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Doctoral thesis, 2014

Computational and comparative investigations of syntrophic acetate-oxidising bacteria (SAOB)

Manzoor, Shahid

Abstract

Today's main energy sources are the fossil fuels petroleum, coal and natural gas, which are depleting rapidly and are major contributors to global warming. Methane is produced during anaerobic biodegradation of wastes and residues and can serve as an alternative energy source with reduced greenhouse gas emissions. In the anaerobic biodegradation process acetate is a major precursor and degradation can occur through two different pathways: aceticlastic methanogenesis and syntrophic acetate oxidation combined with hydrogenotrophic methanogenesis. Bioinformatics is critical for modern biological research, because different bioinformatics approaches, such as genome sequencing, de novo assembly sequencing and transcriptomics sequencing are providing a distinctly better understanding at the genomic level by predicting genes and pathways and by deciphering the relationships between genotype and phenotype. This thesis describes the genomic analysis of three syntrophic acetate-oxidising bacteria (SAOB), namely Tepidanaerobacter acetatoxydans, Clostridium ultunense and Syntrophaceticus schinkii. These isolates have the ability to perform syntrophic acetate oxidation in the presence of a partner methanogen, which ultimately produces methane in the final step of anaerobic digestion. The genomes were assembled using NGS data and the genomic behaviour was determined through genome annotation. Metabolic pathway analysis revealed the physiological attributes of the SAOB regarding substrate utilisation, intermediate metabolism, energy conservation and genes of the Wood- Ljungdahl pathway, which are known to be involved in acetate oxidation. The results showed that the three SAOB use contrasting strategies for syntrophic acetate oxidation (SAO): T. acetatoxydans possesses all genes involved in the W-L pathway except formate dehydrogenase and thus requires a syntrophic formate-utilising methanogenic partner; S. schinkii possesses the complete set of genes required for the W-L pathway to oxidise acetate in the presence of a hydrogen-utilising methanogenic partner; and C. ultunense uses different ways to oxidise acetate because it does not contain the complete set of W-L pathway genes. Moreover, the three SAOB differ from each other as regards organisation of the W-L pathway genes operon.

Keywords

hydrogenotrophic methanogenesis; biogas; Wood-Ljungdahl pathway; next generation sequencing; de novo assembly; acetogenesis; metabolism

Published in

Acta Universitatis Agriculturae Sueciae
2014, number: 2014:56
ISBN: 978-91-576-8060-0, eISBN: 978-91-576-8061-7
Publisher: Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences

Authors' information

Manzoor, Shahid
Swedish University of Agricultural Sciences, Department of Animal Breeding and Genetics

UKÄ Subject classification

Bioinformatics (Computational Biology)

URI (permanent link to this page)

https://res.slu.se/id/publ/60317