Nitrification, the two-step oxidation of NH4+ through NO2- to NO3- is important as an oxygen sink, a source of substrates for denitrification (which leads to loss of fixed nitrogen from the system), in the production of N2O (a greenhouse gas implicated in ozone depletion), and in the supply of NO3- which fuels surface primary productivity. Nitrification is exclusively a bacterial process and is carried out by two genetically similar guilds of chemoautotrophic bacteria (ammonia and nitrite oxidizers). This dissertation describes research on the ammonia oxidizers which, although essential in the biogeochemical cyles of aquatic ecosystems, account for a minor proportion of the total bacterial population.

Questions regarding the role of nitrifying bacteria in natural aquatic environments remain unanswered to date partly because of the lack of simple, rapid, and sensitive detection, identification, and quantification procedures. The goal of this dissertation was to develop techniques that would allow the detection, enumeration, and evaluation of species diversity of ammonia oxidizers in natural aquatic systems, and in turn, to begin investigating the ecology and environmental importance of natural populations of nitrifying bacteria.

Two sets of sensitive and specific PCR primers for the detection of both subclasses of ammonia oxidizers were developed and tested on DNA samples collected from two disparate aquatic environments, an Antarctic lake and the Southern California Bight. Ammonia oxidizers were detected at both locations. These primers were then used to examine the relative abundance and depth distribution of ammonia oxidizers in six perennially ice-covered lakes in the McMurdo Dry Valleys, Antarctica. The observed distribution of nitrifiers in all lakes could be interpreted in terms of patterns predicted from environmental factors known to control nitrifying activity.

To estimate the abundance of nitrifiers in natural samples, three quantitative techniques were compared. Although the overall distribution patterns observed were similar, the subset of the total nitrifying community detected varied with each technique, since each of the techniques relies on a different macromolecular component of a bacterial cell, which responds differently to stages in the cell cycle and to environmental factors. Finally, two PCR-based techniques, RFLP analysis and direct sequencing, were used to examine the genetic diversity of cultured marine beta ammonia-oxidizers and nitrifier 16S rRNA genes retrieved from natural seawater. The marine isolates in culture were nearly identical to the type strain NITOSOMONAS MARINA, while the genes retrieved from seawater did not resemble any of the cultured strains. The results suggest that although Nitrosomonads may be readily isolated from marine systems, they may not be the most dominant nitrifying species present in a community and therefore, not the most ecologically important.