ACTAUNIVERSITATIS

UPSALIENSISUPPSALA

2016

Digital Comprehensive Summaries of Uppsala Dissertationsfrom the Faculty of Science and Technology 1388

Molecular methods for microbialecology

Developments, applications and results

LUCAS SINCLAIR

ISSN 1651-6214ISBN 978-91-554-9620-3urn:nbn:se:uu:diva-297613

Dissertation presented at Uppsala University to be publicly examined in Friessalen,Evolutionary Biology Center, Norbyvägen 14, Uppsala, Thursday, 8 September 2016 at13:15 for the degree of Doctor of Philosophy. The examination will be conducted in English.Faculty examiner: Associate Professor Josh Neufeld (Waterloo University).

AbstractSinclair, L. 2016. Molecular methods for microbial ecology. Developments, applicationsand results. (Systems approach to functional characterization of lentic systems). DigitalComprehensive Summaries of Uppsala Dissertations from the Faculty of Science andTechnology 1388. 52 pp. Uppsala: Acta Universitatis Upsaliensis. ISBN 978-91-554-9620-3.

Recent developments in DNA sequencing technology allow the study of microbial ecologyat unmatched detail. To fully embrace this revolution, an important avenue of research isthe development of bioinformatic tools that enable scientists to leverage and manipulate theexceedingly large amounts of data produced. In this thesis, several bioinformatic tools weredeveloped in order to process and analyze metagenomic sequence data. Subsequently, the toolswere applied to the study of microbial biogeography and microbial systems biology.

A targeted metagenomics pipeline automating quality filtering, joining and taxonomicannotation was developed to assess the diversity of bacteria, archaea and eukaryotes permittingthe study of biogeographic patterns in great detail. Next, a second software package whichprovides annotation based on environmental ontology terms was coded aiming to exploit thecornucopia of information available in public databases. It was applied to resource tracking,paleontology, and biogeography. Indeed, both these tools have already found broad applicationsin extending our understanding of microbial diversity in inland waters and have contributedto the development of conceptual frameworks for microbial biogeography in lotic systems.The programs were used for analyzing samples from several environments such as alkalinesoda lakes and ancient sediment cores. These studies corroborated the view that the dispersallimitations of microbes are more or less non-existant as environmental properties dictating theirdistribution and that dormant microbes allow the reconstruction of the origin and history of thesampled community.

Furthermore, a shotgun metagenomics analysis pipeline for the characterization of total DNAextraction from the environment was put in place. The pipeline included all essential steps fromraw sequence processing to functional annotation and reconstruction of prokaryotic genomes.By applying this tool, we were able to reconstruct the biochemical processes in a selectionof systems representative of the tens of millions of lakes and ponds of the boreal landscape.This revealed the genomic content of abundant and so far undescribed prokaryotes harboringimportant functions in these ecosystems. We could show the presence of organisms with thecapacity for photoferrotrophy and anaerobic methanotrophy encoded in their genomes, traitsnot previously detected in these systems. In another study, we showed that microbes respondto alkaline conditions by adjusting their energy acquisition and carbon fixation strategies. Toconclude, we demonstrated that the "reverse ecology" approach in which the role of microbesin elemental cycles is assessed by genomic tools is very powerful as we can identify novelpathways and obtain the partitioning of metabolic processes in natural environments.

Keywords: bioinformatics, microbiology, metagenomics, ecology, metabolism

Lucas Sinclair, , Department of Ecology and Genetics, Limnology, Norbyv 18 D, UppsalaUniversity, SE-75236 Uppsala, Sweden.

© Lucas Sinclair 2016

ISSN 1651-6214ISBN 978-91-554-9620-3urn:nbn:se:uu:diva-297613 (http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-297613)

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Acta Universitatis UpsaliensisDigital Comprehensive Summaries of Uppsala Dissertationsfrom the Faculty of Science and Technology 1388

Editor: The Dean of the Faculty of Science and Technology

A doctoral dissertation from the Faculty of Science andTechnology, Uppsala University, is usually a summary of anumber of papers. A few copies of the complete dissertationare kept at major Swedish research libraries, while thesummary alone is distributed internationally throughthe series Digital Comprehensive Summaries of UppsalaDissertations from the Faculty of Science and Technology.(Prior to January, 2005, the series was published under thetitle “Comprehensive Summaries of Uppsala Dissertationsfrom the Faculty of Science and Technology”.)

Distribution: publications.uu.seurn:nbn:se:uu:diva-297613

ACTAUNIVERSITATIS

UPSALIENSISUPPSALA

2016