Bacterial Diversity

Common Bacterial Traits

Bacteria are a subset of prokaryotes and while very different, they still have some common features.

Learning Objectives

Identify common bacterial traits

Key Takeaways

Key Points

  • Bacteria vary from species to species, thus assigning many common traits to bacteria is difficult. Bacterial species are typified by their diversity.
  • There are three notable common traits of bacteria, 1) lack of membrane-bound organelles, 2) unicellular and 3) small (usually microscopic) size.
  • Not all prokaryotes are bacteria, some are archaea, which although they share common physicals features to bacteria, are ancestrally different from bacteria.

Key Terms

  • archaea: a taxonomic domain of single-celled organisms lacking nuclei, formerly called archaebacteria but now known to differ fundamentally from bacteria.
  • binary fission: a form of asexual reproduction and cell division used by all prokaryotes, (bacteria and archaebacteria)

Bacteria constitute a large domain of prokaryotic microorganisms. Bacteria were among the first life forms to appear on Earth, and are present in most habitats on the planet. Bacteria grow in soil, acidic hot springs, radioactive waste, water, and deep in the Earth’s crust. In addition, they grow in organic matter and the live bodies of plants and animals, providing outstanding examples of mutualism in the digestive tracts of humans, termites, and cockroaches.

But what defines a bacteria? Bacteria as prokaryotes share many common features, such as:

  1. A lack of membrane-bound organelles
  2. Unicellularity and thus division by binary-fission
  3. Generally small size

Bacteria do not tend to have membrane-bound organelles in their cytoplasm and thus contain few large intracellular structures. They consequently lack a true nucleus, mitochondria, chloroplasts, and the other organelles present in eukaryotic cells, such as the Golgi apparatus and endoplasmic reticulum. Bacteria were once seen as simple bags of cytoplasm, but elements such as prokaryotic cytoskeleton, and the localization of proteins to specific locations within the cytoplasm have been found to show levels of complexity. These subcellular compartments have been called “bacterial hyperstructures”.

image

Bacterial structures: Cell structure of a Gram-positive prokaryote.

Unlike in multicellular organisms, increases in cell size (cell growth and reproduction by cell division) are tightly linked in unicellular organisms. Bacteria grow to a fixed size and then reproduce through binary fission, a form of asexual reproduction.

image

Binary fission: Many bacteria reproduce through binary fission.

Perhaps the most obvious structural characteristic of bacteria is (with some exceptions) their small size. For example, Escherichia coli cells, an “average” sized bacterium, are about 2 micrometres (μm) long and 0.5 μm in diameter. Small size is extremely important because it allows for a large surface area-to-volume ratio which allows for rapid uptake and intracellular distribution of nutrients and excretion of wastes.

The term “bacteria” was traditionally applied to all microscopic, single-cell prokaryotes, having the similar traits outlined above. However, molecular systematics show prokaryotic life to consist of two separate domains, originally called Eubacteria and Archaebacteria, but now called Bacteria and Archaea that evolved independently from an ancient common ancestor. The archaea and eukaryotes are more closely related to each other than either is to the bacteria. It should be noted that Bacteria and Archaea are similar physically, but have different ancestral origins as determined by DNA of the genomes that encode different prokaryotes.

image

Archaea and other domains: Phylogenetic tree showing the relationship between the Archaea and other domains of life. Eukaryotes are colored red, archaea green and bacteria blue.

Unclassified and Uncultured Bacteria

To classify a species of bacteria, one usually needs to isolate and grow up the species that is to be classified.

Learning Objectives

Estimate bacterial diversity

Key Takeaways

Key Points

  • Classification is the attempt to identify and group different species of bacteria together by common traits.
  • If a bacterium cannot be cultured, it is hard to study it to find commonalities and differences from other species of bacteria.
  • Recent advances in molecular technique are allowing uncultured bacteria to be classified.

Key Terms

  • viable but nonculturable: Viable but nonculturable (VBNC) bacteria refers to bacteria that are in a state of very low metabolic activity and do not divide, but are alive and have the ability to become culturable once resuscitated.

Describing Diversity

Classification seeks to describe the diversity of bacterial species by naming and grouping organisms based on similarities. Bacteria can be classified on the basis of cell structure, cellular metabolism, or by differences in cell components such as DNA, fatty acids, pigments, antigens, and quinones.

While these schemes previously allowed the identification and classification of bacterial strains, it was long unclear whether these differences represented variation between distinct species or between strains of the same species. This uncertainty resulted from the lack of distinctive structures in most bacteria, as well as lateral gene transfer that occurred between unrelated species. Because of the existence of lateral gene transfer, some closely related bacteria have very different morphologies and metabolisms.

To overcome these uncertainties, modern bacterial classification emphasizes molecular systematics, using genetic techniques such as guanine cytosine ratio determination, genome-genome hybridization, as well as sequencing genes that have not undergone extensive lateral gene transfer, such as the rRNA gene.

Uni-Species Cultures for Identification

While there are several molecular tools that allow us to classify or distinguish different bacterial species, this is predicated on obtaining uni-species cultures of a given bacteria. Culture techniques are designed to promote the growth and identify particular bacteria, while restricting the growth of the other bacteria in the sample. Often these techniques are designed for specific specimens; for example, a sputum sample will be treated to identify organisms that cause pneumonia, while stool specimens are cultured on selective media to identify organisms that cause diarrhoea while preventing growth of non- pathogenic bacteria. Specimens that are normally sterile, such as blood, urine, or spinal fluid, are cultured under conditions designed to grow all possible organisms. Once a pathogenic organism has been isolated, it can be further characterized by its morphology, by growth patterns such as aerobic or anaerobic growth, by patterns of hemolysis and by staining. If a bacteria can not be cultured, classification can prove to be very difficult.

DNA Sequencing

However, recent advances in molecular techniques do allow the sequencing of DNA from bacterial species, without the reliance on a pure culture of that given bacteria. Diagnostics using such DNA-based tools, such as polymerase chain reaction, are increasingly popular due to their specificity and speed, compared to culture-based methods. These methods also allow the detection and identification of “viable but nonculturable” cells that are metabolically active but non-dividing, which can be applied to isolates of bacterial species that cannot be cultured. However, even using these improved methods, the total number of bacterial species is not known and cannot even be estimated with any certainty. Following present classification, there are a little less than 9,300 known species of prokaryotes, which includes bacteria and archaea. Attempts to estimate the true level of bacterial diversity have ranged from 107 to 109 total species – and even these diverse estimates may be off by many orders of magnitude.