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  • Juottonen, Heli (Helsingin yliopisto, 2008)
    Methanogens are anaerobic Archaea with unique energy metabolism resulting in production of methane (CH4). In the atmosphere methane is an effective greenhouse gas. The largest natural sources of atmospheric methane are wetlands, including peat-forming mires. Methane emissions vary greatly between and within mires, depending on season and hydrological and botanical characteristics. The aim of this work was to elucidate the microbiology underlying the variation. Methanogens and potential methane production were assessed along spatial and temporal gradients of ecohydrology, season, ash fertilization, and peat depth in three Finnish boreal mires. Non-methanogenic Archaea and Bacteria were additionally addressed as potential substrate producers and competitors to methanogens. Characterization of microbial communities targeted the mcrA gene, essential in methane production, and archaeal or bacterial 16S ribosomal RNA gene. The communities were differentiated by analysis of clone libraries, denaturing gradient gel electrophoresis (DGGE), and terminal restriction fragment length polymorphism (T-RFLP) fingerprinting. Methanogen communities and methane production changed markedly along an ecohydrological gradient from fen to bog, with changing vegetation and pH. The most acidic Sphagnum bog showed mainly Methanomicrobiales-associated, hydrogenotrophic Fen cluster methanogens, whereas the oligotrophic and mesotrophic fens with higher pH and sedge coverage had more diverse communities including acetoclastic methanogens. Season had a minor effect on the archaeal community in an acidic oligotrophic fen, but the temporal variation of methane production potential was substantial. Winter potential was unexpectedly high, and active methanogens were detected in winter peat. Ash fertilization, a forestry practice for promoting tree growth, had no substantial effects on methane production or methanogen communities in a drained bog, but the communities changed with peat depth. Comparison of three mcrA primer sets revealed that their coverage of methanogens from the drained bog was similar, but the quantitative representations of communities were primer-dependent. Bacterial and non-methanogenic archaeal groups detected in mires included Deltaproteobacteria, Acidobacteria, Verrucomicrobia, and Crenarchaeota of groups 1.1c and 1.3. Their detection forms a starting point for further studies to distinguish possible interactions with methanogens. Overall, the results indicate that methanogen community composition reflects chemical or botanical gradients that affect methane production, such as mire hydrology. Predictions of methane production in the spatially heterogeneous mires could thus benefit from characterization of methanogens and their ecophysiology.
  • Bomberg, Malin (Helsingin yliopisto, 2008)
    Archaea were long thought to be a group of ancient bacteria, which mainly lived in extreme environments. Due to the development of DNA sequencing methods and molecular phylogenetic analyses, it was shown that the living organisms are in fact divided into three domains; the Archaea, Bacteria and the Eucarya. Since the beginning of the previous decade, it was shown that archaea generally inhabit moderate environments and that these non-extremophilic archaea are more ubiquitous than the extremophiles. Group 1 of non-extreme archaea affiliate with the phylum Crenarchaeota. The most commonly found soil archaea belong to the subgroup 1.1b. However, the Crenarchaeota found in the Fennoscandian boreal forest soil belong to the subgroup 1.1c. The organic top layer of the boreal forest soil, the humus, is dominated by ectomycorrhizal fungal hyphae. These colonise virtually all tree fine root tips in the humus layer and have been shown to harbour distinct bacterial populations different from those in the humus. The archaea have also been shown to colonise both boreal forest humus and the rhizospheres of plants. In this work, studies on the archaeal communities in the ectomycorrhizospheres of boreal forest trees were conducted in microcosms. Archaea belonging to the group 1.1c Crenarchaeota and Euryarchaeota of the genera Halobacterium and Methanolobus were detected. The archaea generally colonised fungal habitats, such as ectomycorrhizas and external mycelia, rather than the non-mycorrhizal fine roots of trees. The species of ectomycorrhizal fungus had a great impact on the archaeal community composition. A stable euryarchaeotal community was detected especially in the mycorrhizas, of most of the tested Scots pine colonising ectomycorrhizal fungi. The Crenarchaeota appeared more sporadically in these habitats, but had a greater diversity than the Euryarchaeota. P. involutus mycorrhizas had a higher diversity of 1.1c Crenarchaeota than the other ectomycorrhizal fungi. The detection level of archaea in the roots of boreal trees was generally low although archaea have been shown to associate with roots of different plants. However, alder showed a high diversity of 1.1c Crenarchaeota, exceeding that of any of the tested mycorrhizas. The archaeal 16S rRNA genes detected from the non-mycorrhizal roots were different from those of the P. involutus mycorrhizas. In the phylogenetic analyses, the archaeal 16S rRNA gene sequences obtained from non-mycorrhizal fine roots fell in a separate cluster within the group 1.1c Crenarchaeota than those from the mycorrhizas. When the roots of the differrent tree species were colonised by P. involutus, the diversity and frequency of the archaeal populations of the different tree species were more similar to each other. Both Cren- and Euryarchaeota were enriched in cultures to which C-1 substrates were added. The 1.1c Crenarchaeota grew anaerobically in mineral medium with CH4 and CO2 as the only available C sources, and in yeast extract media with CO2 and CH4 or H2. The crenarchaeotal diversity was higher in aerobic cultures on mineral medium with CH4 or CH3OH than in the anaerobic cultures. Ecological functions of the mycorrhizal 1.1c Crenarchaeota in both anaerobic and aerobic cycling of C-1 compounds were indicated. The phylogenetic analyses did not divide the detected Crenarchaeota into anaerobic and aerobic groups. This may suggest that the mycorrhizospheric crenarchaeotal communities consist of closely related groups of anaerobic and aerobic 1.1c Crenarchaeota, or the 1.1c Crenarchaeota may be facultatively anaerobic. Halobacteria were enriched in non-saline anaerobic yeast extract medium cultures in which CH4 was either added or produced, but were not detected in the aerobic cultures. They may potentially be involved in anaerobic CH4 cycling in ectomycorrhizas. The CH4 production of the mycorrhizal samples was over 10 times higher than for humus devoid of mycorrhizal hyphae, indicating a high CH4 production potential of the mycorrhizal metanogenic community. Autofluorescent methanogenic archaea were detected by microscopy and 16S rRNA gene sequences of the genus Methanolobus were obtained. The archaeal community depended on both tree species and the type of ectomycorrhizal fungus colonising the roots and the Cren- and Euryarchaeota may have different ecological functions in the different parts of the boreal forest tree rhizosphere and mycorrhizosphere. By employing the results of this study, it may be possible to isolate both 1.1c Crenarchaeota as well as non-halophilic halobacteria and aerotolerant methanogens from mycorrhizospheres. These archaea may be used as indicators for change in the boreal forest soil ecosystem due to different factors, such as exploitations of forests and the rise in global temperature. More information about the microbial populations with apparently low cell numbers but significant ecological impacts, such as the boreal forest soil methanogens, may be of crucial importance to counteract human impacts on such globally important ecosystems as the boreal forests.
  • Helle, Inari (Helsingin yliopisto, 2015)
    Coastal and marine ecosystems across the globe are heavily impacted by various anthropogenic stressors, which has led to a significant loss of biodiversity and ecosystem services in recent decades. In order to find means to counteract this trend, there is a need to develop methods for assessing the environmental impacts of human activities and the effectiveness of management practices to mitigate the harmful effects. However, this is a challenging task due to the complex interactions within and between the ecosystems and human components, and various uncertainties related to them. Bayesian networks (BNs) are graphical models for reasoning under uncertainty. A BN consists of a set of probabilistic variables connected with links describing causalities within the system. As the states of the variables are described with probability distributions, uncertainty can be described in an explicit manner. BNs also enable integration of qualitative and quantitative knowledge from various sources such as observational data sets, models and expert knowledge. In this thesis I have developed BN models to study environmental risks related to anthropogenic stressors in the Gulf of Finland and the Finnish Archipelago Sea. The main aim is to quantify human impacts on the environment, and to assess the ability of different management measures to lessen these impacts. I focus especially on oil spills resulting from potential tanker accidents and I set out to fill various information gaps related to this recently emerged threat. The thesis includes five papers. In paper I, the main aim is to assess the spatial risk posed by oil spills in the Gulf of Finland and the Finnish Archipelago Sea, and identify species and habitat types with the highest risk. In paper II, I focus on the effectiveness of different oil combating methods to mitigate the negative impacts of oil spills on the ecosystem, and paper III widens the approach to a probabilistic cost-benefit analysis of preventive and post-spill measures. Paper IV deals with multiple risks as, in addition to oil spills, eutrophication and harvesting of species are studied. Paper V reviews and discusses various methods that can be applied to evaluate the uncertainty related to deterministic models, which could increase their usefulness in decision-making. The results suggest that risks related to tanker accidents are distributed unevenly between areas, habitats and species. Furthermore, the results support the current Finnish strategy to base oil combating primarily on offshore recovery vessels instead of chemical dispersants. However, as the efficiency of mechanical recovery is dependent on several factors, there is also a need to develop preventive measures. Although major oil accidents are estimated to be rare events, the costs can be very high, if a spill occurs. The work offers new insights to the oil spill risks in the study area and provides examples how Bayesian networks can be applied in environmental risk assessment. The thesis is a part of the work needed in order to develop comprehensive decision support tools related to environmental risk management in the northern Baltic Sea.
  • Santangeli, Andrea (Helsingin yliopisto, 2013)
    Humans are the main cause of the on-going large-scale biodiversity crisis, mostly through processes like habitat loss and fragmentation, and habitat degradation. The recent recognition of the scale and rate of biodiversity erosion has stimulated strong political and institutional reactions, culminating in the implementation of a large number of conservation initiatives. Such efforts have been largely insufficient to revert or slow down the rapid loss of biodiversity. Commonly, conservation resources have been allocated based on decisions supported by traditional knowledge or expert opinion rather than scientific evidence. Therefore, it is relevant that interventions are evaluated, to ultimately allow learning from past actions and taking better decisions in the future. With this thesis I aim to provide evidence needed to improve the effectiveness of different approaches to conservation of some species affected by anthropogenic activities. In doing so, I considered conservation interventions implemented mostly on private land with different underlying approaches: voluntary and inexpensive (based on self-motivation of landowners); voluntary market-based (landowners are compensated); Compulsory land reservation or legislation (landowners have no choice). I first evaluate the effectiveness of a conservation program aimed at protecting raptor nests in private forests of North Karelia in eastern Finland. I show that here an inexpensive voluntary approach, based on self-motivation of landowners, may represent an effective instrument for achieving conservation with very limited financial resources. This approach was effective not only at eliciting participation of local forest owners, but it also provided ecological benefits to the raptor species considered. Relevant outcomes for practical conservation can also emerge when multiple interventions are compared. This was the case for nest protection of the Montagu s harrier breeding in cropland of Spain and France. In France, protection of nests from harvesting operations has been achieved on a voluntary basis. Here I show that the most effective interventions to enhance nest productivity were those that not only protect from harvesting, but also from predation. This was achieved by erecting a protective fence around the nest. On the other hand, some nest protection measures in Spain were more expensive due to payments to farmers. Here, temporary removal of the chicks during harvest operations or relocation of the nest to a nearby safe place, as well as harvest delay, were the most effective measures to enhance nest productivity. Harvest delay was also the most expensive among all measures, therefore removal or relocation of the nest should be prioritized wherever it is operationally feasible. Interestingly, the most commonly employed measure, the retention of a small buffer of un-harvested crop, was also less effective compared to the other means. Unexpected but positive outcomes for conservation management emerged also from an evaluation of the effects of nest site protection for breeding White-tailed eagles in south-western Finland. The species was breeding as often and successfully in protected and unprotected areas, which suggests that compulsory and expensive protection through land reservation may not be necessary under the studied conditions. The species apparently thrives also in unprotected land subject to some levels of anthropogenic activities. I found opposite results in a study on protection of flying squirrel sites in Finland. Here I provide evidence indicating that the enforced legislation to protect the species habitat in Finnish forests is ineffective. The species occupancy at sites protected according to the law strongly declined following tree harvest. This indicates that the primary objective of the legislation (i.e. prevent deterioration of the sites where the species occurs) are not met. This is due to the fact that conservation of flying squirrel s habitat may conflict with forestry interests, and thus restrictions have been largely set in favour of the latter and at the detriment of the former. The case studies presented here indicate that evaluating the effectiveness of past actions is important. This step allows understanding whether past efforts have reached their initial objectives. Only with the strength of this evidence it is possible to adaptively revise current conservation plans and increase the chances of reaching the desired outcome from any given action. This is particularly relevant in the modern era, where conservation challenges are enormous, and the resources limited. Therefore, it is crucial that any implemented effort produces the best possible outcome for conservation.
  • Kiiski, Kirsi (Helsingin yliopisto, 2015)
    Nemaline myopathy (NM) and related disorders constitute a heterogeneous group of congenital myopathies. Mutations in the nebulin gene (NEB) are the main cause of the recessively inherited form. NEB is one of the largest genes in the human genome consisting of 249 kb of genomic sequence. NEB contains 183 exons and a 32 kb homologous triplicate region (TRI) where eight exons are repeated three times. The aims of this Doctoral Thesis study were to develop and implement into diagnostics new efficient variant analysis methods for NEB and other NM-causing genes. The first aim was to design and validate a custom copy number microarray targeting the NM-causing genes for the detection of copy number variations. MLPA (multiplex ligation-dependent probe amplification) and Sanger sequencing were also used. The second aim was to utilise whole-exome sequencing to search for novel disease-causing variants in the known NM genes and try to identify novel NM genes. Lastly, the aim was to collect more data in order to try to find genotype-phenotype correlations of NEB-caused NM. The design and validation of the NM-CGH microarray was successful. Of the total sample cohort of 356 NM families, 196 NM families were studied using the custom-made NM-CGH array. Nine different novel large causative variants were identified in ten NM families. The size of these variants varies greatly, covering only a part of one NEB exon on up to dozens of NEB exons (72bp - 133 kb). In addition, a novel recurrent variation of the NEB TRI region was identified in 13% of the NM families and in 10% of the studied 60 control samples. Deviations of one copy are suggested to be benign but gains of two or more copies might be pathogenic. One novel homozygous deletion was also identified in another NM gene, TPM3, in a patient with severe NM. Furthermore, ten samples were studied using exome sequencing, and for six of those samples, novel disease-causing variant(s) were identified. Two variants were identified in one family in a novel, putative NM gene that is currently under further investigation. 165 NM families from the total cohort of 356 NM families have been identified thus far with two pathogenic NEB variants. Altogether 220 different pathogenic variants were identified in these 165 families, accentuating that the patients in the majority (84%) of the families are compound heterozygous for two different NEB variants. Most of the variants are small single nucleotide changes whereas large variants are more rare. However, copy number variations are much more frequent than previously thought: pathogenic copy number variants were identified in 16% of these 356 NM-families. Genotype-phenotype correlations between the type of NEB mutation and the NM subtypes remained, however, unobtainable. The NM-CGH microarray has been implemented into molecular diagnostics of NM. Using the NM-CGH microarray followed by exome-sequencing has accelerated mutation detection. This combination has increased the coverage of the NM genes and thus improved the diagnostics of NM and NM-related disorders.
  • Rintala, Janne-Markus (Helsingin yliopisto, 2009)
    The seasonal occurrence of sea ice that annually covers almost half the Baltic Sea area provides a unique habitat for halo- and cold temperature-tolerant extremophiles. Baltic Sea ice biology has more than 100 years of tradition that began with the floristic observation of species by the early pioneers using light microscopic techniques that were the only thing available at the time. Since the discovery of life within sea ice, more technologies have become available for taxonomy. Electron microscopy and genetic evidence have been used to identify sea ice biota revealing increased numbers of taxa. Meanwhile ecologists have used light microscopic cell enumeration in addition to the chemical and physical properties of sea ice in attempts to explain the food web structure of sea ice and its functions. Thus, during the Baltic winter, the sea ice hosts more abundant and diverse microbial communities than the water column beneath it. These communities are typically dominated by autotrophic diatoms together with a diverse assortment of dinoflagellates, auto- and heterotrophic flagellates, ciliates, metazoan rotifers and bacteria, which are mostly responsible for the recycling of nutrients. This thesis comprises ecological and systematic studies. In addition to the results of the previous studies carried out on landfast ice, the data presented here provide new insight into the spatial distribution of pelagial sea ice, which has remained largely unexplored. The studies reveal spatial heterogeneity in the pelagial sea ice of the Gulf of Bothnia. There were mismatches in chlorophyll-a concentrations and in photosynthetic efficiencies of the communities studied. The temporal succession was followed and experimental studies performed investigating the community responses towards increased or decreased light in landfast ice in the Gulf of Finland. The systematic studies carried out with established dinoflagellate cultures revealed a new resting cyst belonging to common sea ice dinoflagellate, Scrippsiella hangoei (Schiller) Larsen 1995. The cyst can be used to explain the overwintering of this species during prolonged periods of darkness. The dissimilarities and similarities in the material isolated from the sea ice called for description of a new subspecies Heterocapsa arctica ssp. frigida. The cells obtained in the cultured material were unlike those of the previously described species, necessitating description of ssp. frigida. As a result of its own unique habitus, the subspecies had been noted by Finnish taxonomists during the past three decades and thus its annual occurrence and geographical distribution in the Baltic Sea. This illustrates how combining ecology and systematics increases our understanding of organisms.
  • Lehikoinen, Annukka (Helsingin yliopisto, 2014)
    Environmental risk assessment (ERA) is a process of estimating the probability and consequences of an adverse event due to pressures or changes in environmental conditions resulting from human activities. Its purpose is to search the optimal courses of action under uncertainty when striving for the sustainable use of environment through minimizing the potential losses. As environmental issues are typically multidisciplinary, addressing large amount of eco-societal inter-linkages, an optimal tool for the ERA should enable the efficient integration and meta-analysis of multidisciplinary knowledge. By describing the causalities and studying the interactions among its components, this kind of integrative analysis provides us better understanding about the environmental system in focus. In addition, the functional ERA application should allow exploring, explaining and forecasting the responses of an environmental system to changes in natural and human induced stressors, serving as a decision support model that enables the search of optimal management strategy, also in the presence of imperfect knowledge. Bayesian Network (BN) is a graphical model that enables the integration of both quantitative and qualitative data and knowledge to a causal chain of inference. It is a powerful tool for synthesising knowledge, logic and rules, providing aid for thinking about complex systems that are too demanding to be analysed by human brains alone. In a BN, all the knowledge is handled in the form of probability distributions, thus the result represents the prevailing state of knowledge. The method facilitates analysing the location and amount of uncertainty explicitly, as well as enables studying its significance when it comes to the decision making. The main contribution of this thesis is to share experiences and ideas about the development and use of the ERA applications executed by using the BN as method. The perspective of the work is dichotomic. The objective in the separate studies presented in the articles have been on one hand to develop tools for integrating available knowledge and materials to enable the quantitative assessment of the environmental risks. On the other hand, the ultimate aim has been to learn more about the environmental risks and their potential management in the case study area of the Gulf of Finland. In this thesis, both of these perspectives are considered. Eutrophication and oil transportations at the Gulf of Finland are used as the case issues. The thesis concludes that Bayesian networks have plenty of properties that are useful for ERA and the method can be used for solving problems typical for that field analytically. By planting the developed graphical BNs in the commonly used Drivers-Pressures-States-Impacts-Responses -problem structuring framework, it is also demonstrated that combining these two approaches can be helpful in conceptual modeling, enabling the better framing of the research problem at hand and thinking about it systematically. The greatest challenges concerning the BN-ERA modeling are found to be related to the computational limitations of the current BN software, when it comes to the joint use of the discretised and continuous variables, as well as the restricted capacity to include the spatial resolution to the models. Producing the prior probability distributions by using deterministic models is also noted to be relatively tedious and time-consuming. The issues of end use of the applications, problems related to the scientific publishing of them, as well as the advantages and challenges of working in the multidisciplinary research teams are discussed.
  • Laakkonen, Mika (Helsingin yliopisto, 2007)
    Predation forms one of the main selective forces in nature and in a vast number of prey species the behavioural responses form the main way to avoid predation. World wide numerous captive breeding programs are used to produce fish and other animal species for conservational reintroductions. However, rearing animals in the absence of predators in captivity has been shown to weaken their predator avoidance skills and lead to behavioural divergence between wild and captive-bred populations. In my thesis I studied the effects of predator odour exposures on antipredator behavioural and physiological responses of captive reared Saimaa Arctic charr. This charr population is the most endangered fish population in Finland and a sample of the remaining population has been taken to captive breeding and used for an extensive reintroduction program. Lowered responsiveness to predators is probably one of the major reasons for the poor survival probability of the charr after release into the wild. The main aims of my thesis were to explore the reasons for behavioural phenotypic variation in this charr population and whether naïve charr young could be trained to recognise their natural predators. The predator species in my thesis were burbot (Lota lota) and pikeperch (Sander lucioperca). In my thesis I showed that the captive-bred charr responded to chemical cues from burbot and pikeperch, but the magnitude of responses was linked to the predator species. The burbot odour increased the spatial odour avoidance of the charr young. On the other hand, in the pikeperch treatment charr reduced their relative swimming activity and tended to show more freezing behaviour relative to the burbot treatment. It seems evident that these different responses are related to the different hunting tactics of predator species. Furthermore, I detected wide between-family differences in antipredator responsiveness (i.e. inherited variation in antipredator behaviours) in this captive stock. Detected differences were greater in the response towards burbot than towards pikeperch. These results, in addition to predator-specific antipredator responses, suggest that there is a clear inherited component in antipredator responsiveness in Saimaa charr population and that the detected inherited differences could explain a part of the behavioural phenotypic variation in this population. In my thesis I also found out that both social learning and direct exposure to live predators enhance the antipredator responsiveness of charr young. In addition, I obtained indications that predator odour exposures (i.e. life-skills training) in alevin and fry stages can fine-tune the innate antipredator responsiveness of charr. Thus, all these methods have the potential to enhance the innate antipredator responsiveness of naïve charr young, possibly also improving the post-release survival of these trained individuals in the wild. However, the next logical phase would be to carry out large scale survival studies in the wild to test this hypothesis. Finally, the results of my thesis emphasize that possible long-term life-skills training methods should take into account not only the behavioural but also the physiological effects of training.
  • Sarhan, Alia (Helsingin yliopisto, 2006)
    In my thesis I have been studying the effects of population fragmentation and extinction-recolonization dynamics on genetic and evolutionary processes in the Glanville fritillary butterfly (Melitaea cinxia). By conducting crosses within and among newly-colonized populations and using several fitness measures, I found a strong decrease in fitness following colonization by a few related individuals, and a strong negative relationship between parental relatedness and offspring fitness. Thereafter, I was interested in determining the number and relatedness of individuals colonizing new populations, which I did using a set of microsatellites I had previously developed for this species. Additionally, I am interested in the evolution of key life-history traits. By following the lifetime reproductive success of males emerging at different times in a semi-natural setup, I demonstrated that protandry is adaptive in males, and I was able to rule out, for M. cinxia, alternative incidental hypotheses evoked to explain the evolution of protandry in insects. Finally, in work I did together with Prof. Hanna Kokko, I am proposing bet-hedging as a new mechanism that could explain the evolution of polyandry in M. cinxia.
  • Tuomainen, Ulla (Helsingin yliopisto, 2012)
    When a habitat undergoes change, the first response of an individual is often behavioural adjustment. This immediate response can determine whether the population will survive or not, as behavioural flexibility gives time for genetic changes to arise later on. Habitat changes that alter reproductive behaviours can have long-lasting effects on populations. If the selective regime has changed under the new conditions, mate choice cues may no longer reliably reflect an individual s quality. Thus, animals have to be able to adjust their reproductive behaviours to the local conditions. The aim of my thesis was to discuss if and how animals are able to respond to rapid anthropogenic environmental change, and to study the mechanisms of the responses and the evolutionary consequences. The main focus was on the effects of human-induced eutrophication on the reproductive behaviour of fishes. Eutrophication is the result of increased nutrient input and can cause dense underwater vegetation and algal blooms. I used fishes from two very different ecosystems as model species, the Baltic Sea threespine stickleback (Gasterosteus aculeatus) and the desert goby (Chlamydogobius eremius), an endemic species of the Lake Eyre region in Central Australia. I investigated the effects of increased habitat complexity on courtship behaviour and the possibility of local differentiation in courtship and nest building behaviour depending on the level eutrophication in the habitat of origin. Furthermore, I observed the effect of turbidity on stickleback nest building behaviour. The results show that threespine stickleback males, which were born in areas that have been eutrophied for decades, court females at a higher intensity than males from clear water areas. Similarly, male desert gobies increased their courtship effort in dense vegetation. Intense courtship could be an adjustment to reduced visibility and lowered predation risk in the densely vegetated sites. However, there were no clear differences in nest building between males from clear and eutrophied areas under standardized conditions. This was expected as Baltic Sea sticklebacks prefer to nest under vegetation cover and are fairly rigid in adjusting their nest characteristics. Nest building was affected by increased turbidity: males built smaller nests with a larger nest entrance in turbid water. The large variation in the magnitude of phytoplankton blooms may require a rapid adjustment of the optimal nest structure to the current conditions. This thesis highlights the complex interactions that are set- off by human-induced changes in habitats and are followed by the immediate behavioural responses. It also encourages more research to tease apart the phenotypic and genetic components of the observed behavioural differences.
  • Hellstedt, Paavo (Helsingin yliopisto, 2005)
  • Kanerva, Teri (Helsingin yliopisto, 2006)
    This thesis focuses on how elevated CO2 and/or O3 affect the below-ground processes in semi-natural vegetation, with an emphasis on greenhouse gases, N cycling and microbial communities. Meadow mesocosms mimicking lowland hay meadows in Jokioinen, SW Finland, were enclosed in open-top chambers and exposed to ambient and elevated levels of O3 (40-50 ppb) and/or CO2 (+100 ppm) for three consecutive growing season, while chamberless plots were used as chamber controls. Chemical and microbiological analyses as well as laboratory incubations of the mesocosm soils under different treatments were used to study the effects of O3 and/or CO2. Artificially constructed mesocosms were also compared with natural meadows with regards to GHG fluxes and soil characteristics. In addition to research conducted at the ecosystem level (i.e. the mesocosm study), soil microbial communities were also examined in a pot experiment with monocultures of individual species. By comparing mesocosms with similar natural plant assemblage, it was possible to demonstrate that artificial mesocosms simulated natural habitats, even though some differences were found in the CH4 oxidation rate, soil mineral N, and total C and N concentrations in the soil. After three growing seasons of fumigations, the fluxes of N2O, CH4, and CO2 were decreased in the NF+O3 treatment, and the soil NH4+-N and mineral N concentrations were lower in the NF+O3 treatment than in the NF control treatment. The mesocosm soil microbial communities were affected negatively by the NF+O3 treatment, as the total, bacterial, actinobacterial, and fungal PLFA biomasses as well as the fungal:bacterial biomass ratio decreased under elevated O3. In the pot survey, O3 decreased the total, bacterial, actinobacterial, and mycorrhizal PLFA biomasses in the bulk soil and affected the microbial community structure in the rhizosphere of L. pratensis, whereas the bulk soil and rhizosphere of the other monoculture, A. capillaris, remained unaffected by O3. Elevated CO2 caused only minor and insignificant changes in the GHG fluxes, N cycling, and the microbial community structure. In the present study, the below-ground processes were modified after three years of moderate O3 enhancement. A tentative conclusion is that a decrease in N availability may have feedback effects on plant growth and competition and affect the N cycling of the whole meadow ecosystem. Ecosystem level changes occur slowly, and multiplication of the responses might be expected in the long run.
  • Saarikangas, Juha (Helsingin yliopisto, 2010)
    Plasma membrane adopts myriad of different shapes to carry out essential cellular processes such as nutrient uptake, immunological defence mechanisms and cell migration. Therefore, the details how different plasma membrane structures are made and remodelled are of the upmost importance. Bending of plasma membrane into different shapes requires substantial amount of force, which can be provided by the actin cytoskeleton, however, the molecules that regulate the interplay between the actin cytoskeleton and plasma membrane have remained elusive. Recent findings have placed new types of effectors at sites of plasma membrane remodelling, including BAR proteins, which can directly bind and deform plasma membrane into different shapes. In addition to their membrane-bending abilities, BAR proteins also harbor protein domains that intimately link them to the actin cytoskeleton. The ancient BAR domain fold has evolved into at least three structurally and functionally different sub-groups: the BAR, F-BAR and I-BAR domains. This thesis work describes the discovery and functional characterization of the Inverse-BAR domains (I-BARs). Using synthetic model membranes, we have shown that I-BAR domains bind and deform membranes into tubular structures through a binding-surface composed of positively charged amino acids. Importantly, the membrane-binding surface of I-BAR domains displays an inverse geometry to that of the BAR and F-BAR domains, and these structural differences explain why I-BAR domains induce cell protrusions whereas BAR and most F-BAR domains induce cell invaginations. In addition, our results indicate that the binding of I-BAR domains to membranes can alter the spatial organization of phosphoinositides within membranes. Intriguingly, we also found that some I-BAR domains can insert helical motifs into the membrane bilayer, which has important consequences for their membrane binding/bending functions. In mammals there are five I-BAR domain containing proteins. Cell biological studies on ABBA revealed that it is highly expressed in radial glial cells during the development of the central nervous system and plays an important role in the extension process of radial glia-like C6R cells by regulating lamellipodial dynamics through its I-BAR domain. To reveal the role of these proteins in the context of animals, we analyzed MIM knockout mice and found that MIM is required for proper renal functions in adult mice. MIM deficient mice displayed a severe urine concentration defect due to defective intercellular junctions of the kidney epithelia. Consistently, MIM localized to adherens junctions in cultured kidney epithelial cells, where it promoted actin assembly through its I-BAR andWH2 domains. In summary, this thesis describes the mechanism how I-BAR proteins deform membranes and provides information about the biological role of these proteins, which to our knowledge are the first proteins that have been shown to directly deform plasma membrane to make cell protrusions.
  • Viitasalo, Satu (Helsingin yliopisto, 2007)
    Benthic-pelagic coupling describes processes that operate across and between the seafloor and open-water ecosystems. In soft-sediment communities, bioturbation by sediment-dwelling and epibenthic organisms may strongly shape habitat characteristics and influence processes, e.g. biogeochemical cycling, which supplies bioavailable nutrients to pelagic primary producers. In addition, benthic fauna may mediate benthic-pelagic coupling by affecting the survival and hatching of zooplankton dormant eggs in the sediment. In the shallow waters and seasonally fluctuating environment of the Baltic Sea, emergence from the seafloor essentially contributes to the dynamics of zooplankton pelagic populations. In this thesis, I examine how benthic organisms with different functional traits affect the link between the benthic and pelagic systems in the northern Baltic Sea. By means of experimental laboratory studies, the effects of sediment-dwelling (Monoporeia affinis, Macoma balthica and Marenzelleria spp.) and nectobenthic (Mysis spp.) taxa on the survival and hatching of zooplankton benthic eggs and on benthic nutrient fluxes and sediment structure were investigated. In the predation studies, the nectobenthic mysids Mysis spp. preyed upon benthic eggs of the cladoceran Bosmina longispina maritima (syn. B. coregoni maritima), both in pelagic and benthic environments. Of the sediment-dwelling species, the amphipod M. affinis and the bivalve M. balthica reduced the number of cladoceran eggs in the sediment, whereas the polychaetes Marenzelleria spp. had no effects on cladoceran eggs. Both M. balthica and M. affinis also increased the mortality rates of benthic eggs of copepods and rotifers. It was estimated that zooplankton eggs provide an additional carbon source for food-limited benthic communities. The results indicate that predation pressure on zooplankton benthic eggs may be strong, but varies widely depending on the season and the functional characteristics of the macrofauna. Macoma balthica buried cladoceran eggs and a fluorescent tracer from the sediment surface to a depth of 3 4 cm, indicating efficient sediment mixing. In contrast, the other taxa had fewer effects on particle distributions. In addition to organic matter mineralization, particle mixing is crucial to the success of benthic recruitment of zooplankton, since only eggs close to the sediment surface may hatch. Macoma balthica and M. affinis altered the patterns of zooplankton emergence from the sediment. In general, the highest emergence rates were observed in the absence of macroscopic fauna, and M. balthica exerted a stronger suppressive effect than M. affinis. Moreover, copepods were less severely affected than cladocerans, while only one species (Temora longicornis) clearly benefited from the presence of the macrofauna. These differences probably result from species-specific differences in the resistance of eggs to disturbances. The results show that benthic fauna may considerably alter the patterns of zooplankton emergence from the seafloor, thereby shaping zooplankton pelagic populations. The semi-motile M. balthica and Marenzelleria spp. increased the fluxes of phosphate and ammonium from the sediment to the water, whereas the motile M. affinis and Mysis mixta had a contrasting effect. In the eutrophied Baltic Sea, efficient internal cycling of bioavailable nutrients forms a strong feedback inhibiting the recovery of the ecosystem. Based on the results, a change in species dominance from the two motile taxa, susceptible to oxygen deficiency, to the more tolerant semi-motile taxa provides additional feedback, strengthening internal nutrient cycling and accelerating eutrophication, with deteriorating near-bottom oxygen conditions and changes in the benthic communities. In shallow-water ecosystems, benthic nutrient regeneration plays a key role in determining the overall productivity of the ecosystem. In addition, the results of this study show that the communities in the benthos may essentially contribute to the structure of those in the plankton.