Plasmids and aromatic degradation in Sphingomonas for bioremediation : Aromatic ring cleavage genes in soil and rhizosphere

Microbial degradation pathways play a key role in the detoxification and the mineralization of polyaromatic hydrocarbons (PAHs), which are widespread pollutants in soil and constituents of petroleum hydrocarbons. In microbiology the aromatic degradation pathways are traditionally studied from single bacterial strains with capacity to degrade certain pollutant. In soil the degradation of aromatics is performed by a diverse community of micro-organisms. The aim of this thesis was to study biodegradation on different levels starting from a versatile aromatic degrader Sphingobium sp. HV3 and its megaplasmid, extending to revelation of diversity of key catabolic enzymes in the environment and finally studying birch rhizoremediation in PAH-polluted soil. To understand biodegradation of aromatics on bacterial species level, the aromatic degradation capacity of Sphingobium sp. HV3 and the role of the plasmid pSKY4, was studied. Toluene, m-xylene, biphenyl, fluorene, phenanthrene were detected as carbon and energy sources of the HV3 strain. Tn5 transposon mutagenesis linked the degradation capacity of toluene, m-xylene, biphenyl and naphthalene to the pSKY4 plasmid and qPCR expression analysis showed that plasmid extradiol dioxygenases genes (bphC and xylE) are inducted by phenanthrene, m-xylene and biphenyl whereas the 2,4-dichlorophenoxyacetic acid herbicide induced the chlorocatechol 1,2-dioxygenase gene (tfdC) from the ortho-pathway. A method to study upper meta-pathway extradiol dioxygenase gene diversity in soil was developed. The extradiol dioxygenases catalyse cleavage of the aromatic ring between a hydroxylated carbon and an adjacent non-hydroxylated carbon (meta-cleavage). A high diversity of extradiol dioxygenases were detected from polluted soils. The detected extradiol dioxygenases showed sequence similarity to known catabolic genes of Alpha-, Beta-, and Gammaproteobacteria. Five groups of extradiol dioxygenases contained sequences with no close homologues in the database, representing novel genes. In rhizoremediation experiment with birch (Betula pendula) treatment specific changes of extradiol dioxygenase communities were shown. PAH pollution changed the bulk soil extradiol dioxygenase community structure and birch rhizosphere contained a more diverse extradiol dioxygenase community than the bulk soil showing a rhizosphere effect. The degradation of pyrene in soil was enhanced with birch seedlings compared to soil without birch. The complete 280,923 kb nucleotide sequence of pSKY4 plasmid was determined. The open reading frames of pSKY4 were divided into putative conjugative transfer, aromatic degradation, replication/maintaining and transposition/integration function-encoding proteins. Aromatic degradation orfs shared high similarity to corresponding genes in pNL1, a plasmid from the deep subsurface strain Novosphingobium aromaticivorans F199. The plasmid backbones were considerably more divergent with lower similarity, which suggests that the aromatic pathway has functioned as a plasmid independent mobile genetic element. The functional diversity of microbial communities in soil is still largely unknown. Several novel clusters of extradiol dioxygenases representing catabolic bacteria, whose function, biodegradation pathways and phylogenetic position is not known were amplified with single primer pair from polluted soils. These extradiol dioxygenase communities were shown to change upon PAH pollution, which indicates that their hosts function in PAH biodegradation in soil. Although the degradation pathways of specific bacterial species are substantially better depicted than pathways in situ, the evolution of degradation pathways for the xenobiotic compounds is largely unknown. The pSKY4 plasmid contains aromatic degradation genes in putative mobile genetic element causing flexibility/instability to the pathway. The localisation of the aromatic biodegradation pathway in mobile genetic elements suggests that gene transfer and rearrangements are a competetive advantage for Sphingomonas bacteria in the environment.

Emulgointiaineiden myrkyllisyydestä ja hajoamisesta Suomen oloissa

English summary: Toxicity and biodegradability of emulsifiers in Finnish watercources

Öljypitoisuuksien kartoitustutkimus Suomea ympäröivillä merialueilla vuosina 1971 ja 1972

The study of the occurance of non-polar hydrocarbons in the Finnish coastal waters in 1971-1972.

Bioremediation of diesel oil contaminated soil and water

Diesel spills contaminate aquatic and terrestrial environments. To prevent the environmental and health risks, the remediation needs to be advanced. Bioremediation, i.e., degradation by microbes, is one of the suitable methods for cleaning diesel contamination. In monitored natural attenuation technique are natural processes in situ combined, including bioremediation, volatilization, sorption, dilution and dispersion. Soil bacteria are capable of adapting to degrade environmental pollutants, but in addition, some soil types may have indigenous bacteria that are naturally suitable for degradation. The objectives for this work were (1) to find a feasible and economical technique to remediate oil spilled into Baltic Sea water and (2) to bioremediate soil contaminated by diesel oil. Moreover, the aim was (3) to study the potential for natural attenuation and the indigenous bacteria in soil, and possible adaptation to degrade diesel hydrocarbons. In the aquatic environment, the study concentrated on diesel oil sorption to cotton grass fiber, a natural by-product of peat harvesting. The impact of diesel pollution was followed in bacteria, phytoplankton and mussels. In a terrestrial environment, the focus was to compare the methods of enhanced biodegradation (biostimulation and bioaugmentation), and to study natural attenuation of oil hydrocarbons in different soil types and the effect that a history of previous contamination may have on the bioremediation potential. (1) In the aquatic environment, rapid removal of diesel oil was significant for survival of tested species and thereby diversity maintained. Cotton grass not only absorbed the diesel but also benefited the bacterial growth by providing a large colonizable surface area and hence oil-microbe contact area. Therefore use of this method would enhance bioremediation of diesel spills. (2) Biostimulation enhances bioremediation, and (3) indigenous diesel-degrading bacteria are present in boreal environments, so microbial inocula are not always needed. In the terrestrial environment experiments, the combination of aeration and addition of slowly released nitrogen advanced the oil hydrocarbon degradation. Previous contamination of soil gives the bacterial community the potential for rapid adaptation and efficient degradation of the same type of contaminant. When the freshly contaminated site needs addition of diesel degraders, previously contaminated and remediated soil could be used as a bacterial inoculum. Another choice of inoculum could be conifer forest soil, which provides a plentiful population of degraders, and based on the present results, could be considered as a safe non-polluted inoculum. According to the findings in this thesis, bioremediation (microbial degradation) and monitored natural attenuation (microbial, physical and chemical degradation) are both suitable techniques for remediation of diesel-contaminated sites in Finland.

The potential of microbial ecological indicators to guide ecosophisticated management of hydrocarbon-contaminated soils

Soil is an unrenewable natural resource under increasing anthropogenic pressure. One of the main threats to soils, compromising their ability to provide us with the goods and ecosystem services we expect, is pollution. Oil hydrocarbons are the most common soil contaminants, and they disturb not just the biota but also the physicochemical properties of soils. Indigenous soil micro-organisms respond rapidly to changes in the soil ecosystem, and are chronically in direct contact with the hydrophobic pollutants on the soil surfaces. Soil microbial variables could thus serve as an intrinsically relevant indicator of soil quality, to be used in the ecological risk assessment of contaminated and remediated soils. Two contrasting studies were designed to investigate soil microbial ecological responses to hydrocarbons, together with parallel changes in soil physicochemical and ecotoxicological properties. The aim was to identify quantitative or qualitative microbiological variables that would be practicable and broadly applicable for the assessment of the quality and restoration of oil-polluted soil. Soil bacteria commonly react on hydrocarbons as a beneficial substrate, which lead to a positive response in the classical microbiological soil quality indicators; negative impacts were accurately reflected only after severe contamination. Hydrocarbon contaminants become less bioavailable due to weathering processes, and their potentially toxic effects decrease faster than the total concentration. Indigenous hydrocarbon degrader bacteria, naturally present in any terrestrial environment, use specific mechanisms to improve access to the hydrocarbon molecules adsorbed on soil surfaces. Thus when contaminants are unavailable even to the specialised degraders, they should pose no hazard to other biota either. Change in the ratio of hydrocarbon degrader numbers to total microbes was detected to predictably indicate pollutant effects and bioavailability. Also bacterial diversity, a qualitative community characteristic, decreased as a response to hydrocarbons. Stabilisation of community evenness, and community structure that reflected clean reference soil, indicated community recovery. If long-term temporal monitoring is difficult and appropriate clean reference soil unavailable, such comparison could possibly be based on DNA-based community analysis, reflecting past+present, and RNA-based community analysis, showing exclusively present conditions. Microbial ecological indicators cannot replace chemical oil analyses, but they are theoretically relevant and operationally practicable additional tools for ecological risk assessment. As such, they can guide ecologically informed and sustainable ecosophisticated management of oil-contaminated lands.

Jatrophanviljely ja maankäyttö Vietnamissa

Biofuels are under discussion all over the world today. There are fears that the farming of biofuel plants hurts food production and weakens the food security of the poor. On the other hand, biofuel production could lessen the green house gas emissions caused by transportation, and it could also spread the profits from fuel markets more evenly between countries. The aim of this thesis is to find out how an oil plant called jatropha curcas L., which is used for biodiesel production, can affect the sustainability of livelihoods in Vietnam from the point of view of land use. Special attention is given to the effects of jatropha farming on food production, land productivity, natural resources of livelihoods and global livelihood. Jatropha belongs to the family Euphorbiaceae, and it grows naturally in tropical and subtropical areas. It can be grown on poor soils, its seeds have high oil content, and it cannot be eaten due to its toxicity. The plant grows naturally in Vietnam, and during the past few years it has also begun to be farmed for making biodiesel. Population growth in Vietnam has slowed down, but the population's standard of living and energy consumption are still rising quickly. An interest in the international biodiesel markets has awoken following Vietnam's opening up to international trade. Jatropha diesel plays a significant part in Vietnam’s clean fuel strategy, and many companies have set up jatropha plantations to produce raw material for biodiesel. Diesel made from jatropha is planned to be used both locally and for export. This thesis uses a theoretical concept of sustainable livelihoods. According to the theory, the resources that people have shape their livelihood possibilities. Farming of jatropha affects the livelihoods of people especially through land use, as land use changes have effects on many of the livelihood resources. In addition to the written sources, the material of the thesis is based on 14 interviews in Vietnam and Finland, and on observation during a field trip to Northern Vietnam in the spring of 2008. The results of the thesis show that jatropha diesel can support the sustainability of livelihoods at different scales if it is produced with deliberation. However, positive results are only possible if decisions are made carefully and more experience is collected. The possibilities of sustainable jatropha farming depend mainly on the previous land use methods and ways of production. Farming of jatropha does not threaten food production in Vietnam if the farming plans are implemented as planned. Jatropha may take some land from cassava, but at the same time, food production can be increased if mixed farming is used on some farms. Plenty of new research information and practical experiences on jatropha farming has to be collected before results of the real sustainability of the farming are ready. Carefully considered continuation and documentation of present and future projects would help to understand the possibilities of jatropha diesel in Vietnam and elsewhere.

宽带隙半导体材料SiC 外延生长工艺的研究

Submitted by zhangdi (zhangdi@red.semi.ac.cn) on 2009-04-13T11:45:31Z

量子输运的主方程方法以及在量子点系统中的应用

Submitted by zhangdi (zhangdi@red.semi.ac.cn) on 2009-04-13T11:45:31Z

Optimization of a steel plant utilizing converted biomass

Inom nära framtid kan det vara ekonomiskt lönsamt att investera i träbaserad biomassa-användning inom stålproduktion. En förutsättning är att biomassans bränsle-egenskaper förbättras genom en sorts förkolning, närmare sagt långsam pyrolysering. Som biomassakälla duger skogsrester och dylikt. Nyttan med att använda biomassa är att man reducerar fossila CO2-utsläpp och på så vis minskar på den globala uppvärmningen; detta kräver dock att återplantering görs för att fånga de frigjorda CO2-utsläppen som härstammar från biomassans skörd, transport, processering och förbränning. En investering i en pyrolyseringsanläggning integrerad i ett stålverk kan vara lönsam ifall utsläppskatten är över 20 € per ton CO2 då biomassakostnaden är 40 € per ton torr substans. Detta är dock inte fallet i dagens läge och i Finland är dessa avgifter beroende av politiska beslut på Europeisk nivå. Det kunde dock vara av politiskt intresse att stödja biomassa-användningen inom stålindustrin eftersom detta skulle skapa nya arbetsplatser såväl inom själva stålindustrin som inom skogsindustrin och möjligen även inom kemi-industrin, beroende på hur de resulterande pyrolysprodukterna (träkol, gas och bio-oljor) utnyttjas. Med tanke på att närmare en femtedel av alla CO2-utsläpp härstammande från industrin kommer från stålindustrin så är det uppenbart att mera miljövänligare alternativ kommer att krävas i framtiden. Lähitulevaisuudessa voi olla taloudellisesti kannattavaa käyttää puuperäistä biomassaa teräksen valmistuksessa. Tämä vaatii kuitenkin sen, että biomassa läpikäy eräänlaisen hiillostuksen, eli pyrolyysin, ja tässä tapauksessa, hitaan pyrolyysin. Biomassalähteeksi kelpaavat esimerkiksi hakkuujätteet ja muu puujäte. Hyöty biomassankäytöstä syntyy siitä, kun se osittain korvaa perinteisesti käytettyjä fossiilisia polttoaineita, jolloin fossiiliset hiilidioksidipäästöt vähenevät ja tällöin myös vaikutus ilmaston lämpenemiseen vähenee. Edellytyksenä on tietysti se, että uusia puita ja kasveja istutetaan, jotta biomassan keräyksestä, kuljetuksesta, käsittelystä sekä poltosta vapautunut hiilidioksidi saadaan jälleen talteen. Arvion mukaan pyrolyysiyksikön integroiminen terästehtaaseen tulee taloudellisesti kannattavaksi, kun hiilidioksidivero nousee yli 20 € per tonni, kun biomassan hinnaksi on arvioitu 40 € per tonni kuiva-ainesta. Kyseinen hintataso ei ole tällä hetkellä voimassa ja Suomen tilanne tässä asiassa on vahvasti kytköksissä Euroopan tasolla tehtäviin päätöksiin. Aihe voisi kuitenkin olla poliittisella tasolla kiinnostava ja taloudellisen tuen arvoista, koska biomassan käyttö loisi lisää työpaikkoja niin terästeollisuudessa kuin puuteollisuudessakin ja mahdollisesti myös kemianteollisuudessa, riippuen siitä miten erinäisiä pyrolyysituotteita (puuhiili, kaasu ja bio-öljy) hyödynnettäisiin. Ottaen huomioon, että terästeollisuus maailmanlaajuisesti vastaa noin viidesosasta kaikista teollisuudesta peräisin olevista hiilidioksidipäästöistä on päivänselvää, että ympäristöystävällisemmille vaihtoehdoille on tarvetta tulevaisuudessa.

Valdezin öljyvuodon vaikutus alaskalaiseen alkuperäisväestöön Tundra Times- sanomalehdessä vuoden 1989 huhtikuusta vuoden 1990 huhtikuuhun

Exxon Valdezin tankkerin haaksirikko ja öljyvuoto Prinssi Williamin salmessa Alaskassa olivat vuoden 1989 merkittävimpiä mediatapahtumia 1980-luvun lopussa. Exxon Valdezin öljyvuoto oli Yhdysvaltojen senhetkisen historian pahin öljyvuoto. Prinssi Williamin salmen lähialueen merkittävimpiä maanomistajia olivat aleutit, jotka kuuluvat Alaskan alkuperäisväestöön. Pro gradu-tutkielmani alkuperäisaineistona toimivat alaskalaisen sanomalehden, Tundra Timesin pääkirjoitukset, lukijoiden kirjeet päätoimittajalle, uutiset ja artikkelit. Tutkielmassa tutkitaan Exxon Valdezin öljyvuodon vaikutuksia Alaskan alkuperäisväestöön Tundra Timesissa vuoden 1989 huhtikuusta vuoden 1990 huhtikuuhun. Tutkielma on kvalitatiivinen tutkimus, jonka tärkeimmät tutkimusmetodit ovat etnografinen ja induktiivinen sisällönanalyysi. Tutkielma sijoittuu historiantutkimuskentällä osaksi etnohistoriaa. Tutkimuskysymyksiä ovat muun muassa, mitä Tundra Timesin pääkirjoituksissa kirjoitetaan öljyvuodosta? Mitä tai ketä pääkirjoituksissa kritisoidaan? Mitä teemoja pääkirjoituksissa otetaan esille? Minkälaisia mielipiteitä lehdessä julkaistuissa lukijoiden kirjeissä on suhteessa öljyvuotoon? Miten Prinssi Williamin salmen alueen ja muun Alaskan alkuperäisasukkaat reagoivat öljyvuotoon? Ja miten lehti representoi muutosta öljyvuodon vaikutuksesta ihmisten elämässä? Pääkirjoitusten pohjalta voi todeta, että Tundra Timesin päätoimittaja kritisoi etenkin öljy-yhtiöiden ja –teollisuuden kykyä varautua öljyvuotoihin ja maan hallituksen käyttäytymistä alkuperäisväestöä kohtaan öljyvuodon jälkeen. Pääkirjoituksissa raittiusteema on enemmän esillä tutkimusajankohtana kuin Exxon Valdezin öljyvuoto. Tundra Timesin mukaan alkuperäisväestö oli ensisijaisesti huolissaan öljyvuodon vaikutuksista heidän omavaraistalouteensa. Pääkirjoitusten ja uutisten mukaan omavaraistalous ei ole pelkkä keino toimeentulon hankkimiseen, vaan se on elämäntapa. Huoli omavaraistaloudesta on hallitseva teema Tundra Timesin uutisissa ja artikkeleissa. Pelko alkoholin käytön lisääntymisestä ja toimettomuudesta ovat myös tärkeitä teemoja öljyvuotoon liittyvässä uutisoinnissa.