Archaea, Bacteria, and methane production along environmental gradients in fens and bogs

Metanogeenit ovat hapettomissa oloissa eläviä arkkien pääryhmään kuuluvia mikrobeja, joiden ainutlaatuisen aineenvaihdunnan seurauksena syntyy metaania. Ilmakehässä metaani on voimakas kasvihuonekaasu. Yksi suurimmista luonnon metaanilähteistä ovat kosteikot. Pohjoisten soiden metaanipäästöt vaihtelevat voimakkaasti eri soiden välillä ja yhden suon sisälläkin, riippuen muun muassa vuodenajasta, suotyypistä ja kasvillisuudesta. Väitöskirjatyössä tutkittiin metaanipäästöjen vaihtelun mikrobiologista taustaa. Tutkimuksessa selvitettiin suotyypin, vuodenajan, tuhkalannoituksen ja turvesyvyyden vaikutusta metanogeeniyhteisöihin sekä metaanintuottoon kolmella suomalaisella suolla. Lisäksi tutkittiin ei-metanogeenisia arkkeja ja bakteereita, koska ne muodostavat metaanin tuoton lähtöaineet osana hapetonta hajotusta. Mikrobiyhteisöt analysoitiin DNA- ja RNA-lähtöisillä, polymeraasiketjureaktioon (PCR) perustuvilla menetelmillä. Merkkigeeneinä käytettiin metaanin tuottoon liittyvää mcrA-geeniä sekä arkkien ja bakteerien ribosomaalista 16S RNA-geeniä. Metanogeeniyhteisöt ja metaanintuotto erosivat huomattavasti happaman ja vähäravinteisen rahkasuon sekä ravinteikkaampien sarasoiden välillä. Rahkasuolta löytyi lähes yksinomaan Methanomicrobiales-lahkon metanogeeneja, jotka tuottavat metaania vedystä ja hiilidioksidista. Sarasoiden metanogeeniyhteisöt olivat monimuotoisempia, ja niillä esiintyi myös asetaattia käyttäviä metanogeeneja. Vuodenaika vaikutti merkittävästi metaanintuottoon. Talvella havaittiin odottamattoman suuri metaanintuottopotentiaali sekä viitteitä aktiivisista metanogeeneista. Arkkiyhteisön koostumus sen sijaan vaihteli vain vähän. Tuhkalannoitus, jonka tarkoituksena on edistää puiden kasvua ojitetuilla soilla, ei merkittävästi vaikuttanut metaanintuottoon tai -tuottajiin. Ojitetun suon yhteisöt kuitenkin muuttuivat turvesyvyyden mukaan. Vertailtaessa erilaisia PCR-menetelmiä todettiin, että kolmella mcrA-geeniin kohdistuvalla alukeparilla havaittiin pääosin samat ojitetun suon metanogeenit, mutta lajien runsaussuhteet riippuvat käytetyistä alukkeista. Soilla havaitut bakteerit kuuluivat pääjaksoihin Deltaproteobacteria, Acidobacteria ja Verrucomicrobia. Lisäksi löydettiin Crenarchaeota-pääjakson ryhmiin 1.1c ja 1.3 kuuluvia ei-metanogeenisia arkkeja. Tulokset ryhmien esiintymisestä hapettomassa turpeessa antavat lähtökohdan selvittää niiden mahdollisia vuorovaikutuksia metanogeenien kanssa. Tutkimuksen tulokset osoittivat, että metanogeeniyhteisön koostumus heijastaa metaanintuottoon vaikuttavia kemiallisia tai kasvillisuuden vaihteluita kuten suotyyppiä. Soiden metanogeenien ja niiden fysiologian parempi tuntemus voi auttaa ennustamaan ympäristömuutosten vaikutusta soiden metaanipäästöihin.

Stress responses of Gram-positive bacteria to cationic antimicrobial peptides

As the resistance of bacteria to conventional antibiotics has become an increasing problem, new antimicrobial drugs are urgently needed. One possible source of new antibacterial agents is a group of cationic antimicrobial peptides (CAMPs) produced by practically all living organisms. These peptides are typically small, amphipathic and positively charged and contain well defined a-helical or b-sheet secondary structures. The main antibacterial action mechanism of CAMPs is considered to be disruption of the cell membrane, but other targets of CAMPs also exist. Some bacterial species have evolved defence mechanisms against the harmful effects of CAMPs. One of the most effective defence mechanisms is reduction of the net negative charge of bacterial cell surfaces. Global analysis of gene expression of two Gram-positive bacteria, Bacillus subtilis and Staphylococcus aureus, was used to further study the stress responses induced by different types of CAMPs. B. subtilis cells were treated with sublethal concentrations of a-helical peptide LL-37, b-sheet peptide protegrin 1 or synthetic analogue poly-L-lysine, and the changes in gene expression were studied using DNA macroarrays. In the case of S. aureus, three different a-helical peptides were selected for the transcriptome analyses: temporin L, ovispirin-1 and dermaseptin K4-S4(1-16). Transcriptional changes caused by peptide stress were examined using oligo DNA microarrays. The transcriptome analysis revealed two main cell signalling mechanisms mediating CAMP stress responses in Gram-positive bacteria: extracytoplasmic function (ECF)sigma factors and two-component systems (TCSs). In B. subtilis, ECF sigma factors sigW and sigM as well as TCS LiaRS responded to the cell membrane disruption caused by CAMPs. In S. aureus, CAMPs caused a similar stress response to antibiotics interfering in cell wall synthesis, and TCS VraSR was strongly activated. All of these transcriptional regulators are known to respond to several compounds other than CAMPs interfering with cell envelope integrity, suggesting that they sense cell envelope stress in general. Among the most strongly induced genes were yxdLM (in B. subtilis) and vraDE (in S. aureus) encoding homologous ABC transporters. Transcription of yxdLM and vraDE operons is controlled by TCSs YxdJK and ApsRS, respectively. These TCSs seemed to be responsible for the direct recognition of CAMPs. The yxdLM operon was specifically induced by LL-37, but its role in CAMP resistance remained unclear. VraDE was proven to be a bacitracin transporter. We also showed that the net positive charge of the cell wall affects the signalrecognition of different TCSs responding to cell envelope stress. Inactivation of the Dlt system responsible for the D-alanylation of teichoic acids had a strong and differential effect on the activity of the studied TCSs, depending on their functional role in cells and the stimuli they sense.

Immunological Effects of Probiotic Bacteria in Prevention and Treatment of Allergic Diseases in Children

Epidemiological and experimental studies suggest that changes in gut microbial balance are associated with increases in the prevalence of allergic diseases. Probiotics are proposed to provide beneficial immunoregulatory signals which aid in oral tolerance achievement and alleviation of symptoms of allergic diseases. The present study evaluates both the immunological mechanisms of probiotics in infants with allergic diseases and their preventive aspect among infants prone to allergy. Furthermore, the purpose of the study was to characterise the immunological features of cord blood mononuclear cells (CBMCs) in infants at high genetic risk for allergy. GATA-3 expression (p = 0.03), interleukin (IL) -2(p = 0.026), and IL-5 (p = 0.013) secretion of stimulated CBMCs were higher in IgE-sensitized infants at age 2 than in non-allergic, non-sensitized infants. Lactobacillus GG (LGG) treatment increased secretion of IFN-γ by PBMCs in vitro in infants with cow s milk allergy (CMA) (p = 0.006) and in infants with IgE-associated eczema (p = 0.017), when compared to levels in the placebo group. A probiotic mixture, increased secretion of IL-4 by PBMCs in vitro in infants with CMA (p = 0.028), when compared with placebo-group levels. The LGG treatment induced higher plasma C-reactive protein (CRP) (p = 0.021) and IL-6 (p = 0.036) levels in infants with IgE-associated eczema than in the placebo group. The probiotic mixture induced higher plasma IL-10 levels in infants with eczema (p = 0.016). In the prevention study of allergic dis-eases, the infants receiving the probiotic mixture had higher plasma levels of CRP (p = 0.008), total IgA (p = 0.016), total IgE (p = 0.047), and IL-10 (p = 0.002) than did infants in the placebo group. Increased CRP level at age 6 months was associated with a decreased risk for eczema at age 2 not only in the infants who received probiotics but also in the placebo group (p = 0.034). In conclusion, the priming of the GATA-3 and IL-5 pathway can occur in utero, and a primary feature of T-cells predisposing to IgE-sensitization seems to directly favour Th2 deviation. LGG treatment induced increased plasma levels of CRP and IL-6 in infants with IgE-associated eczema, suggesting an activation of innate immu-nity. The probiotic mixture, when given to allergy-prone infants, induced inflammation, detected as increased plasma CRP levels, which at age 6 months was associated with decreased risk for eczema at age 2.The probiotic-induced response in allergy prone infants was characterized by their higher plasma IL-10, total IgE, and CRP levels, without induction of an allergen-specific IgE response. In this respect, the probiotics in infancy appear to induce protective immune profiles that are characteristic for chronic low-grade inflammation, a response resembling that of helminth-like infections.

Ultrastructure of Biofilms Formed by Bacteria from Industrial Processes

Microorganisms exist predominantly as sessile multispecies communities in natural habitats. Most bacterial species can form these matrix-enclosed microbial communities called biofilms. Biofilms occur in a wide range of environments, on every surface with sufficient moisture and nutrients, also on surfaces in industrial settings and engineered water systems. This unwanted biofilm formation on equipment surfaces is called biofouling. Biofouling can significantly decrease equipment performance and lifetime and cause contamination and impaired quality of the industrial product. In this thesis we studied bacterial adherence to abiotic surfaces by using coupons of stainless steel coated or not coated with fluoropolymer or diamond like carbon (DLC). As model organisms we used bacterial isolates from paper machines (Meiothermus silvanus, Pseudoxanthomonas taiwanensis and Deinococcus geothermalis) and also well characterised species isolated from medical implants (Staphylococcus epidermidis). We found that coating of steel surface with these materials reduced its tendency towards biofouling: Fluoropolymer and DLC coatings repelled all four biofilm formers on steel. We found great differences between bacterial species in their preference of surfaces to adhere as well as their ultrastructural details, like number and thickness of adhesion organelles they expressed. These details responded differently towards the different surfaces they adhered to. We further found that biofilms of D. geothermalis formed on titanium dioxide coated coupons of glass, steel and titanium, were effectively removed by photocatalytic action in response to irradiation at 360 nm. However, on non-coated glass or steel surfaces irradiation had no detectable effect on the amount of bacterial biomass. We showed that the adhesion organelles of bacteria on illuminated TiO2 coated coupons were complety destroyed whereas on non-coated coupons they looked intact when observed by microscope. Stainless steel is the most widely used material for industrial process equipments and surfaces. The results in this thesis showed that stainless steel is prone to biofouling by phylogenetically distant bacterial species and that coating of the steel may offer a tool for reduced biofouling of industrial equipment. Photocatalysis, on the other hand, is a potential technique for biofilm removal from surfaces in locations where high level of hygiene is required. Our study of natural biofilms on barley kernel surfaces showed that also there the microbes possessed adhesion organelles visible with electronmicroscope both before and after steeping. The microbial community of dry barley kernels turned into a dense biofilm covered with slimy extracellular polymeric substance (EPS) in the kernels after steeping in water. Steeping is the first step in malting. We also presented evidence showing that certain strains of Lactobacillus plantarum and Wickerhamomyces anomalus, when used as starter cultures in the steeping water, could enter the barley kernel and colonise the tissues of the barley kernel. By use of a starter culture it was possible to reduce the extensive production of EPS, which resulted in a faster filtration of the mash.

Characterisation of antibiotic-resistant psychrotrophic bacteria in raw milk

Dynamics of raw milk associated bacteria during cold storage of raw milk and their antibiotic resistance was reviewed, with focus on psychrotrophic bacteria. This study aimed to investigate the significance of cold storage of raw milk on antibiotic-resistant bacterial population and analyse the antibiotic resistance of the Gram-negative antibiotic-resistant psychrotrophic bacteria isolated from the cold-stored raw milk samples. Twenty-four raw milk samples, six at a time, were obtained from lorries that collected milk from Finnish farms and were stored at 4°C/4 d, 6°C/3 d and 6°C/4 d. Antibiotics representing four classes of antibiotics (gentamicin, ceftazidime, levofloxacin and trimethoprim-sulfamethoxazole) were used to determine the antibiotic resistance of mesophilic and psychrotrophic bacteria during the storage period. A representative number of antibiotic-resistant Gram-negative isolates retrieved from the cold-stored raw milk samples were identified by the phenotypic API 20 NE system and a few isolates by the 16S rDNA gene sequencing. Some of the isolates were further evaluated for their antibiotic resistance by the ATB PSE 5 and HiComb system. The initial average mesophilic counts were found below 105 CFU/mL, suggesting that the raw milk samples were of good quality. However, the mesophilic and psychrotrophic population increased when stored at 4°C/4 d, 6°C/3 d and 6°C/4 d. Gentamicin- and levofloxacin-resistant bacteria increased moderately (P < 0.05) while there was a considerable rise (P < 0.05) of ceftazidime- and trimethoprim-sulfamethoxazole-resistant population during the cold storage. Of the 50.9 % (28) of resistant isolates (total 55) identified by API 20 NE, the majority were Sphingomonas paucimobilis (8), Pseudomonas putida (5), Sphingobacterium spiritivorum (3) and Acinetobacter baumanii (2). The analysis by ATB PSE 5 system suggested that 57.1% of the isolates (total 49) were multiresistant. This study showed that the dairy environment harbours multidrug-resistant Gramnegative psychrotrophic bacteria and the cold chain of raw milk storage amplifies the antibioticresistant psychrotrophic bacterial population.

Bacteria colonizing paper machines

Bacteria growing in paper machines can cause several problems. Biofilms detaching from paper machine surfaces may lead to holes and spots in the end product or even break the paper web leading to expensive delays in production. Heat stable endospores will remain viable through the drying section of paper machine, increasing the microbial contamination of paper and board. Of the bacterial species regularly found in the end products, Bacillus cereus is the only one classified as a pathogen. Certain B. cereus strains produce cereulide, the toxin that causes vomiting disease in food poisonings connected to B. cereus. The first aim of this thesis was to identify harmful bacterial species colonizing paper machines and to assess the role of bacteria in the formation of end product defects. We developed quantitative PCR methods for detecting Meiothermus spp. and Pseudoxanthomonas taiwanensis. Using these methods I showed that Meiothermus spp. and Psx. taiwanensis are major biofoulers in paper machines. I was the first to be able to show the connection between end product defects and biofilms in the wet-end of paper machines. I isolated 48 strains of primary-biofilm forming bacteria from paper machines. Based on one of them, strain K4.1T, I described a novel bacterial genus Deinobacterium with Deinobacterium chartae as the type species. I measured the transfer of Bacillus cereus spores from packaging paper into food. To do this, we constructed a green fluorescent protein (GFP) labelled derivative of Bacillus thuringiensis and prepared paper containing spores of this strain. Chocolate and rice were the recipient foods when transfer of the labelled spores from the packaging paper to food was examined. I showed that only minority of the Bacillus cereus spores transferred into food from packaging paper and that this amount is very low compared to the amount of B. cereus naturally occurring in foods. Thus the microbiological risk caused by packaging papers is very low. Until now, the biological function of cereulide for the producer cell has remained unknown. I showed that B. cereus can use cereulide to take up K+ from environment where K+ is scarce: cereulide binds K+ ions outside the cell with high affinity and transports these ions across cell membrane into the cytoplasm. Externally added cereulide increased the growth rate of cereulide producing strains in medium where potassium was growth limiting. In addition, cereulide producing strains outcompeted cereulide non-producing B. cereus in potassium deficient environment, but not when the potassium concentration was high. I also showed that cereulide enhances biofilm formation of B. cereus.