Lecture 3. Bacteriology III. Sandra PDF

BIOL2038/2044 Microbiology Bacteriology III: The microbial species concept The microbial species concept Learning objectives: Discuss the challenges associated with describing microbial diversity. Explain the inaccuracy of terminology. Describe the basic underlying mechanisms of microbia...

BIOL2038/2044 Microbiology Bacteriology III: The microbial species concept The microbial species concept Learning objectives: Discuss the challenges associated with describing microbial diversity. Explain the inaccuracy of terminology. Describe the basic underlying mechanisms of microbial speciation. Microbial classification – square peg in a round hole? Disagreement at multiple levels, from domain to ‘species’. Traditional system does not fit in era of molecular classification: – Molecular studies. – Phylogenetic based approach. – Phenotypic plasticity. – Horizontal gene transfer, etc. What are the challenges? Vs What constitutes a species? Recognition of microbial diversity depends heavily on analysis methods. - especially given that 99% are not culturable! Not just semantics – why is a definitive species concept important? It is needed to understand biodiversity (and all aspects outlined above). Lack of agreement over what constitutes a species has led to: – Miscalculations of diversity. – Misunderstanding of environmental systems. – Inability to compare between studies. Traditional species concept ‘species’ – fundamental unit in Linneus’ classification (pre-Darwin) i.e. breeding populations. Mayr (1963) Biological species concept: – A fundamental ecological and genetic unit. – Groups of interbreeding natural populations that are reproductively isolated. But even in eukaryote ecology the A current definition of a ‘Bacterial/Archaeal’ species: “A category that circumscribes a (preferably) genomically coherent group of individual isolates/strains sharing a high degree of similarity in (many) independent features, comparatively tested under highly standardised conditions.” (Stackebrandt et al (2002). Int. J. Syst. Evol. Microbiol. 52: 1043.) What does this mean in practice? No official practical definition of what a species is. Look at approach from historical perspective – what we used to do… Adapt this approach to current technology that offers different ways of characterising other than gross morphology. A classical approach to microbial taxonomy Factors that influence speciation in bacteria Relatively fast generation times. Adaptive mutations. Factors that influence speciation in bacteria Horizontal gene transfer and the ‘core genome’. Brock 12th Ed.  General features of some E. coli sequenced genomes Strain Chromosome Plasmid # # of strain size (Mbp) prophages specific ORFs (%) 536 4.9 No 1 374 (8%) CFT073 5.2 No 5 867 (16%) K12 4.6 No 10 406 (9%) EDL93 5.5 Yes 16 1, 270 3 (24%) pted from Brzuszkiewicz, Elzbieta et al. (2006) Proc. Natl. Acad. Sci. USA 103, 12879-12884 Agents of horizontal gene transfer – prophages and Prophage: plasmids Phage genome inserted into the linear structure of bacterial chromosome Plasmid: Extra-chromosomal DNA molecule Extra genes incorporated into the cell without disrupting it – can alter phenotypic expression.  How does this affect ‘species’ definition? Diversity – biological context Diversity can be measured in terms of the species richness and/or abundance and/or genetic variability of organisms BUT… Defining diversity No coherent solution to questions regarding: – Microbial species concept. – Microbial diversity. Obstacles: – Incomplete information on number of existing microbial species (quantitative estimate limited). – Non-operational definition of ‘microbial niche’ (eukaryote definition not useful in microbial ecology). – Loose definition of ‘species’ and ‘strains’. No definitive approach to characterise microbial Field is moving fast. communities Numerous different approaches. Recognition of microbial diversity – depends on methods used – – Early – gross morphology, cell shapes and colonies. – Then - biochemical attributes. – Now – differences at molecular level. Polyphasic taxonomy Consensus classification – that different information into a classification containing minimum contradictions. Information includes: – Phenotypic data (e.g. biochemical tests, fatty acid composition). – Genotypic data (e.g. DNA fingerprints). – Phylogenetic data (e.g. rDNA sequences).  Assessing microbial diversity Culture-based Culture-independent PCR- PCR- independe based nt Food for thought… How relevant is it to define a species in environmental/medical microbiology? Consider: – Genes used in phylogenetics (not always correlated with functional traits). – Metabolic diversity. – Horizontal gene transfer.