This chapter is from the book
This chapter is from the book
This chapter is from the book
The size of life
Bacteria need only be big enough to hold their vital enzymes, proteins, and genetic machinery. Evolution has eliminated all extraneous structures. Also, a small, simple architecture allows for rapid reproduction, which aids adaptation. Bacterial metabolism is a model of efficiency because of a large surface-to-volume ratio that smallness creates. No part of a bacterial cell is very far from the surface where nutrients enter and toxic wastes exit. Eukaryotic cells that make up humans, algae, redwoods, and protozoa contain varied organelles each surrounded by a membrane. The surface-to-volume ratio in these cells is one-tenth that of bacteria, so shuttling substances across all those organelle membranes, the cytoplasm, and the outer membrane burns energy. Bacterial structure is less demanding and more efficient. Finally, small size contributes to massive bacterial populations that dwarf the populations of any other biota.
Large multicellular beings that produce small litters with long life spans—think whales, elephants, and humans—take a long time to make new, favorable traits part of their genome. Insects evolve faster and can develop a new trait within a few years. In bacteria, evolution occurs overnight. Often, the progeny contain a new trait that makes them better equipped for survival.
No one knows the number of bacterial species. About 5,000 species have been characterized and another 10,000 have been partially identified. Biodiversity authority Edward O. Wilson has estimated that biology has identified no more than 10 percent of all species and possibly as little as 1 percent. Wilson's reasoning would put the total number of bacterial species at 100,000, probably a tenfold underestimate. Most environmental microbiologists believe that less than one-tenth of 1 percent of all bacteria can currently be grown in laboratories so that they can be identified.
Microbial geneticist J. Craig Venter's studies on microbial diversity have correctly pointed out that the number of species may be less important than their diversity and roles in the Earth's biosphere. Venter concluded from a two-year study of marine microbes that for every 200 miles of ocean, 85 percent of the species, judged by unique genetic sequences, changed. The ocean appears to contain millions of subenvironments rather than one massive marine environment, and each milliliter holds millions of bacteria. The actual number of bacteria in the oceans alone may exceed any previous estimates for the entire planet. In future studies of Earth's microbial ecology, the absolute number of species will probably never be determined.
Microbiologists begin defining the microbial world by taking samples from the environment and determining the types of bacteria found there. One of the first questions to answer is: Are any of these bacteria new, previously undiscovered species? To answer this, microbiologists must understand the species that have already been characterized, named, and accepted in biology, such as E. coli.
Taxonomists assign all living things to genus and species according to outward characteristics and the genetics of an organism. Until the late 1970s, microbiologists identified bacteria through enzyme activities, end products, nutrient needs, and appearance in a microscope. In 1977 Carl Woese at the University of Illinois proposed using fragments of a component of cell protein synthesis, ribosomal ribonucleic acid (rRNA). Cellular rRNA takes information contained in genes and helps convert this information into proteins of specific structure and function. Because the genetic information in rRNA is unique to each species, it can act as a type of bacterial fingerprint. Woese's method specifically used a component called 16S rRNA, which relates to a portion of the ribosome, the 16S subunit. This analysis led to a new hierarchy of living things (causing considerable consternation among traditional taxonomists) with bacteria, archaea, and eukaryotes comprising the three domains shown in Figure 1.4. Prior to the new rRNA classifications, biology students had been taught five-, six-, and even eight-kingdom classifications for organizing all plants, animals, and microbes. When I took my first biology classes, the five-kingdom system being taught looked like this:
- Monera, containing the bacteria
- Protista, containing protozoa and algae
- Plantae, containing green plants descended from algae
- Fungi descended from specific members of the Protista
- Animalia descended from specific members of the Protista
Figure 1.4 The three domains. Classification of the world's organisms does not remain static; new technologies constantly force taxonomists to reevaluate and reclassify species.
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New technologies for classifying organisms have yet to end confusion that ensues when attempting to organize the world's biota, and for good reason. Taxonomists and philosophers have been trying to figure out organisms' relationships to each other since Aristotle's first attempts. Additionally, since the emergence of DNA analysis in the 1970s, geneticists have discovered more diversity in biota but also a dizzying amount of shared genes, especially among bacteria. The rRNA analysis introduced by Woese showed the degree to which different species shared genes. The studies revealed a significant amount of horizontal gene transfer, which is the appearance of common genes across many unrelated species.
The evolutionary tree we all learned in which families, genera, and species branched from a major trunk does not depict horizontal gene transfer. The evolutionary tree may look more like a bird's nest than an oak. Nowhere may that be truer than in the bacteria. Gene sharing or gene transfer is now known to take place in bacteria, and possibly archaea, more than ever before imagined. In 2002, the 16S rRNA system became further refined by focusing on certain protein-associated genes. But as biologists dig deeper into the genetic makeup of bacteria, they find more shared genes. Some microbiologists have begun to think that the term "species" makes no sense when speaking about bacteria. Currently, if two different strains of bacteria have less than 97 percent identical genes determined by 16S rRNA analysis, then they can be considered two different species. Some microbiologists suggest that only a 1 percent difference in genes differentiates species, not 3 percent.
When microbiologists first developed the bacterial groups known today as species, they let common characteristics of bacteria guide them. Gram reaction, nutrient requirements, unique enzymes, or motility served as features for putting bacteria into various species. Modern nucleic acid analysis has shown whether the traditional classification system still makes sense. With a high percentage of shared genes among bacteria and the ease with which diverse cells transfer genes around, some microbiologists have suggested that classifying bacteria by species is futile. It seems as if all bacteria belong to one mega-species, and different strains within this species differ by the genes they express and the genes they repress. By classifying bacteria into a single species, all bacteria would obey the definition for a species first proposed by Ernst Mayr in 1942: Members of the same species interbreed and members of different species do not.
Genetic analysis has blurred the lines between bacterial species so that the criteria used to classify other living things cannot apply to bacteria. To preserve their sanity, microbiologists need some sort of taxonomic organization so that they can speak the same language when discussing microbes. The traditional methods of grouping bacteria according to similar characteristics have turned out to be the handiest method regardless of DNA results. Microbiologists use the same classification and naming system for bacteria as used for all other life. The system has changed little since botanists in the mid-1800s, Carl Linnaeus being the most famous, developed it. Species classification and naming uses binomial nomenclature to identify every species by a unique two-part Latin name.
Bacteria of the same genus share certain genes, quite a few as mentioned, but different species have a few unique genes. For example, Bacillus is the genus name of a common soil bacterium. The genus contains several different species: Bacillus subtilis (shortened to B. subtilis), B. anthracis, B. megaterium, and so on. If I were a bacterium, my name would be Maczulak anne or M. anne.
To name a new bacterium, microbiologists have several conventions at their disposal. All that matters is that the new name be different from all other names in biology. Table 1.1 shows common naming conventions.
Table 1.1. Origins of bacteria names
|
Naming Method |
Example |
Reason for the Name |
|
A historic event |
Legionella pneumophila |
Cause of a new disease that occurred at a Legionnaires convention in 1976 |
|
Color |
Cyanobacterium |
Blue-green color |
|
Cell shape and arrangement |
Streptococcus pyogenes |
Long, twisting chains (strepto-) of spherical (-coccus) cells |
|
Place of discovery |
Thiomargarita namibiensis |
Found off the coast of Namibia |
|
Discoverer |
Escherichia coli |
Discovered by Theodor Escherich in 1885 |
|
In honor of a famous microbiologist |
Pasteurella multocida |
Genus named for Louis Pasteur |
|
Unique feature |
Magnetospirillum magnetotacticum |
Spiral-shaped bacteria with magnet-containing magnetosomes inside their cells |
|
Extreme growing conditions |
Thermus aquaticus |
Grows in very hot waters such as hot springs |
Bacterial names will likely never be replaced regardless of scientific advances in classifying and reclassifying the species. Medicine, environmental science, food quality, manufacturing, and biotechnology depend on knowing the identity of a species that causes disease or contamination or makes a useful product. As microbiology fine-tunes its focus from the biosphere to the human body, species identity becomes more important.