CRITICAL PATCH SIZES AND THE SPATIAL STRUCTURE OF SALT MARSH COMMUNITIES

The size, connectivity, and quality of habitat patches can have multifaceted impacts on species and communities. In this dissertation, I combined a multi-year field survey, manipulative field experiments, and a literature review to investigate how spatial structure influences species and their trophic interactions in fragmented habitats. For all empirical work, I used as a study system the arthropod assemblage found on patches of the salt marsh grass Spartina patens. In Chapter 1, I conducted seven surveys of habitat patches over three years to examine the effects of patch size, connectivity, and local environmental conditions on a guild of specialist sap-feeding herbivorous insects and their natural enemies. I found striking differences among species in the effects of both patch size and connectivity, which led to differences in species' relative abundances and trophic structure among these patches. In Chapter 2, I manipulated host plant quality and predator density to experimentally examine mechanisms that might structure this arthropod community. I found that positive responses of herbivores to experimentally-elevated patch quality were limited by dispersal constraints and that predation by abundant generalist spiders may constrain the spatial distribution of certain species. Investigating systems beyond the marsh, I conducted a literature review and analysis in Chapter 3 wherein I examined whether the spatial structure of habitats generally influences trophic interactions. From the literature, I identified 171 studies of trophic interactions in fragmented habitats and found that the influence of fragmentation and related variables on the occurrence or strength of trophic interactions was largely predictable based on the habitat affinity of interacting species. With this dataset, I also identified key gaps in the fragmentation literature, including a heavy bias towards the study of two-species interactions. Therefore, in Chapter 4 I took advantage of my data from the salt marsh to identify how, in addition to the two-species interactions of parasitism and egg predation, more complex food web interactions might depend on variation in the size of habitat patches. Overall, my findings show that variation in patch size can have varied, but predictable, effects on patch occupancy, population density, and interactions between species in fragmented habitats

GRASP [Genomic Resource Access for Stoichioproteomics]: comparative explorations of the atomic content of 12 Drosophila proteomes

“Stoichioproteomics” relates the elemental composition of proteins and proteomes to variation in the physiological and ecological environment. To help harness and explore the wealth of hypotheses made possible under this framework, we introduce GRASP (http://www.graspdb.net), a public bioinformatic knowledgebase containing information on the frequencies of 20 amino acids and atomic composition of their side chains. GRASP integrates comparative protein composition data with annotation data from multiple public databases. Currently, GRASP includes information on proteins of 12 sequenced Drosophila (fruit fly) proteomes, which will be expanded to include increasingly diverse organisms over time. In this paper we illustrate the potential of GRASP for testing stoichioproteomic hypotheses by conducting an exploratory investigation into the composition of 12 Drosophila proteomes, testing the prediction that protein atomic content is associated with species ecology and with protein expression levels. Elements varied predictably along multivariate axes. Species were broadly similar, with the D. willistoni proteome a clear outlier. As expected, individual protein atomic content within proteomes was influenced by protein function and amino acid biochemistry. Evolution in elemental composition across the phylogeny followed less predictable patterns, but was associated with broad ecological variation in diet. Using expression data available for D. melanogaster, we found evidence consistent with selection for efficient usage of elements within the proteome: as expected, nitrogen content was reduced in highly expressed proteins in most tissues, most strongly in the gut, where nutrients are assimilated, and least strongly in the germline. The patterns identified here using GRASP provide a foundation on which to base future research into the evolution of atomic composition in Drosophila and other taxa.https://doi.org/10.1186/1471-2164-14-59

The positive effect of plant diversity on soil carbon depends on climate

Little is currently known about how climate modulates the relationship between plant diversity and soil organic carbon and the mechanisms involved. Yet, this knowledge is of crucial importance in times of climate change and biodiversity loss. Here, we show that plant diversity is positively correlated with soil carbon content and soil carbon-to-nitrogen ratio across 84 grasslands on six continents that span wide climate gradients. The relationships between plant diversity and soil carbon as well as plant diversity and soil organic matter quality (carbon-to-nitrogen ratio) are particularly strong in warm and arid climates. While plant biomass is positively correlated with soil carbon, plant biomass is not significantly correlated with plant diversity. Our results indicate that plant diversity influences soil carbon storage not via the quantity of organic matter (plant biomass) inputs to soil, but through the quality of organic matter. The study implies that ecosystem management that restores plant diversity likely enhances soil carbon sequestration, particularly in warm and arid climates

A Scalable System for Production of Functional Pancreatic Progenitors from Human Embryonic Stem Cells

Development of a human embryonic stem cell (hESC)-based therapy for type 1 diabetes will require the translation of proof-of-principle concepts into a scalable, controlled, and regulated cell manufacturing process. We have previously demonstrated that hESC can be directed to differentiate into pancreatic progenitors that mature into functional glucose-responsive, insulin-secreting cells in vivo. In this study we describe hESC expansion and banking methods and a suspension-based differentiation system, which together underpin an integrated scalable manufacturing process for producing pancreatic progenitors. This system has been optimized for the CyT49 cell line. Accordingly, qualified large-scale single-cell master and working cGMP cell banks of CyT49 have been generated to provide a virtually unlimited starting resource for manufacturing. Upon thaw from these banks, we expanded CyT49 for two weeks in an adherent culture format that achieves 50–100 fold expansion per week. Undifferentiated CyT49 were then aggregated into clusters in dynamic rotational suspension culture, followed by differentiation en masse for two weeks with a four-stage protocol. Numerous scaled differentiation runs generated reproducible and defined population compositions highly enriched for pancreatic cell lineages, as shown by examining mRNA expression at each stage of differentiation and flow cytometry of the final population. Islet-like tissue containing glucose-responsive, insulin-secreting cells was generated upon implantation into mice. By four- to five-months post-engraftment, mature neo-pancreatic tissue was sufficient to protect against streptozotocin (STZ)-induced hyperglycemia. In summary, we have developed a tractable manufacturing process for the generation of functional pancreatic progenitors from hESC on a scale amenable to clinical entry

Crop pests and predators exhibit inconsistent responses to surrounding landscape composition

The idea that noncrop habitat enhances pest control and represents a win–win opportunity to conserve biodiversity and bolster yields has emerged as an agroecological paradigm. However, while noncrop habitat in landscapes surrounding farms sometimes benefits pest predators, natural enemy responses remain heterogeneous across studies and effects on pests are inconclusive. The observed heterogeneity in species responses to noncrop habitat may be biological in origin or could result from variation in how habitat and biocontrol are measured. Here, we use a pest-control database encompassing 132 studies and 6,759 sites worldwide to model natural enemy and pest abundances, predation rates, and crop damage as a function of landscape composition. Our results showed that although landscape composition explained significant variation within studies, pest and enemy abundances, predation rates, crop damage, and yields each exhibited different responses across studies, sometimes increasing and sometimes decreasing in landscapes with more noncrop habitat but overall showing no consistent trend. Thus, models that used landscape-composition variables to predict pest-control dynamics demonstrated little potential to explain variation across studies, though prediction did improve when comparing studies with similar crop and landscape features. Overall, our work shows that surrounding noncrop habitat does not consistently improve pest management, meaning habitat conservation may bolster production in some systems and depress yields in others. Future efforts to develop tools that inform farmers when habitat conservation truly represents a win–win would benefit from increased understanding of how landscape effects are modulated by local farm management and the biology of pests and their enemies

Impact of intra- versus inter-annual snow depth variation on water relations and photosynthesis for two Great Basin Desert shrubs

Snowfall provides the majority of soil water in certain ecosystems of North America. We tested the hypothesis that snow depth variation affects soil water content, which in turn drives water potential (Ψ) and photosynthesis, over 10 years for two widespread shrubs of the western USA. Stem Ψ (Ψ stem) and photosynthetic gas exchange [stomatal conductance to water vapor (g s), and CO2 assimilation (A)] were measured in mid-June each year from 2004 to 2013 for Artemisia tridentata var. vaseyana (Asteraceae) and Purshia tridentata (Rosaceae). Snow fences were used to create increased or decreased snow depth plots. Snow depth on +snow plots was about twice that of ambient plots in most years, and 20 % lower on -snow plots, consistent with several down-scaled climate model projections. Maximal soil water content at 40- and 100-cm depths was correlated with February snow depth. For both species, multivariate ANOVA (MANOVA) showed that Ψ stem, g s, and A were significantly affected by intra-annual variation in snow depth. Within years, MANOVA showed that only A was significantly affected by spatial snow depth treatments for A. tridentata, and Ψ stem was significantly affected by snow depth for P. tridentata. Results show that stem water relations and photosynthetic gas exchange for these two cold desert shrub species in mid-June were more affected by inter-annual variation in snow depth by comparison to within-year spatial variation in snow depth. The results highlight the potential importance of changes in inter-annual variation in snowfall for future shrub photosynthesis in the western Great Basin Desert

Supplement 1. Effect sizes and species traits used in the species abundance meta-analysis.

<h2>File List</h2><div> <p><a href="species_effect_sizes.csv">species_effect_sizes.csv</a> (MD5: 814d3f03927e6dcb0a9cf28c7ea4b5da) </p> </div><h2>Description</h2><div> <p>The file, species effect sizes.csv, presents data utilized in the species abundance meta-analysis. Included are details on the publications used for the analysis (record ‘ID’, ‘Author’, ‘Year’, ‘City’, ‘Country’). Species names are given as per the original publication (‘Given.Name’) along with any modifications to the name due to spelling errors, synonyms, or taxonomic revisions (‘Binomial.Accepted’). All names were verified using Lorenz (2005); an asterisk in the Binomial. Accepted column indicates names that were not listed as accepted names in Lorenz (2005). ‘Subfamily,’ ‘Tribe,’ and ‘Subtribe’ are given, again using Lorenz (2005). Ecological traits were recorded at the species-level: ‘Body.Size’ (median length, in mm), ‘Wing.Morph’, ‘Habitat.Specific’ (listing particular details on habitat use), ‘Habitat.Category’ (used for the analysis), and ‘Trophic.Level.’ The effect size used in the analysis is given as the log response ratio (‘LRR’).</p> </div