Browsing by Subject "microbial communities"

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  • Hyvönen, Tinja (Helsingin yliopisto, 2021)
    The spread of antibiotic resistance is a global health threat. Hospitals are a potential source of antibiotic-resistant bacteria and antibiotic resistance genes (ARGs), which may disseminate into the environment via wastewater. Hospital water environments, such as sink traps and shower drains, are known to harbor antibiotic-resistant bacteria, which might spread from the drains to the patients causing nosocomial infections that are hard to treat because of the limited number of treatments available. However, the current understanding of antibiotic resistance in the drains of residences, and how it relates to the situation in hospitals is limited. The aim of this study was to compare the microbial communities and ARGs in the water environments of homes and hospitals. The sink traps and shower drains of three hospital rooms and eighteen homes were sampled for metagenomic sequencing, and bioinformatic tools were used to detect the microbial taxa and ARGs in the metagenomes. The resistomes of hospital environments were distinct from those of homes and exhibited a higher diversity of ARGs. On the other hand, the microbial communities of homes and hospital rooms could not be clearly distinguished, although there were some differences in the abundances of certain taxa. The abundance of ARGs was higher in the hospital shower drains than in the corresponding samples in homes, but there was no statistical difference in the abundance of ARGs between the sink traps of homes and the hospital. Although the study had limitations, such as the low number of hospital samples, it indicates that the water environments of hospitals have a resistome that is distinct from that of homes and highlights the role of hospital sink traps and shower drains as potential hotspots of antibiotic resistance.
  • Zrim, Jure; Nuutinen, Visa; Simojoki, Asko Juhani; Penttinen, Petri Juhani; Karhu, Laura Kristiina; Glaser, Bruno; Tammeorg, Priit (2018)
    Biochar soil amendment could be used to sequester carbon, enhance soil fertility and potentially increase crop yields. It can have significant impacts on soil organic carbon levels and physicochemical conditions, which consequently affect soil micro- and macro-biota. It is therefore important to understand how key biological components in the soil such as microbial and earthworm communities response to biochar application in the long-term. This study was conducted in Southern Finland in a fertile Stagnosol and a nutrient deficient Umbrisol, four and five years after biochar amendment, respectively. Biochars were produced from spruce (Picea abies (L.) H.Karst.) and pine (Pinus sylvestris L.), and applied at the rates of 10 and 30 t ha-1, respectively. Earthworms and soil samples for microbial analyses were collected in September 2015. Soil microbial communities were studied by using phospholipid fatty acid profiling and 16S rRNA gene amplicon sequencing. Casts from the sampled earthworms were collected to investigate the consumption of biochar and the potential of earthworm bioturbation to affect biochar distribution. Additionally, greenhouse gas emissions from soil were measured. Biochar and fertilizer treatments or their interaction had no statistically significant effects on the earthworm abundance, community composition or greenhouse gas emissions in either field. Earthworms had ingested biochar as earthworm casts from biochar treated-plots contained significantly more black carbon than those in the control plots, demonstrating that earthworm bioturbation is a potentially important factor in the translocation of applied biochar in the soil profile. Microbial community structure data will be presented in the final presentation.
  • Rutanen, Aino (Helsingin yliopisto, 2020)
    Global warming caused by the warming effect of greenhouse gases (GHGs) induces permafrost thaw, which could alter Arctic ecosystems from prominent carbon sinks to potential sources of GHG emissions when polar microorganisms become metabolically more active and have access to carbon compounds that were previously largely unavailable. Polar microbes can have significant contributions to the growing emissions of carbon dioxide (CO2), methane (CH4) and nitrous oxide (N2O) and therefore, studies on their metabolism are important. The aim of my study was to investigate polar microbial community composition and diversity as well as functional potential that was related to GHG-cycling in a subarctic environment with genome-resolved metagenomics. Soil cores were collected at the Rásttigáisá fell that is located in Northern Norway. After DNA extraction, ten mineral soil samples were sequenced. Metagenome-assembled genomes (MAGs) were reconstructed using either the combination of human-guided binning and automatic binning or human-guided binning only. Taxonomy was assigned to the MAGs and the functional potential of the MAGs was determined. I recovered dozens of good-quality MAGs. Notably, the MAGs from the mostly unknown phyla Dormibacterota (formerly candidate phylum AD3) and Eremiobacterota (formerly candidate phylum WPS-2) were reconstructed. There were MAGs from the following bacterial phyla as well: Acidobacteriota, Actinobacteriota, Chloroflexota, Gemmatimonadota, Proteobacteria and Verrucomicrobiota. In addition to the bacterial MAGs, MAGs from the group of ammonia-oxidizing archaea were recovered. Most of the MAGs belonged to poorly studied phylogenetic groups and consequently, novel functional potential was discovered in many groups of microorganisms. The following metabolic pathways were observed: CO2 fixation via the Calvin cycle and possibly via a modified version of 3-hydroxypropionate/4-hydroxybutyrate cycle; carbon monoxide oxidation to CO2; CH4 oxidation and subsequent carbon assimilation via serine pathway; urea, ammonia and nitrite oxidation; incomplete denitrification as well as dissimilatory nitrate reduction to ammonium. My study demonstrates how genome-resolved metagenomics provides a valuable overview of the microbial community and its functional potential.
  • Suominen, Juulia (Helsingin yliopisto, 2020)
    Sourdoughs are a natural habitat for microbial communities predominated by lactic acid bacteria (LAB) and yeasts. How microbial communities assemble and function is, to a large extent, determined by inter-species interactions. However, evidence for LAB-yeast interactions in rich environments, such as sourdough, is yet largely unavailable. In this study, a set of LAB and yeast species was isolated from rye and wheat sourdoughs. While mainly typical sourdough species were identified, Pediococcus parvulus was, to the best of our knowledge, for the first time isolated from sourdoughs. The isolates were characterized in rich chemically defined culture conditions and screened for interactions. Potential interactions were discovered where LAB growth was enabled by a yeast, or where stable communities were formed despite competition. These findings, the resource of naturally co-occurring species, and the designed chemically defined growth medium present the grounds for future research for uncovering the underlying mechanisms of LAB-yeast interactions in rich environments. LAB and yeasts commonly co-occur rich environments of fermented food processes and also in human gut and soil microbiomes. Therefore, the outcomes of this study support not only the optimization of food fermentations but provide also model systems for complex communities directly influencing human health.
  • Lusa, Merja; Bomberg, Malin (2021)
    Microbial communities throughout the 6.5 m depth profile of a boreal ombrotrophic bog were characterized using amplicon sequencing of archaeal, fungal, and bacterial marker genes. Microbial populations and their relationship to oxic and anoxic batch sorption of radionuclides (using radioactive tracers of I, Se, Cs, Ni, and Ag) and the prevailing metal concentrations in the natural bog was investigated. The majority of the detected archaea belonged to the Crenarchaeota, Halobacterota, and Thermoplasmatota, whereas the fungal communities consisted of Ascomycota, Basidiomycota, and unclassified fungi. The bacterial communities consisted mostly of Acidobacteriota, Proteobacteria, and Chloroflexi. The occurrence of several microbial genera were found to statistically significantly correlate with metal concentrations as well as with Se, Cs, I, and Ag batch sorption data. We suggest that the metal concentrations of peat, gyttja, and clay layers affect the composition of the microbial populations in these nutrient-low conditions and that particularly parts of the bacterial and archaeal communities tolerate high concentrations of potentially toxic metals and may concurrently contribute to the total retention of metals and radionuclides in this ombrotrophic environment. In addition, the varying metal concentrations together with chemical, mineralogical, and physical factors may contribute to the shape of the total archaeal and bacterial populations and most probably shifts the populations for more metal resistant genera.
  • Viitamäki, Sirja (Helsingin yliopisto, 2019)
    Soil microbial communities have a critical role in the biogeochemical processes on Earth, but their response to the ongoing climate change is poorly understood. Arctic permafrost harbors approximately 50% of Earth’s below ground carbon, and warmer climate leads to increased rate of microbial decomposition of soil organic matter in polar regions. Without a comprehensive understanding of the soil microbial ecology, the overall impact of climate change to nutrient cycles and greenhouse gas emissions is difficult to predict. My aim was to improve the knowledge of active microbes and their energy sources in subarctic soil. I studied the activity and functions of soil microbial communities by applying metatranscriptomics to soils along a natural climate gradient in subarctic Kilpisjärvi, northwestern Finland. The gradient represents the possible soil conditions, that microbial communities live in as the climate changes. Additionally, I studied the relationship of microbial activity and various environmental factors, including pH and soil organic matter. Results of the thesis showed that the active microbial communities in subarctic soils are diverse taxonomically and by their energy metabolism, and that pH, soil organic matter content and moisture are the main drivers of soil microbial activity and functions.
  • Lindstrom, Stafva; Timonen, Sari; Sundstrom, Liselotte (2021)
    In a subarctic climate, the seasonal shifts in temperature, precipitation, and plant cover drive the temporal changes in the microbial communities in the topsoil, forcing soil microbes to adapt or decline. Many organisms, such as mound-building ants, survive the cold winter owing to the favorable microclimate in their nest mounds. We have previously shown that the microbial communities in the nest of the ant Formica exsecta are significantly different from those in the surrounding bulk soil. In the current study, we identified taxa, which were consistently present in the nests over a study period of three years. Some taxa were also significantly enriched in the nest samples compared with spatially corresponding reference soils. We show that the bacterial communities in ant nests are temporally stable across years, whereas the fungal communities show greater variation. It seems that the activities of the ants contribute to unique biochemical processes in the secluded nest environment, and create opportunities for symbiotic interactions between the ants and the microbes. Over time, the microbial communities may come to diverge, due to drift and selection, especially given the long lifespan (up to 30 years) of the ant colonies.