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

genome-guided analysis of metabolic capacities and energy conserving systems

Manzoor, Shahid (2014). Computational and comparative investigations of syntrophic acetate-oxidising bacteria (SAOB). Diss. (sammanfattning/summary) Uppsala : Sveriges lantbruksuniv., Acta Universitatis agriculturae Sueciae, 1652-6880 ; 2014:56
ISBN 978-91-576-8060-0
eISBN 978-91-576-8061-7
[Doctoral thesis]

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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.

Authors/Creators:Manzoor, Shahid
Title:Computational and comparative investigations of syntrophic acetate-oxidising bacteria (SAOB)
Subtitle:genome-guided analysis of metabolic capacities and energy conserving systems
Series/Journal:Acta Universitatis agriculturae Sueciae (1652-6880)
Year of publishing :2014
Volume:2014:56
Number of Pages:114
Papers/manuscripts:
NumberReferences
I.Manzoor S., Bongcam-Rudloff E., Schnürer A., Müller B. (2013) First genome sequence of a Syntrophic Acetate-Oxidizing Bacterium, Tepidanaerobacter acetatoxydans strain Re1. Genome Announc. 1 :e00213-12; doi:10.1128/genomeA.00213-12.
II.Manzoor S., Müller B., Bongcam-Rudloff E., Schnürer A. (2013) Draft genome sequence of Clostridium ultunense strain Esp, a Syntrophic Acetate-Oxidizing bacterium. Genome Announc. 1: e00107-13; doi:10.1128/genomeA.00107-13.
III.Manzoor S., Müller B., Niazi A., Schnürer A., Bongcam-Rudloff E. (2014) Working draft genome sequence of the mesophilic acetate oxidizing bacterium Syntrophaceticus schinkii strain Sp3. Standards In Genomic Sciences. (Submitted)
IV.Manzoor S., Müller B., Niazi A., Schnürer A., Bongcam-Rudloff E. (2014) Genome guided analysis of the metabolic capacities and energy conserving systems of the SAOB Tepidanaerobacter acetatoxydans. PLOS ONE (Submitted)
V.Manzoor S., Müller B., Niazi A., Schnürer A., Bongcam-Rudloff E. The syntrophic acetate oxidizing bacterium Syntrophaceticus schinkii strain Sp3-A genome scale analysis. (Manuscript)
Place of Publication:Uppsala
Publisher:Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences
ISBN for printed version:978-91-576-8060-0
ISBN for electronic version:978-91-576-8061-7
ISSN:1652-6880
Language:English
Publication Type:Doctoral thesis
Full Text Status:Public
Agris subject categories.:X Agricola extesions > X30 Life sciences
Subjects:(A) Swedish standard research categories 2011 > 1 Natural sciences > 102 Computer and Information Science > 10203 Bioinformatics (Computational Biology) (applications to be 10610)
Agrovoc terms:bacteria, clostridium, acetates, oxidation, biodegradation, anaerobiosis, genes, genomes, genomics, dna sequence
Keywords:hydrogenotrophic methanogenesis, biogas, Wood-Ljungdahl pathway, next generation sequencing, de novo assembly, acetogenesis, metabolism
URN:NBN:urn:nbn:se:slu:epsilon-e-2067
Permanent URL:
http://urn.kb.se/resolve?urn=urn:nbn:se:slu:epsilon-e-2067
ID Code:11443
Faculty:VH - Faculty of Veterinary Medicine and Animal Science
Department:(VH) > Dept. of Animal Breeding and Genetics
External funders:Higher Education Commission, Pakistan
Deposited By: Mr Shahid Manzoor
Deposited On:25 Aug 2014 11:54
Metadata Last Modified:02 Dec 2014 11:08

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