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Open Access Publications from the University of California

Scholarly Works (14 results)

  • Article
  • Peer Reviewed
UC Davis Previously Published Works (2024)
Many 4-year public institutions face significant pedagogical challenges due to the high ratio of students to teaching team members. To address the issue, we developed a workflow using the programming language R as a method to rapidly grade multiple-choice questions, adjust for errors, and grade answer-dependent style multiple-choice questions, thus shifting the teaching teams time commitment back to student interaction. We provide an example of answer-dependent style multiple-choice questions and demonstrate how the output allows for discrete analysis of questions based on various categories such as Fundamental Statements or Blooms Taxonomy Levels. Additionally, we show how student demographics can be easily integrated to yield a holistic perspective on student performance in a course. The workflow offers dynamic grading opportunities for multiple-choice questions and versatility through its adaptability to assessment analyses. This approach to multiple-choice questions allows instructors to pinpoint factors affecting student performance and respond to changes to foster a healthy learning environment.
    Cover page: Dynamic answer-dependent multiple-choice questions and holistic assessment analysis in high-enrollment courses.
    • Thesis
    • Peer Reviewed
    UC Riverside Electronic Theses and Dissertations (2018)

    Microbes can dramatically alter the fitness of host organisms, ranging in effect from mutualistic to antagonistic. Across this spectrum of fitness effects the microbial symbiont is predicted to optimize its own fitness benefits either through positive feedback (i.e., mutualism) or exploitation (i.e., antagonism). The legume-rhizobium symbiosis has emerged as a powerful system to study the control mechanisms of hosts and the corresponding subversion of control by symbionts. Rhizobial bacteria are housed in legume root nodules where they provide the costly services of nitrogen fixation in return for host derived carbon. However, variation in symbiont quality and lifestyle strategies can result in fitness conflict between host and symbiont. I used the symbiosis between Lotus japonicus and Mesorhizobium loti to investigate host control over symbionts across the mutualism-antagonism spectrum. For chapter 1 I investigated the effects of host control on symbiont fitness when symbionts vary in their fitness effects. I found that the L. japonicus host can adaptively alter the fitness of symbionts dependent on symbiotic nitrogen fixation. For chapter 2 I examined how varying host investment into symbiosis affects the fitness of hosts and symbionts. I found host control was maintained when host investment into symbiosis was altered. However, at high levels of host investment in symbiosis with a high-quality symbiont I uncovered evidence that host fitness is optimized, while symbiont fitness continues to increase. For chapter 3 I tested the effects of host control and varying levels of host investment on the evolution of symbiont services to hosts. After experimentally evolving rhizobial symbionts of mediocre quality in multiple experiments, the phenotypic data was most consistent with a shift towards antagonistic phenotypes. Together, these results highlight the intense conflict over resources that can lead to the destabilization or breakdown of the mutualism between legumes and rhizobia.

    • 6 supplemental files
    Cover page: Conflict Over Control in the Legume-Rhizobia SymbiosisCreative Commons 'BY' version 4.0 license
    • Article
    • Peer Reviewed
    UC Riverside Previously Published Works (2018)
    Contents Summary 1199 I. Introduction 1199 II. Selecting beneficial symbionts: one problem, many solutions 1200 III. Control and conflict over legume nodulation 1201 IV. Control and conflict over nodule growth and senescence 1204 V. Conclusion 1204 Acknowledgements 1205 References 1205 SUMMARY: The legume-rhizobia association is a powerful model of the limits of host control over microbes. Legumes regulate the formation of root nodules that house nitrogen-fixing rhizobia and adjust investment into nodule development and growth. However, the range of fitness outcomes in these traits reveals intense conflicts of interest between the partners. New work that we review and synthesize here shows that legumes have evolved varied mechanisms of control over symbionts, but that host control is often subverted by rhizobia. An outcome of this conflict is that both legumes and rhizobia have evolved numerous traits that can improve their own short-term fitness in this interaction, but little evidence exists for any net improvement in the joint trait of nitrogen fixation.
      Cover page: Legumes versus rhizobia: a model for ongoing conflict in symbiosis
      • Article
      • Peer Reviewed
      UC Riverside Previously Published Works (2021)
      Microbial mutualists provide substantial benefits to hosts that feed back to enhance the fitness of the associated microbes. In many systems, beneficial microbes colonize symbiotic organs, specialized host structures that house symbionts and mediate resources exchanged between parties. Mutualisms are characterized by net benefits exchanged among members of different species, however, inequalities in the magnitude of these exchanges could result in evolutionary conflict, destabilizing the mutualism. We investigated joint fitness effects of root nodule formation, the symbiotic organ of legumes that house nitrogen-fixing rhizobia in planta. We quantified host and symbiont fitness parameters dependent on the number of nodules formed using near-isogenic Lotus japonicus and Mesorhizobium loti mutants, respectively. Empirically estimated fitness functions suggest that legume and rhizobia fitness is aligned as the number of nodules formed increases from zero until the host optimum is reached, a point where aligned fitness interests shift to diverging fitness interests between host and symbiont. However, fitness conflict was only inferred when analyzing wild-type hosts along with their mutants dysregulated for control over nodule formation. These data demonstrate that to avoid conflict, hosts must tightly regulate investment into symbiotic organs maximizing their benefit to cost ratio of associating with microbes.
        Cover page: Dysregulation of host-control causes interspecific conflict over host investment into symbiotic organs.
        • Article
        • Peer Reviewed
        UC Davis Previously Published Works (2023)
        Microbial symbionts range from mutualistic to commensal to antagonistic. While these roles are distinct in their outcome, they are also fluid in a changing environment. Here, we used the Lotus japonicus-Mesorhizobium japonicum symbiosis to investigate short-term and long-term shifts in population abundance using an effective, fast, and low-cost tracking methodology for M. japonicum. We use quantitative polymerase chain reaction (qPCR) to track previously generated signature-tagged M. japonicum mutants targeting the Tn5 transposon insertion and the flanking gene. We used a highly beneficial wild type and moderately beneficial and non-beneficial mutants of M. japonicum sp. nov. to demonstrate the specificity of these primers to estimate the relative abundance of each genotype within individual nodules and after serial transfers to new hosts. For the moderate and non-beneficial genotypes, qPCR allowed us to differentiate genotypes that are phenotypically indistinguishable and investigate host control with suboptimal symbionts. We consistently found the wild type increasing in the proportion of the population, but our data suggest a potential reproductive trade-off between the moderate and non-beneficial genotypes. The multi-generation framework we used, coupled with qPCR, can easily be scaled up to track dozens of M. japonicum mutants simultaneously. Moreover, these mutants can be used to explore M. japonicum genotype abundance in the presence of a complex soil community.
          Cover page: Evaluation of qPCR to Detect Shifts in Population Composition of the Rhizobial Symbiont Mesorhizobium japonicum during Serial in Planta Transfers.Creative Commons 'BY' version 4.0 license
          • Article
          • Peer Reviewed
          UC Riverside Previously Published Works (2017)

          Premise of the study

          To maximize benefits from symbiosis, legumes must limit physiological inputs into ineffective rhizobia that nodulate hosts without fixing nitrogen. The capacity of legumes to decrease the relative fitness of ineffective rhizobia-known as sanctions-has been demonstrated in several legume species, but its mechanisms remain unclear. Sanctions are predicted to work at the whole-nodule level. However, whole-nodule sanctions would make the host vulnerable to mixed-nodule infections, which have been demonstrated in the laboratory and observed in natural settings. Here, we present and test a cell-autonomous model of legume sanctions that can resolve this dilemma.

          Methods

          We analyzed histological and ultrastructural evidence of sanctions in two legume species, Acmispon strigosus and Lotus japonicus. For the former, we inoculated seedlings with rhizobia that naturally vary in their abilities to fix nitrogen. In the latter, we inoculated seedlings with near-isogenic strains that differ only in the ability to fix nitrogen.

          Key results

          In both hosts, plants inoculated with ineffective rhizobia exhibited evidence for a cell autonomous and accelerated program of senescence within nodules. In plants that received mixed inoculations, only the plant cells harboring ineffective rhizobia exhibited features consistent with programmed cell death, including collapsed vacuoles, ruptured symbiosomes, and bacteroids that are released into the cytosol. These features were consistently linked with ultrastructural evidence of reduced survival of ineffective rhizobia in planta.

          Conclusions

          Our data suggest an elegant cell autonomous mechanism by which legumes can detect and defend against ineffective rhizobia even when nodules harbor a mix of effective and ineffective rhizobial genotypes.
            Cover page: Cell autonomous sanctions in legumes target ineffective rhizobia in nodules with mixed infections
            • Article
            • Peer Reviewed
            UC Riverside Previously Published Works (2017)
            Rhizobial bacteria are known for their capacity to fix nitrogen for legume hosts. However ineffective rhizobial genotypes exist and can trigger the formation of nodules but fix little if any nitrogen for hosts. Legumes must employ mechanisms to minimize exploitation by the ineffective rhizobial genotypes to limit fitness costs and stabilize the symbiosis. Here we address two key questions about these host mechanisms. What stages of the interaction are controlled by the host, and can hosts detect subtle differences in nitrogen fixation? We provide the first explicit evidence for adaptive host control in the interaction between Lotus japonicus and Mesorhizobium loti. In both single inoculation and co-inoculation experiments, less effective rhizobial strains exhibited reduced in planta fitness relative to the wildtype M. loti. We uncovered evidence of host control during nodule formation and during post-infection proliferation of symbionts within nodules. We found a linear relationship between rhizobial fitness and symbiotic effectiveness. Our results suggest that L. japonicus can adaptively modulate the fitness of symbionts as a continuous response to symbiotic nitrogen fixation.
              Cover page: Lotus japonicus alters in planta fitness of Mesorhizobium loti dependent on symbiotic nitrogen fixation.
              • Article
              • Peer Reviewed
              UC Riverside Previously Published Works (2020)
              Bacterial mutualists generate major fitness benefits for eukaryotes, reshaping the host phenotype and its interactions with the environment. Yet, microbial mutualist populations are predicted to generate mutants that defect from providing costly services to hosts while maintaining the capacity to exploit host resources. Here, we examined the mutualist service of symbiotic nitrogen fixation in a metapopulation of root-nodulating Bradyrhizobium spp. that associate with the native legume Acmispon strigosus. We quantified mutualism traits of 85 Bradyrhizobium isolates gathered from a 700 km transect in California spanning 10 sampled A. strigosus populations. We clonally inoculated each Bradyrhizobium isolate onto A. strigosus hosts and quantified nodulation capacity and net effects of infection, including host growth and isotopic nitrogen concentration. Six Bradyrhizobium isolates from five populations were categorized as ineffective because they formed nodules but did not enhance host growth via nitrogen fixation. Six additional isolates from three populations failed to form root nodules. Phylogenetic reconstruction inferred two types of mutualism breakdown, including three to four independent losses of effectiveness and five losses of nodulation capacity on A. strigosus. The evolutionary and genomic drivers of these mutualism breakdown events remain poorly understood.
                Cover page: Recurrent mutualism breakdown events in a legume rhizobia metapopulation.
                • Article
                • Peer Reviewed
                UC Riverside Previously Published Works (2019)
                Microbial symbionts exhibit broad genotypic variation in their fitness effects on hosts, leaving hosts vulnerable to costly partnerships. Interspecific conflict and partner-maladaptation are frameworks to explain this variation, with different implications for mutualism stability. We investigated the mutualist service of nitrogen fixation in a metapopulation of root-nodule forming Bradyrhizobium symbionts in Acmispon hosts. We uncovered Bradyrhizobium genotypes that provide negligible mutualist services to hosts and had superior in planta fitness during clonal infections, consistent with cheater strains that destabilise mutualisms. Interspecific conflict was also confirmed at the metapopulation level - by a significant negative association between the fitness benefits provided by Bradyrhizobium genotypes and their local genotype frequencies - indicating that selection favours cheating rhizobia. Legumes have mechanisms to defend against rhizobia that fail to fix sufficient nitrogen, but these data support predictions that rhizobia can subvert plant defenses and evolve to exploit hosts.
                  Cover page: Interspecific conflict and the evolution of ineffective rhizobia
                  • Article
                  • Peer Reviewed
                  UC Riverside Previously Published Works (2019)
                  Efficient host control predicts the extirpation of ineffective symbionts, but they are nonetheless widespread in nature. We tested three hypotheses for the maintenance of symbiotic variation in rhizobia that associate with a native legume: partner mismatch between host and symbiont, such that symbiont effectiveness varies with host genotype; resource satiation, whereby extrinsic sources of nutrients relax host control; and variation in host control among host genotypes. We inoculated Acmispon strigosus from six populations with three Bradyrhizobium strains that vary in symbiotic effectiveness on sympatric hosts. We measured proxies of host and symbiont fitness in single- and co-inoculations under fertilization treatments of zero added nitrogen (N) and near-growth-saturating N. We examined two components of host control: 'host investment' into nodule size during single- and co-inoculations, and 'host sanctions' against less effective strains during co-inoculations. The Bradyrhizobium strains displayed conserved growth effects on hosts, and host control did not decline under experimental fertilization. Host sanctions were robust in all hosts, but host lines from different populations varied significantly in measures of host investment in both single- and co-inoculation experiments. Variation in host investment could promote variation in symbiotic effectiveness and prevent the extinction of ineffective Bradyrhizobium from natural populations.
                    Cover page: Host investment into symbiosis varies among genotypes of the legume Acmispon strigosus, but host sanctions are uniform
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