Bergey’s Manual of Classification of Microorganisms – General Features

Microorganisms are diverse in morphology, physiology, and genetics. Proper classification of

these organisms is essential for their identification, study, and application. In 1923, David
Bergey, a Professor of Bacteriology at University of Pensylvania and four collegues
published classification of bacteria that could be used for identification of Bacterial species.
One of the most widely used references for bacterial classification is the Bergey’s Manual of
bacterial classification.

Bergey’s Manual is published in two main versions:

1. Bergey’s Manual of Determinative Bacteriology – designed for identification based

on phenotypic traits and genotypic analysis.
2. Bergey’s Manual of Systematic Bacteriology – focuses on classification and
phylogeny, emphasizing evolutionary relationships.

Historical Background

 First Edition (1923): Edited by D.H. Bergey, primarily based on morphological and
staining characteristics.
 Later editions incorporated biochemical properties and metabolic capabilities.
 Since the 1980s, the Systematic Bacteriology series has been published in multiple
volumes, incorporating molecular phylogenetics (especially 16S rRNA gene
analysis) as the main framework for classification.

General Features

1. Authoritative Reference

Bergey’s Manual is recognized worldwide as the official standard for bacterial taxonomy. It
is produced with contributions from hundreds of microbiologists and taxonomists, ensuring
that information is current, validated, and globally accepted. It follows the rules of the
International Code of Nomenclature of Prokaryotes (ICNP)

2. Basis of Classification

The classification criteria have evolved over time.

Earlier editions:

 Relied heavily on phenotypic features, including:

o Morphology: cell shape (coccus, bacillus, spiral), arrangement (chains,
clusters), and cell size.
o Staining reactions: Gram-positive vs. Gram-negative based on Gram staining.
o Motility: flagella type, gliding motility, or non-motile.
o Spore formation: presence or absence of endospores.
o Metabolism: aerobic or anaerobic, chemoorganotrophic, chemolithotrophic,
phototrophic.
o Biochemical activities: sugar fermentation patterns, enzyme production,
nitrogen fixation, etc.
o Nutritional requirements: minimal or complex media requirements.
Modern editions:

 Incorporate molecular systematics, especially:

o 16S rRNA gene sequencing for determining phylogenetic relationships.
o DNA G+C content (mol%).
o Whole-genome sequencing and comparative genomics.
o Signature sequences(short sequences in DNA,RNA and proteins) and
conserved protein-coding genes(Remained unchanging through out evolution
in different species).

This combination of classical and molecular data ensures more accurate classification.

3. Phylogenetic Organization

Bergey’s Manual organizes prokaryotes into a hierarchical taxonomic structure:

 Domain
 Phylum
 Class
 Order
 Family
 Genus
 Species

This structure is based largely on molecular phylogeny rather than purely morphological
similarity. For example:

 Gram-negative bacteria are divided into distinct phyla such as Proteobacteria,

Bacteroidetes, Cyanobacteria.
 Gram-positive bacteria are classified into Firmicutes (low G+C) and Actinobacteria
(high G+C) groups.

4. Structure of the Manual

The Systematic Bacteriology series is published in volumes that group related organisms
together.
Example (as in the 2nd edition):

 Volume 1: The Archaea, deeply branching bacteria, and phototrophic bacteria.

 Volume 2: Proteobacteria.
 Volume 3: Firmicutes(Low G+C Gram positive bacteria)
 Volume 4: Actinobacteria(High G+CGram positive bacteria)
 Volume 5: Bacteroidetes, Spirochaetes, Tenericutes, and other phyla.

Within each section, each genus and species is described under standardized headings:

 Morphological description (cell shape, arrangement, Gram reaction)

 Cultural characteristics (growth temperature, pH, oxygen requirements)
 Biochemical properties (enzyme activities, substrate utilization)
 Habitat and ecological significance
  Pathogenicity (if applicable)
 Type strain designation

5. Two Versions – Identification vs. Classification

 Bergey’s Manual of Determinative Bacteriology:

o Intra specific classification: For diagnostic and epidemiological

purposes,it is necessary to sub classify bacterial [Link] may be
based on biochemical properties(biotypes),antigenic features
(serotypes), bacteriophage susceptibility(Phage types) or production of
bacteiocin(colicin type).The intra specific typing of bacteria has been
achieved by Phenotypic and genotypic. Phenotypic method includes
electrophoretic typing of bacterial proteins and immunoblotting.
Genotypic methods include plasmid profile analysis, restricted
endonuclease analysis of chromosomal DNA with sourthen
blotting,PCR and nucleotide sequence analysis.

 Bergey’s Manual of Systematic Bacteriology:

o Comprehensive classification based on evolutionary relationships.
o More suitable for researchers and taxonomists.
o Integrates molecular phylogenetics with classical bacteriology.

6. Use of Dichotomous Keys

In the Determinative version, dichotomous keys are provided to aid identification:

 Bacteria are divided into sections (e.g., Gram-negative rods, Gram-positive cocci).
 Step-by-step questions about morphology, physiology, and biochemical behavior
narrow down possibilities to a genus or species.

7. Integration of Molecular Data

Recent editions rely heavily on 16S rRNA gene sequences to determine relatedness between
organisms. This has led to:

 Reclassification of many bacteria into new genera or families.

 Discovery of entirely new phyla.
 Recognition that some bacteria previously grouped together phenotypically are
genetically very distant.
8. Constantly Updated

Microbial taxonomy is a rapidly changing field. New species are described almost every
week, and genome sequencing frequently reveals novel relationships. Bergey’s Manual
undergoes periodic revisions to:

 Add newly discovered taxa.

 Update nomenclature.
 Reflect changes in phylogenetic understanding.

9. Global Standardization

Bergey’s Manual is accepted worldwide as the taxonomic gold standard for bacteria and
archaea. It ensures that:

 Scientists from different countries use the same names for the same organisms.
 Data from different laboratories can be compared accurately.

The Five Kingdoms Classification

In 1969, Robert H. Whittaker proposed the Five Kingdom Classification, which addressed
both structural and nutritional differences among organisms, making it more scientific and
comprehensive.

Basis of Whittaker’s Classification

Whittaker used multiple criteria for grouping organisms:

1. Cell structure – prokaryotic or eukaryotic.

2. Level of organization – unicellular or multicellular.
3. Mode of nutrition – autotrophic (photosynthesis, chemosynthesis) or heterotrophic
(ingestion, absorption).
4. Reproduction – asexual or sexual.

[Link] relationships – evolutionary history.

Summary Table

Kingdom Cell Type Organization Cell Wall Nutrition Mode Examples

Bacteria,
Monera Prokaryotic Unicellular Peptidoglycan Auto/heterotrophic
Cyanobacteria
Protista Eukaryotic Mostly unicellular Variable Auto/heterotrophic Amoeba, Euglena
Multicellular (except Heterotrophic
Fungi Eukaryotic Chitin Mushrooms, Yeast
yeast) (absorptive)
Plantae Eukaryotic Multicellular Cellulose Autotrophic Ferns, Angiosperms
Animalia Eukaryotic Multicellular Absent Heterotrophic (ingestive) Insects, Humans
Whittaker’s classification divided all living organisms into Monera, Protista, Fungi,
Plantae, and Animalia.

1. Kingdom Monera

 Cell Type: Prokaryotic (no true nucleus or membrane-bound organelles).

 Organization: Unicellular.
 Nutrition: Autotrophic (chemosynthetic or photosynthetic) or heterotrophic
(saprophytic, parasitic).
 Examples: Bacteria, cyanobacteria (blue-green algae), mycoplasma.
 Special features:
o DNA is circular and not enclosed in a nucleus.
o Reproduction mostly by binary fission.
o Some bacteria can fix nitrogen (e.g., Rhizobium, Anabaena).

2. Kingdom Protista

They are eukaryotic mostly unicellular, some simple multicellular forms. Nutrition is
autotrophic (algae), heterotrophic (protozoa), or [Link]: Amoeba,
Paramecium, Euglena, diatoms.

 Special features:
o Exhibit both plant-like and animal-like characteristics.e.g. Euglena
o Reproduction by binary fission, budding, or sexual reproduction.
o Often aquatic, forming plankton in water bodies.

3. Kingdom Fungi: They are eukaryotic, multicellular (except yeasts which are
unicellular).Cell Wall is made of chitin (not cellulose).Nutrition is heterotrophic, absorptive
mode (saprophytic, parasitic, or mutualistic).Examples: Mushrooms (Agaricus), yeasts
(Saccharomyces), molds (Rhizopus, Penicillium).

 Special features:
o Body usually organized into mycelium made of hyphae.
o Non-motile, reproduce by spores.
o Play important roles in decomposition, fermentation, and symbiosis
(mycorrhiza).

4. Kingdom Plantae

They are eukaryotic,[Link] Wall is made of [Link] autotrophic

(photosynthetic) — chlorophyll a and b [Link]: Mosses, ferns, gymnosperms,
angiosperms.

 Special features:
 o Reproduction can be sexual or asexual.
o Alternation of generations in life cycle.
o Immobile, have specialized tissues for transport (in higher plants).

5. Kingdom Animalia: They are eukaryotic,[Link] wall is [Link] is

heterotrophic, ingestive [Link]: Sponges, insects, fish, mammals, birds.

 Special features:
o Show locomotion (at least in some stage of life cycle).
o Nervous system present for coordination (except in simple animals like
sponges).
o Reproduction mostly sexual.

Advantages of the Five Kingdom Classification

 Distinguishes prokaryotes (Monera) from eukaryotes.

 Separates fungi from plants, recognizing their unique heterotrophic absorptive
nutrition.
 Places unicellular eukaryotes in their own kingdom (Protista) rather than grouping
them with plants or animals.
 Reflects evolutionary relationships better than the old two-kingdom or three-kingdom
systems.
 Helps in systematic study of biodiversity.

Limitations

 Protista is a heterogeneous group — includes both plant-like and animal-like

organisms, making it less natural.
 Does not account for the domain concept (Bacteria, Archaea, Eukarya) proposed later
by Woese.

 Viruses are excluded since they are acellular and not considered true living organisms.

Carl Woese’s Three-Domain Classification

In 1977, Carl R. Woese and colleagues, using 16S ribosomal RNA (rRNA) gene
sequencing, discovered that prokaryotes are not a single uniform group. Instead, they fall
into two fundamentally distinct lineages — Bacteria and Archaea — which are as different
from each other as they are from eukaryotes.

This led to the proposal of the Three-Domain Classification System in 1990, which
recognizes:

1. Bacteria
2. Archaea
3. Eukarya

Basis of Classification
  Molecular phylogeny: 16S rRNA (for prokaryotes) and 18S rRNA (for eukaryotes)
sequences are compared.
 Differences in ribosomal RNA sequences indicate deep evolutionary divergence.
 Other supporting evidence:
o Differences in cell wall composition
o Membrane lipid structure
o Sensitivity to antibiotics
o RNA polymerase structure
o Presence or absence of introns

The Three Domains

1. Domain Bacteria

 Cell Type: Prokaryotic.

 Cell Wall: Contains peptidoglycan.
 Membrane Lipids: Fatty acids linked to glycerol by ester bonds.
 Genome: Circular DNA, no introns (in most species).
 Ribosomes: 70S type with unique RNA and proteins.
 Examples: Escherichia coli, Bacillus subtilis, Cyanobacteria.
 Other features:
o Reproduce by binary fission.
o Sensitive to traditional antibiotics like streptomycin and chloramphenicol.
o Includes both pathogenic and beneficial species

2. Domain Archaea

 Cell Type: Prokaryotic, but with unique molecular traits.

 Cell Wall: Lacks peptidoglycan (may have pseudopeptidoglycan).
 Membrane Lipids: Branched-chain hydrocarbons linked to glycerol by ether bonds.
 Genome: Circular DNA, often with introns in some genes.
 Ribosomes: 70S, but RNA sequences and proteins resemble eukaryotes more than
bacteria.
 Examples: Methanogens (Methanobacterium), halophiles (Halobacterium),
thermophiles (Thermoproteus).
 Other features:
o Often inhabit extreme environments (hot springs, salt lakes, deep-sea vents).
o Not sensitive to most bacterial antibiotics.
o Some produce methane as a metabolic by-product.

3. Domain Eukarya

 Cell Type: Eukaryotic (true nucleus, membrane-bound organelles).

 Cell Wall: Present in some groups (plants: cellulose; fungi: chitin), absent in animals.
 Membrane Lipids: Fatty acids linked to glycerol by ester bonds.
 Genome: Linear DNA molecules organized into chromosomes; introns present.
 Ribosomes: 80S type in the cytoplasm, 70S type in mitochondria and chloroplasts.
 Examples: Protists (Paramecium), Fungi (Saccharomyces), Plants (Pisum sativum),
Animals (Homo sapiens).
 Other features:
 o Reproduce sexually or asexually.
o Includes both unicellular and multicellular organisms.

Significance of Woese’s System

 Highlights that Archaea are a distinct and ancient lineage, not just “odd bacteria.”
 Shows that molecular data can reveal relationships not apparent from morphology.
 Forms the basis of modern microbial taxonomy and evolutionary biology.
 Used as a universal framework in genomics and microbial ecology.

Limitations

 Mainly it applicable to cellular life; viruses are excluded.