Abstract:
Much effort is currently directed at understanding the extent of biodiversity in the natural environment. Until recently microbial diversity was poorly understood, but it now appears that many bacteria have some unique characteristics which may simplify the task. Bacterial diversity in three aqueous environments, a pond, a stream and the human mouth, was examined for breadth and similarity. To identify members of the domain Bacteria which inhabit such environments, we used PCR to construct a library of 16S rRNA genes (16S rDNAs) cloned from DNA extracted from the waters of each environment. A segment of the 16S rRNA gene was examined using DNA extraction, amplification and sequencing protocols. 7 total varieties of bacteria were detected, showing marked similarities in all three environments, however both the stream and mouth were found to be low in overall diversity. Phylogenetic diversity among the various representative microbes found was low perhaps due to limited cloning success. The results point to the utility of molecular analysis for positive identification of bacterial “species” and cataloging of elements key to microbial ecology.

Introduction:
Bacteria are the driving force of global biogeochemical cycles and make up the base of the food web in many environments 1. Bacteria are ubiquitous and are the dominant life-form in terms of pure numbers of every ecological niche. The average human bacterial load is approximately 2 to 9 pounds.2 But one claim, formerly regarded as wildly improbable but now quite plausible, if still unproven, grant bacteria as making up the main biomass of our planet.3 To understand the Earth system as a whole, it is therefore necessary to improve our knowledge of bacterial biodiversity, the interactions among microbes, and their responses to human activities.

The taxonomy of many, perhaps most aquatic bacteria is undescribed.4 Classical taxonomy, using morphology and biochemical methods, can be inappropriate or impracticable given the organisms size. Even the species concept is of questionable validity for many of these organisms. However, molecular techniques and the application of functional gene probes now offer the opportunity for rapid gains in both evolutionary, ecological and biodiversity knowledge.

This project focuses on the information which resides within discrete regions of bacterial genomes (the basis for molecular taxonomy). It thereby provides the means to investigate bacterial biodiversity of aquatic ecosystems. Bacterial biodiversity in aqueous habitats is relevant to industrial applications because of the novel biochemistry evolved. There are also strong applied interests in horizontal gene exchange and chemical signaling systems at the molecular level, and the wide range of symbioses in which bacteria are components.

1http://www.ucmp.berkeley.edu/bacteria/bacteria.html
2 http://answers.google.com/answers/main?cmd=threadview&id=208733
3 http://www.stephenjaygould.org/library/gould_bacteria.html
4 Wise, Mark G., McArthur, J. Vaun and Shimkets, Lawrence. Bacterial
Diversity of a Carolina Bay as Determined by 16S rRNA Gene Analysis: Confirmation of Novel Taxa. Applied and Environmental Microbiology. April 1997, p. 1505-1514.