Adverse effects of anthropogenic impact on the environment have become conspicuous in thepast century and among others include the gradual increase in the global CO2 levels, thecontamination of air, soil and water by toxic chemicals, and the emergence of antimicrobialresistance among pathogenic microbial species. Microorganisms partake in an extremediversity of activities in the environment, and hence, constitute the prime candidates to beinvestigated in understanding of the progression and effects of the aforementionedenvironmental hazard scenarios. The spectacular rise of massively parallel sequencing (nextgeneration sequencing, NGS) technologies in mid 2000s initiated a renaissance in microbialecology by allowing the in situ investigation of environmental samples at metagenome level,largely eliminating prior laboratory culturing steps. Metagenomics has thereby beenestablished as a new interdisciplinary field and methodology, harmonizing the accumulatedknowledge in microbial ecology and genetics with the high-throughput environmental DNAsequence data through the means of bioinformatics analysis resources.One of the emerging application areas that require a comprehensive microbialinvestigation is the study of the effects of toxic chemicals on biota in the environment,namely ecotoxicology. In this PhD thesis, bioinformatics software development and microbialecological data analysis projects are integrated within the field of ecotoxicology. Theobjective of the thesis is to implement metagenomics as a robust tool in the field ofecotoxicology to gain both community and molecular level insights. Paper I presentsFANTOM (Functional and Taxonomic Analysis of Metagenomes), a graphical user interface(GUI)-based metagenomic data analysis tool that provides various statistical analysis andvisualization features for biologists with limited bioinformatics experience. PACFM(Pathway Analysis with Circos for Functional Metagenomics), another GUI-based softwaretool, is presented in Paper II, and it provides researchers in metagenomics with a novel plotand various biochemical pathway analysis features. Paper III is an exploratory study of themarine biofilms (also known as periphython), constituting the first study to sequence the totalgenomic DNA content of these microbial communities that inhabit the aquatic environment.The metagenomic analysis of the marine biofilms revealed that Proteobacteria, Bacteroidetesand Cyanobacteria are the most abundant organisms in these biofilm communities. Inaddition, the functional repertoire within the metagenome involved signatures of anaerobicprocesses including denitrification and methanogenesis, which suggests the presence of lowoxygenzones within the micro-ecosystem formed by the marine biofilms. Paper III alsoconstituted the pilot study for Paper IV, where an experimental design was set up toinvestigate the toxic effects of the broad spectrum antimicrobial agent, triclosan, on themarine biofilms. High and low levels of triclosan exposure was shown to cause significantchanges in the community structure and the functioning of the marine biofilms. A sulfurbasedmicrobial consortium together with several algal groups were hypothesized to partakein the detoxification of triclosan. Hence, metagenomics is shown to be a powerful researchtool in the field of ecotoxicology.This PhD thesis presents novel software tools and applications in the field ofmetagenomics, combining a wide range of paradigms from several disciplines within aunified solution framework as an attempt to practice and transcend interdisciplinary research.
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