Bacteria

A

A New Classification System

The development of the field of molecular phylogeny in the 1970s changed our view of bacteria. Phylogeny relates organisms through their evolutionary origins. In molecular phylogeny, scientists look for similarities in the molecules of organisms to figure out relationships. Initially, scientists looked at proteins, which are made up of long strings of amino acids. They figured that if a particular protein in two organisms contained exactly the same amino acids in the same order, then the two were very closely related or even identical. If there were only a few differences, the organisms were closely related. The more differences there were, the more distant the relationship would be.

Carl Woese, a microbiologist at the University of Illinois, discovered that it was easier to work with nucleic acids, such as DNA and RNA. He found that the best molecules were ribonucleic acid molecules from ribosomes (rRNA). Ribosomes are the biochemical machines inside cells that coordinate the synthesis of proteins. It was relatively easy to obtain rRNA, to identify its chemical building blocks known as nucleotides, and to determine the order of the nucleotides in the molecule. Because rRNA shows relatively little variation from one generation to the next, it proved to be an excellent tool for determining evolutionary relationships.

Molecular phylogeny indicated that there are three major groups, or kingdoms, of organisms. One kingdom, called Eukaryotae, consists of all organisms with a true nucleus and includes all plants and animals. The two other kingdoms, called Archaea and Eubacteria, consist of prokaryotic bacteria without a true nucleus. Archaea, or archaeabacteria, were once classified with other bacteria and the two kingdoms share many characteristics. Many of the archaea are extremophiles and can live in extremely hot, salty, or acid environments, but so can many eubacteria.

The classification of bacteria into two kingdoms, a system proposed by Woese, is based almost entirely on the structure of ribosomal RNA. But it appears to agree with other findings regarding the basic structures of the organisms, their metabolism, and their evolution.

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B

Sequencing Bacterial DNA

Amazing advances in technology have enabled scientists to sequence the entire genome of many bacteria—that is, identify the nucleotides that make up the DNA and the order in which the nucleotides are arranged. This knowledge, and the sciences that have developed around it, will enable scientists to harness the useful capabilities of bacteria in agriculture, industry, and other fields and to develop new drugs. In one example, scientists have turned bacteria into factories for producing the hormone insulin by inserting human insulin-producing genes into bacteria. The insulin produced can be used to treat human diabetes.

Insulin is a protein, and genes govern the production of proteins by a cell. The study of protein production will help scientists understand the process of disease at a cellular level and help them develop new means of combating diseases. As scientists study how bacteria attach to and enter healthy cells, cause illness, and spread, they are learning useful details about the molecular structure of cells.

V

Evolution of Bacteria

The oldest fossils of bacteria-like organisms date back as many as 3.5 billion years, making them the oldest-known fossils. These early bacteria could survive in the inhospitable conditions when Earth was young, extremely hot, and without oxygen. With the help of molecular phylogeny, scientists have pieced together a view of the evolution of bacteria. They believe that the kingdoms Archaea and Eubacteria had a common ancestor but separated very early on, a few billion years ago. Archaea may be the most common organisms on Earth today. Many of them can live without oxygen and without sunlight and inhabit such places as deep-sea vents. However, scientists currently know much more about the kingdom Eubacteria than the kingdom Archaea, because humans have more contact with disease-causing Eubacteria, such as streptococci and Escherichia coli, and with Eubacteria such as lactobacilli used in food processing and other industries.

Over time, bacteria evolved to capture energy from the Sun’s light and thereby carry out the process of photosynthesis, converting sunlight into nutrients. Next they developed the sort of photosynthesis that plants today carry out by splitting water molecules to produce oxygen. With oxygen available, organisms that require it, such as animals, could inhabit Earth.

Recent discoveries suggest that Eukaryotae (plants and animals) probably evolved from Eubacteria. Many of the organelles (structures within the cytoplasm) of plant and animal cells are actually bacterial. Among organelles derived from bacteria that invaded plant or animal cells are mitochondria and chloroplasts. Mitochondria in plants and animals convert nutrients into energy-storage molecules. Chloroplasts house the photosynthetic machinery of plant cells. Not only do bacteria live on us and in us, but we ourselves are in a way partly bacterial.

VI

Scientific Study of Bacteria

Before the development of the microscope, some people speculated that small, invisible particles caused diseases and fermentations. But not until the late 1600s did anyone actually see bacteria. In the 1670s Dutch lens maker Antoni van Leeuwenhoek first saw what he called “wee animalcules” under his single-lens microscopes. Leeuwenhoek noticed cells of different shapes within a variety of specimens, including scrapings from his teeth and rainwater from gutters. His findings laid the foundation for the growth of microbiology.

The microscope was improved over the following centuries, but bacteria still appeared as tiny objects, even with magnifications of 1,000 times. In the 1930s, the first electron microscopes were developed. Using beams of electrons instead of light, these microscopes could magnify objects at least 200 times more than light microscopes could. With magnifications of 200,000 times actual size, it became possible to see structures within bacterial cells in detail.

Early studies of bacteria were difficult. In any environment many types of bacteria compete and cooperate, and all this activity makes it nearly impossible to figure out what each organism is doing. The first step was to separate different types of bacteria. One way of isolating bacteria was to grow them on a solid surface. Scientists first used kitchen foods, such as a potato slice cut with a sterile knife, on which to grow bacteria that attack plants. This method was not very convenient, however.

The perfect medium (environment) for growing bacteria also came from the kitchen, although its usefulness was demonstrated in the laboratory of German scientist Robert Koch. The medium was agar, a gel-forming substance that comes from seaweed. A coworker of Koch’s noted that his wife’s puddings remained solid in summer heat, whereas the gelatin on which he grew bacteria dissolved or got eaten by the bacteria. The firm puddings contained agar.

Agar dissolves in water only at temperatures close to boiling. When it cools, it forms a stable gel. Most bacteria cannot digest it. Bacteriologists could transfer a bacterial specimen onto a plate of agar using sterile wires or loops, and obtain a colony of organisms. If more than one type of bacteria formed a colony, the scientists could repeat the process, growing each type on a separate agar plate to obtain a pure culture (laboratory-grown specimen) for study. They could also add nutrients to agar to provide the bacteria with the food they need for growth. In addition, they could add substances to suppress the growth of unwanted bacteria but not the growth of those the bacteriologist wished to isolate. Growing bacteria on agar has become routine in laboratories.

Bacteriologists have become accustomed to studying individual types of bacteria in pure cultures. In nature, however, bacteria usually live in diverse communities, often with hundreds of types of organisms. These communities form sticky masses called biofilms on soil particles, ocean debris, plants and animals, and just about any solid or liquid surface. In our bodies, biofilms develop on teeth, on the soft tissues of the mouth and throat, on the membrane lining the nose and sinuses, in the gut, and on all other exposed body surfaces. In nature, organisms form microbial mats on surfaces between water and air. In sewage treatment, bacteria clump together in masses. All these communities are highly diverse, harboring many kinds of organisms. They can be compared to cities in which the different members have different functions, all important to maintaining the community.

Bacteriologists are realizing more and more the need to move from studying pure cultures containing only a single species to the study of communities in biofilms and microbial mats. The growth of molecular biology and the capacity to study bacteria in molecular detail have demonstrated that the bacterial world is far more diverse than previously thought. It seems possible that we currently have discovered only a small fraction of existing types of bacteria in the world. Perhaps as many as 95 percent of total types remain unknown.

Recent information on the true diversity of bacteria comes from a study published in 2006 that used a new DNA-identification technique to study microbes taken from the ocean. Scientists found more than 20,000 types of bacteria in a liter of sea water—over ten times the biodiversity predicted. Much of the diversity came from rare bacteria that had not been detected in previous studies of marine microbes. Samples were taken at eight sites in the Atlantic Ocean and Pacific Ocean from a wide range of depths and environments, including the North Sea and hydrothermal vents. The work will be expanded in the future to sample marine microbes from more than 1,000 ocean sites with even more types of environments. The international research is being conducted as part of the global Census of Marine Life, a ten-year project that began in 2000. The newly recognized complexity of ocean bacteria could lead to a much greater gene pool for a range of scientific work.

Scientists have already sequenced the entire genome for many bacteria. Researchers can cut pieces from bacterial DNA and replicate it in many copies. Through DNA transfer, the pieces can be inserted in bacterial cells. The cells with the new DNA may then start to make new proteins they were unable to make previously. Thus, bacteria can be genetically engineered to make a whole range of products and to develop new functions. Genetic engineering has opened up a new world of biology and a tremendous opportunity to explore bacteria and other microorganisms and to benefit humanity from the resulting knowledge.

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