Published Abstracts

University of Minnesota Long-Term Agricultural Research Network

Peer-Reviewed Journal Articles

Denison, R.F., G. Johnson, F. Izuno (in preparation) How widely applicable are conclusions from single-site long-term experiments?

Muller, K., R.F. Denison (in preparation) Prolonged host absence selects for rhizobia strains that divert twice as much energy from N fixation to polyhydroxybutyrate during symbiosis.

Oono, R., K. Muller, R. Ho, A,J, Salinas, R.F. Denison. 2020. How do less-expensive nitrogen alternative affect legume sanctions on rhizobia?  Ecology and Evolution (in press).

Sadras,V., J. Alston, P. Aphalo, D. Connor, R.F. Denison, T. Fischer, R. Gray, P. Hayman, J. Kirkegaard, H. Kirchmann, M. Kropff, H.R. Lafitte, P. Langridge, J. Lenne, M.I. Minguez, J. Passioura, J.R. Porter, T. Reeves, D. Rodriguez, M. Ryan, F.J. Villalobos, and D.
Wood. 2020. Making science more effective for agriculture. Advances in Agronomy (in press).

Castle, S. C., Sadowsky, M. J., Samac, D. A., Gutnecht, J. L., Rosen, C. J., and Kinkel, L. L. 2020. Impacts of cropping system composition and nitrogen fertilization on soil fungal and bacterial communities. Soil Biol. Biochem. Submitted.

Liu, S, H.L. Rusch, G. Johnson, and A. Garcia y Garcia. 2020. Crops water use in corn-soybean rotation with cover crops. In preparation.

Oono, R., K. Muller, R. Ho, A.J. Salinas, R.F. Denison. 2020. How do less-expensive nitrogen alternatives affect legume sanctions on rhizobia? Submitted to Proceedings of the Royal Society.

Muller, K.E. and R.F. Denison. 2020. Prolonged absence of hosts favors rhizobia that hoard more resources during symbiosis with soybean. In revision.

 

Rusch, Hannah L.; Jeffrey A. Coulter, Julie M. Grossman; Gregg A. Johnson, Paul M. Porter, and A. Garcia y Garcia. 2020. Towards sustainable maize production in the U.S. upper Midwest with interseeded cover crop. PLoS ONE 15(4): e0231032. 

Abstract
The incorporation of cover crops into the maize (Zea mays L.)-soybean [Glycine max (L.) Merr.] rotation in the U.S. upper Midwest may improve sustainability. Long, cold winters in the region make identifying successful cover crop species and management practices a challenge. Two experiments were conducted in Minnesota, USA from fall 2016 through spring 2019 to examine the effect of cover crops interseeded at four- to six-leaf collar (early-interseeded) and dent to physiological maturity (late-interseeded) on biomass and grain yield of maize. Annual ryegrass (Lolium multiflorum L.) and cereal rye (Secale cereale L.) were evaluated as monocultures and in mixtures with crimson clover (Trifolium incarnatum L.) and forage radish (Raphanus sativusL.). Differences in canopy cover and biomass of late-interseeded cover crops were observed at the southernmost location in 2018. Additional accumulated growing-degree days in fall 2018 did not translate into increased cover crop canopy coverage of late-interseeded cover crops. Differences in cover crop canopy cover and biomass of early-interseeded cover crops were observed by fall frost at all locations in 2017 and at the northernmost location in 2018. Cover crop canopy cover and biomass at termination before planting maize, soil moisture at maize planting as well as maize aboveground biomass and yield were not affected by spring cereal rye regrowth of cover crops late-interseeded the previous year. Similarly, early-interseeded cover crops did not affect maize aboveground biomass or yield. We attribute these results to limited cover crop growth. This highlights the potential of a variety of cover crop strategies interseeded into maize in the U.S. upper Midwest; however, efforts to fine-tuning cover crop management and weather conditions are needed to benefit from such practice.

 

Joshi, V.R., K.R. Thorp, J.A. Coulter, G.A. Johnson, P.M. Porter, J.S. Strock, and A. Garcia y Garcia. 2020. Improving site-specific maize yield estimation by integrating satellite multispectral data into a crop model. Agronomy, 9:719.  doi:10.3390/agronomy9110719

Abstract
Integrating remote sensing data into crop models offers opportunities for improved crop yield estimation. To compare site-specific yield estimation accuracy of a stand-alone crop model with a data-integration approach, a study was conducted in 2016–2017 with nitrogen (N)-fertilized and unfertilized treatments across a heterogeneous 7-ha maize field. For each treatment, yield data were grouped into five classes resulting in 109 spatial zones. In each zone, the Crop Environment Resource Synthesis (CERES)-Maize model was run using the GeoSim plugin within Quantum GIS. In the data integration approach, maize biomass values estimated using satellite imagery at the five (V5) and ten (V10) leaf collar stages were used to optimize the total soil nitrogen concentration (SLNI) and soil fertility factor (SLPF) in CERES-Maize. Without integration, maize yield was simulated with root mean square error (RMSE) of 1264 kg ha−1. Optimization of SLNI improved yield simulations at both V5 and V10. However, better simulations were obtained from optimization at V10 (RMSE 1026 kg ha−1) as compared to V5 (RMSE 1158 kg ha−1). Optimization of SLPF together with SLNI did not further improve the yield simulations. This study shows that integrating remote sensing data into a crop model can improve site-specific maize yield estimations as compared to the stand-alone crop modeling approach. 

 

Denison, R.F. 2019. Evolutionary tradeoffs are key to beneficial manipulation of crops by microbes. American Journal of Botany 106:1529-1531.

Abstract
Microbes associated with roots may benefit plants by defending them from pathogens, by providing them with resources like nitrogen or phosphorus, or by manipulating plant phenotypes (Pérez‐Montaño et al., 
2014). This essay argues that beneficial manipulation of crop plants by microbes will often be constrained by trade‐offs between benefits to plants and the Darwinian fitness of individual microbes. However, I also suggest some potential opportunities, linked to similar trade‐offs among plants.

 

Castle, S. C., Samac, D. A., Sadowsky, M. J., Rosen, C. J., Gukneckt, J. L. M., and Kinkel, L. L. 2019. Impacts of sampling design on estimates of microbial community diversity and composition in agricultural soil. Mol. Ecol. 78:753-763  https://doi.org/10.1007/s00248-019-01318-6.

Abstract
Soil microbiota play important and diverse roles in agricultural crop nutrition and productivity. Yet, despite increasing efforts to characterize soil bacterial and fungal assemblages, it is challenging to disentangle the influences of sampling design on assessments of communities. Here, we sought to determine whether composite samples—often analyzed as a low cost and effort alternative to replicated individual samples—provide representative summary estimates of microbial communities. At three Minnesota agricultural research sites planted with an oat cover crop, we conducted amplicon sequencing for soil bacterial and fungal communities (16SV4 and ITS2) of replicated individual or homogenized composite soil samples. We compared soil microbiota from within and among plots and then among agricultural sites using both sampling strategies. Results indicated that single or multiple replicated individual samples, or a composite sample from each plot, were sufficient for distinguishing broad site-level macroecological differences among bacterial and fungal communities. Analysis of a single sample per plot captured only a small fraction of the distinct OTUs, diversity, and compositional variability detected in the analysis of multiple individual samples or a single composite sample. Likewise, composite samples captured only a fraction of the diversity represented by the six individual samples from which they were formed, and, on average, analysis of two or three individual samples offered greater compositional coverage (i.e., greater number of OTUs) than a single composite sample. We conclude that sampling design significantly impacts estimates of bacterial and fungal communities even in homogeneously managed agricultural soils, and our findings indicate that while either strategy may be sufficient for broad macroecological investigations, composites may be a poor substitute for replicated samples at finer spatial scales.

 

Xie, C., C. Yang, A. Hummel Jr., G.A. Johnson, and F. T. Izuno. 2018. Spectral reflectance response to nitrogen fertilization in field grown corn. Int. J. Agric. Biol. Eng. 11(4):118-126.

Abstract
This study was carried out to analyze the spectral reflectance response of different nitrogen levels for corn crops. Four different nitrogen treatments of 0%, 80%, 100% and 120% BMP (best management practice) were studied. Principal component analysis-loading (PCA-loading) was used to identify the effective wavelengths. Partial least squares (PLS) and multiple linear regression (MLR) models were built to predict different nitrogen values. Vegetation indices (VIs) were calculated and then used to build more prediction models. Both full and selected wavelengths-based models showed similar prediction trends. The overall PLS model obtained the coefficient of determination (R2) of 0.6535 with a root mean square error (RMSE) of 0.2681 in the prediction set. The selected wavelengths for overall MLR model obtained the R2 of 0.6735 and RMSE of 0.3457 in the prediction set. The results showed that the wavelengths in visible and near infrared region (350- 1000 nm) performed better than the two either spectral regions (1001-1350/1425-1800 nm and 2000-2400 nm). For each data set, the wavelengths around 555 nm and 730 nm were identified to be the most important to predict nitrogen rates. The vogelmann red edge index 2 (VOG 2) performed the best among all VIs. It demonstrated that spectral reflectance has the potential to be used for analyzing nitrogen response in corn.

 

Muller K.E. and R.F. Denison. 2018. Resource acquisition and allocation traits in symbiotic rhizobia with implications for life-history outside of legume hosts. Royal Society Open Science 5:181124

Abstract
Resources that microbial symbionts obtain from hosts may enhance fitness during free-living stages when resources are comparatively scarce. For rhizobia in legume root nodules, diverting resources from nitrogen fixation to polyhydroxybutyrate (PHB) has been discussed as a source of host – symbiont conflict. Yet, little is known about natural variation in PHB storage and its implications for rhizobial evolution. We therefore measured phenotypic variation in natural rhizobia populations and investigated how PHB might contribute to fitness in the free-living stage. We found that natural populations of rhizobia from Glycine max and Chamaecrista fasciculata had substantial, heritable variation in PHB acquisition during symbiosis. A model simulating temperature-dependent metabolic activity showed that the observed range of stored PHB per cell could support survival for a few days, for active cells, or over a century for sufficiently dormant cells. Experiments with field-isolated Bradyrhizobium in starvation culture suggest PHB is partitioned asymmetrically in dividing cells, consistent with individual- level bet-hedging previously demonstrated in E. meliloti. High-PHB isolates used more PHB over the first month, yet still retained more PHB for potential long-term survival in a dormant state. These results suggest that stored resources like PHB may support both short-term and long-term functions that contribute to fitness in the free-living stage.

 

Castle, S. C., Song, Z., Gohl, D. M., Gutknecht, J., Rosen, C., Sadowsky, M. J., Samac, D. A., and Kinkel, L. L. 2018. DNA template dilution greatly impacts amplicon-sequencing based estimates of soil fungal diversity. Phytobiomes J. 2:100-107.

Next generation sequencing of taxonomically relevant marker genes has enabled researchers to sample the richness, diversity, and composition of environmental microbiomes at previously unattainable depths. However, molecular methods may have unintended downstream consequences and the inadvertent undersampling of microbial communities may be a significant pitfall in microbiome profiling. One such procedure, dilution of the DNA template prior to polymerase chain reaction (PCR), may improve marker gene amplification by reducing chimeric read formation and decreasing PCR inhibitor concentrations. However, dilution unavoidably reduces target DNA template number per sample. We evaluated the effects of pre-PCR DNA template dilution on estimates of soil fungal microbiome diversity, composition, and species abundance distributions across a collection of 144 agricultural soil samples. Fungal DNA templates were serially diluted at 0-, 10-, 100-, and 1,000-fold and sequence data of diluted templates were compared with those of an identical set of undiluted templates. For three prairie soil samples, in addition to evaluating variation among replicates of individual samples, we serially diluted fungal DNA extracts from soil samples in triplicate and sequenced undiluted and diluted samples. DNA template dilution significantly reduced estimates of fungal richness and diversity, as compared with undiluted samples. Dilution of DNA template also resulted in reduced relative abundances of rare operational taxonomic units (OTUs) and increased relative abundances of common OTUs. Collectively, changes in OTU abundance distributions following dilution produced substantial shifts in overall fungal community composition. Our results highlight risks associated with sample dilution and point to the potential utility of quantifying pre-PCR template concentration in the estimation of microbiomes. We urge researchers to thoroughly document methods and to reconsider routine dilution of pre-PCR DNA templates particularly for low abundance microbiome samples. As efforts to profile environmental microbiomes using molecular sequencing approaches accelerate, developing an adequate understanding of potential methodological bottlenecks will increase our ability to accurately characterize and compare datasets.

 

Cao, Y., Miller, S. S., Dornbusch, M. R., Castle, S., Lenz, P., Ferguson, J., Sadowsky, M. J., Nelson, M. S., Klatt, C., and Samac, D. A. 2018. Widespread occurrence of Sinorhizobium meliloti strains with a type IV secretion system. Symbiosis 75:81-91.

Improving symbiotic nitrogen fixation would reduce reliance on synthetic fertilizers, but establishment of effective bacterial strains is hampered due to competition by indigenous, less effective rhizobia. This study investigated the origins, diversity, and competitiveness of Sinorhizobium meliloti (syn. Ensifer meliloti) strains isolated from root nodules of alfalfa (lucerne; Medicago sativa L.) grown in soils that had not been in alfalfa cultivation for over 30 years. Sets of PCR primers were developed to identify Sinorhizobium spp. and to identify strains with virD 4 , the defining gene for a type IV secretion system (T4SS), which has been implicated in increasing strain competitiveness for nodule colonization of M. truncatula, an annual species closely related to alfalfa. A collection of S. meliloti isolates was made from nodules of field-grown plants and from seeds used for establishing field plots that had been inoculated with rhizobia by the manufacturer prior to packaging. Diversity among strains was examined by repetitive element palindromic PCR (rep-PCR) DNA fingerprinting using the BOXA1R primer. Strains originating from the seed inoculant could not be detected in nodules, even in the first year of alfalfa establishment, which were occupied exclusively by indigenous rhizobia originating from soil. Field strains were very diverse within and among field sites, and genetically distinct from inoculant strains. Approximately 33% of field strains were positive for virD 4 , a component of the T4SSb gene cluster, which putatively mobilizes effector proteins across the bacterial cell envelop into the host cell. Strains with virD 4 , the presence of which suggests that they have a functional T4SS, had more rapid nodulation kinetics than did those lacking virD 4 . These results provide additional support for the role of the S. meliloti T4SS in competitiveness for nodule occupancy.