General Characteristics & Classification of Eubacteria

Economic Importance of Bacteria

• Bacteria act as both “friends and foes” due to their beneficial and harmful activities.

Agriculture

• Decomposition – saprophytic bacteria mineralise organic matter, releasing nutrients for plants.
• Biocontrol agents – e.g. Bacillus thuringiensis (Bt) produces protein-based toxins against insect pests.
• Symbiotic nitrogen fixation – rhizobia in legume root nodules; cyanobacteria such as Nostoc and Anabaena also contribute.

Industries (Selected products & organisms)

• Alcohols/acetone – \textit{Clostridium acetobutylicum} ferments molasses to butyl & methyl alcohol + acetone.
• Retting of fibres – \textit{Clostridium tertium} separates bast fibres.
• Vitamins – \textit{Escherichia coli} in the gut forms vitamin K & B-complex; industrial vitamin B production via \textit{C. acetobutylicum} fermentation.
• Curing/fermentation – special flavour & aroma of tea/tobacco via \textit{Mycococcus candisans}, \textit{Bacillus megatherium}.

Medicine

• Antibiotic producers.
• Vaccines from killed/attenuated bacteria – tuberculosis, whooping cough, DTP, pneumonia.

Ecological Roles

• Nutrient cycling – nitrogen fixation (rhizobia, cyanobacteria); nitrification (e.g. Nitrosomonas, Nitrobacter); denitrification (Pseudomonas denitrificans, Thiobacillus denitrificans).
• Sulfur & phosphorus cycles – redox transformations.
• Plant symbioses – enhanced nutrient uptake, stress protection, disease resistance, mycorrhiza-associated.
• Animal symbioses – gut microbiota (digestion, immunity), bioluminescence, pathogen exclusion; termites rely on cellulose-digesting bacteria.

Environmental Protection

• Biogas (gobar gas) production stages:
– Hydrolysis (e.g. Clostridium, Pseudomonas)
– Acidogenesis – organic acids
– Methanogenesis (Methanobacterium, Methanococcus).
• Sewage treatment – secondary aerobic stage lowers BOD; tertiary stage anaerobic methanogens produce biogas.

Harmful Effects

• Plant diseases – e.g. Xanthomonas citri → citrus canker.
• Human pathogens – Bacillus anthracis, Vibrio cholerae, Yersinia pestis; botulinum toxin (biowarfare).
• Food spoilage/poisoning – putrefaction by numerous bacteria; Salmonella typhimurium, Clostridium botulinum.
• Denitrification – loss of soil \text N by anaerobes in water-logged soils.

Historical & Conceptual Foundations of Taxonomy

• Carolus Linnaeus – “Father of Taxonomy”; hierarchic ranks: KINGDOM → PHYLUM → CLASS → ORDER → FAMILY → GENUS → SPECIES; binomial nomenclature.
• Successive kingdom models:
– Linnaeus \to 2-kingdom (1758)
– Haeckel \to 3-kingdom
– Copeland \to 4-kingdom (Monera added)
– Whittaker (1969) \to 5-kingdom (Fungi separated).

Five-Kingdom Snapshot (Whittaker)

• Monera – unicellular prokaryotes (bacteria, cyanobacteria).
• Protista – unicellular eukaryotes.
• Plantae – multicellular autotrophs with cellulose walls.
• Fungi – chitin walls, absorptive heterotrophy.
• Animalia – multicellular, no walls, ingestive heterotrophy.

Modern Approaches

• Numerical taxonomy – Sokal & Sneath; every character equal weight, phenetic similarity.
• Polyphasic taxonomy – integrates phenotypic, physiological & phylogenetic (16S rRNA) data; handles big data, many strains, data fusion.
• Highly conserved genes (small-subunit rRNA) now central.
• Genome flux – lateral gene transfer revealed by full-genome sequencing; \ge 99\% of bacterial diversity remains uncultured.

General Characteristics of Eubacteria

• Prokaryotic, no membrane-bound nucleus; genome in nucleoid (usually circular, sometimes linear).
• Size typically 0.5{-}5\,\mu\text m diameter.
• Morphology: cocci, bacilli, vibrios, spirilla, filamentous, spirochetes; may form endospores.
• Cell wall of peptidoglycan (Gram + thick; Gram − thin with outer membrane).
• Asexual reproduction – binary fission (doubling time E. coli ≈20\text{ min}), budding, fragmentation; no meiosis.
• Motility – flagella (H antigen), pili (adhesion, conjugation).
• Metabolic range – photoautotrophy, chemoautotrophy, heterotrophy; aerobes, anaerobes, facultatives.
• Ribosome type 70\text S; plasmids enable horizontal gene transfer.

Bacterial Associations

• Free-living, facultative/obligate symbioses, opportunistic pathogens.
• Endosymbiotic theory – chloroplasts & mitochondria evolved from bacteria.

Classical & Phenotypic Classification Schemes

By Shape (Cohn 1872)

• Cocci – monococcus, diplococcus, streptococcus, tetracoccus, staphylococcus, sarcina.
• Bacilli – rods / chains.
• Vibrios – comma shaped.
• Spirilla – rigid helices with polar flagella.

By Gram Stain

• Gram + (retain crystal violet) – e.g. \textit{Streptococcus}.
• Gram − (safranin counterstain) – e.g. \textit{Escherichia coli}.

By Flagella

• Atrichous, monotrichous, lophotrichous, amphitrichous, peritrichous.

Temperature Niches

• Psychrophiles 0{-}20^\circ\text C
• Mesophiles 25{-}40^\circ\text C (optimum 37^\circ\text C)
• Thermophiles >45^\circ\text C
• Hyperthermophiles >80^\circ\text C

pH Preferences

• Acidophiles, neutrophiles 6.5{-}7.5, alkalophiles (e.g. Vibrio cholerae optimum \text{pH}=8.2).

Salt Requirement

• Halophiles (require \text{NaCl}), halotolerant, halolabile.

Oxygen Requirement

• Obligate aerobes, facultative anaerobes, aerotolerant, microaerophiles, obligate anaerobes, capnophiles (CO_2 loving).

Spore Formation

• Endospore formers – Bacillus, Clostridium, Sporosarcina.
• Exospore formers – Methylosinus.

Enzyme Tests

• Catalase (+) Staphylococcus / (−) Streptococcus.
• Oxidase (+) Pseudomonas / (−) E. coli.
• Coagulase (+) S. aureus; differentiates pathogenic staphylococci.

Energy & Carbon Class Matrix

• Phototrophs vs chemotrophs; autotrophs (CO2) vs heterotrophs (organic C). • Photoautotrophs – oxygenic (plants, cyanobacteria) vs anoxygenic (green & purple bacteria). • Chemoautotrophs – \text{H}2, \text{S}^{2-}, \text{Fe}^{2+} oxidisers.
• Chemoheterotrophs – most bacteria, animals.

Bergey’s Manuals & Species Concept

Bergey’s Manual of Determinative Bacteriology (1923 → 9ᵗʰ ed.)

• Phenetic emphasis – morphology, staining, biochemical traits.

Bergey’s Manual of Systematic Bacteriology–1ᵗ ed. (4 vols, 1984 – 2000)

• Vol 1 Gracilicutes (Gram −), Vol 2 Firmicutes (Gram +), Vol 3 Mendosicutes (Archaea + Tenericutes), Vol 4 Actinomycetes.

Bergey’s Manual –2ⁿᵈ ed. (5 vols, 2001 – 2012)

• Phylogenetic, 16S rRNA-based.
• Vol I Archaea & phototrophs; Vol II Proteobacteria; Vol III Firmicutes; Vol IV Spirochaetes → Planctomycetes; Vol V Actinobacteria (not listed above but implied).

Online “Bergey’s Manual of Systematics of Archaea & Bacteria” (2015- )

• Continuously updated; \approx100 new genera & >600 new species yr$^{-1}$.

Microbial Species – ICSP “Gold Standard”

• Phenotypic similarity, \ge70\% DNA-DNA hybridisation, \le5^{\circ}\text C T_m difference (GC %), <3\% divergence in 16S rRNA.
• Debate persists owing to asexuality, HGT & limited morphology in prokaryotes.

Major Phyla / Groups (Bergey’s, rRNA phylogeny)

Proteobacteria (Gram −)

• Five classes.
• Alpha – nitrogen fixers (Rhizobium), plant pathogen Agrobacterium, human pathogens Brucella, Rickettsia.
• Beta – mucosal pathogens Neisseria spp.
• Gamma – Pseudomonas, Legionella, enterics (E. coli, Salmonella, Proteus, Serratia).
• Delta – myxobacteria, sulfate reducers.
• Epsilon – gut symbionts/pathogens; Helicobacter pylori.

Oxygenic Phototrophs

• Cyanobacteria – blue-green algae; heterocysts for \text N fixation (Nostoc, Oscillatoria, Spirulina).
• Chlorobi – anoxygenic “green sulfur” photoautotrophs, some photoferrotrophs.

Spirochaetes

• Endoflagella; pathogens Treponema pallidum (syphilis), Leptospira.

Gram + : Firmicutes (low GC) & Actinobacteria (high GC)

• Firmicutes – endospore formers Clostridium (tetanus, botulism, C difficile), Bacillus anthracis; cocci Staphylococcus aureus (MRSA), Streptococcus pneumoniae (pneumonia).
• Actinobacteria – high GC filamentous forms (not detailed in slides).

Thermophiles

• Phyla Aquificae, Deinococcus-Thermus, Thermotogae.
• Thermus aquaticus – Taq DNA polymerase fundamental to PCR.

Laboratory Identification Flowcharts (high-level)

• Initial plating: MacConkey agar (lactose fermenters), blood agar (haemolysis).
• Gram stain → Gram + vs Gram − decision tree.
• Gram + cocci → catalase test → staph vs strep → coagulase for S. aureus.
• Gram + bacilli → catalase (+) Bacillus vs (−) Corynebacterium, Listeria, etc.
• Gram − bacilli → oxidase test; oxidase (+) Pseudomonas, Pasteurella; oxidase (−) Enterobacteriaceae → TSI, urea, citrate.

Key Take-Home Connections

• Bacterial metabolic diversity underpins biogeochemical cycles and vast habitat range.
• Modern taxonomy increasingly relies on molecular phylogeny (16S rRNA, whole genome) while retaining phenotypic tests for routine diagnostics.
• Understanding ecological roles & physiological limits (temperature, pH, salinity, oxygen) is essential for biotechnology, environmental management & clinical microbiology.
• Continuous taxonomic revisions (Bergey’s online) reflect rapid discovery of uncultured diversity driven by genomics and metagenomics.