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Specialeemner i mikrobiel økologi og mikrobiologi

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Forekomst og skæbne af mikroorganismer i atmosfæren

Baggrund

Man ved godt at der findes luftbårne mikroorganismer. Men hvor kommer de fra, hvor er de på vejen hen, og hvad har de gang i? Måske påvirker de ikke kun planter, dyr og mennesker, men også klimaet…? Disse spørgsmål undersøger vi ved at indsamle mikroorganismer fra forskellige luftlag og at analysere dem i laboratoriet.

Kontaktperson: Seniorforsker Ulrich Bay Gosewinkel, uka@dmu.dk, tlf. 87 15 86 17.


Bacillus thuringiensis – naturens eget insektbekæmpelsesmiddel

Background

Bacillus thuringiensis er en Gram positiv sporedannende bakterie som er naturligt forekommende overalt i miljøet. For mere end 100 år siden fandt man ud af at bakterien kunne slå visse insekter ihjel. I dag anvendes B. thuringiensis i en række produkter til bekæmpelse af larver af biller, myg og sommerfugle. I Danmark anvendes B. thuringiensis primært til bekæmpelse af sørgemyg i gartnerier, men der anvendes også en del til bekæmpelse af forskellige sommerfugle larver i f. eks. kålafgrøder. En af fordelene ved at anvende B. thuringiensis til insektbekæmpelse er at den enkelte stamme ikke er særlig bredspektret og således i høj grad kan anvendes til målrettet bekæmpelse. Desuden har den insektgiftige aktivitet en meget kort holdbarhed, hvilket er medvirkende til at det er meget sjældent at insekterne udvikler resistens overfor B. thuringiensis.

Når B. thuringiensis sporulerer dannes der en protein krystal uden for sporen. Dette krystal kan ses ved fase-kontrast mikroskopi, og indeholder proteiner som er giftige for nogle insekt larver. Evnen til at danne disse protein krystaller er kodet på store plasmider, og det er netop denne evne som adskiller B. thuringiensis fra den nærtbeslægtedeBacillus cereus, som især er kendt for at være en relativt mild human pathogen. B. thuringiensistilhører B. cereus gruppen indenfor slægten Bacillus. De andre arter i denne gruppe er B. mycoides, B. pseudomycoides, B. weihenstephanensis, B. anthracis og B. cereus. Disse seks arter er så tæt beslægtede at mange mener de burde samles til én art, men fordi de seks bakterier hver især har specifikke fænotypiske karakteristika, som ofte er plasmidbundne, vil den nuværende artsopdeling sandsynligvis bibeholdes. Under alle omstændigheder er det en meget divers gruppe af bakterier lige fra B. anthracis som kan slå pattedyr (incl. mennesker) ihjel og B. thuringiensis som anvendes til insektbekæmpelse til B. cereus som kan forårsage mave-tarm infektioner, men som også kan anvendes som et probiotika til behandling af diarré hos dyr og mennesker. Ud over at kunne dræbe insekter ser det ud til at B. thuringiensis, ja måske hele B. cereus gruppen, kan leve i et symbiotisk samspild med invertebrater i deres tarme. Vi har fundet aktiveB. thuringiensis i tarmen hos regnorme og stankelben larver uden at disse øjensynligt påvirkes af den grund. Således ser det ud til at B. thuringiensis måske kan have to aktive livsformer, et samliv med nogle invertebrater i deres tarme, og et liv som insekt pathogen hos andre.

Vi har mange B. thuringiensis-relaterede forskningsaktiviteter, som alle dog har en relevans for risikovurdering af B. thuringiensis :

  • Vi har en stammesamling med flere tusinde bakterier fra B. cereus gruppen.
  • Vi undersøger slægtskabs forholdende og diversiteten indenfor B. cereus gruppen med genetiske og fænotypiske metoder, herunder udvikling af detektionsmetoder.
  • Vi arbejder på at belyse hvorvidt det at sprøjte grøntsager med B. thuringiensis kan give en øget risiko for B. cereus lignende infektioner hos mennesker.
  • Vi undersøger vekselvirkningerne med invertebrater.
  • Vi undersøger overlevelsen af udsprøjtede B. thuringiensis i miljøet.
  • Vi undersøger forekomsten af B. cereus gruppens bakterier i luften i landbruget.
  • Vi udvikler nye typer B. thuringiensis ved overførsel af plasmider som koder for krystalline proteiner til andre medlemmer indenfor B. cereus gruppen.
  • Vi analyserer toksicitet ved hjælp af eucaryote cellelinier og nematoder.
  • Vi kloner og sekventerer specifikke gener.

Kontaktperson: Seniorforsker Niels Bohse Hendriksen, nbh@dmu.dk, tlf. 87 15 84 73.


Eco-toxicology of silver-based nanomaterials (SNMs) - with emphasis on soil microorganisms and bacterial antibiotic resistance

Background

The objective is to study: 1) eco-toxicological aspects of SNMs in microbial communities in soil and sewage-treatment plants, and 2) if SNMs facilitate emergence of antibiotic resistance in pathogenic bacteria when used in anti-bacterial therapy.

The student may decide to deal with only one of the two objectives.

Silver-based nanomaterials (SBNs) are widely used as anti-microbial agents in medical applications (e.g. bandages) and in clothes and technical equipment where reduced microbial growth is required. However, via disposal, wear, washing etc., SNM is released to sewage-treatment plants, soil (via sludge application) and aquatic environments. Taken the intrinsic biocidal activity of the SNMs into account, this may devastate the microbial functionality vital for effective treatment of sewage effluents and turnover of organic matter. Medical equipment (e.g. bandages and catheters) is coated with SNM to diminish infection with inflammatory pathogens. It is well known that genes coding for various heavy metals are exchanged both between related and non-related bacteria. These genes are often found on plasmids and linked with genes coding for antibiotics. Hence, there is a risk that increased use of SNM may also increase the presence of multi-resistant pathogens. In the project we study 1) how survival, growth dynamics and genetic and functional diversity of bacterial communities (especially from sewage plants) are affected by SNMs (various formulations and concentrations); 2) if SNM induce the horizontal transfer of silver resistant genes as well as the co-transfer of antibiotic-resistance genes using (non-hazardous) model bacteria and plasmids typically found in medical treatment scenarios.

Advisor: Anders Johansen, PhD, Senior Scientist, Section of Environmental Microbiology and Biotechnology, Aarhus University Institute in Roskilde.

Internal advisor: Erik Baatrup, lector, PhD, Biologisk Institut. Aarhus Universitet.

Contact person: Seniorforsker Anders Johansen, ajo@dmu.dk, tlf. 87 15 85 86.


Plants and microorganisms help clean the environment – bioremediation

Background

Many soils are heavily contaminated with heavy metals which constitute a huge problem because they are toxic to both the environment and humans. This leaves the contaminated soils with a need for expensive treatments and in many cases also a continuous risk of contaminating plants, animals and ground water. Some plant species are known to be able to take up and accumulate heavy metals in their tissues at much greater rates than normal plants. In this way plants may help clean up contaminated soils for heavy metals. Obviously, the tissues of such plants cannot be used for food but maybe utilized for producing bioenergy (biogas, bioethanol).

The main objective of the present project is to study the possibility of using specific heavy-metal accumulating plant species to reduce these compounds in contaminated soil. The remediation of soils may be further facilitated, or sometimes maybe even inhibited, by the soil microorganisms – depending on factors like soil type, climate etc. Experimentally, we will add heavy metals to soil as well as use soil already contaminated with heavy metals. These soils will be grown with plant species able to accumulate high proportions of heavy metals. Additionally, we may study how the soil microorganisms influence the plant uptake of the contaminants. Ultimately the project may evaluate if the this approach for heavy metal remediation can actually clean up contaminated soils and how long time this will eventually take. Other issues which can be included in the project are the energy potentials of such remediation cropping systems and the possibility to remove the heavy metals from the bioenergy residues/wastes so that they can be stored in a safe way or reused in technical applications.

Advisor: Anders Johansen, PhD, Senior Scientist, Section of Environmental Microbiology and Biotechnology, Aarhus University Institute in Roskilde.

Contact persons: Senior Scientist Anders Johansen, ajo@dmu.dk, tlf. 87 15 85 86; or Department Head: Senior Scientist Ulrich Bay Gosewinkel, uka@dmu.dk, tlf. 87 15 86 17.


Microbial community diversity in agricultural soils with no to low carbon input

Danish agricultural soils are declining carbon content which can affect the soil quality and fertility. However, the agricultural practice of low to no input and return of carbon to soil yields crops of very high quality.

In this project, agricultural practice of no organic carbon and nitrogen input will be compared to conventional agricultural practice with regard to microbial and protist abundance, community structure and diversity, using molecular methods as quantitative PCR and next generation sequencing.

Specific focus will be on nitrogen and phosphate cycling enzymatic activity and microbial diversity.

Supervisor: Anne Winding (senior scientist) (aw@envs.au.dk)

              


Biochar as a carrier of plant growth promoting bacteria

When introducing beneficial microorganisms into soil they usually have a very poor survival and this fact has limited the extensive use of plant growth promoting bacteria and microbial pest control agents.

Biochar is an acclaimed soil quality improver with potential of sequestering carbon in soil to mitigate increasing CO2 in the atmosphere. Our results have so far shown biochar to increase soil organic carbon content and have no significant effect on microbial processes.

In this project we will explore the potentials of using biochar as a carrier of beneficial bacteria upon introduction to soil. This is hypothesised to increase and prolong survival of the beneficial bacteria and hence their positive effects towards sustainable agricultural practises.

Supervisor: Anne Winding (senior scientist) (aw@envs.au.dk)

            

        


Biochar as cleaning agent in soil and water

Biochar can provide a niche for survival of bacteria and at the same time attract organic contaminants. This facilitates the contact between degrading bacteria and the contaminants.

The hypothesis to be tested is the increased contaminant degradation and cleaning of soil and water. This will be tested in microcosm experiments of increasing complexity.

Supervisor: Anne Winding (senior scientist) (aw@envs.au.dk)

  


Interaction between protists and bacteria in soil

Unicellular eukaryotic protists as e.g. flagellates, amoebae and ciliates have very important roles in the soil turn-over of organic matter and as predators of bacteria, regulation their abundance and diversity.

In this project, the capacity of biochar as a survival niche for bacteria – and protists – will be studied in controlled laboratory conditions of increasing complexity with soil and plants.

Supervisor: Anne Winding (senior scientist) (aw@envs.au.dk)


Environmental DNA

Environmental DNA (eDNA) has a great potential of detection rare species of plants, animals and microorganisms in the environment as well as describing and monitoring the diversity of the communities.

In this project eDNA will be developed and tested for monitoring bathing water quality as regard to pathogenic bacteria and protists, using next generation sequencing, qPCR and other relevant techniques.

Supervisor: Anne Winding (senior scientist) (aw@envs.au.dk)


Forekomst af den sygdomsfremkaldende bakterie Pasteurella multocida i ederfugle og redemateriale fra Saltholm

Baggrund

Pasteurella multocida er en sygdomsfremkaldende bakterie, der forårsager fuglekolera hos fugle, både husdyr og vilde fugle. I Nordamerika er fuglekolera en væsentlig årsag til sygdomsudbrud med mange dødsfald blandt vilde fugle, specielt vandfugle, og der er bekymring for spredning til ederfugle langs Grønlands kyster. I Danmark forekommer der sporadisk epidemier af fuglekolera. Det er uklart om og i hvilket omfang P. multocida kan overleve i det ydre miljø som redemateriale, jord og vand, samt hvorvidt raske fugle kan være bærere af sygdommen. I specialet vil der blive arbejdet med allerede indsamlet materiale fra ederfugle og deres nærmiljø, og forekomst af P. multocida samt diversiteten af mikroorganismerne i miljøet kan undersøges. Det vil give ny relevant viden om denne sygdomsfremkaldende bakteries livsmønster.

Kontaktperson: Seniorforsker Anne Winding, aw@dmu.dk, tlf. 87 15 86 15.