Microbiology Helmut Pospiech

Transcription

1 Microbiology Helmut Pospiech

2 The Species Concept in Microbiology No universally accepted concept of species for prokaryotes Current definition of prokaryotic species Collection of strains sharing a high degree of similarity in several independent traits Most important traits include 70% or greater DNA-DNA hybridization and 97% or greater 16S rrna gene sequence identity Brock Biology of Microorganisms, 12th ed.

3 The Species Concept in Microbiology Biological species concept not meaningful for prokaryotes as they are haploid and do not undergo sexual reproduction Genealogical species concept is an alternative Prokaryotic species is a group of strains that based on DNA sequences of multiple genes cluster closely with others phylogenetically and are distinct from other groups of strains Brock Biology of Microorganisms, 12th ed.

4 Multi-Gene Phylogenetic Analysis 16S rrna genes gyrb genes luxabfe genes Figure Brock Biology of Microorganisms, 12th ed.

5 The Species Concept in Microbiology Ecotype Population of cells that share a particular resource Different ecotypes can coexist in a habitat Bacterial speciation may occur from a combination of repeated periodic selection for a favorable trait within an ecotype and lateral gene flow Brock Biology of Microorganisms, 12th ed.

6 A Model for Bacterial Speciation Figure Brock Biology of Microorganisms, 12th ed.

7 The Species Concept in Microbiology This model is based solely on the assumption of vertical gene flow New genetic capabilities can also arise by horizontal gene transfer; the extent among bacteria is variable Brock Biology of Microorganisms, 12th ed.

8 Trouble with the Tree of Life Concept Ring of Life rather than a tree of life since the eukaryotic genome represents a fusion of a bacterial and archaeal genome (Riviera and Lake (2004), Nature 431, 152) A reticulated tree would better describe the genotypic relationship of organisms due to vast horizontal gene transfer (Doolittle (1999), Science 284, 2124; Martin (1999), BioEssays 21, 99)

9 Universal common ancestry of life on earth? a, The multiple-ancestry possibility: depicted here is life originating from two separate forms, with proteins with similar functions arising independently. Transfers, by endosymbiosis or by lateral gene transfers, are shown by dotted lines. b, A single origin (universal common ancestry), at least after the advent of protein synthesis. Correlations between patterns at different amino-acid positions are used to test between the two possibilities. Steel M & Penny D (2010) Nature 465,168.

10 The Species Concept in Microbiology No firm estimate on the number of prokaryotic species Nearly 7,000 species of Bacteria and Archaea are presently known

11 Classification and Nomenclature Classification Organization of organisms into progressively more inclusive groups on the basis of either phenotypic similarity or evolutionary relationship

12 Classification and Nomenclature Prokaryotes are given descriptive genus names and species epithets following the binomial system of nomenclature used throughout biology Assignment of names for species and higher groups of prokaryotes is regulated by the Bacteriological Code - The International Code of Nomenclature of Bacteria

13 Taxonomic Hierarchy for Allochromatium warmingii Brock Biology of Microorganisms, 13th ed.

14 14.14 Classification and Nomenclature Major references in bacterial diversity Bergey s Manual of Systematic Bacteriology (Springer) The Prokaryotes (Springer)

15 Classification and Nomenclature Formal recognition of a new prokaryotic species requires Deposition of a sample of the organism in two culture collections Official publication of the new species name and description in the International Journal of Systematic and Evolutionary Microbiology (IJSEM) The International Committee on Systematics of Prokaryotes (ICSP) is responsible for overseeing nomenclature and taxonomy of Bacteria and Archaea

16

17 Uneven distribution of components of the archaeal cell division (FtsZ, CdvBC, and actin), DNA maintenance (topoisomerases IA and IB, eukaryotic-like histones), protein ubiquitinylation, and transcription (Rpb8) systems. Such uneven distributions could result from ancient HGTs among the archaeal lineages and/or differences in the loss of multiple systems present in the last common archaeal ancestor (orange circle). Dark purple indicates a character present in all members of the corresponding lineage, whereas light purple indicates a character present in only some representatives of the lineage. Uncertainties, given the lack of a complete genome sequence for Nitrososphaera gargensis, are noted by question marks. Brochier-Armanet, Forterre & Gribaldo (2011) Current Opinion in Microbiology 14,

18 Methanogens

19 Phylogeny of Bacteria Brock Biology of Microorganisms, 13th ed.

20 Proteobacteria Largest and metabolically most diverse group of bacteria Most bacteria of industrial, agricultural or medical importance Gram-negative Metabolically extremely diverse Phenotypic classification does not match the phylogenetic relationship between the proteobacteria Brock Biology of Microorganisms, 13th ed.

21 Important groups of Proteobacteria Purple sulfur bacteria Anoxigenic photosynthesis E.g. Chromatium Non-sulfur purple bacteria Anoxigenic photosynthesis Often facultative phototrophic E.g. Rhodobacter Chemolithotrophs Nitrifying bacteria Sulfur- and iron-oxidising bacteria Hydrogen-oxidising bacteria Brock Biology of Microorganisms, 13th ed.

22 Important groups of Proteobacteria Pseudomonas and Pseudomonads Obligatory respiratory Oxidase-positive Ecologically important for aerobic decomposition of organic material in nature Often nutritionally versatile Common in soil and water Some important pathogens Brock Biology of Microorganisms, 13th ed.

23 Important groups of Proteobacteria Gram-negative cocci Include Neisseria and Moraxella Important pathogens of human N. gonorrhoeae gonerrhea N. menigitidis meningitis Vibrio and relatives Facultative anaerobes Oxidase positive Marine environments, e.g. in and on fish Often bioluminescence V. cholerae causes cholera Brock Biology of Microorganisms, 13th ed.

24 Important groups of Proteobacteria Enteric Bacteria Include many medically important pathogens Escherichia, Salmonella, Shigella, Proteus, Klebsiella and Serratia In the enterogastric tracts of mammals, on plants, aquatic environments etc. Brock Biology of Microorganisms, 13th ed.

25 Important groups of Proteobacteria Rickettsias Obligate parasites Live inside host cells Brock Biology of Microorganisms, 13th ed.

26 Important groups of Proteobacteria Spirillia Spiral-shaped bacteria Microaerophilic aerobes Bdellovibrio Prays on bacteria! Brock Biology of Microorganisms, 13th ed.

27 Important groups of Proteobacteria Myxobacteria social bacteria Forming fruiting bodies with spores But not endospores Brock Biology of Microorganisms, 13th ed.

28 Gram-positive bacteria - Firmicutes Lactic acid bacteria Streptococcus / Lactococcus Lactobacillus Endospore formers Bacillus (aerobe) Clostridium (strictly anaerobe) Heliobacteria photosynthetic

29 Gram-positive bacteria - Mullicutes Mycoplasms Parasites Without cell wall Small Smallest genomes

30 Gram-positive bacteria - Actinobacteria Corynebacteria Propionic acid bacteria Mycobacteria Many pathogens Streptomyces