Source: UTAH STATE UNIVERSITY submitted to
MICROBIAL/PLANT NITROGEN INTERACTIONS IN ANIMAL WASTE MANAGEMENT
Sponsoring Institution
National Institute of Food and Agriculture
Project Status
TERMINATED
Funding Source
Reporting Frequency
Annual
Accession No.
0161906
Grant No.
(N/A)
Project No.
UTA00323
Proposal No.
(N/A)
Multistate No.
(N/A)
Program Code
(N/A)
Project Start Date
Jul 1, 1999
Project End Date
Jun 30, 2004
Grant Year
(N/A)
Project Director
Norton, J. M.
Recipient Organization
UTAH STATE UNIVERSITY
(N/A)
LOGAN,UT 84322
Performing Department
PLANTS, SOILS & BIOMETEOROLOGY
Non Technical Summary
Application of animal wastes in excess of plant needs can contribute to water pollution. Nitrogen transformations are of particular concern due to the potential for excess N to be transported off site. Appropriate use of animal wastes requires predictive ability for the release of nitrogen from organic forms and subsequent conversions. An improved understanding of the microbial processes involved will allow for appropriate management of a variety of wastes.
Animal Health Component
85%
Research Effort Categories
Basic
15%
Applied
85%
Developmental
(N/A)
Classification

Knowledge Area (KA)Subject of Investigation (SOI)Field of Science (FOS)Percent
1020110104025%
1022499104025%
1330110104025%
1332499104025%
Goals / Objectives
1) Molecular markers for ammonia oxidizing bacteria will be refined for application to soil systems receiving animal wastes. 2) Assess the correlation between changes in nitrification rates and population size and determine the kinetic parameters for ammonia oxidation in these same soils. 3) Determine in situ N cycle rates for dairy waste nitrogen, focusing on mineralization and nitrification. 4) Assess the suitability of nitrapyrin for nitrification inhibition in soils receiving dairy wastes. 5) Examine the feasibility of establishing nitrifying bioreactors based on a zeolite mineral.
Project Methods
The Norton laboratory will maintain and extend a culture collection of AOB. These cultures will be used to complete additional molecular studies on the amo genes and their regulation and evolution in collaboration with M. G. Klotz (Univ. Louisville). Standard process methods for following nitrification in soils will be combined with the molecular techniques for the examination of the community composition of AOB. Replicated field experiments at the Greenville Farm (UAES) will be used to examine N cycling rates (mineralization, nitrification, N immobilization) and plant N availability in response to different rates and sources of dairy waste. Manipulative laboratory experiments will examine the link between ammonia oxidzer communities and the kinetics of ammonia oxidation. Laboratory and field experiments (subplots) will examine the interaction of nitrapyrin with the AOB.

Progress 07/01/99 to 06/30/04

Outputs
We examined nutrient and C dynamics in relationship to microbial transformations in soils that have received repeated applications of dairy wastes from 1997-2003. Data analysis and multi-year comparisons are being completed. Silage corn yield was significantly increased by all of the N treatments with the highest yield being associated with dairy waste compost treatment. Compost applications applied to maximize silage yields have resulted in accumulations of C, N, P and K in surface and subsurface soils. In the high level compost treated soil, organic C and N pools have increased by 96% and 60% respectively over the control soil values. C storage in soil organic matter can be increased significantly by the application of high levels of stabilized dairy waste compost. Dairy waste lagoon effluent supplied a large proportion of its total N as NO3- several months after it was amended to an agricultural soil, whereas compost provided only a small fraction of its total N as mineral N. Differences in N availability in the wastes predicted by laboratory incubations were confirmed by silage corn yields and plant N contents. Compost treated soils maintained N supply to the plants through continuous mineralization as shown by mineralization rate estimates, inorganic N pools and plant N analysis. While effluent mineralized a greater proportion of the N applied (up to 90%) the compost treated soils consistently supported higher corn yields. This indicates that synchronization of N availability is as important as the amount of N mineralized. Five-year averages for gross mineralization, nitrification and ammonium consumption were significantly increased with compost treatment. Microbial nitrate consumption was not significantly different among the treatments. Increased nitrification potentials for soils receiving dairy waste indicate that these soils are maintaining higher nitrifier populations. Nitrification potentials increased in the ammonium sulfate fertilized soils but to a lesser degree than with the waste treatments. Ammonia oxidizing bacteria (AOB) responded differentially to dairy waste and ammonium fertilizer treatments after six years of application. The community structure of the AOB as indicated by sequencing of amplified genes encoding ammonia monooxygenase (amo) was most similar for soils receiving the same N-source. PCR amplification of the intergenic region between amoC and amoA was shown to be a quick and effective method of profiling changes in community structure. Ammonium sulfate and effluent treated plots had similar AOB community structure profiles that were distinct from the compost treated plots. Congruent with the change in AOB community profiles, the compost treatments resulted in significantly higher nitrification rates, indicating that changes in AOB community structure and function were related. The high and low levels of compost and the high level of the effluent treatment had increased urease activity. Elevated urease activity may not be desirable in agricultural soils because of the potential for ammonia volatilization and rapid nitrification.

Impacts
We improved understanding of N release in soils treated with dairy-waste compost and effluent. As waste N content varied considerably, producers are being advised to base waste application rates on actual N analysis. Estimates of 10% mineralizable N in the first year and 5% in the following year were reasonable predictors of available N in compost based on yield comparisons. Peak plant N demand can easily be met by compost, but continued high N mineralization after harvest makes nitrate leaching post-growing season and the next spring likely. We suggest that careful management of dairy compost needs to account for soil accumulation of available P & K, mineralizable N and the timing of N release from these multiple year applications. We are collaborating with outreach personnel to incorporate our results into new recommendations for treated wastes. Appropriate dairy waste application will increase economic returns for growers while minimizing potential N losses to the environment.

Publications

  • Shi, W., B.E. Miller, J. M. Stark and J. M. Norton. 2004. Microbial nitrogen transformations in response to treated dairy waste in an agricultural soil. Soil Sci. Soc. Am. J. 68:1867-1874.
  • Koper T.E., A.L. El-Sheikh, J.M. Norton, and M.G. Klotz. 2004. Urease-encoding genes in autotrophic ammonia-oxidizing bacteria. Appl. Environ. Microbiol.70:2342-2348.
  • Habteselassie M. Y. and J. M. Norton 2004. Shifts in Activity and Structure of Ammonia Oxidizer Communities following Dairy Waste Application. ASA-CSSA-SSSA Abstracts Annual meetings. Seattle, WA.


Progress 01/01/03 to 12/31/03

Outputs
We examined the trajectory of nutrient and C dynamics in relationship to microbial transformations in soils that have received repeated applications of dairy wastes. Compost applications applied to maximize silage yields have resulted in accumulations of N, P and K in surface and subsurface soils. Compost treated soils maintained N supply to the plants through continuous mineralization as shown by mineralization rate estimates, inorganic N pools and plant N analysis. The nitrification potential increases in soils receiving dairy waste indicate that these soils are also maintaining higher nitrifier populations. Nitrification potentials also increased in the ammonium sulfate fertilized soils but to a lesser degree than with the dairy waste treatments. Silage corn yield was significantly increased by all of the N treatments with the highest yield being associated with compost treatment. Five-year averages for gross mineralization, nitrification and ammonium consumption were significantly increased with dairy waste compost treatment. Microbial nitrate consumption was not significantly different among the treatments. The high and low levels of dairy waste compost and the high level of dairy waste liquid treatments have significantly increased urease activity. Elevated urease activity may not be desirable in agricultural soils because of associated ammonia volatilization and the potential for rapid nitrification. The results demonstrate the change in N processes associated with dairy waste application and importance of management of the timing of N release versus plant demand to prevent undesirable environmental impacts. Understanding microbial dynamics focused on nitrification and urea hydrolysis by targeting the microbial genes encoding the key enzymatic processes in these transformations. The complete genome sequence of Nitrosomonas europaea was finalized and published. The genome sequence for this chemolithoautotrophic bacterium had the full-complement of genes enabling the creation of biomass from carbon dioxide and inorganic nutrients but was lacking almost all genes necessary for assimilation of organic compounds. The DOE has accepted a collaborative proposal to accomplish draft genome sequences for several ammonia oxidizing and nitrite oxidizing bacteria for comparative genome analysis. The interactions of invasive annual grasses and nitrogen were examined in collaborative projects. Cheatgrass was found to be associated with increases in nitrate availability compared to native vegetation and was relatively more responsive to N deprivation in comparison to native perennial grasses.

Impacts
In recent decades, increasing US land area has been classified as exceeding recommended nutrient loading due to animal waste application. Yet, our knowledge of the recovery phase of soils impacted by wastes is limited. The project has contributed to the understanding of N release in soils treated with dairy-waste compost and liquid dairy-waste. Our understanding of the microbial transformations controlling nitrate production has been improved. Our evidence of nitrate leaching from soils receiving composted dairy manure and yields will be used to adjust recommended compost application rates. Management of N has potential as a tool for promoting rehabilitation of cheatgrass infested rangelands. The completed genome sequence of Nitrosomonas europaea is a complete genetic map of the potential biochemistry of this organism.

Publications

  • Monaco T.M., C.T. Mackowan, D. A. Johnson, T. A. Jones, J.M. Norton, K.J. Connors, J.B. Norton, M. B. Redinbaugh. 2003. Nitrogen effects on seed germination and seedling growth. J. Range Manage. 56: 646-653.
  • Monaco T.M., D. A. Johnson, J.M. Norton, T. A. Jones, K.J. Connors, J.B. Norton, M. B. Redinbaugh. 2003. Contrasting responses of Intermountain West grasses to soil nitrogen. J. Range Manage. 56: 282-290.
  • Chain, P., J. Lamerdin, F. Larimer, W. Regala, V. Lao, M. Land, L. Hauser, A. Hooper, M. Klotz, J. Norton, L. Sayavedra-Soto, D. Arciero, N. Hommes, M. Whittaker, D. Arp. 2003. Complete genome sequence of the ammonia oxidizing bacterium and obligate chemolithoautotroph Nitrosomonas europaea. J. of Bacteriol. 185: 2759-2773.


Progress 01/01/02 to 12/31/02

Outputs
Ultimately, the environmental consequences of animal waste disposal will depend upon our ability to manage the changes in soil biology and chemistry that are the result of repeated waste applications. This project has examined the trajectory of nutrient and C dynamics in relationship to microbial transformations in soils that have received repeated applications of dairy wastes for five years. We continued to monitor soil levels for ammonium, nitrate, organic N and extractable P and K. Compost applications applied to maximize yields have resulted in accumulations of N, P and K in surface and subsurface soils. In preseason sampling of soils after five years of repeated compost treatment, surface soils had 10 mg /kg nitrate-N, 150 mg/kg P and 1500 mg/kg K compared to 2 mg/kg N, 10 mg/kg P and 200 mg/kg K for the control soils. Compost treated soils maintained N supply to the plants through continuous mineralization as shown by mineralization rate estimates, inorganic N pools and plant N analysis. Understanding microbial dynamics focused on nitrification and urea hydrolysis by targeting the microbial genes encoding the key enzymatic processes in these transformations. The highest potentials for nitrification (12 mg/ kg*day) and urea hydrolysis (20 mg /kg*h) were found in soils receiving compost applications. The interactions of grass roots on soil biology and chemistry was examined in two collaborative projects. Cheatgrass was found to be associated with increases in nitrate availability compared to native vegetation. Annotation of the sequence of the complete genome of Nitrosomonas euraopaea was finalized.

Impacts
In recent decades, increasing US land area has been classified as exceeding recommended nutrient loading due to animal waste application. Yet, our knowledge of the recovery phase of soils impacted by wastes is limited. The project has contributed to the understanding of N release in soils treated with dairy-waste compost and liquid dairy-waste. Our understanding of the microbial transformations controlling nitrate production has been improved. Our evidence of nitrate leaching from soils receiving composted dairy manure and yields will be used to adjust recommended compost application rates. The completed genome sequence of Nitrosomonas europaea is a complete genetic map of the potential biochemistry of this organism.

Publications

  • Habteselassie M.Y., T.E. Koper, W. Shi and J.M. Norton. 2002. Trajectory of soil nitrogen transformations after five years of applications of organic and inorganic N-sources. In 2002 Agronomy Abstracts. ASA, Madison WI.
  • Henry A., J.Chard, M. Petersen, J. Norton and B. Bugbee. 2002. Water and nutrient stress increase root exudation. In 2002 Agronomy Abstracts. ASA, Madison WI.
  • Monaco, T.A., J.M. Norton, T.A. Jones, D.A. Johnson, K.J. Connors, and J.B. Norton. 200X. Contrasting responses of invasive annual and native perennial grasses to soil nitrogen form and availability: Seedling establishment and growth. Accepted for publication in J. Range Mgmt.
  • Norton, J.B. T.A. Monaco J.M. Norton D.A. Johnson, and T.A. Jones. 2002. Cheatgrass invasion alters soil morphology and organic matter dynamics in shrub-steppe grasslands. In 2002 Agronomy Abstracts. ASA, Madison WI.


Progress 01/01/01 to 12/31/01

Outputs
The control and utilization of the nitrogen (N) contained in animal wastes is essential for the sustainability of western agroecosystems. To effectively manage animal waste N in treatment systems or in soils, we need to understand the microbial transformations controlling nitrate production. We continued both laboratory and field experiments to investigate the N transformations in dairy waste amended soils. The genes for the ammonia monooxygenase enzyme were used as functional markers for the ammonia oxidizing bacteria (AOB). Using these molecular tools, we observed shifts in the types of AOB in soils treated with different wastes that coincided with changes in process rates. The N-15 field experiment was repeated in August 2001. We are continuing to analyze the data on N process rates from isotope dilution experiments performed in 1998-2001. In 1999 through 2001, the highest nitrification potentials were found in soils treated with the high rate compost. Post-harvest in 1998- 2001, we sampled soils down to 1.8 m depths to check for nitrate leaching below the root zone. Movement of nitrate below the rooting depth was observed for the compost treatments. Highest values for nitrate accumulation (up to 50 mg/kg soil) were observed for the high rate compost (equivalent to 200 kg available N/ha application rate) at the 1.2 to 1.5 m depth. The movement of nitrate downward indicates that nitrate in excess of plant demand is being produced in surface soils that have been repeatedly amended with dairy-waste compost applied at rates sufficient to maximize yields. Production of nitrate from organic nitrogen continued during the post harvest and preplant season resulting in considerable nitrate accumulation in surface soils. No leaching was observed for the other treatments. In a DOE funded project, the genome sequence of Nitrosomonas europaea was completed in November 2001. We are collaborating with the research groups of Prof. Daniel Arp (Oregon State University), Alan Hooper (University of Minnesota) and Martin Klotz (Univ. of Louisville) to interpret and annotate the complete genome sequence of this model nitrifier. In a collaborative project with Dr. Bruce Bugbee and Dawn Muhlestein (USU), we used microbial and isotopic techniques to assess nitrification rates in hydroponic wheat systems with high ammonium/nitrate ratios. Nitrification was detectable in all systems however; the rate was decreased significantly in planted systems while in unplanted bottles nitrification was considerable.

Impacts
The project has contributed to the understanding of N release from dairy-waste compost and liquid dairy-waste. Our understanding of the microbial transformations controlling nitrate production has been improved. Our evidence of nitrate leaching from soils receiving composted dairy manure and yields will be used to adjust recommended compost application rates. The completed genome sequence of Nitrosomonas europaea is a complete genetic map of the potential biochemistry of this organism.

Publications

  • Norton J.M., J.J Alzerreca, Y.Suwa and M. G. Klotz. 200X. Diversity of ammonia monooxygenase operon in autotrophic ammonia-oxidizing bacteria. Archives of Microbiology.
  • Norton J.M., T.E. Koper, W.Shi. 2001. Ammonia Oxidizer Communities and Nitrification Kinetics in Soils Treated with Dairy Wastes. Abstract for International Symposium on Microbial Ecology.
  • Muhlestein, D, J.M.Norton, and B. Bugbee. 2001. Nitrification rates in liquid hydroponics with ammonium nitrogen. Abstract for ASHS.
  • Norton, J.M., Klotz, M.G., Alzerreca, J. and Kelly, D. 2000. Nitrosomonas cryotolerans, amo operon. GenBank Accession AF314753.
  • Norton,J.M. and Klotz,M.G. 2001. Nitrosospira multiformis strain 24C 16S ribosomal RNA gene, partial. GenBank Accession AF408634


Progress 01/01/00 to 12/31/00

Outputs
The control and utilization of the nitrogen (N) contained in animal wastes is essential for the sustainability of western agroecosystems. To effectively manage animal waste N in treatment systems or in soils, we need to understand the microbial transformations controlling nitrate production. We have used both laboratory and field experiments to investigate the N transformations in dairy waste amended soils. We examined effects of waste management techniques such as composting, anaerobic lagoon digestion and liquid separation treatments on the N released from dairy manure to the soil. The project focused on nitrification because nitrate (the product of nitrification) is extremely mobile in the environment. We have used the genes for the ammonia monooxygenase enzyme (AMO) as functional markers for the AOB. Using these molecular tools, we assessed the community composition of soil AOB. We have observed shifts in the types of AOB in soils treated with different wastes that coincide with changes in process rates. We are analyzing the data on N process rates from isotope dilution experiments performed in 1998 and 1999. The N-15 field experiment was repeated in August 2000. Soils treated with dairy waste compost (48 tons/acre) have high N mineralization rates (1.7 mg N/kg soil/day), nitrification rates (2.9 mg N/kg soil/day), and nitrification potentials (8.1 mg N/kg soil/day). The ratio of potential to actual rate of 0.39 revealed that the nitrifiers were supplied with sufficient ammonium substrate to grow and maintain a higher population in the compost treated plots. In 1999 and 2000, the highest nitrification potentials were found in the high rate compost treatment, while the highest yield occurred in the low rate compost treatment. The soils treated with high rates of compost also had elevated EC and inorganic P in pre-planting. Possible effects of excessive salt from high rates compost application and the high residual mineralization capacity after three years of application are being assessed. Post-harvest in 1999 and 2000, we sampled soils down to 1.8 m depths to check for nitrate leaching below the root zone. Movement of nitrate was observed for the compost treatment. Highest values for nitrate accumulation (up to 50 mg/kg soil) were observed for the high rate compost at the 1.2 to 1.5 m depth. The movement of nitrate downward indicates that nitrate in excess of plant demand is being produced in surface soils that have been repeatedly amended with dairy-waste compost applied at rates sufficient to maximize yields. In a DOE funded project, we are collaborating with the research groups of Prof. Daniel Arp at Oregon State University and Alan Hooper at University of Minnesota to interpret and annotate the Nitrosomonas europaea complete genome sequence. In a collaborative project, we investigated the extent of nitrification in hydroponic solutions with high ammonium/nitrate ratios using microbial and isotopic techniques. The necessity of inoculation of nitrifying organisms to hydroponic systems was assessed.

Impacts
The project has contributed to the understanding of N release from dairy-waste compost and liquid dairy-waste. Interaction with soil extension specialists will help to disseminate quantitative information to effectively manage animal waste N and P in treatment systems or in soils. Our understanding of the microbial transformations controlling nitrate production has been improved.

Publications

  • Shi, W. and J.M. Norton. 2000. Microbial control of nitrate concentrations in an agricultural soil treated with dairy waste compost or ammonium fertilizer. Soil Biol. Biochem.32:1453-1457
  • Shi, W. and J.M. Norton. 2000. Effect of long-term, biennial, fall-applied ammonia and nitrapyrin on soil nitrification. Soil Sci. Soc. Am. J. 64:228-234.
  • Lamerdin, J. , F. Larimer, D. Arp, A. Hooper, J. Norton, M. Klotz, L. Sayavedra-Soto3, D. Arciero, N. Hommes, and M. Whittaker. 2000. The Genome of Nitrosomonas: Specialization for Growth Only on Ammonia and CO2. American Society of Microbiology Abstracts.


Progress 01/01/99 to 12/31/99

Outputs
The management of animal wastes is a key issue for sustainability of western agro-ecosystems. One area of particular concern is the control and utilization of the nitrogen (N) contained in wastes. To effectively manage animal waste N in treatment systems or in soils, we need to understand the microbial transformations controlling nitrate production. We have used both laboratory and field experiments to investigate the N transformations, particularly mineralization and nitrification, in dairy waste amended soils. We have examined effects of waste management techniques such as composting, anaerobic lagoon digestion and liquid separation treatments on the N released from dairy manure to the soil. The project focused on nitrification because nitrate (the product of nitrification) plays a central role in the soil N cycle and is extremely mobile in the environment. Ammonia oxidation, the first step in the nitrification process, is mediated primarily by the ammonia oxidizing bacteria and is generally considered rate limiting. The enzyme ammonia monooxygenase (AMO) catalyses the first step in nitrification. Because all ammonia oxidizing bacteria (AOB) must contain AMO, we have used the genes that encode this enzyme as functional markers for the AOB. Molecular approaches are especially important for these bacteria as culture based approaches are difficult and may not be appropriate for these slow growing chemolithotrophs. Our research strategy has been to make our database accessible to the public (as GenBank entries) thereby fostering collaboration with other investigators. Analysis of the sequences from our culture collection of AOB allowed us to identify conserved and variable regions of the amo genes, which we are using to assess the community composition of soil AOB. We are analyzing the data on N process rates from isotope dilution experiments performed in 1998 and 1999. We are currently characterizing the ammonia oxidizer community using molecular techniques. We have observed shifts in the types of AOB in soils treated with different wastes that coincide with changes in process rates. Soils treated with dairy waste compost (48 tons/acre) have high N mineralization rates (1.7 mg N/kg soil/day), nitrification rates (2.9 mg N/kg soil/day), and nitrification potentials (8.1 mg N/kg soil/day). In a dryland wheat system that received repeated biennial applications of the nitrification inhibitor, nitrapyrin, for 8 years, we observed residual impacts on nitrification kinetics that lasted at least two years.

Impacts
The project has contributed to the understanding of N release from dairy-waste compost and liquid dairy-waste. Interaction with soil extension specialists will help to disseminate quantitative information to effectively manage animal waste N in treatment systems or in soils. Our understanding of the microbial transformations controlling nitrate production has been improved.

Publications

  • Shi W. and J.M. Norton. 2000. Effect of long-term, biennial, fall-applied ammonia and nitrapyrin on soil nitrification. Soil Sci. Soc. Am. J.
  • Shi W., J.M. Norton, B.E. Miller and M.G. Pace. 1999. Aeration and moisture effects during windrow composting on the N fertilizer value of composts. Applied Soil Ecology.11: 17-28.
  • Alzerreca, J.J., J.M. Norton and M.G. Klotz. 1999. The amo operon in marine, ammonia-oxidizing g-proteobacteria. FEMS Microbiol. Lett.180: 21-29.
  • Alzerreca, J.J. 1999. Molecular Characterization of soil ammonia-oxidizing bacteria based on the genes encoding ammonia monooxygenase. M.S. Thesis. Utah State Univ. Logan. 151p.
  • Norton, J.M. 1999. Soil Bacteria: a Dynamic Pool of Soil Organic Matter and Catalysts of Key Belowground Processes. p. 59-67 In: Meurisse, R.T., Ypsilantis, W.G., and Seybold, C. A. eds. Proceedings: Pacific Northwest Forest and Rangeland Soil Organism Symposium. Gen. Tech. Rep. PNW-GTR-461. U.S. Department of Agriculture, Forest Service, Pacific Northwest Research Station.
  • Norton, J.M. 1999. Nitrogen Mineralization and Immobilization Turnover. Pages C148-C160 in Handbook of Soil Science, M. Sumner (Editor), CRC Press, Inc., Boca Raton, FL.
  • Norton, J.M. 1999. Nitrification. Pages C160-C181in Handbook of Soil Science, M. Sumner (Editor), CRC Press, Inc., Boca Raton, FL.
  • Alzerreca, J.J., J.M. Norton, and M.G. Klotz. 1999. Nitrosococcus sp. C-113 strain C-113 ammonia monooxygenase subunit A (amoA) and ammonia monooxygenase subunit B (amoB) genes, complete cds.GenBank Accession AF153344.
  • Alzerreca,J.J., J.M. Norton, and M.G Klotz. 1999. Nitrosococcus sp. C-113 strain C-113 16S ribosomal RNA gene, partial sequence.GenBank Accession AF15334.
  • Shi W.,and J.M. Norton. 1999. Microbial control of nitrate concentrations in an agricultural soil treated with dairy-waste compost or ammonium fertilizer. Agronomy Abstracts, ASA, Madison WI.
  • Muhlestein, D.J., T.J Hooten, J.M. Norton, R. Koenig, P.Grossl and B. Bugbee. 1999. The effects of highammonium/nitrate ratios on yield and nitrification in hydroponic wheat. Agronomy Abstracts, ASA, Madison WI.


Progress 01/01/98 to 12/31/98

Outputs
The management of animal wastes is a key issue for sustainability of western agro-ecosystems. One area of particular concern is the control and utilization of the nitrogen (N) contained in wastes. To effectively manage animal waste N in treatment systems or in soils, we need to understand the microbial transformations controlling nitrate production. We have used both laboratory and field experiments to investigate the N transformations, particularly mineralization and nitrification, in dairy waste amended soils. We have examined effects of waste management techniques such as composting, anaerobic lagoon digestion and liquid separation treatments on the N released from dairy manure to the soil. Composted dairy manure has a lower mineralization rate than fresh manure or liquid wastes, with only 6% of the organic nitrogen in the potentially mineralizable (rapidily available) fraction. The information on application rates of wastes and N fertility is useful to agricultural producers. The project focuses on nitrification because nitrate (the product of nitrification) plays a central role in the soil N cycle and is extremely mobile in the environment. Ammonia oxidation, the first step in the nitrification process, is mediated primarily by the ammonia oxidizing bacteria and is generally considered rate limiting. The enzyme ammonia monooxygenase (AMO) catalyses the first step in nitrification. Because all ammonia oxidizing bacteria (AOB) must contain AMO, we have used the genes which encode this enzyme as functional markers for the AOB. Molecular approaches are especially important for these bacteria as culture based approaches are difficult and may not be appropriate for these slow growing chemolithotrophs. Our research strategy has been to make our database accessible to the public (19 GenBank entries related to amo genes) thereby fostering collaboration with other investigators. Analysis of the sequences from our culture collection of AOB allowed us to identify conserved and variable regions of the amo genes which we can use to assess the community composition of soil AOB. We are currently measuring N process rates using isotope dilution while characterizing the ammonia oxidizer community using molecular techniques. We have observed strong shifts in the types of AOB in soils treated with different wastes which coincide with changes in process rates. Soils treated with dairy waste compost (48 tons/acre) have high N mineralization rates (1.7 mg N/kg soil/day), nitrification rates (2.9 mg N/kg soil/day), and nitrification potentials (8.1 mg N/kg soil/day). We are collaborating with the research group of Prof. Daniel Arp at Oregon State University on projects related to the regulation of amo transcription and expression. We have now developed the tools needed to investigate the link between changes in the ammonia oxidizer community and nitrification in the soil environment. Collaborative projects on the availability of ammonium bound to clinoptilolite to AOB are ongoing. In dryland wheat systems, the longterm repeated use of the nitrification inhibitor, nitrapyrin, had a residual effect on the AOB which lasted at least two years.

Impacts
(N/A)

Publications

  • Shi, W. Management of Microbial Nitrate Production in Agricultural Soils. PhD Dissertation. Logan (UT). Utah State University; 1998. 172p.
  • Shi W., J.M. Norton, B.E. Miller and M.G. Pace. 1999. Aeration and moisture effects during windrow composting on the N fertilizer value of composts. Applied Soil Ecology.11:17-28
  • Sayavedra-Soto, L. A., N. G. Hommes, J.J. Alzerreca, D. J. Arp, J. M. Norton, and M. G. Klotz. 1998. Transcription of the amoC, amoA and amoB genes in Nitrosomonas europaea and Nitrosospira sp. NpAV. FEMS Microbiol. Lett. 167: 81-88.
  • Perrin T.S., J.L. Boettinger, D.T. Drost, and J.M. Norton. 1998. Decreasing nitrogen leaching from sandy soil with ammonium-loaded clinoptilolite. J. Environ. Qual. 27:656-663
  • Perrin T.S., D.T. Drost, J.L. Boettinger and J.M. Norton. 1998. Ammonium-loaded clinoptilolite: a slow-release fertilizer for sweet corn. J. Plant. Nutrition 21: 515-530
  • Norton J.M. 1999. Soil Bacteria: a Dynamic Pool of Soil Organic Matter and Catalysts of Key Belowground Processes. Gen. Tech. Rep. PNW-GTR-xxx. Portland, OR: U.S. Department of Agriculture, Forest Service, Pacific Northwest Research Station. XX p. In: Meurisse, R.T., Ypsilantis, W.G., and Seybold, C. A. eds. Soil Organisms in Pacific Northwest Forest and Rangeland Ecosystems-Population Dynamics, Functions and Applications to Management. Proceedings of a Symposium. 1998 March 17-19; Corvallis. Corvallis, Oregon State University, College of Forestry.
  • Norton J.M. 1999. Nitrogen Mineralization and Immobilization Turnover. Pages C148-C160 in Handbook of Soil Science, M. Sumner (Editor), CRC Press, Inc., Boca Raton, FL.
  • Norton J.M. 1999. Nitrification. Pages C160-C181 in Handbook of Soil Science, M. Sumner (Editor), CRC Press, Inc.Boca Raton, FL.
  • Alzerreca,J.J., Norton,J.M. and Klotz,M.G. 1998. GenBank Accession [AF047705] Nitrosococcus oceanus ammonia monooxygenase subunit A (amoA) and ammonia monooxygenase subunit B (amoB) genes, complete cds; and unknown gene.
  • Shiozawa,T.L., Norton,J.M., Alzerreca,J.J. and Klotz,M.G. 1998. GenBank Accession [AF042170] Nitrosospira sp. Np39-19 ammonia monooxygenase subunit C1 (amoC1) gene, partial cds; ammonia monooxygenase subunit A1 (amoA1) gene, complete cds; and ammonia monooxygenase subunit B1 (amoB1) gene, partial cds.
  • Alzerreca,J.J., Norton,J.M. and Klotz,M.G. 1998. GenBank Accession [AF071774] Nitrosospira sp. NpAV ammonia monooxygenase subunit C-4 (amoC-4) gene, complete cds.
  • Alzerreca,J.J., Norton,J.M. and Klotz,M.G. 1998. GenBank Accession [AF042171] Nitrosolobus multiformis (strain 24-C) ammonia monooxygenase subunit AmoA (amoA) gene, complete cds.
  • Sayavedra-Soto,L.A., Hommes,N.G., Alzerreca,J., Arp,D.J., Norton,J.M. and Klotz,M.G. 1998. GenBank Accession [AF073793] Nitrosomonas europaea ammonia monooxygenase 3 subunit C (amoC3) gene, complete cds.


Progress 01/01/97 to 12/31/97

Outputs
We used PCR to amplify the genes encoding ammonia monooxygenase from various strains of ammonia oxidizing bacteria . A sequence database for ammonia oxidizing bacteria is available in the National Center for Biotechnology Information, Genbank. The level of genetic diversity in the amoA gene is better suited to fine-scale differentiation of ammonia oxidizer strains than the alternative 16S rDNA target sequences. PCR primers are capable of amplifying the amoA gene using DNA isolated from soil as template. We have prepared enrichment cultures from an aerobic lagoon treating dairy waste, the genetic diversity of these ammonia oxidizers is being investigated. In field experiments, we found that composted dairy manure was a good source for sustained release of N over the growing season of field corn, especially when compared to liquid waste or ammonium sulfate fertilizer. While initial N availability was high for all N sources, the ammonium sulfate and liquid waste would have to be reapplied to maintain optimum N availability late season (split-application). End of season soil nitrate pool size and cornstalk nitrate values indicated that at the highest compost treatment (48 tons/acre) there would be excess nitrate that may be leached. However, this treatment also had the best feed nutritional value of all the treatments. Optimum compost application rate would be between 24-48 tons /acre. In laboratory incubations, nitrification was found to be active in the composted manure, application to soil increased nitrification potentials indicating the growth of the nitrifying population. Approximately 5% of the organic N was released by mineralization during 80 days. Compost that is turned and watered has higher mineralizable N than that from static piles. The long-term effect of the application of the nitrification inhibitor N-serve on populations of nitrifying bacteria in dryland wheat systems and the ability of nitrifying bacteria to use the ammonium bound to zeolite are under investigation in collaborative projects.

Impacts
(N/A)

Publications

  • Klotz M.G, J. Alzerreca and J.M. Norton. 1997. A gene encoding a membrane protein exists upstream of the amoA/amoB genes in ammonia-oxidizing bacteria; a third member of the amo operon? FEMS Microbiol. Lett.: 150: 65-73.
  • Norton J.M. 1997. Soil Microbiology p 645-647 in McGraw-Hill Encyclopedia of Science and Technology 8th Edition. McGraw-Hill Inc. New York.
  • Klotz, M.G. and J.M. Norton. 1997. Molecular analysis of the ammonia monooxygenase operons in chemolithoautotrophic soil bacteria. 41st annual meeting on procaryotic biology (Wind River Conference), Allenspark, CO.
  • Boettinger, J.L. J.M. Norton, L.M. Dudley, D.T. Drost, T.S. Perrin, I.S. MacQueen and P.T. Kolesar. 1997. Developing sustainable agricultural systems based on nitrogen cycling with clinoptilolite. Zeolite '97. Ischia, Italy.
  • Norton J. M., J. J. Alzerreca and M.G. Klotz. 1997. A gene encoding a membrane protein exists upstream of the amoA/amoB genes in ammonia-oxidizing bacteria; a third member of the amo operon? American Society of Microbiology Abstracts.
  • Shi W., J.M. Norton, B.E. Miller and M.G. Pace. 1997. Aeration and moisture effects during windrow composting on the N fertilizer value of composts. Western Society of Soil Science, Pacific Division AAAS.


Progress 01/01/96 to 12/30/96

Outputs
We used PCR to amplify the genes encoding ammonia monooxygenase from various strains of ammonia oxidizing bacteria . PCR products were obtained, cloned and sequenced from Nitrosospira sp. NpAV, Nitrosolobus multiformis, Nitrosospira briensis, Nitrosomonas eutropha, Nitrosovibrio tenuis and environmental isolates. These sequences have been submitted to the Genbank. The significance of the observed genetic diversity in the amoA gene is under investigation. Analysis of the amoA sequence from several ammonia oxidizers allowed us to identify conserved regions which possibly encode the catalytic region and are useful as probes or primers in environmental samples. The designed primers are capable of amplifying the amoA gene using DNA isolated from soil as template. We have prepared enrichment cultures from an aerobic lagoon treating dairy waste, the genetic diversity of these ammonia oxidizers is being investigated. We found that multiple copies of the amo genes within an individual strains are nearly identical. The long-term effect of the application of the nitrification inhibitor N-serve on populations of nitrifying bacteria in dryland wheat systems and the ability of nitrifying bacteria to use the ammonium bound to zeolite are under investigation in a collaborative projects.

Impacts
(N/A)

Publications

  • Norton, J.M., J. M. Low and M.G. Klotz. 1996. The gene encoding ammonia monooxygenase subunit A exists in three nearly identical copies in Nitrosospira sp. NpAV. FEMS Microbiol. Lett. 139: 181-188.
  • Norton, J.M. and M.K. Firestone. (1996) N dynamics in the rhizosphere of Pinus ponderosa seedlings. Soil Biol. Biochem. 28:351-362.
  • Boettinger J.L., L.M. Dudley, J.M. Norton and P.T. Kolesar. 1995. Zeolite Efficiency in Reducing Nitrate Contamination. Clean Water- Clean Environment Conference Proceedings. Am Soc. Ag. Eng. 2:19-22.
  • Norton, J.M. C.A. Brunson and J. L. Boettinger. 1996. Effects of Soil Properties on Ammonium Release from Zeolite during Laboratory Incubations. Agronomy Abst., Am. Soc. of Agronomy.
  • Perrin, T.S. D.T. Drost, J.L. Boettinger and J.M. Norton. 1996. The effectiveness of clinoptilolite as a slow-release nitrogen fertilizer. Agronomy Abst., Am. Soc. of Agronomy.
  • Norton J. M., J. M. Low and M.G. Klotz. 1996. The Gene Encoding Ammonia Monooxygenase Subunit-A Exists in Three Nearly Identical Copies in Nitrosospira sp. NpAV. American Society of Microbiology.
  • Boettinger J. L., L.M. Dudley, J.M. Norton and I.S. MacQueen. 1995. Dynamics of ammonium loading on clinoptilolite. Agronomy Abst., Am. Soc. of Agronomy.
  • Norton, J.M., Alzerreca, J. and Klotz, M.G. 1996. Nitrosomonas eutropha ammonia.


Progress 01/01/95 to 12/30/95

Outputs
We used amoA and amoB genes from Nitrosomonas europaea and several additional ammonia oxidizing bacteria to design degenerate oligomers which can be used to amplify similar genes from soil ammonia oxidizers. Various PCR products were obtained, cloned and sequenced from Nitrosospira sp. NpAV, Nitrosolobus multiformis, Nitrosospira briensis, Nitrosomonas eutropha, Nitrosovibrio tenuis and environmental isolates. The significance of the observed genetic diversity in the amoA gene and the multiple copies of this gene in the individual strains is under investigation. Analysis of the amoA sequence from several ammonia oxidizers allowed us to identify conserved regions which possibly encode the catalytic region and are useful as probes or primers in environmental samples. The designed primers are capable of amplifying the amoA gene using DNA isolated from soil as template. We are isolating additional ammonia oxidizer strains from an aerobic lagoon treating dairy waste. The long-term effect of the application of the nitrification inhibitor N-serve on populations of nitrifying bacteria in dryland wheat systems is under investigation in a collaborative project. The effects of zeolite on nitrification in soils and animal manures are being examined.

Impacts
(N/A)

Publications

  • Klotz, M.G. and Norton, J.M. 1995. Sequence of an ammonia monooxygenase subunit A-encoding gene from Nitrosospira sp. NpAV. Gene 163:159-160.
  • Norton, J.M. and Firestone, M.K. (in press) Nitrogen dynamics in the rhizosphere of ponderosa pine seedlings. Soil Biol. Biochem.
  • Boettinger J.L., Dudley, L.M., Norton, J.M. and Kolesar P. T. 1995. Zeolite Efficiency in Reducing Nitrate Contamination. Clean Water- Clean Environment. Am Soc. Ag. Eng. 2:19-22.
  • Norton J.M. 1995. Book Review of Soil Microbial Ecology-Applications in Agricultural and Environmental Management. Arid Soil Research and Rehabilitation 9 (4): 503.
  • Boettinger J. L., Dudley, L.M., Norton, J.M. and MacQueen, I.S. 1995. Dynamics of ammonium loading on clinoptilite. Agronomy Abst., Madison WI.
  • Norton J. M. and Klotz, M.G. 1995. Development and application of molecular tools for investigations of ammonia oxidizer functional diversity. Ecological Society of America Abst.
  • Norton J. M. and Klotz, M.G. 1995. Homology among Ammonia Monooxygenase Genes from Ammonia Oxidizing Bacteria. American Society for Microbiology Abst.


Progress 01/01/94 to 12/30/94

Outputs
1) Development & application of nucleic acid probes for ammonia oxidizers. We used amoA & amoB genes from Nitrosomonas europaea as heterologous probes to examine homology of these genes in strains from the Nitrosolobus & Nitrosospira genera. The gene encoding the catalytic AMO subunit, amoA, exists in multiple copies in all strains examined. Degenerate oligomers were designed based on N.europaea amoA sequence. By using these oligomers as primers & Nitrosolobus multiformis genomic DNA as template, various PCR products were obtained,cloned & sequenced. The obtained sequence for one copy of N. multiformis amoA was highly similar to the N.europaea amoA gene (75% identity) its deduced amino acid sequence (82% identity). All investigated Nitrosospira strains contained sequences similar to amoA but with different restriction patterns than N.europaea or N. multiformis. Analysis of the sequences from ammonia oxidizers will allow us to identify conserved regions which may encode the catalytic region. 2) Nitrogen Cycling Rates in Composted Manure. Aerobic incubations of dairy manure composted in a factorial experiment (factors: length of composting, turning & water application) have been completed. We are analyzing the data to determine significance of these factors in the nitrogen supplying potential of composted manure. In future experiments, we will determine N-15 pool dilution rate estimates of mineralization, immobilization & nitrification. Results will be used in models of N release from manure.

Impacts
(N/A)

Publications


    Progress 01/01/93 to 12/30/93

    Outputs
    Research was conducted in the following areas: 1) Development and application ofnucleic acid probes for nitrifying and denitrifying organisms. The usefulness of gene sequences of ammonia monooxygenase (amo) and nitrite reductase (dnir) for application in the soil are being assessed. A culture collection of nitrifying and denitrifying organisms has been initiated. Our laboratory system for culturing ammonia oxidizers has been developed. A gene probe has been constructed from the Nitrosomonas europaea amoA gene which was used to screen for homology in the ammonia oxidizing organism Nitrosolobus multiformis, significant homology was found. The gene from N. multiformis will be cloned and sequenced. Conserved regions of the amoA gene in these organisms have potential as a function targeted DNA probe. Planning and collaborative efforts are in progress on the dnir gene probe. Denitrifier and nitrifier populations will be investigated in agricultural soils which have received excessive manure inputs. 2) Nitrogen Cycling Rates in Composted Manure. In collaboration with Bruce Miller, ASTE, Utah State University, aerobic incubations of dairy manure composted in a factorial experiment (factors: turning and water application) are in preparation. Throughout the incubation 15N pool dilution rate estimates of mineralization, immobilization, nitrification and nitrate immobilization will be made. Results will be useful in models of N release from manure.

    Impacts
    (N/A)

    Publications

    • NORTON, J.M., TIEDJE, J.M., PAUL, E.A. 1993. DNA probes for enzymatic functions in the soil environment: problems and potential. 1993 Agronomy Abstracts, pp. 255. American Society of Agronomy.