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Functional Genomics and Ecology of Nitrifying Bacteria

Non-Technical Summary: Human activities have dramatically altered the global nitrogen cycle by increasing the amount of reactive nitrogen in the environment; human associated inputs of industrially produced N fertilizers and N fixation by crops now exceed the natural N inputs to terrestrial systems. Nitrifying microorganisms play critical roles in the movement of this reactive nitrogen through ecosystems and in the availability of nitrogen for plant growth. In many agricultural soils when available nitrogen supply exceeds plant demand, nitrification increases leading to accumulation of nitrate that is reactive and mobile in the environment. The nitrogen use efficiency of our N fertilizers in agricultural systems remains quite low, typically only around 30% in cereal crops. Nitrification may lead to losses of nitrogen by leaching and denitrification. Nitrate leaching from agricultural systems is a significant contribution to the contamination of surface and groundwater. Nitrification therefore needs to be managed to protect the quality of surface waters and soils. Information is needed on the physiology and ecology of the bacteria and archaea responsible for cycling nitrate in ecosystems. We will improve understanding of the genomics of nitrifiers, characterize the processes in agricultural and wildland systems and examine links between nitrification and plants in soils. Improved understanding of nitrifying bacteria and archaea in soils and in wastewater systems may suggest management options for particular environments. Delineation of the limiting factors for nitrification in water delivery and wastewater treatment systems will help municipal and other government entities in preventing water pollution and planning for water reuse in the semi-arid and arid Intermountain West region.

Utah Agricultural Experiment Station Project Objectives
Objective 1. Functional genomics of nitrifying bacteria. Supply genomic DNA of selected nitrifying bacteria for draft-level and complete genome sequencing. Work with the Joint Genome Institute and the DOE to facilitate genome sequencing and analysis. Annotate and check functional designations for selected genes especially those encoding enzymatic functions. Perform comparative genome analysis on nitrifying bacteria sequenced. Write collaborative papers
Objective 2. Ecology of nitrification in agricultural systems in the Intermountain West.
Collaborate in ongoing agricultural systems experiments comparing conventional and organic fertility management for effects on nitrification. Examine the role of tannins in the regulation of nitrification rates and changes in nitrifier communities in soil environments in pasture systems.
Objective 3. Ecology of nitrification in wildland systems in the Intermountain West. Collaborate in ongoing experiments in wildland systems examining plant species diversity and function to assess nitrifier functional diversity and ecology of nitrification. This area of research will require establishment of collaborative relationships, site assessment and selection and the collection of baseline data on nitrification in a variety of ecosystems in Colorado and Utah.
Objective 4. Characterization of N cycling in wastewater treatment systems.
Explore wastewater N cycle in selected wastewater treatment systems in Utah. Assess the key microbial communities, specifically ammonia oxidizing bacteria and archaea by the application of molecular tools to waste treatment systems. Determine rate parameters for nitrification in lagoon, artificial wetland, and storage pond environments. Identify key vulnerability points of the N cycling processes needed to maintain effluent water quality.

Research Coordination Network: Nitrification, a bacterial process at the interface of the carbon and nitrogen cycles
Funded NSF 2006-2011
Investigator Institution Disciplines
Dan Arp* Oregon State University Biochemistry, Microbiology, Genomics
Bill Hickey University of Wisconsin Soil Science, Proteomics
Martin Klotz University of Louisville Physiology, Molecular Evol. & Gen., Genomics
Jenny Norton Utah State University Soil Science, Microbial Ecology
Bess Ward Princeton University Microbial Ecology, Oceanography, Geochemistry

Project Summary
Nitrification, the oxidation of ammonia to nitrate, is a bacterially mediated process that is an
essential part of the biogeochemical N cycle. By controlling available N for growth, nitrification
also influences the C cycle. Despite extensive studies of the N-cycle for over 100 years and the
heightened awareness due to concerns about its balance, the anthropogenic influence on the Ncycle
is at present greater than on any of the other biogeochemical cycles. Anthropogenic input
has changed from about 40% to nearly 200% of the natural contribution in just the last 50 years.
This relatively recently elevated input to the cycle has a myriad of effects on waters, soils, and
the atmosphere. There is a continuing and urgently growing need to understand the details of the
nitrification process in order to provide the tools to manage nitrification at local levels for a
global impact. The study of nitrification has been dramatically altered in the last few years due to
recent advances in the areas of genomics, structural biology, physiology, and ecology. As the
study of nitrification becomes ever more cross-disciplinary and collaborative, there is a need to
coordinate the activities of those studying nitrification. A Research Coordination Network
would provide the appropriate structure to organize activities of researchers in this field as well
as to disseminate results within and outside the field.

Current Genome Project
Funded Dept. of Energy, Joint Genome Institute, genomes completed 2011, analysis in progress
Genome Sequencing for Nitrosomonas sp. AL212 and Isolate IS-79; Ammonia-oxidizing Bacteria Adapted for Growth at Low Ammonia Concentrations
Abstract
As candidates for draft sequencing, we recommend two ammonia-oxidizing bacteria that mediate the first step in the process of nitrification. These bacteria are classified in the genus Nitrosomonas but have contrasting physiology to N. europaea and N. eutropha. Nitrosomonas sp.(strain AL212) and Isolate IS-79 belong to a cluster of the Nitrosomonas with higher substrate affinity (low Km), lower growth rates and increased sensitivity to high ammonia concentrations compared to N. europaea and N. eutropha. These unique physiological attributes improve their ability to grow at low concentrations of their substrate, ammonia. Similar oligotrophic ammonia-oxidizing bacteria have been found to be widely distributed in the environment although their importance was often overlooked because they were rarely isolated in the typical high nutrient media.

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