Bacterial Genomes and Evolution Concepts

Evolution (to bacteria)

Genetic change (altered genotype) leading to a change in observable traits (altered phenotype), new ability, or different appearance, resulting in a fitness advantage in a given environment.

Microbial taxonomy

Names and identifies organisms based on genomic information that predicts traits of related organisms.

Bacterial genetic exchange

The process by which bacteria share genetic material without sexual reproduction, forming 'clonal' populations.

Horizontal gene transfer

Moving DNA from one bacterium to another through transformation, conjugation, or transduction.

Transformation

Taking up free DNA from the environment into bacterial cells, a property inherent to many bacterial species.

Conjugation

A method of DNA transfer that requires intimate cell contact, typically initiated by a sex pilus from the donor cell.

Transduction

Virus-mediated transfer of DNA from one bacterium to another, involving bacteriophages that can package host DNA.

Generalized recombination

An enzyme-mediated process where two DNA molecules exchange portions, requiring long stretches of sequence similarity.

Homologs / homologous

Genes that are similar, having similar DNA coding sequences, similar protein products, and similar functions.

Paralogs

Similar genes in the same organism that encode for two different proteins with different functions.

Orthologs

Similar genes in different organisms that encode for proteins with the same function.

Natural transformation

A property inherent to many bacterial species that allows them to take up free DNA from the environment.

Artificially competent

Bacteria that have been manipulated to take up free DNA from the environment.

Bacteriophages

Bacterial viruses that can move DNA from one bacterium to another, composed of nucleic acid and a capsid.

Specialized transduction

A process where a virus genome becomes part of the bacterial chromosome.

Mobile genetic elements

Genetic elements that can move around within the genome and facilitate genetic exchange.

Clonal populations

Populations of bacteria that arise from a single ancestor, lacking sexual reproduction.

Fitness advantage

An increased likelihood of survival and reproduction due to advantageous traits in a given environment.

Accidental DNA transfer

The process by which a phage accidentally packages a small piece of host DNA during transduction.

Capsid

The protein shell of a virus that encases its nucleic acid.

Lysing

The process of breaking down a cell, often used to release newly assembled phage particles.

Site specific recombination

Requires very little sequence homology but does require a short sequence recognized by a special recombination enzyme.

Recombination advantages to microbes

Use their own DNA to fix mutations or restart stalled replication forks, repair damaged chromosomes using DNA donated by others of the same species, and obtain genes from other organisms that might enhance the competitive fitness of the cell.

Recombination

DNA molecules are cleaved and reattached to other DNA (chromosome to chromosome or plasmid to chromosome).

Origins and Evolution

All life originated from microbes, and species continue to evolve through changes to genomes.

Genomes change

Via processes of random mutation and natural selection.

Common ancestor

All three domains of life (Archaea, Bacteria, Eukarya) originated from a common ancestor but branched apart and developed unique characteristics.

Genetic relatedness

Arises from common ancestry.

Divergence

As organisms reproduce over many generations, their offspring acquire mutations, leading to divergence.

Family tree of organisms

The gradual divergence of organisms generates a 'family tree' of related organisms, known as phylogeny.

Sources of divergence

Besides mutation, another source of divergence is gene mobility.

Instant speciation

Gain or loss of a large number of genes can lead to a more sudden change.

Natural selection

Favors the organism that produces more offspring in that environment (competitive advantage).

Selective pressure

Genes encoding traits that influence the survival of offspring are said to be under 'selective pressure'.

Reductive evolution

A trait no longer needed for growth or survival is no longer under selective pressure.

Three domains of life

Three major groups called Domains: Bacteria, Archaea, and Eukarya.

Eukaryotes

Possess many complex membranous organelles.

Bacteria

Have a distinctive gene expression apparatus and all bacterial cell walls are made of peptidoglycan.

Archaea

Have distinctive ether-linked membrane lipids and no known Archaea are human pathogens.

Endosymbiotic theory

A free living Bacterium was engulfed by a larger Archaeon, leading to the formation of mitochondrion and eventually Eukaryotes.

Fitness

Depends on environment and is determined by the traits that influence survival and reproduction.

Endosymbiosis

A mutualistic relationship between the host and the symbiont where each is required for normal growth and development.

Degenerative evolution

Loss of traits in the absence of selection pressure.

Microbial species

Defined by the principle that members of different species do not normally interbreed with each other.

Asexual reproduction in bacteria and archaea

Occurs through binary fission, making interbreeding not a basis for classification.

70% DNA hybridization

A metric used to define microbial species based on genetic similarity.

97% similarity of 16S rRNA gene

A threshold used to classify microbial species.

95% identity in ortholog sequence

Another metric for defining microbial species.

Phylogeny

Classification based on DNA relatedness.

Ecology

Classification based on shared traits and ecological niche.

Taxonomy

Description of distinct life forms and their organization into different categories.

Identification

The process of determining the identity of a microbe.

Classification

The arrangement of organisms into categories.

Nomenclature

The system of naming organisms.

Genome sequencing

The most conclusive way to identify a microbe.

DNA-based methods

Preferred methods in clinical practice for identifying microbes.

Dichotomous key

A series of yes/no decisions that narrow down possible categories of species.

Probabilistic indicator

An alternative means of identification that uses biochemical tests and a predefined database.

Bacterial Diversity

Millions of species with thousands isolated and characterized.

Major groups of bacteria

Include Gram-positive, Gram-negative, Spirochetes, Cyanobacteria, Deep Branching, and Chlamydia.

Environmental effects on diversity

Genes are sampled from thousands of species, influencing the evolution of pathogens.

Genetic changes

Occur and are maintained when the change is neutral or beneficial.

Geographic separation

Leads to the development of new species over time.