Genetic diversity of Atlantic salmon (Salmo salar) and European whitefish (Coregonus lavaretus) in the Baltic Sea

We described the patterns and extent of microsatellite DNA variation in historical and present-day Atlantic salmon (Salmo salar L.) stocks in the Baltic Sea and neighbouring areas, and in European whitefish (Coregonus lavaretus) ecotypes, populations and run-timing types in Finland. Moreover, the amount and pattern of genetic diversity in historical salmon populations before human impact were described, and the proportion of diversity maintained in the present hatchery stocks evaluated. Salmon populations in the Baltic Sea were, on average, significantly less variable than eastern Atlantic populations, and the diversity of landlocked populations (Lakes Vänern, Saimaa, Onega and Ladoga) was in turn significantly lower than that of anadromous salmon populations in the Baltic Sea populations. Within the Baltic Sea, the anadromous populations of Atlantic salmon formed three clear groups, corresponding to the northern (Gulf of Bothnia), eastern (Gulf of Finland and eastern Baltic Main Basin) and southern (western Baltic Main Basin) regions. Based on microsatellite data, three salmon population groups in the Baltic Sea were considered potentially different colonization lineages. In short- and long-term breeding programmes of Atlantic salmon, the average observed rate of loss of alleles was 4.9% and 2.0% per generation and the average rate of loss of heterozygosity was 1.4% and 1% per generation, respectively. When comparing the genetic parameters of stocks before and after hatchery breeding of several successive generations (Rivers Iijoki and Oulujoki), statistically significant changes in allele frequencies were common, while large wild stock in the Teno River has remained temporally very stable over 56 years. Despite the observed losses of genetic diversity in broodstock breeding, a large proportion of the genetic resources of the extirpated stocks are still conserved in the broodstocks. Genetic differentiation among European whitefish ecotypes was generally low, thus giving support to the hypothesis of one native European whitefish species in Fennoscandia. Among the ecotypes, the northern, large sparsely rakered, bottom-dwelling whitefish was the most unique. The known genetic differences in quantitative traits have thus either developed independently of potential phylogenetic lineages, or the lineages have mixed and the quantitative traits of the ecotypes, like gill-raker number, have later changed according to environment and selection pressures. Overall, genetic distances between the anadromous whitefish populations along the Finnish coast, especially in the Bothnian Bay area, were small. Wild whitefish populations studied had slightly higher allelic diversity than hatchery-reared populations in corresponding rivers.

Nile Basin Initiative diskursiivisena areenana

Pro gradu -tutkielma käsittelee Niilin alueen poliittista kehitystä käyttäen viitekehyksenä Barry Buzanin, Ole Wæverin sekä Jaap de Wilden muodostaman Kööpenhaminan koulukunnan teoriaa turvallistamisesta sekä turvallisuuskomplekseista. Niilin kymmenen valtiota kattavan jokialueen poliittista historiaa on vuosikymmenet hallinnut valtioiden välinen epäluottamus, ja erityisesti Egypti, joka on täysin riippuvainen Niilin vesivaroista, on julistanut Niilin vesivarojen olevan sille kansallinen turvallisuuskysymys, ja se on uhannut käyttää myös voimakeinoja puolustaakseen vedenkäyttöoikeuksiaan. Egyptiä on myös voitu Niilin alueen hegemonina, sillä vanhat, alun perin siirtomaa-ajalta peräisin olevat sopimukset ovat antaneet sille lähes yksinoikeuden Niilin vesivarojen käyttöön. Samanaikaisesti erityisesti Etiopia, jonka alueelta suurin osa joen vesivaroista on peräisin, on pitänyt vanhoja sopimuksia epäreiluina, ja vedonnut maassa kasvavaan nälänhätään ja ruokapulaan, mutta myös useat muut alueen valtiot ovat esittäneet tyytymättömyytensä vanhoihin sopimuksiin. Vuonna 1999 kehityksessä tapahtui kuitenkin käänne, sillä jokilaakson valtiot perustivat tuolloin Niilin jokialueen yhteistyöjärjestön Nile Basin Initiativen (NBI). Tutkielma keskittyy NBI:n perustamisen jälkeiseen ajanjaksoon. Keskeinen tutkimuskysymys on, millä tavalla Niilin alueen jäsenvaltiot pyrkivät 2000-luvun alkupuolella keskinäisellä toiminnallaan muuttamaan alueella vallitsevaa kilpailu- ja konfliktiasetelmaa rauhanomaiseen suuntaan. Aineistona käytetään NBI:n omia kausijulkaisuja vuosilta 2006–2010, ja tutkimuksen menetelmänä käytetään diskurssianalyysia. Tutkitun aineiston perusteella on esitettävissä, että Niilin alueen poliittisesta kehityksestä on selvästi erotettavissa diskursseja, jotka ovat NBI:n toiminnan taustalla. Nämä ovat luottamuksen rakentamisen, yhteisten haasteiden voittamisen, yhteistyön tärkeyden sekä saavutusten diskurssit. Aineiston perusteella on nähtävissä, että valtioiden välisen luottamuksen vähitellen lisääntyessä yhteistyötä aletaan yhä enemmän legitimoida aikaisemmin yhteistyöstä saavutetuilla hyödyillä. Toisaalta diskurssianalyysin perusteella on myös nähtävissä, että alueella on ratkaisematta yhä fundamentaalisia ongelmia; uutta vesisopimusta ei ole vielä vuoteen 2010 mennessä aikaansaatu ja NBI:n jäsenvaltioiden suhteissa on myös nähtävissä kiistaa periaatteista, joihin yhteistyön olisi pohjauduttava. Tutkielma pyrkii analyysin avulla kehittämään myös Kööpenhaminan koulukunnan teoriaa turvallistamisesta. Kööpenhaminan koulukunta jättää turvallistamisen purkamiskehityksen kirjoituksissaan taka-alalle keskustelun painottuessa siihen, kuinka jokin asia tuodaan esille julkiseen turvallisuuskeskusteluun. Tältä osin tutkimuksen tavoitteena on esittää mahdollinen kehityskulku turvallistamisen purkamisdiskurssista. Teoriaosuudessa käytetyt keskeiset lähteet: Allan 2001,2009; Buzan 1991; Buzan ja Wæver 2003; Buzan, Wæver ja de Wilde 1998; Jutila 2008; Schulz 1995; Stritzel 2007; Turton 2001; Wæver 1995; Wendt 1992, 1999.

Lower Gastrointestinal Microbiota in Health and Irritable Bowel Syndrome : Characterisation and Effect of Probiotic Intervention

The human gastrointestinal (GI) microbiota is a complex ecosystem that lives in symbiosis with its host. The growing awareness of the importance of the microbiota to the host as well as the development of culture-free laboratory techniques and computational methods has enormously expanded our knowledge of this microbial community. Irritable bowel syndrome (IBS) is a common functional bowel disorder affecting up to a fifth of the Western population. To date, IBS diagnosis has been based on GI symptoms and the exclusion of organic diseases. The GI microbiota has been found to be altered in this syndrome and probiotics can alleviate the symptoms, although clear links between the symptoms and the microbiota have not been demonstrated. The aim of the present work was to characterise IBS related alterations in the intestinal microbiota, their relation to IBS symptoms and their responsiveness to probiotic theraphy. In this thesis research, the healthy human microbiota was characterised by cloning and sequencing 16S rRNA genes from a faecal microbial community DNA pool that was first profiled and fractionated according to its guanine and cytosine content (%G+C). The most noticeable finding was that the high G+C Gram-positive bacteria (the phylum Actinobacteria) were more abundant compared to a corresponding library constructed from the unfractionated DNA pool sample. Previous molecular analyses of the gut microbiota have also shown comparatively low amounts of high G+C bacteria. Furthermore, the %G+C profiling approach was applied to a sample constructed of faecal DNA from diarrhea-predominant IBS (IBS-D) subjects. The phylogenetic microbial community comparison performed for healthy and IBS-D sequence libraries revealed that the IBS-D sample was rich in representatives of the phyla Firmicutes and Proteobacteria whereas Actinobacteria and Bacteroidetes were abundant in the healthy subjects. The family Lachnospiraceae within the Firmicutes was especially prevalent in the IBS-D sample. Moreover, associations of the GI microbiota with intestinal symptoms and the quality of life (QOL) were investigated, as well as the effect of probiotics on these factors. The microbial targets that were analysed with the quantitative real-time polymerase chain reaction (qPCR) in this study were phylotypes (species definition according to 16S rRNA gene sequence similarity) previously associated with either health or IBS. With a set of samples, the presence or abundance of a phylotype that had 94% 16S rRNA gene sequence similarity to Ruminococcus torques (R. torques 94%) was shown to be associated with the severity of IBS symptoms. The qPCR analyses for selected phylotypes were also applied to samples from a six-month probiotic intervention with a mixture of Lactobacillus rhamnosus GG, L. rhamnosus Lc705, Propionibacterium freudenreichii ssp. shermanii JS and Bifidobacterium breve Bb99. The intervention had been previously reported to alleviate IBS symptoms, but no associations with the analysed microbiota representatives were shown. However, with the phylotype-specific assays applied here, the abundance of the R. torques 94% -phylotype was shown to be lowered in the probiotic-receiving group during the probiotic supplementation, whereas a Clostridium thermosuccinogenes 85% phylotype, previously associated with a healthy microbiota, was found to be increased compared to the placebo group. To conclude, with the combination of methods applied, higher abundance of Actinobacteria was detected in the healthy gut than found in previous studies, and significant phylum-level microbiota alterations could be shown in IBS-D. Thus, the results of this study provide a detailed overview of the human GI microbiota in healthy subjects and in subjects with IBS. Furthermore, the IBS symptoms were linked to a particular clostridial phylotype, and probiotic supplementation was demonstrated to alter the GI microbiota towards a healthier state with regard to this and an additional bacterial phylotype. For the first time, distinct phylotype-level alterations in the microbiota were linked to IBS symptoms and shown to respond to probiotic therapy.

Seasonal variation in nitrification and nitrate-reduction pathways in coastal sediments in the Gulf of Finland, Baltic Sea

The Baltic Sea is one of the most eutrophic marine areas in the world. The role of nitrogen as a eutrophicating nutrient in the Baltic Sea has remained controversial, due to lack of understanding of nitrogen cycling in the area. We investigated the seasonal variation in sediment nitrification, denitrification, anaerobic ammonium oxidation (anammox), and dissimilatory nitrate reduction to ammonium (DNRA) at two coastal sites in the Gulf of Finland. In addition to the in situ rates, we assessed the potential for these processes in different seasons. The nitrification and nitrogen removal processes were maximal during the warm summer months, when the sediment organic content was highest. In colder seasons, the in situ rates of the nitrification and nitrate reduction processes decreased, but the potential for nitrification remained equal to or higher than that during the warm months. The denitrification and nitrification rates were usually higher in the accumulation basin, where the organic content of the sediment was higher, but the transportation area, despite lower denitrification rates and potential, typically had higher potential for nitrification than the accumulation basin. Anammox and DNRA were not significant nitrate sinks in any of the seasons sampled. The results also show that the denitrification rates in the coastal Gulf of Finland sediment have decreased, and that benthic denitrification might be a less important sink for fixed nitrogen than previously assumed.

Effect of drainage basin characteristics on the diffuse load of phosphorus and nitrogen.

Tiivistelmä: Valuma-alueen vaikutus fosforin ja typen hajakuormitukseen.