A Basic Introduction

All of the organisms on earth have been classified into one of three major divisions.

  1. eubacteria
  2. archaea
  3. eukaryotes

Most of the genetic diversity on Earth is represented by microbes. Recent data have shown that humans differ from chimpanzees by only 1.5% of their DNA sequences. Eukaryotic DNA sequences are so similar that the genome of one species can be used to predict the genome of others. In a typical bacterium, however,  25-50% of the genes are unique to that species.


Archaea (formerly known as the archaebacteria) are single-celled microbes mostly represented by extremophiles, organisms that live under conditions where other types of organisms cannot survive. Until recently the archaea were classified in the same group as eubacteria; however, comparisons of transcription factors and membrane ATPases suggest that archaea are more closely related to eukaryotes than eubacteria. Substantially less is known about the archaea than about the eubacteria which are thus often referred to as just ‘bacteria’.

True Bacteria

The eubacteria consist of a wide variety of single- and multi-cellular species, some with complex developmental cycles. They are divided into two subgroups based on the results of a Gram stain test.

  1. gram-negative cells (stain pink)
  2. gram-positive cells (stain purple)

There are four basic steps of the Gram stain. A primary stain (crystal violet) is applied to a heat-fixed smear of a bacterial culture, followed by the addition of a mordant (Gram’s iodine), rapid decolorization with alcohol or acetone, and counterstaining with safranin or basic fuchsin. Gram-negative bacteria are surrounded by thin inner and outer membranes which retain little of the dye resulting in a pink cell. Gram positive bacteria have a thick cell wall made of peptidoglycan which retains much of the dye resulting in a deep blue or purple cell.

Gram stained cerebrospinal fluid showing gram-positive anthrax baccilli (purple rods).

Gram stained cerebrospinal fluid showing gram-positive anthrax baccilli (purple rods).

Eubacteria Examples

The genus Myxococcus consists of gram-negative bacterium that exist as free-living single-celled organisms during part of their lifecycle and can aggregate and self-organize to form fruiting bodies in response to environmental cues. Epulopiscium fishelsoni is one of the largest bacterium known, and because of this it has evolved some curious adaptations. The gram-positive Epulopiscium reproduces exclusively through an unusual form of sporulation reminiscent of vivipary. Anywhere from one to twelve daughter cells are grown inside of the parent cell until the cell eventually lyses and the new bacteria burst through the cell wall. Another member of the eubacteria, the actinomycetes, are used by the Attine tribe of ants for the antibiotics produced by the fungus-like bacteria. The actinomycete-produced antibiotics protect the ants’ fungal gardens from infection by a parasitic fungus (Escovopsis).

Chloroplasts and Mitochondria

Current evidence indicates that eukaryotic mitochondria and chloroplasts are descended from free-living eubacteria that formed a symbiosis with eukaryotes. Comparisons of highly conserved ribosomal RNA (rRNA) gene seuences suggest mitochondria are descended from the proteobacteria and chloroplasts are descended from the cyanobacteria. In fact, some dinoflagellates (eukaryotes) are known to engulf cyanobacteria when it is light out, allowing the dinoflagellates to photosynthesize, then discard the cyanobacteria at night when they have no use for them.

Why more is known about some bacteria than is known about any other type of organism.

What is currently know about the basic molecular mechanisms in cells is a result of studies of bacteria. This is because bacteria are relatively easy to manipulate genetically. Bacteria are haploid organisms. In diploid organisms most mutations are recessive making them difficult to identify. Mutations in haploid organisms usually have an immediate, easily identifiable effect. Bacteria also hav short generation times. The shorter the generation time the more experiments that can be done. Some strains of Escherichia coli (E. coli) can reproduce every 20 minutes under ideal conditions. The asexual reproduction used by bacteria makes it is easy to obtain a large number of identical organisms to perform experiments on. Every daughter cell is a clone of the mother. With bacteria there is no sex to complicate genetic experiments. The ability to grow colonies on agar plates allows researchersto produce a large number of organisms in a small place, and no matter how crowded the bacteria are on the original agar plate, it is possible to isolate a pure strain of the bacterium in one or a few steps of colony purification. Using serial dilutions a measurable number of discrete colonies can easily be obtained from a densely concentrated culture. One of the major advantages of bacterial genetics is the opportunity to isolate rare mutants or other strains of bacterium. Using the proper selective growth conditions a single bacterium can be seleted from among billions placed on an agar plate. Finally, the three methods of genetic exchange between bacteria (transformation, conjugation, and transduction) allow for the possibility of all the genetic exepriments performed on microbes.

(Header Image: Epulopiscium)


The Attini tribe rely solely on the cultivation of Fungus Gardens for food. When an Attine Daughter Queen leaves her maternal home, she must carry within her mouth a Nucleus of Fungus to serve as the Starting Culture for her new Garden (Schultz and Brady 2008).


In a paper published in PNAS in 2008, Schultz and Brady provide detailed insights into the transition from simple agriculture to complex agriculture of the Attini tribe. The study suggests the Attini first developed agriculture approximately 50 million years ago in the forests of South America, coinciding with the early Eocene climatic optimum (50-55 mya). During this time there was a period of global warming and an extraordinary diversity of tropical plants occurring at middle and high latitudes in South America. The methods used in Attine agriculture have been divided into five distinct systems:

1. Lower Agriculture (practiced by the majority of the Attine)
2. Coral Fungus Agriculture (practiced by the “Pilosum Group”)
3. Yeast Agriculture (practiced by the “Rimosus Group”)
4. Generalized Higher Agriculture (practiced by the “Higher Attine”)
5. Leaf Cutting Agriculture (practiced by the Atta and Acromyrmex)

(Schultz and Brady 2008)

All five systems of agriculture utilize remarkably proficient planting, manuring, weeding, and sheltering techniques (Mueller and Rabeling 2008).


The original Attine agriculturalists collected withered plant bits and other debris on which to cultivate an unspecialized fungus that retained close genetic ties to free-living fungal populations (Mueller and Rabeling 2008). The “parasol mushrooms” grown using this method are, so far as is known, entirely capable of free-living existence without the help of the Attine growers. A paraphyletic grade of Escovopsis is known to infect the the paraphyletic fungal food sources used by the Lower Attine; but, like all Attine agriculturalists, they utilize an antibiotic produced by Actinomycete bacteria to control the parasite.


The “Pilosum Group” of the Attini tribe began to cultivate coral fungi (Pterulaceae) between 10 and 20 million years ago. Recent research indicates that Coral Fungus Agricultural products are infected by a specialized grade of Escovopsis that is derived from an Escovopsis species that infects Lower Agricultural products. This species subsequently gave rise to a clade that switched hosts and began infecting the Higher Attine food sources (Schultz and Brady 2008).


Unlike typical Attine Mycelial Gardens, Yeast Gardens consist of small, irregularly shaped nodules of fungus growing in the yeast phase. Yeast Agriculture is confined to the “Rimosus Group” and originated sometime between 5 and 25 million years ago. The yeast grown are capable of a free-living, feral existence; however, they grow in the mycelial phase rather than the yeast phase. Indeed, these fungi are only known to grow in the yeast phase when attended by the Attine growers (or depending on conditions in artificial culture). The parasite Escovopsis is unknown to Yeast Agriculture (Schultz and Brady 2008).


The transition to higher agriculture and the subsequent origin of leaf cutting are arguably the two most ecologically significant developments in the history of the Attini tribe. The fungi grown by the Higher Attine suggest a significant degree of “domestication”, or modification for life with the Attine. These fungi do not appear capable of free-living existence separable from their growers. And only the fungi grown by the Higher Attine produce “gongylidia”, nutritious swollen hyphal tips that are harvested by the Higher Attine for food(Schultz and Brady 2008).


The development of Leaf Cutting Agriculture (rather than the debris collecting that is used in all the other systems) coincided with marked ecological transitions in South America (5-15 mya). The coincidence of grassland expansion with the development of Leaf Cutting Agriculture supports the hypothesis that early Leaf Cutters may have been Grass Cutting specialists with specializations in Broadleaf Cutting developing later. The most wide ranging Leaf Cutting Agriculturalists originated and expanded within the last 1 to 2 million years. Such a rapid acceleration in diversification and expansion of the Attini tribe underscores the belief that Leaf Cutting Agriculture represents one of the key innovations in Attine history (Mueller and Rabeling 2008).

Mueller, U., & Rabeling, C. (2008). A breakthrough innovation in animal evolution Proceedings of the National Academy of Sciences, 105 (14), 5287-5288 DOI: 10.1073/pnas.0801464105

Schultz, T., & Brady, S. (2008). Major evolutionary transitions in ant agriculture Proceedings of the National Academy of Sciences, 105 (14), 5435-5440 DOI: 10.1073/pnas.0711024105
-Bryan Perkins