Taxonomy and Bacterial Diversity—BIOL 212 Microbiology PDF

Taxonomy and bacterial diversity Linfeng Huang Associate Professor of Biology BIOL 212 Microbiology  Classification system Carl Linnaeus classification system (for plant and animal) invented in 1700s: – Using...

Taxonomy and bacterial diversity Linfeng Huang Associate Professor of Biology BIOL 212 Microbiology  Classification system Carl Linnaeus classification system (for plant and animal) invented in 1700s: – Using a two-part binary name for a species’ name: for example, Homo sapiens. – A hierarchy of rank in ascending scale: genus, family upward to order, class, phyla, kingdom and domain. – Currently there are three domains of microorganisms: the Eukaryotes, Bacteria and Archaea https://ucmp.berkeley.edu/ history/linnaeus.html  Bacterial taxonomy Bergey's Manual (1923 by David Hendricks Bergey) largely based on gram staining and phenotypical properties. In 1987 Carl Woese divided the Eubacteria into 11 divisions based on 16S ribosomal RNA (SSU) sequences, which with several additions are still used today. Escherichia coli Domain: Bacteria Phylum: Proteobacteria Class: Gammaproteobacteria Order: Enterobacteriales Family: Enterobacteriaceae Genus: Escherichia Species: E. coli https://www.ncbi.nlm.nih.gov/pmc/articles/PMC432104/pdf/pnas00033-0388.pdf Pronunciation of Biological Latin: http://capewest.ca/pron.html#current  Molecular Phylogeny: Making Sense of Molecular Sequences Systematics: Study of diversity of organisms and relationships, links phylogeny with taxonomy Taxonomy: Characterizes, names, classifies organisms Bacterial taxonomy incorporates multiple methods for identifying and describing new species. The polyphasic approach to taxonomy uses three methods: 1. phenotypic (morphological, metabolic, physiological, chemical characteristics) analysis 2. genotypic (genome) analysis 3. phylogenetic (evolutionary) analysis  Phylogenetic trees: Diagrams depicting evolutionary history Difference in nucleotide sequence between two organisms is a function of number of mutations accumulated since they shared a common ancestor. Obtaining DNA sequences isolate genomic DNA and sequence directly or use polymerase chain reaction (PCR) SSU (small subunit) ribosomal RNA (rRNA) genes highly conserved and easily sequenced and analyzed (Figure 13.15) can amplify SSU rRNA from environmental samples or to sequence environmental using metagenomics estimate evolutionary changes from number of sequence differences across SSU rRNA Primary and secondary structure of 16S rRNA from Escherichia coli. The 16S rRNA from Archaea is similar in secondary structure (folding) but has numerous differences in primary structure (sequence). The molecule is composed of conserved and variable regions (V1–V9). The approximate positions of the variable regions are indicated in color. Figure 13.15 E. coli total RNA nt 3.0 2.5 2.0 1.5 1 0.5 ThermoFisher Figure 13.24 13.10 Classification and Nomenclature Taxonomy and describing new species taxonomy: how organisms are classified and named classification: organization of organisms into progressively more inclusive groups on the basis of either phenotypic similarity or evolutionary relationship Species is one to several strains. Genus (genera) groups several species. families, orders, classes, phyla, domains (Table 13.2) Table 13.2  Chromatium okenii Phacus sp. Microcystis sp. in water environment Chromatium okenii Phacus sp. Microcystis sp. Domain: Bacteria Domain: Eukaryota Domain: Bacteria Phylum: Pseudomonadota Phylum: Euglenozoa Phylum: Cyanobacteria Class: Gammaproteobacteria Class: Euglenoidea Class: Cyanophyceae Order: Euglenida Order: Chroococcales Order: Chromatiales Family: Chromatiaceae Family: Phacaceae Family: Microcystaceae Genus: Chromatium Genus: Phacus Genus: Microcystis  Diversity of Bacteria Phylogenetic overview of Bacteria (Figure 16.1a) More than 90 percent of characterized genera and species come from four phyla Proteobacteria Actinobacteria Firmicutes Bacteroidetes  Numbers of cultured and characterized species (green bars) Known 16S rRNA gene Figure 16.1  I. Proteobacteria 16.1 Alphaproteobacteria 16.2 Betaproteobacteria 16.3 Gammaproteobacteria: Enterobacteriales 16.4 Gammaproteobacteria: Pseudomonadales and Vibrionales 16.5 Deltaproteobacteria and Epsilonproteobacteria  Proteobacteria is the largest classes of bacteria Named after a Greek sea god “Proteus”, the oldest son of Poseidon. He is capable of assuming many different shape, versatile and mutable - “protean”. Illustration of Proteus by Andrea Alciato from The Book of Emblems (1531)  Proteobacteria Proteobacteria (Figure 16.2) largest and most metabolically diverse phylum includes more than one-third of characterized species majority of known medically, industrially, and agriculturally significant bacteria all gram-negative divided into six classes Alpha-, Beta-, Delta-, Gamma-, Epsilon-, Zeta- horizontal gene flow important in shaping metabolic diversity