Progress 10/01/02 to 09/30/07
Outputs
1) Management and nitrogen contribution of legume cover-crops in agroecosystems. Nitrogen was traced from isotopically-enriched legume cover-crop hay into grapevines in field experiments. Cover-crop derived nitrogen was rapidly detected in the vines; vine N uptake was much lower in mature vines in the field than in young plants in lysimeter experiments. Seasonal uptake of cover-crop derived nitrogen by mature vines depended on placement of the cover crop in relation to the woody perennial root system, and timing of application. In addition, a perennial clover cover crop provided improved N and water status in grapevines, compared with a perennial grass cover. 2) Gene expression, nodule organization and nitrogen assimiliation in actinorhizal root nodules (DATISCA GLOMERATA and ALNUS spp.). A novel nodule organization of primary N assimilatory organization was demonstrated in the root nodules of DATISCA GLOMERATA, which involves storage of assimilated N as arginine. We
are now investigating transcriptional patterns of genes coding for enzymes of N assimilation in FRANKIA, within nodules of DATISCA GLOMERATA. A novel class of FRANKIA hemoglobins has been characterized in root nodules of DATISCA GLOMERATA. Thirdly, we showed that DATISCA GLOMERATA is evolutionarily distant both from legumes and from other actinorhizal hosts. In root nodules of ALNUS spp., arabinogalactan proteins were localized at sites of early FRANKIA infection, indicating a role for these extracellular glycoproteins at the symbiotic interface. 3) Continued characterization of hopanoid lipid genes from the nitrogen-fixing microsymbiont, FRANKIA. Previous results showed that hopanoid lipids play a key role in oxygen regulation of nitrogen fixation in FRANKIA. Cloning and whole genome studies of FRANKIA ALNI revealed two gene copies of squalene-hopene cyclase (shc1 and shc2), the central enzyme in hopanoid biosynthesis. Likely functional differences between the gene regions
encompassing these two copies were characterized. The phylogeny of shc indicated that the gene sequences of shc1 and shc2 are more divergent than shc1 and the homologous gene in ACIDOTHERMUS CELLULOLYTICUS, a close phylogenetic relative. Evidence for an interaction between phenylpropanoid metabolism in the root nodule and biosynthesis of nitrogen-fixation specific hopanoids in Frankia was uncovered. Current genomic comparison of ACIDOTHERMUS and FRANKIA within the actinobacteria reveals new potential genes for carbohydrate and aromatic compound degradation,as well as potential incidents of lateral gene transfer and other genomic properties. 4) As part of the first ever phylogenomic research on FRANKIA, comparing sequenced genomes from 3 major genetic groupings revealed both an environmental and a phytogeographic (host-dependent) component in FRANKIA speciation. We are currently in process of sequencing a fourth FRANKIA genome, an obligate symbiont from DATISCA GLOMERATA nodules. The
resulting genome sequence will provide a wealth of information about this evolutionarily distinct FRANKIA group, and its resulting unusual nodule symbioses.
Impacts
This research examined aspects of the biology and biogeochemistry of plant-associated biological nitrogen fixation and nitrogen cycling. Organic matter derived from N-fixing plants has value for soil-building and agroecological applications. Nitrogen-fixing plants contribute to sustainable productivity and biodiversity in disturbed or depleted soils, often in extreme environments. During the project, understanding was gained about the metabolic and evolutionary mechanisms underlying symbiotic nitrogen fixation in root nodules, and methods were tested for improving management approaches. These findings will permit new applications and better use of agricultural and natural systems.
Publications
- Pawlowski K., K.R. Jacobsen, N. Alloisio, R.F. Denison, M. Klein, J.D. Tjepkema, T. Winzer, A. Sirrenberg, C. Guan, A.M. Berry. 2007. Truncated hemoglobins in actinorhizal nodules of Datisca glomerata. Plant Biology 9, 776-785.
- Solomeshch A.I., S.N. Long, M.G. Barbour, and A.M. Berry. In Press. Floristic Composition of Roadside Grasslands, Yolo County, California. IN: T. Van Devender (Ed.), Proceedings, Weeds Across Borders 2006, Hermosillo, Mexico, University of Arizona Press.
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Progress 01/01/06 to 12/31/06
Outputs
Research projects related to biological nitrogen fixation and plant-microbe associations have been focused in 3 areas: 1) Continuing studies on gene expression and nitrogen assimiliation in actinorhizal root nodules. Based on earlier findings (Berry et al. 2004, Plant Physiol. 135:1849) we are investigating transcriptional patterns of genes coding for enzymes of N assimilation in FRANKIA, within nodules of DATISCA GLOMERATA. 2. We concluded one phase of our comparative analysis of FRANKIA genomes (Normand et al. 2006), the first ever genomic research on FRANKIA. The evidence from the comparison of 3 genomes from major genetic groupings revealed both an environmental and a phytogeographic component in FRANKIA speciation. We are now in process of sequencing a fourth FRANKIA genome, again the first ever from the fourth major FRANKIA group. 3) Comparison of the genomes of ACIDOTHERMUS and FRANKIA with closely-related actinobacteria reveals new potential genes for
carbohydrate and aromatic compound degradation, features associated with thermostability and motility, as well as potential incidents of lateral gene transfer and other genomic properties. We are confirming some genomic features with biochemical experiments.
Impacts
This research examines aspects of the biology and biogeochemistry of symbiotic nitrogen fixation and plant symbiosis. Organic matter derived from N-fixing plants has value for soil-building and agroecological applications. Plant biomass is also useful as a feedstock source in bioconversion. Nitrogen-fixing plants contribute to sustainable productivity and biodiversity in disturbed or depleted soils, often in extreme environments. Understanding the regulatory mechanisms of nitrogen fixation, nodulation and plant biomass degradation will permit new applications in agricultural systems.
Publications
- Normand,P., P. Lapierre, L. S. Tisa, J. P. Gogarten, N. Alloisio, E. Bagnarol, C. A. Bassi, A. M. Berry, D. M. Bickhart, N. Choisne, A. Couloux, B. Cournoyer, S. Cruveiller, V. Daubin, N. Demange, M. P. Francino, E. Goltsman, Y. Huang, O. R. Kopp, L. Labarre, A. Lapidus, C. Lavire, J. Marechal, M. Martinez, J. E. Mastronunzio, B. C. Mullin, J. Niemann, P. Pujic, T. Rawnsley, Z. Rouy, C.l Schenowitz, A. Sellstedt, F. Tavares, J. P. Tomkins, D. Vallenet, Cl. Valverde, L. G. Wall, Y. Wang, C. Medigue, and D. R. Benson. 2006. Genome characteristics of facultatively symbiotic Frankia sp. strains reflect host range and host plant biogeography. Genome Research 17:7-15.
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Progress 01/01/05 to 12/31/05
Outputs
Research projects on biological nitrogen fixation have been focused in 3 areas: 1) Management and nitrogen contribution of legume cover-crops in winegrape vineyards. Nitrogen was traced from isotopically-enriched legume cover-crop hay into grapevines in field experiments. A perennial clover cover crop provided improved N and water status in grapevines, compared with a perennial grass cover. Seasonal uptake of cover-crop derived nitrogen by mature vines depends on placement of the cover crop in relation to the woody perennial root system. Whole-vine experiments were carried out to determine total N uptake and annual partitioning patterns. 3) Gene expression and nitrogen assimiliation in actinorhizal root nodules. The new type of primary N assimilatory organization observed previously in nodules of Datisca glomerata will be studied further in 2006. 2) Continued characterization of hopanoid lipid genes from the nitrogen-fixing microsymbiont, FRANKIA. Cloning and whole
genome studies of F. alni revealed two gene copies for squalene-hopene cyclase (shc1 and shc2), the central enzyme in hopanoid biosynthesis. Functional differences between the gene regions that encompass these two copies were characterized. The phylogeny of shc was elucidated, indicating that the gene sequences of shc1 and shc2 are more divergent than shc1 and the homologous gene in A. cellulolyticus . shc2 is located adjacent to a redox response regulator, suggesting a specialized function in relation to oxygen and nitrogen fixation.
Impacts
This research examines aspects of the biology and biogeochemistry of symbiotic nitrogen fixation. Organic matter derived from N-fixing plants has value for soil-building and agroecological applications. Nitrogen-fixing trees contribute to sustainable productivity and biodiversity in disturbed or depleted soils, often in extreme environments. Understanding the regulatory mechanisms of nitrogen fixation, and improving management approaches, will permit better use of agricultural and natural systems.
Publications
- King AP and Berry AM. 2005. Vineyard delta-15-N, nitrogen and water status in perennial clover and bunch grass cover crop systems of California's Central Valley. Agriculture Ecosystems & Environment. 109(3-4). 262-272.
- Alloisio N, Marechal J, Vanden Heuvel B, Normand P, and Berry AM. 2005. Characterization of a gene locus containing squalene-hopenecyclase (shc) in Frankia alni ACN14a, and an shc homolog in Acidothermus cellulolyticus. Symbiosis 39, 83-90.
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Progress 01/01/04 to 12/31/04
Outputs
Research projects on biological nitrogen fixation have been focused in 3 areas: 1) Management and nitrogen contribution of legume cover-crops in winegrape vineyards. Nitrogen was traced from isotopically-enriched legume cover-crop hay into grapevines in field experiments. Seasonal uptake of cover-crop derived nitrogen by mature vines is of the same order of magnitude as uptake in lysimeter experiments. 2) Continuing studies on gene expression and nitrogen assimiliation in actinorhizal root nodules. A new type of primary N assimilatory organization was demonstrated in nodules of Datisca glomerata, which involves storage of assimilated N as arginine. We also showed that Datisca glomerata is evolutionarily distant both from legumes and from other actinorhizal hosts. 3) Continued characterization of hopanoid lipid genes from the nitrogen-fixing microsymbiont, FRANKIA. Cloning and whole genome studies of Frankia alni revealed two gene copies for squalene-hopene cyclase,
the central enzyme in hopanoid biosynthesis. Functional differences between the gene regions that encompass these two copies were characterized.
Impacts
This research examines aspects of the biology and biogeochemistry of symbiotic nitrogen fixation. Organic matter derived from N-fixing plants has value for soil-building and agroecological applications. Nitrogen-fixing trees contribute to sustainable productivity and biodiversity in disturbed or depleted soils, often in extreme environments. Understanding the regulatory mechanisms of nitrogen fixation, and improving management approaches, will permit better use of agricultural and natural systems.
Publications
- Pawlowski, K., Swensen, S., Guan, C-H, Hadri, A-E, Berry, A.M., Bisseling, T. 2003. Distinct patterns of symbiosis-related gene expression in actinorhizal nodules from different plant families. Mol Plant Microbe Interactions 16:796-807.
- Berry, A.M., Murphy, T.M., Okubara, P.A., Jacobsen, K.R., Swensen, S.M., and K. Pawlowski. 2004. Novel expression pattern of cytosolic glutamine synthetase in nitrogen-fixing root nodules of the actinorhizal host, Datisca glomerata. Plant Physiology 135:1849-1862
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Progress 01/01/03 to 12/31/03
Outputs
Research projects on biological nitrogen fixation have been focused in 3 areas: 1) Effects of legume cover-crops as nitrogen sources in a winegrape vineyard. Nitrogen was traced from isotopically-enriched legume cover-crop hay into grapevines in field experiments. Cover-crop derived nitrogen was rapidly detected in the vines, but vine N uptake was much lower in the field than in lysimeter experiments. 2) Role of plant cell wall components in nodule establishment and function. Arabinogalactan proteins were localized at sites of early infection in root nodules of ALNUS, indicating a role for these extracellular glycoproteins at the symbiotic interface. 3) Continued characterization of hopanoid lipid genes and gene products from the nitrogen-fixing microsymbiont, FRANKIA. Evidence for an interaction between phenylpropanoid metabolism in the root nodule and biosynthesis of nitrogen-fixation specific hopanoids in FRANKIA was uncovered.
Impacts
This research examines aspects of the biology and biogeochemistry of symbiotic nitrogen fixation. Organic matter derived from N-fixing plants has value for soil-building and agroecological applications. Nitrogen-fixing trees contribute to sustainable productivity and biodiversity in disturbed or depleted soils, often in extreme environments.
Publications
- SALYARDS, J., EVANS, R.Y. and BERRY, A.M. 2003. Mycorrhizal development and plant growth in inoculated and non-inoculated plots of California native grasses and shrubs. Native Plants J 4: 143-149.
- McDERMOTT, E.L. and BERRY, A.M. 2003. Mycorrhizal fungi. Native Plants J 4:141-142.
- WALL, L.G. and BERRY, A.M. 2003. Early interactions, infection and nodulation in actinorhizal symbiosis. IN: (K. Pawlowski and W.E. Newton, eds.) ACTINORHIZAL SYMBIOSIS. Kluwer Publishers, The Netherlands. In Press
- WHEELER, C.T., AKKERMANS, A.D.L. and BERRY, A.M. 2003. FRANKIA and Actinorhizal Plants: A Historical Perspective. IN: (K. Pawlowski and W.E. Newton, eds.) ACTINORHIZAL SYMBIOSES. Kluwer Publishers, The Netherlands. In Press
- PATRICK, A.E., SMITH, R., KECK, K. and BERRY, A.M. 2003. Grapevine uptake of 15N-labeled nitrogen derived from a winter annual leguminous cover crop mix. Am J Enology & Viticulture. In Press
- HAMMAD, Y., NALIN, R., MARECHAL, J., FIASSON, K., PEPIN, R., BERRY, A.M., NORMAND, P. and DOMENACH, A.M. 2003. A possible role for phenyl acetic acid (PAA) on ALNUT GLUTINOSA nodulation by FRANKIA. Plant & Soil 254: 193-205.
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