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Open Access Publications from the University of California

Scholarly Works (34 results)

  • Article
  • Peer Reviewed
UC Davis Previously Published Works (2024)
BACKGROUND: Despite being among the most abundant biological entities on earth, bacteriophage (phage) remain an understudied component of host-associated systems. One limitation to studying host-associated phage is the lack of consensus on methods for sampling phage communities. Here, we compare paired total metagenomes and viral size fraction metagenomes (viromes) as methods for investigating the dsDNA viral communities associated with the GI tract of two bee species: the European honey bee Apis mellifera and the eastern bumble bee Bombus impatiens. RESULTS: We find that viromes successfully enriched for phage, thereby increasing phage recovery, but only in honey bees. In contrast, for bumble bees, total metagenomes recovered greater phage diversity. Across both bee species, viromes better sampled low occupancy phage, while total metagenomes were biased towards sampling temperate phage. Additionally, many of the phage captured by total metagenomes were absent altogether from viromes. Comparing between bees, we show that phage communities in commercially reared bumble bees are significantly reduced in diversity compared to honey bees, likely reflecting differences in bacterial titer and diversity. In a broader context, these results highlight the complementary nature of total metagenomes and targeted viromes, especially when applied to host-associated environments. CONCLUSIONS: Overall, we suggest that studies interested in assessing total communities of host-associated phage should consider using both approaches. However, given the constraints of virome sampling, total metagenomes may serve to sample phage communities with the understanding that they will preferentially sample dominant and temperate phage. Video Abstract.
    Cover page: Targeted viromes and total metagenomes capture distinct components of bee gut phage communities.
    • Article
    • Peer Reviewed
    UC Davis Previously Published Works (2016)
    Secondary metabolites that are present in floral nectar have been hypothesized to enhance specificity in plant-pollinator mutualism by reducing larceny by non-pollinators, including microorganisms that colonize nectar. However, few studies have tested this hypothesis. Using synthetic nectar, we conducted laboratory and field experiments to examine the effects of five chemical compounds found in nectar on the growth and metabolism of nectar-colonizing yeasts and bacteria, and the interactive effects of these compounds and nectar microbes on the consumption of nectar by pollinators. In most cases, focal compounds inhibited microbial growth, but the extent of these effects depended on compound identity, concentration, and microbial species. Moreover, most compounds did not substantially decrease sugar metabolism by microbes, and microbes reduced the concentration of some compounds in nectar. Using artificial flowers in the field, we also found that the common nectar yeast Metschnikowia reukaufii altered nectar consumption by small floral visitors, but only in nectar containing catalpol. This effect was likely mediated by a mechanism independent of catalpol metabolism. Despite strong compound-specific effects on microbial growth, our results suggest that the secondary metabolites tested here are unlikely to be an effective general defense mechanism for preserving nectar sugars for pollinators. Instead, our results indicate that microbial colonization of nectar could reduce the concentration of secondary compounds in nectar and, in some cases, reduce deterrence to pollinators.
      Cover page: Nectar microbes can reduce secondary metabolites in nectar and alter effects on nectar consumption by pollinators
      • Article
      • Peer Reviewed
      UC Davis Previously Published Works (2018)

      Background and aims

      Flowers can be highly variable in nectar volume and chemical composition, even within the same plant, but the causes of this variation are not fully understood. One potential cause is nectar-colonizing bacteria and yeasts, but experimental tests isolating their effects on wildflowers are largely lacking. This study examines the effects of dominant species of yeasts and bacteria on the hummingbird-pollinated shrub, Mimulus aurantiacus, in California.

      Methods

      Wildflowers were inoculated with field-relevant titres of either the yeast Metschnikowia reukaufii or the bacterium Neokomagataea sp. (formerly Gluconobacter sp.), both isolated from M. aurantiacus nectar. Newly opened flowers were bagged, inoculated, harvested after 3 d and analysed for microbial abundance, nectar volume, and sugar and amino acid concentration and composition.

      Key results

      Yeast inoculation reduced amino acid concentration and altered amino acid composition, but had no significant effect on nectar volume or sugar composition. In contrast, bacterial inoculation increased amino acid concentration, enhanced the proportion of nectar sugars comprised by monosaccharides, and reduced nectar volume.

      Conclusions

      The results presented suggest that microbial inhabitants of floral nectar can make nectar characteristics variable among flowers through divergent effects of yeasts and bacteria on nectar chemistry and availability, probably modifying plant-pollinator interactions.
        Cover page: Contrasting effects of yeasts and bacteria on floral nectar traits
        • Thesis
        • Peer Reviewed
        UC Davis Electronic Theses and Dissertations (2024)

        Host-microbe interactions underlie the development and fitness of many macroorganisms; microbial symbionts can facilitate digestion, mitigate pathogens, and even produce essential developmental cues. My dissertation focuses on the impacts of microbes within the plant-pollinator system, investigating the crucial and complex interactions between bees, plants, and microbes- with a focus on how microbes use specialized tools to influence pollen processes, bee development, and the wider microbial community. Through use of classical natural history observations combined with entirely novel experimental and sampling approaches, I have been able to discover unique phenomena in microbial ecology that not only have important implications for pollinator systems but have changed broader perception and understanding of ecology and evolution. Chapter 1 explores the role of nectar-associated bacteria, particularly Acinetobacter pollinis, in facilitating pollen digestion. By inducing pollen germination and bursting, these bacteria access critical nutrients, with implications for pollinator nutrition and the role of flower associated microbes in pollinator systems. Chapter 2 examines the developmental microbiome of a solitary bee, revealing that immature stages of Anthophora bomboides standfordiana host a distinct core microbiome dominated by Actinobacteria and a yeast-like fungus, Moniliella spathulata. Data from microbial community profiling, qPCR, and functional experiments support the hypothesis that the bee’s microbial community may provide critical fitness advantages, such as pathogen protection (Streptomyces) and enhanced cold tolerance (M. spathulata) during the bees’ diapausing larval stage- suggesting that microbes play a vital role in the bees’ overwintering success and long-term survival. Chapter 3 builds on these findings by describing two novel species, Streptomyces solapis sp. nov. and Streptomyces nidicoloris sp. nov., isolated from the brood of A. bomboides. These new bee- associated species display unique biosynthetic gene clusters that correlate with antifungal activity, underscoring the potential of leveraging the diversity of microbial symbionts to support discovery of new bioactive compounds. Collectively, this dissertation highlights the profound influence of microbes on macroorganisms, offering broader insights into the dynamics of pollination ecology, host-microbe symbioses, and the unique evolutionary strategies of microbes in these environments.

          • Article
          • Peer Reviewed
          UC Davis Previously Published Works (2023)
          Floral nectar is frequently colonised by microbes. However, nectar microbial communities are typically species-poor and dominated by few cosmopolitan genera. One hypothesis is that nectar constituents may act as environmental filters. We tested how five non-sugar nectar compounds as well as elevated sugar impacted the growth of 12 fungal and bacterial species isolated from nectar, pollinators, and the environment. We hypothesised that nectar isolated microbes would have the least growth suppression. Additionally, to test if nectar compounds could affect the outcome of competition between microbes, we grew a subset of microbes in co-culture across a subset of treatments. We found that some compounds such as H2 O2 suppressed microbial growth across many but not all microbes tested. Other compounds were more specialised in the microbes they impacted. As hypothesised, the nectar specialist yeast Metschnikowia reukaufii was unaffected by most nectar compounds assayed. However, many non-nectar specialist microbes remained unaffected by nectar compounds thought to reduce microbial growth. Our results show that nectar chemistry can influence microbial communities but that microbe-specific responses to nectar compounds are common. Nectar chemistry also affected the outcome of species interactions among microbial taxa, suggesting that non-sugar compounds can affect microbial community assembly in flowers.
            Cover page: Nectar compounds impact bacterial and fungal growth and shift community dynamics in a nectar analog.
            • Article
            • Peer Reviewed
            UC Davis Previously Published Works (2017)
            Insect pests cause serious economic, yield, and food safety problems to managed crops worldwide. Compounding these problems, insect pests often vector pathogenic or toxigenic microbes to plants. Previous work has considered plant-insect and plant-microbe interactions separately. Although insects are well-understood to use plant volatiles to locate hosts, microorganisms can produce distinct and abundant volatile compounds that in some cases strongly attract insects. In this paper, we focus on the microbial contribution to plant volatile blends, highlighting the compounds emitted and the potential for variation in microbial emission. We suggest that these aspects of microbial volatile emission may make these compounds ideal for use in agricultural applications, as they may be more specific or enhance methods currently used in insect control or monitoring. Our survey of microbial volatiles in insect-plant interactions suggests that these emissions not only signal host suitability but may indicate a distinctive time frame for optimal conditions for both insect and microbe. Exploitation of these host-specific microbe semiochemicals may provide important microbe- and host-based attractants and a basis for future plant-insect-microbe chemical ecology investigations.
              • Article
              • Peer Reviewed
              UC Davis Previously Published Works (2023)
              Bee-fungus associations are common, and while most studies focus on entomopathogens, emerging evidence suggests that bees associate with a variety of symbiotic fungi that can influence bee behavior and health. Here, we review nonpathogenic fungal taxa associated with different bee species and bee-related habitats. We synthesize results of studies examining fungal effects on bee behavior, development, survival, and fitness. We find that fungal communities differ across habitats, with some groups restricted mostly to flowers (Metschnikowia), while others are present almost exclusively in stored provisions (Zygosaccharomyces). Starmerella yeasts are found in multiple habitats in association with many bee species. Bee species differ widely in the abundance and identity of fungi hosted. Functional studies suggest that yeasts affect bee foraging, development, and pathogen interactions, though few bee and fungal taxa have been examined in this context. Rarely, fungi are obligately beneficial symbionts of bees, whereas most are facultative bee associates with unknown or ecologically contextual effects. Fungicides can reduce fungal abundance and alter fungal communities associated with bees, potentially disrupting bee-fungi associations. We recommend that future study focus on fungi associated with non-honeybee species and examine multiple bee life stages to document fungal composition, abundance, and mechanistic effects on bees.
                Cover page: Bees just wanna have fungi: a review of bee associations with nonpathogenic fungi.
                • Article
                • Peer Reviewed
                UC Davis Previously Published Works (2019)
                Background and aim: Root-associated microbial communities influence plant phenotype, growth and local abundance, yet the factors that structure these microbial communities are still poorly understood. California landscapes contain serpentine soils, which are nutrient-poor and high in heavy metals, and distinct from neighboring soils making them ideal for studying the factors that structure root microbiomes and their functions. Method: Here, we surveyed the rhizoplane of serpentine-indifferent plants, which grow on and off serpentine soil, to determine the relative influence of plant identity and soil chemistry on rhizoplane microbial community structure using 16S rRNA metabarcoding. Additionally, we experimentally examined if serpentine vs. non-serpentine microorganisms differentially affected plant growth in serpentine soil. Results: Rhizoplane bacterial communities differed among plant species, soil types, and the interaction between them in both the field and experimental soils. In the experiment, soil microbial community source influenced seedling survival, but plant growth phenotypes were largely invariant to microbial community with a few exceptions. Conclusions: Rhizosplane bacterial species composition differed between plant species and soil types, and Amplicon Sequence Variants (ASVs) from the phyla Acidobacteria and Proteobacteria (Genus: Microvirga) were characteristic of serpentine soils. While soil microbial community composition influenced seedling survival in the current study, further study is required to disentangle the role of microbial associations and plant tolerance to serpentine.
                  • Article
                  • Peer Reviewed
                  UC Davis Previously Published Works (2024)
                  Plant-systemic neonicotinoid (NN) insecticides can exert non-target impacts on organisms like beneficial insects and soil microbes. NNs can affect plant microbiomes, but we know little about their effects on microbial communities that mediate plant-insect interactions, including nectar-inhabiting microbes (NIMs). Here we employed two approaches to assess the impacts of NN exposure on several NIM taxa. First, we assayed the in vitro effects of six NN compounds on NIM growth using plate assays. Second, we inoculated a standardised NIM community into the nectar of NN-treated canola (Brassica napus) and assessed microbial survival and growth after 24 h. With few exceptions, in vitro NN exposure tended to decrease bacterial growth metrics. However, the magnitude of the decrease and the NN concentrations at which effects were observed varied substantially across bacteria. Yeasts showed no consistent in vitro response to NNs. In nectar, we saw no effects of NN treatment on NIM community metrics. Rather, NIM abundance and diversity responded to inherent plant qualities like nectar volume. In conclusion, we found no evidence that NIMs respond to field-relevant NN levels in nectar within 24 h, but our study suggests that context, specifically assay methods, time and plant traits, is important in assaying the effects of NNs on microbial communities.
                    Creative Commons 'BY-NC-ND' version 4.0 license
                    • Thesis
                    • Peer Reviewed
                    UC Davis Electronic Theses and Dissertations (2024)

                    Insect-fungi associations are common, with effects on insect hosts ranging from detrimental to beneficial. Fungi can provide multiple benefits to insects, including nutritional benefits, detoxification of food resources, and protection from detrimental microbes. In contrast, fungi can also harm insect hosts, acting as pathogens or food-spoiling saprotrophs. Bees (clade Anthophila) commonly associate with fungi, which can be found within their gastrointestinal tracts, in stored provisions within their nests, and in the flowers that they forage on. While certain pathogenic fungi (Ascosphaera, Aspergillus, Nosema) have been well-studied for the negative impacts they have on bee hosts, the majority of the fungi associated with bees are non-pathogenic, with unknown impacts on bee health. My dissertation focuses on understanding these associations between bees and their symbiotic fungi. Chapter 1 provides a review of existing literature on bee-fungi interactions, highlighting the fungal genera most commonly associated with bees and their nests. Notably, the yeast genera Starmerella and Zygosaccharomyces are commonly found in association with a wide variety of bee species, particularly with social bees, and exhibit adaptations to the bee nest environment. Chapters 2 and 3 utilize bumble bee systems to test the impacts of these common yeast symbionts on bee health. In Chapter 2, the impacts of fungicide exposure and yeast supplementation on the health of two bumble bee species (Bombus impatiens, B. vosnesenskii) are assessed. Impacts of treatments varied by bee species, with yeasts assisting B. vosnesenskii workers in recovering from the negative impacts of fungicide exposure. For B. impatiens, yeasts were beneficial to bee survival and reproduction regardless of fungicide exposure. In Chapter 3, the mechanisms behind the positive impacts of yeasts are tested using B. impatiens. Bees were fed treatment solutions varying in the presence of living yeast cells and yeast-modified media, and bee performance was measured. Impacts of yeast treatments were variable, and depended on the source colony bees were derived from, suggesting that benefits of yeast are context dependent. Overall, this research shows that many bee species are consistently associated with fungi which can benefit bee health and reproduction. However, the effects of these yeasts are inconsistent, with context-dependent benefits. Discovering the contexts in which yeasts are beneficial to bees, and the mechanisms underlying these benefits, is necessary to fully understand the roles that these microbes play in bee health.  

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