Browsing by Subject "environmental microbiology"

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  • Yan, Lijuan (Helsingin yliopisto, 2016)
    Soil pollution by petroleum hydrocarbons (PHCs) as a result of anthropogenic activities poses significant threats in the environment. In particular, used motor oil that contains high concentrations of aliphatics, polycyclic aromatic hydrocarbons (PAHs) and heavy metals (e.g. lead, zinc, chromium, barium and arsenic) contribute to chronic hazards including carcinogenicity. Microorganisms are able to degrade and utilize many recalcitrant compounds as carbon and energy sources in a natural attenuation process. However, in boreal regions this process is limited by the cool climate. The main goal of most bioremediation designs should be an optimization of environmental conditions for microbial growth and metabolic activities. Plant growth can stimulate the activities of soil microflora in the rhizosphere, thus enhancing the bioremediation of oil-polluted soil. Nitrogen deficiency is a frequent limiting factor of biomediation in oil-contaminated soils. Legumes that form symbiotic association with N-fixing bacteria are able to assist the biodegradation of PHCs. The planting of oil-tolerant perennial crops, especially legumes, in oil-contaminated soil holds promise for great economic benefits for bioenergy production while accelerating the oil degradation process. Fodder galega (Galega orientalis Lam.), a perennial forage legume, and smooth brome (Bromus inermis L.), a cool-season perennial sod-forming grass, are both persistent in boreal zones and have been shown to grow well together in crop mixtures without N-fertilizer supply. The oil tolerance and oil-rhizoremediation potential of G. orientalis and its microsymbiont Neorhizobium galegae have been demonstrated at microcosm and mesocosm scales. Plant growth promoting bacteria (PGPB) have potential to increase nodulation of galega, mitigate plant stress response and increase the bioavailability of soil contaminants, therefore enhancing the degradation of contaminants. These components can form a powerful combination to be used for bioremediation of oil-contaminated soil. However, the competitiveness and effectiveness of the crop- and PGPB-assisted bioremediation system need to be evaluated in field conditions. To date, there were no systematically described studies on bioremediation of oil-contaminated soil combined with crop biomass production in boreal regions. This multidisciplinary research project was conducted to fill this knowledge gap by evaluating the sustainability of the legume-cropping bioremediation system economically in terms of crop yield, and environmentally in terms of oil degradation rate and the dynamics of bacterial communities. To reach these aims, we established a multi-year bioremediation field experiment at the Viikki Experimental Farm, University of Helsinki, Finland (60°14'N, 25°01'E, 8 m AMSL) with crop treatments (brome grass, fodder galega, their mixture and bare fallow) as the main plots in four replicated blocks, and used motor oil treatments (7000 ppm +/-) and PGPB (+/-) treatments as the sub-plot factors. Soil samples were taken from the top 20 cm layer at six time points (July 2009, May 2010, November 2010, May 2011, May 2012 and October 2012). Soil chemical properties e.g. pH, electrical conductivity (EC), total C, total N and C:N ratio of three sample sets (July 2009, November 2010 and May 2012) were measured. Oil concentration was determined based on the difference of total solvent extractable material (TSEM) concentration between the oil-spiked plot and the average of control plots at each sampling time using the gravimetrical method. Crop physiological properties e.g. annual DM yield, total C, total N, C: N ratio, chlorophyll and BNF of the legume were measured. Soil-borne bacterial communities were investigated using i) LH-PCR community fingerprinting technique (all samples) and ii) Illumina s MiSeq sequencing (spring-summer samples). Oil contamination had a significant impact on soil chemical properties, e.g. pH, EC, total C and C:N ratio. The oil degradation was incomplete 40 months after the oil spike, with a dissipation of 73% - 92% of oil concentration (Paper I). As the field soil condition was good for oil degradation, the advantage of using crops to assist oil degradation was not evident. The oil degradation followed firstorder kinetics with the reduction rates decreasing as follows: bare fallow > galega-brome grass mixture > brome grass > galega. Oil, surprisingly, increased crop dry matter and nitrogen yield, particularly in the fourth year (Paper I). The legume-grass mixture produced significantly higher crop dry biomass than the pure stands. For instance, the unfertilized galega-brome grass mixture out-yielded the Nfertilized pure grass swards over years by an average of 32% (Paper I), suggesting that the inoculated galega could fully replace N-fertilizer for brome grass. PGPB enhanced the efficiency of biological nitrogen fixation of the legume, especially in legume-grass mixture plots (Paper I). The LH-PCR community fingerprinting technique produced similar results as the 16S rRNA gene amplicon sequencing. Both time and oil contamination were the main drivers of bacterial community dynamics (Papers II and III). The effect of oil was initially negative on overall bacterial diversity (Papers II and III), but variable on the diversity of bacterial sub-communities (Paper III). The bacterial communities responded quickly to oil contamination, but the effect of oil on community composition was recoverable over time (Papers II and III). Crop cultivation had a small impact on the composition of bacterial community (Paper III). The oil-favored taxa that discriminated bacterial communities between oil-contaminated and non-contaminated soils were mainly assigned to the two prevalent phyla Actinobacteria and Proteobacteria (Paper III). The operational taxonomic units (OTUs) with significantly different oil-specific abundance changes over time were all favored by oil; therefore, these oil-specific taxa were suggested as suitable bio-indicators to monitor the ecological impact of oil contamination (Paper III). Besides oil concentration, the changes in soil chemical properties, e.g. soil pH and EC, significantly affected bacterial community structure (Paper II and III). To summarize, oil contamination affected soil chemical and biological properties (e.g. crop growth and bacterial community), but the impact of oil decreased with time. The cultivation of oil-tolerant perennial crops, especially galega-brome grass mixture, in oil-contaminated soil can hopefully produce considerable biomass for bioenergy industry. Bacterial communities underwent a significant time- and season-dependent succession, regardless of oil contamination. Therefore, studies restricted to a single snapshot of time without any non-contaminated samples as reference cannot reveal oil contaminationrelated changes in the dynamic patterns of bacterial communities in the field soil. With the development and decreasing cost of high-throughput sequencing (NGS), NGS-based metagenomics analysis has become the mainstream method in microbial ecology research, providing in-depth view on bacterial populations at different taxonomic levels in the community. However, the LH-PCR technique is still suggested as a cost-effective method to monitor microbial community dynamics for assessing the ecological impact of oil contamination. Oil degradation was rather slow in the boreal climate. Long-term stimulation and monitoring of soil chemical properties, oil concentration, crop growth and microbial community are still needed for risk control. All these suggestions can be applied to soil contaminated by PHC contaminants other than used motor oil, despite hydrocarbon compositional differences.
  • Castro, Hanna; Douillard, Francois; Korkeala, Hannu; Lindström, Miia (2021)
    Listeria monocytogenes is a foodborne pathogen and a resilient environmental saprophyte. Dairy farms are a reservoir of L. monocytogenes, and strains can persist on farms for years. Here, we sequenced the genomes of 250 L. monocytogenes isolates to investigate the persistence and mobile genetic elements (MGEs) of Listeria strains inhabiting dairy farms. We performed a single-nucleotide polymorphism (SNP)-based phylogenomic analysis to identify 14 monophyletic clades of L. monocytogenes persistent on the farms for ≥6 months. We found that prophages and other mobile genetic elements were, on average, more numerous among isolates in persistent than nonpersistent clades, and we demonstrated that resistance genes against bacitracin, arsenic, and cadmium were significantly more prevalent among isolates in persistent than nonpersistent clades. We identified a diversity of mobile elements among the 250 farm isolates, including three novel plasmids, three novel transposons, and a novel prophage harboring cadmium resistance genes. Several of the mobile elements we identified in Listeria were identical to the mobile elements of enterococci, which is indicative of recent transfer between these genera. Through a genome-wide association study, we discovered that three putative defense systems against invading prophages and plasmids were negatively associated with persistence on farms. Our findings suggest that mobile elements support the persistence of L. monocytogenes on dairy farms and that L. monocytogenes inhabiting the agroecosystem is a potential reservoir of mobile elements that may spread to the food industry. IMPORTANCE Animal-derived raw materials are an important source of L. monocytogenes in the food industry. Knowledge of the factors contributing to the pathogen's transmission and persistence on farms is essential for designing effective strategies against the spread of the pathogen from farm to fork. An increasing body of evidence suggests that mobile genetic elements support the adaptation and persistence of L. monocytogenes in the food industry, as these elements contribute to the dissemination of genes encoding favorable phenotypes, such as resilience against biocides. Understanding of the role of farms as a potential reservoir of these elements is needed for managing the transmission of mobile elements across the food chain. Because L. monocytogenes coinhabits the farm ecosystem with a diversity of other bacterial species, it is important to assess the degree to which genetic elements are exchanged between Listeria and other species, as such exchanges may contribute to the rise of novel resistance phenotypes.
  • Purkamo, Lotta; Kietavainen, Riikka; Nuppunen-Puputti, Maija; Bomberg, Malin; Cousins, Claire (2020)
    The deep bedrock surroundings are an analog for extraterrestrial habitats for life. In this study, we investigated microbial life within anoxic ultradeep boreholes in Precambrian bedrock, including the adaptation to environmental conditions and lifestyle of these organisms. Samples were collected from Pyhasalmi mine environment in central Finland and from geothermal drilling wells in Otaniemi, Espoo, in southern Finland. Microbial communities inhabiting the up to 4.4 km deep bedrock were characterized with phylogenetic marker gene (16S rRNA genes and fungal ITS region) amplicon and DNA and cDNA metagenomic sequencing. Functional marker genes (dsrB, mcrA, narG) were quantified with qPCR. Results showed that although crystalline bedrock provides very limited substrates for life, the microbial communities are diverse. Gammaproteobacterial phylotypes were most dominant in both studied sites. Alkanindiges -affiliating OTU was dominating in Pyhasalmi fluids, while different depths of Otaniemi samples were dominated by Pseudomonas. One of the most common OTUs detected from Otaniemi could only be classified to phylum level, highlighting the uncharacterized nature of the deep biosphere in bedrock. Chemoheterotrophy, fermentation and nitrogen cycling are potentially significant metabolisms in these ultradeep environments. To conclude, this study provides information on microbial ecology of low biomass, carbon-depleted and energy-deprived deep subsurface environment. This information is useful in the prospect of finding life in other planetary bodies.