What is Microbial Diversity?

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What is the point?

  1. To introduce the amazing range of variation in the microbial world
  2. To define and use the terms chemo/photo-hetero/auto-troph
  3. To introduce the phylogenetic perspective to be used in this course

Classic pen-and-ink drawing of Bacteria Source unknown

Classic pen-and-ink drawing of Bacteria
Source unknown

What is diversity? How exactly are organisms either similar to or different than each other? This seems easy in the macroscopic world, but what about microbes?

Morphological diversity

Microbes are often divided into those that are rod-shaped, cocci, or spirals. And these are the most common cells shapes. But bacterial and archaeal cells also come in a wide range of over shapes: filaments (branched or unbranched), irregular, pleomorphic (different shapes under different conditions, or even in the same culture), star-shaped, stalked, &c. Haloquadratum is a flat square organism, just like a bathroom tile!

Haloquadraticum:  Wikimedia commons Haloquadratum walsbyi00.jpg
Haloquadraticum:
Wikimedia commons Haloquadratum walsbyi00.jpg

Individual cells of whatever shape can be found in a variety of multicellular arrangements, from simple pairs and tetrads to multicellular filaments, sheets, rosettes, and true multicellular organisms. Many species form highly structured multi-species mats that resemble the tissues of animals and plants that carry out complex biochemical transformations.

Microbial matt Photo by John R. Spear and Norman R. Pace
Microbial matt
Photo by John R. Spear and Norman R. Pace

Most Bacteria and Archaea are 1-5 microns in size, but they range from 0.1 in diameter to over a millimeter! At the low end, it is hard to understand how everything that's needed for life could fit into the cell. At the high end, they can be easily seen without a microscope.

The bacterium Epulopiscium fishelsoni and the protist Paramecium Photo by Esther Angert
The bacterium Epulopiscium fishelsoni and the protist Paramecium
Photo by Esther Angert

Structural diversity

Many Bacteria have “typical” Gram-positive (single membrane, thick cell wall) or Gram-negative (double membrane, thin cell wall) cell envelops. However, there is a wide range of variation within these two types. Many Gram-positive Bacteria have an outer membrane; made of mycolic acids rather than glyercol-phospahte esters. Many Gram-negative Bacteria lack the lipopolysaccharide layer. Many Archaea and Bacteria (both Gram positive and negative) have an orderly protein coat, the S-layer. In Bacteria, cell walls are composed of peptioglycan, but there is a surprizing range of chemical variations within this type of material. Archaea do not have peptidoglycan cells walls, although some have a related material, pseudomurein.

Korarchaeum cryptophilum S layer Elkins JG … KO Stetter 2008 PNAS 105:8102-7
Korarchaeum cryptophilum S layer
Elkins JG … KO Stetter 2008 PNAS 105:8102-7

Microbes have a wide range of external structures: flagella, pili, fibrils, holdfasts, stalks, buds, capsules, and sheaths, &c. They also have a wide variety of internal structures such as spores, daughter cells, thylakoids, mesosomes, and the nucleoid. In reality, microbial cells are just as structurally organized, and diverse, as are eukaryotic cells.

Metabolic diversity

Macroscopic eukaryotes are not metabolically diverse; they are either chemoheterotrophic (e.g. animals) or photosynthetic (e.g. plants). Bacteria and Archaea have a much broader range of energy and carbon sources, which can be generally divided into four broad types:

Chemoheterotrophs obtain both carbon & energy from organic compounds. Some organisms can use a wide range of organics, and can either oxidize or ferment them. Others can only use a very narrow range of organic compounds and process them in a specific way. Saprophytes and pathogenic microbes are examples of this group.

Chemoautotrophs obtain cell carbon by fixing CO2. Energy is obtained from inorganic chemical reactions such as the oxidation or reduction of sulfur or nitrogen compounds, iron, hydrogen, &c. These organisms don't need organic compounds for either energy or cell carbon. Sulfur-oxidizing bacteria and methane-producing Archaea are examples of this group.

Photoheterotrophs obtain cell carbon from organic compounds, but energy is harvested from light. Halophilic Archaea and most purple photosynthetic bacteria are examples of this group.

Photoautotrophs (photosynthetic) obtain cell carbon by fixing CO2. Energy is from light. These organisms don't need organic compounds for either energy or cell carbon. Most cyanobacteria, some purple photosynthetic bacteria, and plants are examples of this group.

Ecological diversity

Microbes live in an amazing range of habitats, from laboratory distilled water, through freshwater and marine environments, to saturated brines like the Great Salt Lake or the Dead Sea. They grow at temperature of from -5°C to over 118°C; Pyrodictium cultures are sometimes incubated in autoclaves! Organisms are know to grow at pH 0 (0.5M sulfuric acid), and at pH 11 (Draino). Very often, these extremes are combined; Acidianus grows in 0.1M sulfuric acid at 80°C! Many Bacteria grow in the water droplets that make up the clouds, and other live deep in underground aquifers or deep sea sediments. Many microbes live in intimate symbiosis with other creatures, in complex communities or as permanent intracellular “guests”.

Moose Pool, YNP Photo by James W. Brown
Moose Pool, YNP
Photo by James W. Brown

In fact, if you’re on or around Earth and find liquid water, there’s almost certainly something living in it.

Behavioral diversity

It may seem odd to consider the behavior of microscopic organisms, but they do have behavior. Motility and taxis are one form of behavior, both of whoch come in a variety of forms, from the phototactic Chlorobium that use gas vacuoles to adjust their place in the water column to the chemotactic Rhizobium that sense and swim (via flagella) toward chemical signals send by receptive plants roots. Magnetotactic Bacteria have a built-in magnetic compass that allows them to use the Earths magnetic field for orientation!

Chlorobium consortium  Croome RL, Tyler PA. The microanatomy and ecology of "Chlorochromatium aggregatum" in two meromictic lakes in Tasmania. J Gen Microbiol 1984; 130:2717–23.
Chlorobium consortium
Croome RL, Tyler PA. The microanatomy and ecology of "Chlorochromatium aggregatum" in two meromictic lakes in Tasmania. J Gen Microbiol 1984; 130:2717–23.

All organisms have developmental cycles; at very least the ability to switch between active growth (e.g. log phase) to resting or slow growth (e.g. stationary phase) stages. Other developmental cycles include sporulation, the production of swarmers cells, cysts or akinetes, and even terminal differentiation and distinct germ and somatic cell types, such as heterocysts in filaments of cyanobacteria, “slugs” in Myxobacteria, or the very complex life cycles of Streptomyces.

Streptomyces antibioticus Nora Ausmees, University of Uppsala
Streptomyces antibioticus
Nora Ausmees, University of Uppsala

Microbes also respond to their environments metabolically, by expressing the genes needed to compete for the resources available at the time. An example of this would be converting over its metabolism from oxidative to fermentation when the oxygen is exhausted in a culture, or from glucose to galactose when the glucose is used up in a mixed sugar medium.

In addition, microbes act communally. Cells within a specie (or group) communicate by sending and receiving chemical signals, or by direct contact. For example, Myxococcus swarming begins with a chemical signal propagated through the community, which brings them into proximity. Direct contact between cells then directs aggregation and formation of the fruiting body. Microbes also form specific symbioses, with other microbes or with macroscopic creatures. Complex communities of microbes associate into ‘mats’ that process and recycle resources throughout the community.

A swarm of Myxococcus xanthus (left) invading a colony of E.coli (right). John Kirby, University of Iowa Carver College of Medicine
A swarm of Myxococcus xanthus (left) invading a colony of E.coli (right).
John Kirby, University of Iowa Carver College of Medicine

Underlying all these is Evolutionary diversity

Underlying all of these different aspects of diversity is genetic diversity, perhaps more properly viewed as evolutionary diversity. Microbes are far more evolutionarily diverse than are macroscopic creatures; the macroscopic world is just the tip of the iceberg of Life. Even most plants and animals are microscopic! So microbial diversity is actually the same as biological diversity, with just a few of the more ponderous organisms overlooked.

3-Domain tree Redrawn from Norm Pace
3-Domain tree
Redrawn from Norm Pace


Evolutionary diversity is usually expressed in terms of trees; branched graphs that trace the genealogies of organisms. When these trees are based on genetic diversity (gene sequences), they can be both quantitative and objective.

This is the perspective on diversity we’ll be using in this course.