Curriculum Development > High School 9-12 > Other Supplemental Programs > Frontiers in Microbiology > Microbial Genomics   Microbiologists have known for a long time that the small number of microbes that had been cultured in the laboratory represents but a tiny fraction of the existing microbial diversity. Over the past 10 years, new types of laboratory and computer analyses have given researchers tools to more accurately estimate the numbers and types of microbes in our surroundings. GenBank (the sequence database hosted by the National Center for Biotechnology Information) now includes data from over 30,000 different bacterial species. Recent estimates suggest that the sea may contain more than 2 million bacterial species and a ton of soil may contain 4 million species (NCBI, 2004). Similar species diversity is likely among the Archaea. Traditionally, scientists have studied microbes by obtaining samples from the environment and taking them back to the lab, where, by trial and error, they attempt to identify growth conditions that allow the microbes to be cultured indefinitely. Not only is this procedure time-consuming and costly, but it also excludes many species of microbes for which suitable growth conditions cannot be found. New techniques associated with genomics are giving scientists approaches to studying microbes in their natural environments. Often, scientists investigating microbial diversity focus on the genes encoding the 16S ribosomal RNA. This gene was selected because it has been conserved across vast taxonomic distances, yet still shows some sequence variation among closely related species. After data are obtained from environmental samples, the DNA sequences are compared to each other and to all known 16S rRNA genes. Such studies have found new uncultured species even in well-studied environments such as the human mouth. One scientist, J. Craig Venter, began an ambitious two year project in August 2003 that is attempted to assess the microbial diversity of the world’s oceans (Shreeve, 2004). Aboard his yacht, the Sorcerer II, Venter sailed a route similar to that taken by Charles Darwin aboard the HMS Beagle in the 19th century. After every 200 miles, the crew pumped 53 gallons of seawater taken from a depth of about five feet on board the yacht. The seawater was forced through a series of filters to collect the microbes. The filters were then sent back to Venter’s lab in Rockville, Maryland for analysis. Once in the lab, the filters were treated to remove everything but microbe DNA. This DNA, which represented all the different microbe species that were collected on the filter was then forced through a pinhole under pressure to generate a series of millions of shorter DNA fragments. The fragments were amplified using PCR and subjected to DNA sequencing reactions. The resulting DNA sequences were analyzed by computer. The computer algorithms searched for overlapping sequences to create longer ones. Using bioinformatics tools, the number of species was estimated by comparing the sample DNA to that from known microbial species. Venter chose the Sargasso Sea near Bermuda as the site for a pilot test of his approach. This area of the ocean was chosen because it is low in nutrients and thought to be somewhat of an oceanic desert. To his surprise, everywhere he went the samples were teeming with microbial life. In a report of his Sargasso Sea results, Venter (2004) reported that his group sequenced more than 1 billion bases. The DNA sequences represented approximately 1800 species, including 148 unknown groups. About 1.2 million new genes were found. A follow-up study conducted in Long Island Sound identified DNA sequences from nearly 1000 different species. Only 1 percent of the Long Island species overlapped with those from the Sargasso Sea (Pennisi, 2004). Although Venter’s study concentrates on bacteria, his approach should also work for investigating the prevalence of plasmids, phages, viruses, and eukaryotic microbes. An even more recent analysis of soil microbes has suggested that the inferred microbial diversity in these environments has been greatly underestimated. It has long been known that if the DNA from a single organism is heated, the double helix melts and the two strands separate. If the sample is allowed to slowly cool, then the DNA strands will reassociate or reanneal. Larger and more complex genomes require longer times for this reannealing to occur than do smaller genomes. Such an approach has been used for decades to estimate the size and complexity of genomes from diverse organisms. About 15 years ago, Torsvik and coworkers recognized that pooled genomic DNA from a microbial community could reanneal like that from a single large genome. Indeed, when they isolated DNA from a soil microbe community, it reannealed slowly, much like DNA from an organism with a genome about 7000 times that of a typical bacterium (Torsvik, Goksoyr, & Daae, 1990). This suggested that the sample may have contained the genomes of 7000 different taxa. In 2005, Gans and coworkers realized that the pattern of DNA reassociation reflects the underlying diversity of the microbial community. They applied new mathematical analyses to existing data from bacterial communities and came to a startling conclusion. Each 10 grams of healthy soil contains 10 million different bacterial species. Most of this diversity is found among rare bacteria that are present in small numbers (Gans, Wolinsky, & Dunbar, 2005). The overwhelming number of species found within microbial communities makes it impossible to study them using bacteria cultured in the laboratory. It is estimated that 99 percent of the bacterial species found in the soil cannot be cultured in the laboratory (Gewin, 2006). Metagenomics is the name given to the study of gene function and interaction regardless of species within large microbial communities. Researchers today rely on methods of genomics to study the diversity and interactions that take place within these communities. The use of whole- genome shotgun sequencing gives an indication of the diversity that resides within a microbial community. It also allows scientists to study the community in its entirety, almost as though it were a single organism. Previous Table of Contents Next

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