Progress 10/01/99 to 09/30/04
Outputs
Rhizobia are soil bacteria best known for their symbiosis with legume plants like alfalfa and bean. Once inside a root nodule, rhizobia often benefit their plant hosts by fixing (taking up) atmospheric nitrogen and providing it to the plant. However, rhizobium strains that fix little or no nitrogen are also widespread, and significantly limit legume growth in some areas. My research is figuring out why such diversity among rhizobium strains has persisted over the course of evolution, and how to bias future evolution in favor of the best strains. Last year, we showed that rhizobia prevented from fixing nitrogen (using a nitrogen-free atmosphere) reproduced only half as much as otherwise identical rhizobia. The plant monitored the symbiotic performance of individual root nodules and imposed sanctions on nonfixing cheaters, apparently by reducing their oxygen supply. This explains why cheating rhizobia (which use plant resources for their own reproduction, rather than for
the nitrogen fixation that benefits the plant) have not taken over. But if sanctions reduce the reproduction of cheaters to half that of nitrogen fixers, why the nitrogen-fixers taken over? One possible explanation for the long-term coexistence of fixing and nonfixing strains is that each nodule that contains a mixture of fixers and nonfixers could release mostly nonfixers into the soil when the plant dies. Or, even if numbers are similar, the nonfixers might have hoarded more resources than fixers, which used those resources for nitrogen fixation. To test this mixed-nodule hypothesis, we needed to determine 1) how common mixed nodules are under field conditions, 2) what kind of sanctions, if any, plants impose on nodules that fix intermediate amounts of nitrogen (as expected with a mixed nodule), and 3) whether cheaters escape from mixed nodules in greater numbers, or with more resources, than nitrogen fixing strains. This year, we used DNA fingerprinting to determine the number of
strains per nodule in a representative sample of nodules collected from Steve Temple common bean and California Blackeye plots. As a control for the effects of human intervention on legume evolution, we are also assaying lupine nodules collected from Bodega Bay Marine Laboratory. To measure sanctions at intermediate levels of fixation, we exposed nodules to low, but not zero, concentrations of nitrogen gas, and then counted the rhizobia inside after 10 days. We have not yet been able to conduct a complete test of the effects of sharing nodules on reproduction and resource hoarding by nonfixing rhizobia, but have made substantial progress in developing the methods we will use for these experiments. In particular, we are have developed methods based on flow cytometry that let us determine the proportional representation of two rhizobium strains in a mixture and also obtain statistics on the size and resource status of each.
Impacts
Basic research is a cornerstone of US agriculture, but economically or ecologically important results can often take years to implement. For example, many of the publications listed below resulted from my earlier project titled Long-term research on agricultural systems. Real-world impact, such as greater use of winter cover crops, or changes in organic transition regulations (both possible future impacts of the paper by Martini et al.), usually takes even longer. An eventual on-farm impact expected from this work is the development of legume crops and forages that selectively enrich soils with the most consistently beneficial strains of nitrogen-fixing bacteria, leading to reductions in the excessive use of nitrogen fertilizer. The scientific impact of the research is already evident in invitations to write review articles and to speak at both the European and the International meetings on nitrogen fixation. The citation impact (number of times a given publication is
referring to in other publications) for the first paper I published on this topic in 2000 currently stands at 33, well above average.
Publications
- E.T. Kiers, S.A. West, and R.F. Denison. 2005 Maintaining cooperation in the legume-rhizobia symbiosis: identifying selection pressures and mechanisms. In: J. Sprent and E. James (eds.) Leguminous Symbioses. Kluwer Academic Publishers (in press).
- Hasegawa, H., and R.F. Denison. 2004 Model predictions of winter rainfall effects on N dynamics of winter wheat rotation following legume cover crop or fallow. Field Crops Research (in press).
- R.F. Denison and E.T. Kiers. 2004. Why are most rhizobia beneficial to their plant hosts, rather than parasitic? (Invited review.) Microbes and Infection 6:1235-1239.
- R.F. Denison and E.T. Kiers. 2004. Lifestyle alternatives for rhizobia: mutualism, parasitism, and forgoing symbiosis. (Invited review.) FEMS Microbiology Letters 237:187
- Martini, E.A., J.S. Buyer, D.C. Bryant, T.K. Hartz, and R.F. Denison. 2004. Yield increases during the organic transition: improving soil quality or increasing experience? Field Crops Research 86:255-266.
- Okano, Y., K.R. Hristova, C. Leutenegger, L. Jackson, R.F. Denison, B. Gebreyesus, D. LeBauer, and K.M. Scow. 2004. Effects of ammonium on the population size of ammonia-oxidizing bacteria in soil -- Application of real-time PCR. Applied and Environmental Microbiology 70:1008-1016.
- R.F. Denison and E.T. Kiers. 2005 Sustainable crop nutrition: constraints and opportunities. In: M. Broadley (ed.) Plant Nutritional Genomics. Blackwell Publishing (in press).
|
Progress 01/01/03 to 12/31/03
Outputs
Steve Kaffka took over as director of the 100-year Long-Term Research on Agricultural Systems (LTRAS) project in 2003, but I remained involved in some aspects, especially analyzing results and writing papers. I have also been working with the project databases, correcting a few errors and holding a training session for potential users. Scientific results from this multi-investigator project, including some not yet published, have been diverse. There have been dramatic shifts in weed species differing between cropping systems. Organic systems produce more dust. Low-input and alternative systems have generally had lower yields, but this was not true of tomato, the most valuable crop. Improvements in yield-limiting aspects of soil quality from organic methods (particularly the use of winter legume cover crops) were apparent only a few months into the organic transition, in contrast to the widely held view that such benefits develop only over years. Residual soil N made a
substantial contribution to yields of unfertilized controls even after 9 years. This shows that short-term soil fertility experiments can be very misleading a crop dependent only on a green manure or low fertilizer rate might actually be using significant amounts of soil N and underscores the importance of a long-term approach. LTRAS has also hosted UCD classes and many visitors from around the world each year. The recent move of the SAFS team to the LTRAS site creates exciting new opportunities for collaborative research, making LTRAS arguably the most ambitious sustainable agriculture experiment in the world.
Impacts
LTRAS provides a credible source of field data to answer important questions about the sustainability, profitability, resource use, and environmental impact of conventional and alternative field crop production practices.
Publications
- Okano, Y., K.R. Hristova, C. Leutenegger, L. Jackson, R.F. Denison, B. Gebreyesus, D. LeBauer, and K.M. Scow. 2003 Effects of ammonium on the population size of ammonia-oxidizing bacteria in soil. Application of real-time PCR. Applied and Environmental Microbiology (submitted).
- Denison, R.F., D.C. Bryant, and T.E. Kearney. 2003. Crop yields over the first nine years of LTRAS, a long-term comparison of field crop systems in a Mediterranean climate. Field Crops Research (in press).
- Martini, E.A., J.S. Buyer, D.C. Bryant, T.K. Hartz, and R.F. Denison. 2003. Yield increases during the organic transition: improving soil quality or increasing experience? Field Crops Research (in press).
- Denison, R.F., E.T. Kiers, and S.A. West. 2003. Darwinian Agriculture: When can humans find solutions beyond the reach of natural selection? http://www.agronomy.ucdavis.edu/denison/DarwinianAgriculture.pdf Quarterly Review of Biology 78:145-168.
|
Progress 01/01/02 to 12/31/02
Outputs
A paper summarizing the first nine years of this 100-year experiment is ready to submit as soon as corn yield samples have been processed. A companion paper on soil quality during the "organic transition" will be submitted at the same time. LTRAS is, in part, an early warning system to identify agricultural practices that may be unsustainable. So far, only our two unfertilized controls have been shown to be unsustainable, based on statistical analyses showing significant negative yield trends over years. These trends were not statistically significant if only the first 8 years of data were used. Other systems may be shown to unsustainable over the next decade or two. Organic tomato yields actually increased significantly over years. There are historical examples of such trends reversing, but trends in soil properties typically provide some indication of problems in such cases. This year LTRAS was visited and endorsed by an external review team (see LTRAS.ucdavis.edu
for their report) and discussions are underway about the possibility of the Sustainable Agriculture Farming Systems project relocating to the LTRAS site.
Impacts
Outgoing LTRAS Director, R. Ford Denison, got rave reviews for his talk, mostly based on LTRAS, to leading journalists enrolled in a course at the UC Berkeley School of Journalism. This led to articles in the LA Times and Sacramento Bee (at least) and interviews broadcast on KQED on Oct. 21 and as part of National Public Radio's All Things Considered on Nov. 12. The latter called for greater cooperation between agricultural and environmental groups, cooperation that should be facilitated by results from LTRAS.
Publications
- No publications reported this period
|
Progress 01/01/01 to 12/31/01
Outputs
This 100-year experiment on the sustainability and environmental impact of field crop systems is now beginning its ninth year. Although yields of nonirrigated wheat grown in a two-year rotation with a winter legume cover crop suggest that the legume provides enough nitrogen to meet the wheat's needs, wheat yield in our unfertilized control remain surprisingly high. Until soil organic nitrogen reserves in the control decrease enough to severely limit yields, we cannot be sure that nitrogen from the legume is sufficient to sustain good wheat yields. Plots managed organically for 1-2 years had yields as high or higher than those managed organically for 6-7 years, when both sets of plots were managed identically. (Previous comparisons by other researchers were confounded by changes in management over years.) This same experiment also showed that organic tomatoes can sometimes outyield conventional tomatoes, apparently due to beneficial effects of the winter legume cover
crop on soil physical properties. These results disprove the popular hypotheses that 1) organic yields are always lower at first, and 2) that yields increase over years due to improvements in soil quality. Important infrastructure improvements during the past year include automated twice-daily update of data from our on-site weather station on the web; a new web-based application process for approving research at the site; and completion of the design for our replacement barn. Refer to our web site (LTRAS.ucdavis.edu) or previous reports for additional information on this project.
Impacts
Over the decades, our long-term yield trends will provide farmers and policy makers with unambiguous information as to which agricultural practices are most sustainable. Meanwhile, our organic transition study suggests that farmers with adequate knowledge, skill, and resources could achieve the full yield potential of organic methods right from the first year.
Publications
- Martini, E.A., J.S. Buyer, D.C. Bryant, T.K. Hartz, D. Barrett, and R.F. Denison. Grower experience, not soil quality, may explain yield trends during the "organic transition". Submitted to Agronomy Journal. Tuli, A., K. Kosugi, and J.W. Hopmans. 2001. Simultaneous scaling of water retention and unsaturated hydraulic conductivity functions assuming lognormal pore-size distribution. Advances in Water Resources 24:677-688. Timm, L., Pearson, D., and Jaffee, B. 2001. Nematode-trapping fungi in conventionally- and organically-managed corn-tomato rotations. Mycologia 93:25-29
|
Progress 01/01/00 to 12/31/00
Outputs
This 100-year experiment on the sustainability and environmental impact of field crop systems is now in its eighth year. Noteworthy results for the past year include: 1) unfertilized control plots are finally beginning to show N deficiency, both in terms of crop yields, and in increased dominance of nitrogen-fixing leguminous weeds, which were scarcely present when the experiment began, 2) water use by our legume cover crops, which has no adverse effects in the first few years, because of wet winters, resulted in lower yields in wheat following a cover crop than in the unfertilized control, and 3) the "organic transition effect" (reportedly lower yields in the early years of organic farming, followed by yield increases hypothesized to be due to improving "soil quality") disappears when proper controls are used, at least under our conditions. We are also making progress on the installation of a radiotelemetry system that will allow us to display "live" data on our web
site, beginning with data from our weather station and from a system we are developing to monitor runoff from systems with and without winter cover crops. Refer to our web site (LTRAS.ucdavis.edu) or previous reports for additional information on this project.
Impacts
Comparisons of productivity, profitability, efficiency, sustainability, and environmental impact are of interest in long-term planning of public policy related to agriculture. For example, what would be the long-term effects of a decrease in water allocations for irrigation? Are some agricultural practices degrading the soil in ways that will have long-term effects on crop productivity?
Publications
- Timm, L., Pearson, D., and Jaffee, B. 2001. Nematode-trapping fungi in conventionally- and organically-managed agriculture: Early data from the LTRAS project. Mycologia (in press)
- Hasegawa, H., D.C. Bryant, and R.F. Denison. 2000. Testing CERES model predictions of crop growth and N dynamics, in cropping systems with leguminous green manures in a Mediterranean climate. Field Crops Res. 67:239-255.
- R.F. Denison. 2000. Studying soil trends linked to increased sustainability. NRI Research Highlights, November 2000.
|
Progress 01/01/99 to 12/31/99
Outputs
LTRAS is a one-hundred year experiment comparing the sustainability and environmental impact of various field crop systems. The first six years were unusually wet, which may have obscured differences between our irrigated vs. nonirrigated systems, whereas the winter of nineteen hundred ninety-nine through two thousand (through early January) has been dry. Nonirrigated wheat has grown poorly so far this year, especially in systems that had a legume cover crop last winter. In addition to the main, one-hundred year experiment, we are conducting the first controlled and replicated comparison of soil quality and resulting performance of identically-managed cropping systems differing only in the duration of organic management. In contrast to the widely-held belief that soil microbial communities develop gradually during the 'organic transition', microbial communities in the transitional organic plots were not intermediate between conventional and established organic plots.
Vegetative growth (trends in leaf area index) and final yield of tomatoes did not differ between the established organic and transitional organic systems. Yield increases reported during the early years of organic farming may reflect the 'learning curve' of new organic growers, rather than trends in 'soil quality', as was previously thought. Growth and yield of tomato in the most-directly comparable conventional system were lower than in transitional or organic systems, apparently because the conventional system was more susceptible to soil compaction under wet spring of nineteen hundred ninety-nine conditions. Even a system that had a green manure in alternate years (most recently, over a year prior to spring planting for nineteen hundred ninety-nine) had higher yield than the conventional system, which has never had a green manure crop. The beneficial effect of cover crops on soil physical properties needs to be considered along with the N benefit and with possible adverse effects
related to weeds (see last year's report) and water use.
Impacts
The results above should affect such issues as the transition requirement in any national organic standard, although there are other factors to consider. Agricultural policy related to water use should also be influenced by our results, but only after we have more data for dry years.
Publications
- Hasegawa, H., D.C. Bryant, and R.F. Denison. 2000. Evaluation of CERES models for predicting N dynamics during crop growing periods following legume cover crop incorporation. Field Crops Res. (submitted).
- Hasegawa, H.,J.M. Labavitch, A.M. McGuire, D.C. Bryant, and R.F. Denison. 1999. Testing CERES model predictions of N release from legume cover crop residue. Field Crops Res. 63:255-267.
- Lundquist, E.J., L.E. Jackson, and K.M. Scow. 1999. Effects of wet or dry cycles on dissolved organic carbon in two California agricultural soils. Soil Biol. Biochem. 31:1031-1038.
- Devevre, OC and WR Horwath. 1999. Soil Humic Fractions as Indicators of the Transition from Conventional to Low-Input-Organic Farming Systems: Evaluation of SOM Maintenance. International Humic Society, Brisbane, Australia. September Nineteen Hundred Ninety-Eight.
- Kosugi, K., and J.W. Hopmans. 1998. Scaling of soil water retention curves for soils with a lognormal pore size distribution. Soil Sci. Soc. Amer. J. 62:1496-1505.
|
Progress 01/01/98 to 12/31/98
Outputs
The sustainability of agricultural systems depends on long-term trends in the soil properties that control yield, resource-use efficiency, and off-farm environmental impacts. As LTRAS begins its sixth year, yield trends are still obscured by yearly variation in weather, but some trends in soil properties are evident. Soil organic matter has increased about 20 percent with organic management. Because external inputs of compost to the organic system exceed statewide supply by up to eight-fold, we continue to explore the use of winter legume cover crops (WLCC). Although our main WLCC (a mixture of woollypod vetch and peas) has proved highly competitive with many weed species, winter weeds with a short life cycle (e.g., chickweed) have increased, especially when a WLCC is grown every year (organic system), while decreasing in wheat-fallow rotations in which herbicides are used every winter. Summer weed populations have been relatively stable in our conventional systems,
but have increased (with species shifts) in the organic system. Ongoing research at the LTRAS site will reveal the net effect of positive changes (e.g., increasing organic matter) and negative changes (increasing weed populations) in the organic system. Meanwhile, we are beginning the first properly-controlled test of the hypothesis that yield trends during the early, "transitional" years of organic management reflect changes in soil quality.
Impacts
(N/A)
Publications
- Hasegawa, H., Labavitch, J.M., McGuire, A.M., Bryant, D.C., and Denison, R.F. Testing CERES model predictions of N release from legume cover crop residue. Field Crops Res. (Accept for pub).
|
Progress 01/01/97 to 12/01/97
Outputs
LTRAS made a brief appearance on NBC Evening News in 1997, but we expect our scientific publications to have much greater long-term impact. Results from the first four cropping years of this 100-year experiment will be submitted for publication over the next year. In three of four years, yield differences among fertilized wheat, wheat following a legume cover crop, and an unfertilized wheat control were smaller than expected, apparently due to unusually heavy winter rains that limited potential growth or resulted in significant losses of fertilizer N. Yields of organic tomatoes were comparable to conventional tomatoes in two of four years (and higher than conventional following the wettest winter), but costs for weed control were higher. Soil organic matter increased 20% in the organic system over four years, mainly due to application of composted manure at rates comparable to those used by organic farmers but exceeding statewide per-acre manure supply. Weeds have
also increased in organic system. A balance between these two trends, plus changes in other soil properties, may determine future yield trends. Methods developed at LTRAS for analysis of aerial photos are currently being used in on-farm research. Faculty from several departments have obtained grants from various sources to support research by their students at LTRAS (see publications). LTRAS hosted field trips from Davis, Berkeley and Stanford this year, as well as Weed Day participants and many visitors from around the world.
Impacts
(N/A)
Publications
- Lundquist, E.J., L.E. Jackson, and K.M. Scow. Effects of wet/dry cycles on dissolved organic carbon in two California agricultural soils. Soil Biol. Biochem. (submitted).
- Kosugi, K., and J.W. Hopmans. Scaling of soil water retention curves for soils with a lognormal pore size distribution. Soil Sci. Soc.
- McGuire, A.M., D.C. Bryant, and R.F. Denison. Wheat yields, nitrogen uptake, and soil moisture following green manure vs. fallow. Agron.
- Denison, R.F., and R. Russotti. 1997. Field estimates of green leaf area index using laser-induced chlorophyll fluorescence. Field Crops
- Denison, R.F. 1997. Review of "Long-Term Experiments in Agricultural and Ecological Sciences." Field Crops Res. 54:74-75.
- Phillips, D. A., C.M. Joseph, and P.R. Hirsch. 1997. Occurrence of flavonoids and nucleosides in agricultural soils. Appl. Environ.
- Heike Clausnitzer and Michael J. Singer. 1997. Intensive land preparation emits respirable dust. Calif. Agric. 51(2):27-30.
|
Progress 01/01/96 to 12/30/96
Outputs
LTRAS is halfway through its third year (of 100), comparing ten different two-year rotations differing in external inputs of water and nitrogen. For cropping systems based on two-year rotations, four years is the minimum for publication in leading agronomic journals. Therefore, the first summary of agronomic results will be submitted for publication sometime after fall harvests in 1997. Meanwhile, LTRAS has been the site of some interesting short-term research projects. Methods developed at LTRAS were featured as the cover story of a recent issue of California Agriculture. These methods are now being applied in a multidisciplinary on-farm research project on precision farming and have been incorporated into proposals by other UCD faculty to the cotton and tomato industries. More recently, LTRAS has been the principal test site for a new laser-based instrument that allows rapid, nondestructive estimates of leaf area index (LAI). LTRAS continues to attract researchers
from across the campus and around the world, mostly with interests in some aspect of soil quality and its relationship to sustainability. Among research projects funded by this year's competitive grants to LTRAS collaborators are (1) a long-term comparison of weed control strategies and (2) a comparison of soil organic matter turnover in various cropping systems, based on stable isotope analysis. The latter is an example of research that uses our archival soil samples (collected in anticipation of such "unanticipated" applications).
Impacts
(N/A)
Publications
- DENISON, R.F. AND RAY RUSSOTTI. 1997. Field estimates of green leaf area indexusing laser-induced chlorophyll fluorescence. Field Crops Research (in press).
|
Progress 01/01/95 to 12/30/95
Outputs
In October of 1995, the Long Term Research on Agricultural Systems (LTRAS) project completed its first two-year cropping cycle. The most striking result was the outstanding early season growth of corn and especially tomatoes in the organic system, relative to their conventional counterparts. For tomatoes, this strong early growth also resulted in a higher final yield for the organic system -- the opposite of our results for last year. The winter and spring of 1994-1995 were unusually wet, and soil compaction may have limited productivity of the conventional system. In the organic system, water consumption by the winter cover crop during early spring was probably beneficial under these conditions. Soil bulk density at depths of 10-22 cm was significantly higher in the conventional system. The organic tomatoes also received composted manure at 4 ton/acre. Soil nitrate levels were higher in the organic system early in the season, as were tomato plant tissue N concentrations
(4.46 vs. 3.12%) in May. Other soil and tissue analyses (P, K, Ca, etc.) are in progress. Note that the statewide supply of manure is only about 1 ton/acre. At least 19 faculty members from at least 5 departments currently have grants for specific research projects at LTRAS, including nitrate leaching, soil microbiology, PM-10 dust production, and computer-enhanced aerial photography for site-specific management.
Impacts
(N/A)
Publications
|
|