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Publications & Scholarly Works
Holdridge, E.M., M. Emmen, and L.S. Bittleston. 2022. A diverse community of bacteriophage may contribute to insect prey degradation in pitcher plants. Submitted. Preprint available: 10.22541/au.166618890.06191324/v1
Summary: As primary determinants of microbial community dynamics, viruses play a central role in key ecological processes, including respiration, organic and inorganic nutrient cycling, and greenhouse gas production and sequestration. However, the majority of studies of viruses in natural environments are from oceans, where the size and complexity of ecological communities pose major challenges for studying detailed mechanisms and gaining a full picture of host-virus networks. We characterize viruses in 16 metagenomes from carnivorous pitcher plant natural microcosms, which are an emerging model system for studying community ecology and ecosystem function. We find that pitcher plant microcosms possess a relatively high proportion of lysogenic viruses compared to other freshwater systems. In addition, viruses from pitcher plant microcosms appear to possess auxiliary metabolic genes for chitin degradation, an important ecological function in pitcher plants where the primary energy source is the plant's insect prey. The reduced size and complexity of pitcher plant natural microcosms, as well as their well-defined ecological function, position them as an excellent model system for characterizing whole host-virus networks and understanding the mechanisms through which viruses alter microbial diversity and function.
Summary: As primary determinants of microbial community dynamics, viruses play a central role in key ecological processes, including respiration, organic and inorganic nutrient cycling, and greenhouse gas production and sequestration. However, the majority of studies of viruses in natural environments are from oceans, where the size and complexity of ecological communities pose major challenges for studying detailed mechanisms and gaining a full picture of host-virus networks. We characterize viruses in 16 metagenomes from carnivorous pitcher plant natural microcosms, which are an emerging model system for studying community ecology and ecosystem function. We find that pitcher plant microcosms possess a relatively high proportion of lysogenic viruses compared to other freshwater systems. In addition, viruses from pitcher plant microcosms appear to possess auxiliary metabolic genes for chitin degradation, an important ecological function in pitcher plants where the primary energy source is the plant's insect prey. The reduced size and complexity of pitcher plant natural microcosms, as well as their well-defined ecological function, position them as an excellent model system for characterizing whole host-virus networks and understanding the mechanisms through which viruses alter microbial diversity and function.
Holdridge, E.M., and D.A. Vasseur. 2022. Intraspecific variation promotes coexistence under competition for essential resources. Theoretical Ecology. DOI: 10.1007/s12080-022-00539-9
Summary: Intraspecific variation may be key to coexistence in diverse communities, with some even suggesting it is necessary for large numbers of competitors to coexist. However, theory provides little support for this argument, instead finding that intraspecific variation generally makes it more difficult for species to coexist. Our paper presents a model of competition where two species compete for two essential resources and individuals within populations vary in their ability to take up different resources. We found a range of cases where intraspecific variation expands the range of conditions under which coexistence can occur. We demonstrate that this result relies on nonlinearity in the function that describes how traits map onto ecological function. A sigmoid mapping function is necessary in order to model essential resources because it allows for variation in an unbounded trait while maintaining biologically realistic boundaries on uptake rates, and differs from other kinds of nonlinearity, which only unidirectionally increase or decrease ecological function. The sigmoid function’s nonlinearity spreads individuals unevenly along the growth function, which allows positive growth contributions from some individuals to compensate for growth loses from others, akin to source-sink dynamics, leading to coexistence. In this way, intraspecific trait variation is able to amplify niche differences, thereby strengthening coexistence. We discuss empirical systems beyond competition for essential resources in which piecewise functions (i.e., thresholds) are important.
Summary: Intraspecific variation may be key to coexistence in diverse communities, with some even suggesting it is necessary for large numbers of competitors to coexist. However, theory provides little support for this argument, instead finding that intraspecific variation generally makes it more difficult for species to coexist. Our paper presents a model of competition where two species compete for two essential resources and individuals within populations vary in their ability to take up different resources. We found a range of cases where intraspecific variation expands the range of conditions under which coexistence can occur. We demonstrate that this result relies on nonlinearity in the function that describes how traits map onto ecological function. A sigmoid mapping function is necessary in order to model essential resources because it allows for variation in an unbounded trait while maintaining biologically realistic boundaries on uptake rates, and differs from other kinds of nonlinearity, which only unidirectionally increase or decrease ecological function. The sigmoid function’s nonlinearity spreads individuals unevenly along the growth function, which allows positive growth contributions from some individuals to compensate for growth loses from others, akin to source-sink dynamics, leading to coexistence. In this way, intraspecific trait variation is able to amplify niche differences, thereby strengthening coexistence. We discuss empirical systems beyond competition for essential resources in which piecewise functions (i.e., thresholds) are important.
Rodríguez, Z.C., E.M. Holdridge, and T.E. Miller. 2022. Understanding spatially complex cryptic coloration in the green lynx spider Peucetia viridans. Ecological Entomology. DOI: 10.1111/een.13132
Summary: Many species are thought to use cryptic coloration to evade predators or catch prey. However, colour patterns are historically difficult to document and compare when coloration is continuous and spatially complex. The authors studied colour variation in the green lynx spider, Peucetia viridans, a sit-and-wait predator often found in the tops of inflorescences feeding on pollinators. Spiders were collected from three distinct plant species that provided different original colour backgrounds and photographed under standard lighting and background. A novel colour analysis method (Colormesh) was used to quantify spatially explicit contributions of red, green, and blue along the spider abdomen from digital photographs. Spiders collected from green backgrounds were found to have significantly greater contributions of green abdomen colours; red and blue body colours showed no significant correlation with spider background. This is the first study of colour-matching in a natural population of this wide-spread generalist predator and also demonstrates a novel method for quantifying complex, continuous colour patterns.
Summary: Many species are thought to use cryptic coloration to evade predators or catch prey. However, colour patterns are historically difficult to document and compare when coloration is continuous and spatially complex. The authors studied colour variation in the green lynx spider, Peucetia viridans, a sit-and-wait predator often found in the tops of inflorescences feeding on pollinators. Spiders were collected from three distinct plant species that provided different original colour backgrounds and photographed under standard lighting and background. A novel colour analysis method (Colormesh) was used to quantify spatially explicit contributions of red, green, and blue along the spider abdomen from digital photographs. Spiders collected from green backgrounds were found to have significantly greater contributions of green abdomen colours; red and blue body colours showed no significant correlation with spider background. This is the first study of colour-matching in a natural population of this wide-spread generalist predator and also demonstrates a novel method for quantifying complex, continuous colour patterns.
Holdridge, E.M., G.E. Flores, and C.P. terHorst. 2017. Predator trait evolution alters prey community composition. Ecosphere. DOI: 10.1002/ecs2.1803
Summary: Predators have strong effects on the growth, abundance, and traits of their prey. The strength and magnitude of these effects depend on predators traits, which can evolve on ecologically relevant timescales. Our study experimentally manipulated temperature and nutrient input in laboratory populations of bacterivorous ciliates and a diverse community of bacteria. We measured how ciliate traits responded to selection under different temperature and nutrient regimes, and how the composition of the bacterial community was altered by these regimes directly and indirectly through ciliate trait evolution. We found that nutrient enrichment directly decreased bacterial species richness, but indirectly increased bacterial richness through changes to ciliate traits. These effects were pronounced in some contemporary environments and undetectable in others, emphasizing that both contemporary and historical environments contribute to the ways in which trait evolution can affect community structure.
Summary: Predators have strong effects on the growth, abundance, and traits of their prey. The strength and magnitude of these effects depend on predators traits, which can evolve on ecologically relevant timescales. Our study experimentally manipulated temperature and nutrient input in laboratory populations of bacterivorous ciliates and a diverse community of bacteria. We measured how ciliate traits responded to selection under different temperature and nutrient regimes, and how the composition of the bacterial community was altered by these regimes directly and indirectly through ciliate trait evolution. We found that nutrient enrichment directly decreased bacterial species richness, but indirectly increased bacterial richness through changes to ciliate traits. These effects were pronounced in some contemporary environments and undetectable in others, emphasizing that both contemporary and historical environments contribute to the ways in which trait evolution can affect community structure.
Holdridge, E.M., C. Cuellar‐Gempeler, and C.P. terHorst. 2016. A shift from exploitation to interference competition with increasing density affects population and community dynamics. Ecology and Evolution. DOI: 10.1002/ece3.2284
Summary: Intraspecific competition occurs via two mechanisms. Exploitative competition is an indirect effect that occurs through use of a shared resource and depends on resource availability. Interference competition occurs by obstructing access to a resource and may not depend on resource availability. Our study tested whether the strength of interference competition changes with protozoa population density. Our study tested whether the strength of interference competition changes with protozoa population density, using experimental microcosms and a dynamic predator–prey model. We found that the strength of interference competition increased with protozoan density and that bacterial community composition changed with protozoan density and resource availability.
Summary: Intraspecific competition occurs via two mechanisms. Exploitative competition is an indirect effect that occurs through use of a shared resource and depends on resource availability. Interference competition occurs by obstructing access to a resource and may not depend on resource availability. Our study tested whether the strength of interference competition changes with protozoa population density. Our study tested whether the strength of interference competition changes with protozoa population density, using experimental microcosms and a dynamic predator–prey model. We found that the strength of interference competition increased with protozoan density and that bacterial community composition changed with protozoan density and resource availability.
Holdridge, E.M. 2015. Effects of environmental change on the eco-evolutionary dynamics of species in natural microcosm communities. CSUN Electronic Theses & Dissertations.
Summary: Natural communities are expected to undergo shifts in composition and species interactions as a result of environmental change. Predicting how communities will respond is complicated by three factors: non-additive effects of multiple stressors, differences in response among trophic levels, and trait evolution leading to adaptation. This study addressed all three of these factors experimentally using a natural microcosm, the inquiline community of the purple pitcher plant (Sarracenia purpurea). The results of this study show that the ways in which communities respond to environmental change can differ in light of evolutionary responses, the trophic levels being considered, and additivity of multiple stressors.
Summary: Natural communities are expected to undergo shifts in composition and species interactions as a result of environmental change. Predicting how communities will respond is complicated by three factors: non-additive effects of multiple stressors, differences in response among trophic levels, and trait evolution leading to adaptation. This study addressed all three of these factors experimentally using a natural microcosm, the inquiline community of the purple pitcher plant (Sarracenia purpurea). The results of this study show that the ways in which communities respond to environmental change can differ in light of evolutionary responses, the trophic levels being considered, and additivity of multiple stressors.
Holdridge, E.M. 2013. Trophic ecology of ariid catfishes in the Gulf of Mexico. Honors Theses. Paper 184.
Summary: When species are able to coexist within the same geographic region, niche theory would predict that they partition their resources such that each species occupies a separate niche. Two species of ariid catfishes, Bagre marinus and Ariopsis felis, are among the most abundant teleosts in the Gulf of Mexico. This study used gut contents analysis to test an often stated but never tested idea that the larger B. marinus forages throughout the water column while A. felis is a more archetypical bottom-feeding catfish. Although their diets differ in a few qualitative ways, their diets do not differ significantly by percent weight or number of prey items.
Summary: When species are able to coexist within the same geographic region, niche theory would predict that they partition their resources such that each species occupies a separate niche. Two species of ariid catfishes, Bagre marinus and Ariopsis felis, are among the most abundant teleosts in the Gulf of Mexico. This study used gut contents analysis to test an often stated but never tested idea that the larger B. marinus forages throughout the water column while A. felis is a more archetypical bottom-feeding catfish. Although their diets differ in a few qualitative ways, their diets do not differ significantly by percent weight or number of prey items.