Soil Microbial Ecology

Professor Jeanette M. Norton (Jenny) is Professor of Soil Microbiology in the Department of Plants, Soils and Climate, an Ecology Center Associate and an Adjunct Professor in Biology at Utah State University. Dr. Norton’s research focuses on understanding key organisms in the nitrogen and carbon cycles of terrestrial systems on many different levels -  from individual genes to ecosystem processes. Dr. Norton is on the steering committee for the Nitrification Network (nitrificationnetwork.org).

Dr. Norton has served on the editorial boards of Applied Environmental Microbiology and Soil Science Society America Journal and as panelist for NSF and USDA. She is dedicated to student research mentoring on the graduate and undergraduate levels. Dr. Norton graduated with a Bachelor of Science in Forest Biology from the State University of New College of Environmental Science and Forestry in 1980, received her PhD. in Soil Science (Microbiology) under the mentoring of Prof. Mary Firestone at University of California, Berkeley in 1991 and gained further experience as a post-doctoral researcher at the NSF Center for Microbial Ecology, Michigan State University with Professor Eldor Paul and Professor James Tiedje. Dr. Norton is a member of the American Society of Microbiology, Soil Science Society of America, International Society of Microbial Ecology and the Society for the Advancement of Chicanos and Native Americans in Science (SACNAS).Curriculum Vita

Brittany Johnson

Research Assistant

Wayne Breon

Undergraduate Research Assistant

Currently funded projects in these areas include (click on links below for proposal abstracts):

• Functional Genomics and Ecology of Nitrifying Bacteria:
  • Improving the understanding of the genomics of nitrifiers, characterizing the processes in agricultural and wildland systems, and delineation of limiting factors for nitrification in water delivery/wastewater treatment systems. (UAES)
  • Development of a Research Coordination Network to organize activities of researchers in this field and to disseminate results. (NSF)
  • Genome sequencing for Nitrosomonas sp. AL212 and Isolate IS-79, ammonia-oxidizing bacteria adapted for growth at low ammonia concentrations. (JGI)
• Functional and Molecular Diversity in Nitrogen Cycle Enzymes Under Contrasting Agricultural Management Systems (USDA):
  • Describing functional diversity in the root-zone of microbial communities responsible for selected N transformations in agroecosystems under contrasting nitrogen management.
  • Recovering and characterizing novel bacterial and fungal genes encoding key enzymatic functions in N transformations.
  • Delineation of the role of bacterial and archaeal ammonia oxidizers in soil nitrification.
• Below Ground Feedbacks in Plant Communities in Western Rangelands: 
  • Delineating positive feedbacks from cheatgrass-induced changes in nutrient cycling, and developing management strategies to speed reestablishment of perennial plant species on cheatgrass-dominated rangelands (USDA).
  • Determining plant-soil feedbacks in the shrub steppe ecosystem - collaboration with investigators to characterize microbial communities using next-generation sequencing of phylogenetic and functional genes extracted from soils (see A. Kumultiski).

Functional And Molecular Diversity In Nitrogen Cycle Enzymes Under Contrasting Agricultural Management Systems

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.

PI John Stark, USU Biology, Norton Co-PI, Funded USDA 2007-2011

Cheatgrass establishment results in stable exotic plant communities that resist re-invasion by native perennials. We hypothesize that positive feedbacks resulting from shifts in nutrient cycling and microbial activity are responsible for the long-term persistence of cheatgrass. To test this hypothesis we will revisit a set of restoration plots set up by John Stark (PI) in 1984 in Western Colorado. We will examine the soil microbial structure and nutrient cycling characteristics in these well-replicated experimental plots to determine whether during the past 26 years, cheatgrass-dominated or native perennial-dominated plant communities have 'cultured' different soil characteristics.The study will provide new information on the mechanisms by which cheatgrass establishes stable, persistent plant communities. Through these experiments we will address the CSREES priority of establishing 'mechanisms determining the abundance and distribution of weedy and invasive species on western rangelands. In addition, our results will provide information essential for developing management strategies that will speed the reestablishment of perennial plant species on cheatgrass-dominated rangelands.

Plant-Soil Feedbacks in the Shrub Steppe Ecosystem

Norton Cooperator with Andrew Kulmatiski and Karen Beard

J. Norton will be working with these investigators to characterize microbial communities using next-generation sequencing of phylogenetic and functional genes extracted from the soils from the Washington State manipulative plots. See Kulmatiski A., Beard, K.H. 2011. Long-term plant growth legacies overwhelm short-term plant growth effects on soil microbial community structure. Soil Biology and Biochemistry.

Professor of Soil Microbiology
Dept. of Plants, Soils and Climate
Utah State University, Logan, UT 84322-4820
Email: jeanette.norton@usu.edu