1. Microbial ecology According to Caumette et al. (2015) the term ecology is derived from the Greek words “oikos” (the house and its operation) and “logos” (the word, knowledge or discourse) and can, therefore, be defined as the scientific field engaged in the “knowledge of the laws governing the house”. This, in extension, results in the simple conclusion that microbial ecology represents the study of the relationship between microorganisms, their co-occurring biota and the prevailing environmental conditions (Caumette et al. 2015). The term microbial ecology has been in use since the early 1960s (Caumette et al. 2015) and microbial ecologists have made astonishing discoveries since. Microbial life at extremes such as in the hydrothermal vents (see Dubilier et al. 2008 and references therein) or the abundance of picophytoplankton (Waterbury et al. 1979; Chisholm et al. 1988) in the deep and surface waters of the oceans, respectively, are only a few of many highlights. Nevertheless, a microbial ecologist who, after leaving the field early in their career, now intends to return would hardly recognise again their former scientific field. The main reason for this hypothesis is to be found in the advances made to the methodologies employed in the field. Most of these were developed for biomedical research and were subsequently hijacked, sometimes followed by minor modifications, by microbial ecologists. The Author presents in this thesis scientific findings which, although spanning only a fraction of the era of research into microbial ecology, have been obtained using various modern tools of the trade. These studies were undertaken by the Author during his employment as postdoctoral scientist at Warwick University (UK), as member of staff at Plymouth Marine Laboratory (UK) and as scientist at the TU Bergakademie Freiberg. Although the scientific issues and the environmental habitats investigated by the Author changed due to funding constraints or due to change of work place (i.e. from the marine to the mining environment) the research shared, by and large, a common aim: to further the existing understanding of microbial communities. The methodological approach chosen to achieve this aim employed both isolation followed by the characterisation of microorganisms and culture independent techniques. Both of these strategies utilised again a variety of methods, but techniques in molecular biology represent a common theme. In particular, the polymerase chain reaction (PCR) formed the work horse for much of the research since it has been routinely used for the amplification of a marker gene for strain identification or analysis of the microbial diversity. To achieve this, the amplicons were either directly sequenced by the Sanger approach or analysed via the application of genetic fingerprint techniques or through Sanger sequencing of individual amplicons cloned into a heterologous host. However, the Author did not remain at idle while with these ‘classical’ approaches for the analysis of microbial communities, but utilised the advances made in the development of nucleotide sequence analysis. In particular, the highly parallelised sequencing techniques (e.g. 454 pyrosequencing, Illumina sequencing) offered the chance to obtain both high genetic resolution of the microbial diversity present in a sample and identification of many individuals through sequence comparison with appropriate sequence repositories. Moreover, these next generation sequencing (NGS) techniques also provided a cost-effective opportunity to extent the characterisation of microbial strains to non-clonal cultures and to even complex microbial assemblages (metagenomics). The work involving the high throughput sequencing techniques has been undertaken in collaboration with Dr Jack Gilbert (PML, lateron at Argonne National Laboratory, USA) and, since at Freiberg, with Dr Anja Poehlein (Goettingen University). These colleagues are thanked for their support with sequence data handling and analyses.

No description available.

Microorganisms play crucial roles in aquatic environments in determining ecosystemstability and driving the turnover of elements essential to life. Understanding thedistribution and evolution of aquatic microorganisms will help us predict how aquaticecosystems will respond to Global Change, and such understanding can be gained bystudying these processes of the past. In this project, we investigate the evolutionaryrelationship between brackish water bacteria from the Baltic Sea and Caspian Seawith freshwater and marine bacteria, with the goal of understanding how brackishwater bacteria have evolved. 11,276 bacterial metagenome-assembled genomes(MAGs) from seven metagenomic datasets were used to conduct a comparativeanalysis of freshwater, brackish and marine bacteria. When clustering the genomes bypairwise average nucleotide identity (ANI) at the approximate species level (96.5%ANI), the Baltic Sea genomes were more likely to form clusters with the Caspian Seagenomes than with Swedish lakes genomes, even though geographic distancesbetween Swedish lakes and the Baltic Sea are much smaller. Phylogenomic analysisand ancestral state reconstruction showed that approximately half of the brackishMAGs had freshwater ancestors and half had marine ancestors. Phylogeneticdistances were on average shorter to freshwater ancestors, but when subsampling thetree to the same number of freshwater and marine MAG clusters, the distances werenot significantly different. Brackish genomes belonging to Acidimicrobiia,Actinobacteria and Cyanobacteriia tended to originate from freshwater bacteria, whilethose of Alphaproteobacteria and Bacteroidia mainly had evolved from marinebacteria. / Mikroorganismer spelar avgörande roller i akvatiska ekosystem där de driverkretsloppen av näringsämnen. En ökad förståelse för hur mikroorganismer anpassarsig till miljöförändringar är viktigt för att förutsäga hur akvatiska ekosystem kommeratt förändras som en konsekvens av global uppvärmning, och sådan förståelse kanuppnås genom att studera tidigare skeenden i evolutionen. I detta projekt undersökervi det evolutionära förhållandet mellan brackvatten-bakterier från Östersjön ochKaspiska havet med sötvattens- och marina bakterier, med målet att förstå hurbrackvatten-bakterier har utvecklats. 11,276 bakteriella arvsmassor somrekonstruerats med metagenomik från sju data-set användes för att utföra enjämförande analys av bakterie-genom från söt-, brack och havsvatten. Klustring avgenomen baserat på parvis genomsnittlig nukleotididentitet (ANI) på ungefärligartnivå (96,5% ANI), grupperade Östersjöns bakterier tillsammans med Kaspiskahavets bakterier mer än med bakterier från svenska sjöar, trots att det geografiskaavståndet mellan svenska sjöar och Östersjön är mycket mindre. Fylogenetisk analysvisade att ungefär hälften av brackvatten arterna hade anfäder från sötvatten ochhälften från havsvatten. De fylogenetiska avstånden var i genomsnitt kortare tillanfaderna i sötvatten, men när man reducerade trädet till att ha samma antal sötvattenoch marina arter var avstånden inte längre signifikant olika. Brackvatten-arter somtillhörde Acidimicrobiia, Actinobacteria och Cyanobacteriia tenderade att härstammafrån sötvattenbakterier, medan de från Alphaproteobacteria och Bacteroidia främsthärstammade från marina bakterier.

No description available.

1. Microbial ecology According to Caumette et al. (2015) the term ecology is derived from the Greek words “oikos” (the house and its operation) and “logos” (the word, knowledge or discourse) and can, therefore, be defined as the scientific field engaged in the “knowledge of the laws governing the house”. This, in extension, results in the simple conclusion that microbial ecology represents the study of the relationship between microorganisms, their co-occurring biota and the prevailing environmental conditions (Caumette et al. 2015). The term microbial ecology has been in use since the early 1960s (Caumette et al. 2015) and microbial ecologists have made astonishing discoveries since. Microbial life at extremes such as in the hydrothermal vents (see Dubilier et al. 2008 and references therein) or the abundance of picophytoplankton (Waterbury et al. 1979; Chisholm et al. 1988) in the deep and surface waters of the oceans, respectively, are only a few of many highlights. Nevertheless, a microbial ecologist who, after leaving the field early in their career, now intends to return would hardly recognise again their former scientific field. The main reason for this hypothesis is to be found in the advances made to the methodologies employed in the field. Most of these were developed for biomedical research and were subsequently hijacked, sometimes followed by minor modifications, by microbial ecologists. The Author presents in this thesis scientific findings which, although spanning only a fraction of the era of research into microbial ecology, have been obtained using various modern tools of the trade. These studies were undertaken by the Author during his employment as postdoctoral scientist at Warwick University (UK), as member of staff at Plymouth Marine Laboratory (UK) and as scientist at the TU Bergakademie Freiberg. Although the scientific issues and the environmental habitats investigated by the Author changed due to funding constraints or due to change of work place (i.e. from the marine to the mining environment) the research shared, by and large, a common aim: to further the existing understanding of microbial communities. The methodological approach chosen to achieve this aim employed both isolation followed by the characterisation of microorganisms and culture independent techniques. Both of these strategies utilised again a variety of methods, but techniques in molecular biology represent a common theme. In particular, the polymerase chain reaction (PCR) formed the work horse for much of the research since it has been routinely used for the amplification of a marker gene for strain identification or analysis of the microbial diversity. To achieve this, the amplicons were either directly sequenced by the Sanger approach or analysed via the application of genetic fingerprint techniques or through Sanger sequencing of individual amplicons cloned into a heterologous host. However, the Author did not remain at idle while with these ‘classical’ approaches for the analysis of microbial communities, but utilised the advances made in the development of nucleotide sequence analysis. In particular, the highly parallelised sequencing techniques (e.g. 454 pyrosequencing, Illumina sequencing) offered the chance to obtain both high genetic resolution of the microbial diversity present in a sample and identification of many individuals through sequence comparison with appropriate sequence repositories. Moreover, these next generation sequencing (NGS) techniques also provided a cost-effective opportunity to extent the characterisation of microbial strains to non-clonal cultures and to even complex microbial assemblages (metagenomics). The work involving the high throughput sequencing techniques has been undertaken in collaboration with Dr Jack Gilbert (PML, lateron at Argonne National Laboratory, USA) and, since at Freiberg, with Dr Anja Poehlein (Goettingen University). These colleagues are thanked for their support with sequence data handling and analyses.

No description available.