Biology subjects

Murray-Stoker, D.

Publications and source records attributed to Murray-Stoker, D..

7 recordsLinked to original sources

bioRxiv2024

Diversity and assembly of the microbiome of a leguminous plant along an urbanization gradient

Interactions between plants and bacterial communities are essential for host physiology and broader ecosystem functioning, but plant-microbiome interactions can be disrupted by environmental change like urbanization. Here, we evaluated how urbanization affected the diversity and assembly of soil and white clover (Trifolium repens) microbiome communities. We sampled 35 populations of white clover and associated roots and soil along an urbanization gradient. Soil alpha diversity was greater at the urban and rural limits of the gradient and lower in suburban habitats, while root alpha diversity was not influenced by urbanization. Root and soil bacterial communities had distinct compositions, with greater beta diversity for root compared to soil microbiomes. We found that urbanization directly and indirectly affected soil microbiome assembly, particularly through soil carbon. In contrast, root microbiome assembly was not linked to urbanization, which suggested that the host plant acted as an additional filter on microbiome assembly independent of urbanization. We also found that key pathogenic bacteria like Legionella and Clostridium varied in abundance with urbanization, which has implications for human health. Together, our study underscores the importance of examining how urban-driven environmental change alters the ecology and function of soil and root microbiomes.

ecology↗

bioRxiv2024

Comparing approaches to quantify urbanization on a multicontinental scale

Urbanization is an increasingly prevalent driver of environmental, ecological, and evolutionary change in both terrestrial and aquatic systems, and it is important that our sampling designs accurately capture this urban environmental change. Common approaches to sampling urban environments include: urban-nonurban transects, which sample along urbanization gradients; random points, which sample locations at random within an area of interest; and systematic points, which sample locations based on a regularly-spaced grid from a predetermined starting point within the area of interest. Presently, we lack a comparative analysis of the efficacy of these different sampling designs in capturing variation in urban environments. Here, we compare the environmental variation captured by transect- and point-based sampling designs in 136 cities across six continents. We quantified and compared a common set of environmental variables for each sampling design, with variables capturing landcover, climate, and socioeconomic facets of urban environments. Mean landcover and socioeconomic metrics consistently differed among sampling designs, in contrast to climate variables that primarily varied among cities. Additionally, changes in environmental variables with distance from the city centre depended on the sampling design, with this distance-by-sampling design interaction present in 27%-51% of cities, depending on the environmental variable. This implies that the rate of environmental change along urban-nonurban gradients frequently depends on the sampling design used. We also examined potential causes of deviations between transect- and point-based sampling designs and identified human population density and city area as common predictors of deviations between transect- and point-sampling designs. Our results show that sampling design can dictate how the urban environment is characterized, with sampling design as important - or more important - as the selected environmental variable. We further developed R code so researchers can implement these methods as they develop and validate sampling designs in novel or unstudied urban environments.

ecology↗

bioRxiv2023

Mosaic of local adaptation between white clover and rhizobia along an urbanization gradient

O_LIUrbanization frequently alters the biotic and abiotic environmental context. Variation in both the biotic and abiotic environment can result in selection mosaics that lead to locally adapted phenotypes. Ecological changes to urban environments have been found to result in evolutionary responses across a diverse array of plants and animals, but the effects of urbanization on local adaptation and coevolution between species remains largely unstudied. C_LIO_LIUsing a common garden experiment of 30 populations and 1080 plants, we tested for local adaptation in the mutualism between white clover (Trifolium repens) and rhizobia (Rhizobium leguminosarum symbiovar trifolii) along an urbanization gradient. We asked: (Q1) are white clover and rhizobia locally adapted? (Q2) Does nitrogen (N) addition mediate the strength of local adaptation? (Q3) Is the strength of local adaptation in host plants related to the strength of local adaptation in rhizobia, as expected if white clover and rhizobia are co-adapting? And (Q4) How does the degree of local adaptation vary with urbanization? C_LIO_LIWe found evidence for local adaptation for both white clover and rhizobia, with stronger signatures of local adaptation for rhizobia than white clover (Q1). While N addition positively affected plant biomass and negatively affected nodule density, N addition did not consistently mediate patterns of local adaptation (Q2). The strength of local adaptation was positively related between white clover and rhizobia under N addition, suggesting that soil N mediates co-adaptation between white clover and rhizobia (Q3). We did not find a consistent relationship between measures of urbanization and local adaptation (Q4). Additionally, fitness responses for white clover and rhizobia were unrelated to Rhizobium abundance and local adaptation was unrelated to the broader bacterial microbiome in the soil inoculants or root endosphere. C_LIO_LISynthesis. Our results show a spatial mosaic in local adaptation, with stronger local adaptation for rhizobia than white clover. While urbanization does influence the ecology of plant-microbe interactions, our study suggests urbanization does not disrupt local adaptation and coevolution among mutualists. C_LI

evolutionary biology↗

bioRxiv2022

Environmental filtering and habitat (mis)matching of riverine invertebrate metacommunities

AimMetacommunities are assembled through a combination of local and regional processes, with the relative importance of the drivers of assembly depending on ecological context. Global change can alter community assembly at both local and regional levels, potentially shifting communities into disequilibrium with their local environmental conditions. In this study, we evaluated the spatial variation in environmental filtering and habitat matching of 1078 riverine macroinvertebrate communities distributed across nine ecoregions within the conterminous United States. LocationConterminous United States. TaxonFreshwater macroinvertebrates. MethodsWe first quantified spatial patterns in environmental filtering, habitat matching, and functional trait diversity. We then used boosted regression trees to identify (1) functional trait predictors of environmental filtering and habitat matching and (2) environmental, landscape, and network variables that predict functional trait abundances. ResultsOur results demonstrated that environmental filtering but not habitat matching varied strongly by ecoregion. We also found that functional trait diversity varied by ecoregion, but not as strongly as the signatures of environmental filtering. We did not identify consistent functional trait predictors for both environmental filtering and habitat matching, with trait predictors instead varying by individual traits, trait categories, and ecoregions. Notwithstanding inconsistent trait predictors, environmental filtering was primarily influenced by habitat preference traits while habitat matching was primarily influenced by both habitat preference and dispersal traits. Predictors of functional traits also varied by trait category and ecoregion, with habitat preference and dispersal traits primarily influenced by network variables. Main conclusionsOur study demonstrates the contingent patterns and drivers of environmental filtering and habitat matching on a macroecological scale. We aim for this work to provide the foundation on which trait-environment relationships can be further quantified and causal explanations established in the context of community disequilibrium and applied to conservation and management of freshwater systems.

ecology↗

bioRxiv2021

Ecological consequences of urbanization on a legume-rhizobia mutualism

Mutualisms are key determinants of community assembly and composition, but urbanization can alter the dynamics of these interactions and associated effects on ecosystem functions. Legume-rhizobia mutualisms are a model interaction to evaluate the ecological and ecosystem-level effects of urbanization, particularly urban-driven eutrophication and nitrogen (N) deposition. Here, we evaluated how urbanization affected the ecology of the mutualism between white clover (Trifolium repens) and its rhizobial symbiont (Rhizobium leguminosarum symbiovar trifolii) along an urbanization gradient. We found that the abundance of rhizobium nodules on white clover decreased with urbanization. White clover acquired N from mixed sources of N fixation and uptake from the soil for the majority of the urbanization gradient, but white clover primarily acquired N from the soil rather than N fixation by rhizobia at the urban and rural limits of the gradient. Importantly, we identified soil N as a critical nexus for urban-driven changes in the white clover-rhizobium mutualism. Taken together, our results demonstrate that urbanization alters the ecological consequences of a legume-rhizobium mutualism, with direct and indirect effects of the urban landscape on an ecologically-important mutualistic interaction.

ecology↗

bioRxiv2019

On the efficacy of restoration in stream networks: comment and critique

Swan and Brown (2017) recently addressed the effects of restoration on stream communities under the meta-community framework. Using a combination of headwater and mainstem streams, Swan and Brown (2017) evaluated how position within a stream network affected the outcome of restoration on invertebrate communities. Ostensibly, their hypotheses were partially supported as restoration had stronger effects in headwater streams: invertebrate taxonomic richness was increased and temporal variability decreased in restored reaches; however, these results were not consistent upon closer scrutiny for both the original paper (Swan and Brown 2017) and the later erratum (Swan and Brown 2018). Here, I provide a secondary analysis of the data, with hypotheses and interpretations in the context of stream, meta-community, and restoration ecology. Swan and Brown (2017, 2018) evaluated the effect of restoration on sites receiving various combinations of in-channel manipulation and riparian reforestation treatments. Given the difference in the relative importance of environmental filtering and dispersal between headwaters and mainstems and the structure of river networks, I contend that different restoration treatments have differential effects between headwaters and mainstems. I hypothesized in-channel manipulations would have more consistent effects between headwaters and mainstems compared to riparian reforestation, and I used this hypothesis to guide site selection in the re-analysis. I then compared results from the re-analysis to those presented by Swan and Brown (2017, 2018). I did not find any effects of restoration on local diversity, spatial dissimilarity, or temporal variability, let alone differential effects of restoration between headwaters and mainstems; these results are contrary Swan and Brown (2017, 2018), who reported that restoration increased taxonomic richness, increased spatial dissimilarity, and decreased temporal variability in restored headwater streams. I demonstrate further that the statistical tests conducted by Swan and Brown (2017, 2018) were invalid and, therefore, recommend the use of the results presented here. More broadly, I suggest, in agreement with Swan and Brown (2017, 2018) and a growing body of research, that river and stream restoration will likely have greater success if a regional approach is taken to designing and implementing restoration projects.

ecology↗

bioRxiv2019

Functional diversity plays a role in driving β-diversity: Or does it?

Patrick and Brown (2018) suggest that functional diversity of the species pool has an important role in generating {beta}-diversity. Using a combination of path analysis and model selection, they ostensibly provide support for this hypothesis; however, they neglected to put theory and modeling into proper ecological and statistical context. Here, I present a re-analysis of their data. I conclude that the drivers of {beta}-diversity are variable, with functional diversity typically having a reduced, if any, role compared to consistently stronger roles played by {gamma}-diversity or environmental variation on structuring {beta}-diversity.

ecology↗