrease metabolic disorders and to improve animal nutritional management and health. In the experiment I, dairy cows were fed a grass silage based diet either on a controlled energy level (on average 99 MJ/d metabolizable energy (ME), n = 8) during the last six weeks of the dry period or high energy level (on average 141 MJ/d ME, n = 8) for the first three weeks and then gradually decreasing energy allowance during three weeks to 99 MJ/d ME by parturition. In experiment II, dairy cows were fed ad libitum either grass silage (144 MJ/d ME, n = 8) or a mixture of grass silage, wheat straw and rapeseed meal (TMR, 55%: 40%: 5%, 109 MJ/d ME, n = 8) during the 8-wk dry period. Liver and adipose tissue biopsies and blood samples were collected during the transition period in experiments I and II. In the experiment III, the impact of grazing either on cultivated high-yielding pasture (CG) or semi-natural grassland pasture (NG) on fat deposition, insulin resistance status and adipose tissue gene expression of Finnhorse mares was studied. Body measurements, intravenous glucose tolerance tests (IVGTT), and sampling for the determination of neck and tailhead adipose tissue gene expressions were conducted in May and September. In experiments I and II, overfed cows had greater total dry matter and ME intakes and ME balance before parturition than control cows, but no differences were observed after calving. Increases in body weight and body condition score were greater in the overfed cows of the experiment II during the dry period. In the experiment I, there was greater plasma insulin and lower glucagon/insulin ratio in overfed cows than in control cows, while in the experiment II, there were no differences in blood parameters between overfed and TMR group during the transition period. Down-regulation of key genes linked to hepatic gluconeogenesis and fatty acid β-oxidation in the overfed group of cows in the experiment I was found, suggesting impaired liver function compared to a controlled energy diet. In the experiment II, ad libitum feeding of grass silage throughout the dry period may have attenuated the increase of hepatic gluconeogenic capacity from propionate compared to a controlled TMR diet. However, there was no difference in the expression of genes related to hepatic glucose release during the transition period (II). In adipose tissue, there was some evidence that the level of energy overfeeding may have exacerbated the inflammatory status postpartum and temporarily decreased lipogenesis very near parturition relative to control energy diet (I). In the experiment II, prepartal ad libitum feeding of grass silage decreased lipogenesis and insulin sensitivity early postpartum compared to the TMR control group. In the experiment III, CG mares had higher median body condition score and body weight, and larger waist circumference than NG mares at the end of grazing. In September, greater basal and peak insulin concentrations, and faster glucose clearance rate during IVGTT were observed in CG mares than in NG mares. In addition, a greater decrease in plasma non-esterified fatty acids during IVGTT was noticed in CG mares. There were no differences in the expression of genes related to insulin resistance, inflammation and lipogenesis between the two groups. Significant temporal differences in the expression profiles of genes related to insulin resistance and lipogenesis were observed during the grazing season. Grazing on CG had moderate effects on responses during IVGTT, but did not exacerbate insulin resistance. In conclusion, overfeeding energy with concomitant weight gain moderately altered the expression of genes related to insulin resistance, inflammation and lipogenesis in adipose tissue of dairy cows. Prepartal overfeeding energy affected the expression of genes related to hepatic gluconeogenesis and fatty acid oxidation in dairy cows, but the extent of these effects differed depending on the dietary composition during the close-up period (e.g. feeding of cereal grain). In mares, the diets with variable energy content did not affect the expression of insulin resistance- or inflammation-related genes, although mares were different in their body condition scores.