scholarly journals It's what's on the inside that counts: stress physiology and the bacterial microbiome of a wild urban mammal

2019 ◽  
Vol 286 (1913) ◽  
pp. 20192111 ◽  
Author(s):  
Mason R. Stothart ◽  
Rupert Palme ◽  
Amy E. M. Newman
Keyword(s):  
Environmental Change ◽  
Hpa Axis ◽  
Careful Consideration ◽  
Sciurus Carolinensis ◽  
Grey Squirrel ◽  
Nutrient Sources ◽  
Neutrophil Lymphocyte Ratio ◽  
Trade Offs ◽  
Faecal Glucocorticoid Metabolites ◽  
Host Physiology

The microbiome's capacity to shape the host phenotype and its mutability underlie theorization that the microbiome might facilitate host acclimation to rapid environmental change. However, when environmental change occurs, it is unclear whether resultant microbiome restructuring is proximately driven by this changing external environment or by the host's physiological response to this change. We leveraged urbanization to compare the ability of host environment (urban or forest) versus multi-scale biological measures of host hypothalamic–pituitary–adrenal (HPA) axis physiology (neutrophil : lymphocyte ratio, faecal glucocorticoid metabolites, hair cortisol) to explain variation in the eastern grey squirrel ( Sciurus carolinensis ) faecal microbiome. Urban and forest squirrels differed across all three of the interpretations of HPA axis activity we measured. Direct consideration of these physiological measures better explained greater phylogenetic turnover between squirrels than environment. This pattern was strongly driven by trade-offs between bacteria which specialize on metabolizing digesta versus host-derived nutrient sources. Drawing on ecological theory to explain patterns in intestinal bacterial communities, we conclude that although environmental change can affect the microbiome, it might primarily do so indirectly by altering host physiology. We demonstrate that the inclusion and careful consideration of dynamic, rather than fixed (e.g. sex), dimensions of host physiology are essential for the study of host–microbe symbioses at the micro-evolutionary scale.

scholarly journals Shades of Grey: Host Phenotype Dependent Effect of Urbanization on the Bacterial Microbiome of a Wild Mammal

2021 ◽  
Author(s):  
Mason R Stothart ◽  
Amy E.M. Newman
Keyword(s):  
Built Environment ◽  
Environmental Change ◽  
Habitat Heterogeneity ◽  
Spatial Scales ◽  
Coat Colour ◽  
Intestinal Microbiome ◽  
Rrna Gene ◽  
Sciurus Carolinensis ◽  
Grey Squirrel ◽  
Grey Squirrels

Abstract Background Host-associated microbiota are integral to the ecology of their host and may help wildlife species cope with rapid environmental change. Urbanization is a globally replicated form of severe environmental change which we can leverage to better understand wildlife microbiomes. Does the colonization of separate cities result in parallel changes in the intestinal microbiome of wildlife, and if so, does within-city habitat heterogeneity matter? Using 16S rRNA gene amplicon sequencing, we quantified the effect of urbanization on the microbiome of eastern grey squirrels (Sciurus carolinensis). Eastern grey squirrels are ubiquitous in rural and urban environments throughout their native range, across which they display an apparent coat colour polymorphism (agouti, black, intermediate). Results Grey squirrel microbiomes differed between rural and city environments; however, comparable variation was explained by habitat heterogeneity within cities. Our analyses suggest that operational taxonomic unit (OTU) community structure was more strongly influenced by local environmental conditions (rural and city forests versus human built habitats) than urbanization of the broader landscape (city versus rural). The bacterial genera characterizing the microbiomes of built-environment squirrels are thought to specialize on host-derived products and have been linked in previous research to low fibre diets. However, despite an effect of urbanization at fine spatial scales, phylogenetic patterns in the microbiome were coat colour phenotype dependent. City and built environment agouti squirrels displayed greater phylogenetic beta-dispersion than those in rural or forest environments, and null modelling results indicated that the phylogenetic structure of urban agouti squirrels did not differ greatly from stochastic expectations. Conclusions Habitat heterogeneity at fine spatial scales affects host-associated microbiomes, however, we found little evidence that this pattern was the result of similar selective pressures acting on the microbiome within environments. Further, this result, those of phylogeny-independent analyses, and patterns of beta-dispersion lead us to suggest that microbiota dispersal and ecological drift are integral to shaping the inter-environmental differences we observed. These patterns were partly mediated by squirrel coat colour phenotype. Given a well-known urban cline in squirrel coat colour melanism, grey squirrels provide a useful free-living system with which to study how host genetics mediate environment x microbiome interactions.

scholarly journals Shades of grey: Coat-colour dependent effect of urbanization on the bacterial microbiome of a wild mammal

2021 ◽  
Author(s):  
Mason R. Stothart ◽  
Amy E.M. Newman
Keyword(s):  
Built Environment ◽  
Environmental Change ◽  
Habitat Heterogeneity ◽  
Spatial Scales ◽  
Coat Colour ◽  
Intestinal Microbiome ◽  
Rrna Gene ◽  
Sciurus Carolinensis ◽  
Grey Squirrel ◽  
Grey Squirrels

AbstractBackgroundHost-associated microbiota can be fundamental to the ecology of their host and may even help wildlife species colonize novel niches or cope with rapid environmental change. Urbanization is a globally replicated form of severe environmental change which we can leverage to better understand wildlife microbiomes. Does the colonization of separate cities result in parallel changes in the intestinal microbiome of wildlife, and if so, does within-city habitat heterogeneity matter? Using 16S rRNA gene amplicon sequencing, we quantified the effect of urbanization on the microbiome of eastern grey squirrels (Sciurus carolinensis). Eastern grey squirrels are ubiquitous in both rural and urban environments throughout their native range, across which they display an apparent coat colour polymorphism (agouti, black, intermediate).ResultsGrey squirrel microbiomes differed between rural and city environments; however, comparable variation was explained by habitat heterogeneity within cities. Our analyses suggest that operational taxonomic unit (OTU) community structure was more strongly influenced by local environmental conditions (rural and city forests versus human built habitats) than urbanization of the broader landscape (city versus rural). Many of the bacterial genera identified as characterizing the microbiomes of built-environment squirrels are though to specialize on host-derived products and have been linked in previous research to low fibre diets. However, despite an effect of urbanization at fine spatial scales, phylogenetic patterns in the microbiome were coat colour phenotype dependent. City and built environment agouti squirrels displayed greater phylogenetic beta-dispersion than those in rural or forest environments, and null modelling results indicated that the phylogenetic structure of urban agouti squirrels did not differ greatly from stochastic phylogenetic expectations.ConclusionsHabitat heterogeneity at fine spatial scales affects host-associated microbiomes, however, we found little evidence that this pattern was the result of similar selective pressures acting on the microbiome within environments. Further, this result, those of phylogeny-independent analyses, and patterns of beta-dispersion lead us to suggest that microbiota dispersal and ecological drift are integral to shaping the inter-environmental differences we observed. These patterns were partly mediated by squirrel coat colour phenotype, and therefore putatively, host physiology. Given a well-known urban cline in squirrel coat colour melanism, grey squirrels provide an ideal free-living system with which to study how host genetics mediate environment x microbiome interactions.

scholarly journals Shades of grey: host phenotype dependent effect of urbanization on the bacterial microbiome of a wild mammal

2021 ◽  
Vol 3 (1) ◽  
Author(s):  
Mason R. Stothart ◽  
Amy E. M. Newman
Keyword(s):  
Built Environment ◽  
Environmental Change ◽  
Habitat Heterogeneity ◽  
Spatial Scales ◽  
Coat Colour ◽  
Intestinal Microbiome ◽  
Rrna Gene ◽  
Sciurus Carolinensis ◽  
Grey Squirrel ◽  
Grey Squirrels

Abstract Background Host-associated microbiota are integral to the ecology of their host and may help wildlife species cope with rapid environmental change. Urbanization is a globally replicated form of severe environmental change which we can leverage to better understand wildlife microbiomes. Does the colonization of separate cities result in parallel changes in the intestinal microbiome of wildlife, and if so, does within-city habitat heterogeneity matter? Using 16S rRNA gene amplicon sequencing, we quantified the effect of urbanization (across three cities) on the microbiome of eastern grey squirrels (Sciurus carolinensis). Grey squirrels are ubiquitous in rural and urban environments throughout their native range, across which they display an apparent coat colour polymorphism (agouti, black, intermediate). Results Grey squirrel microbiomes differed between rural and city environments; however, comparable variation was explained by habitat heterogeneity within cities. Our analyses suggest that operational taxonomic unit (OTU) community structure was more strongly influenced by local environmental conditions (rural and city forests versus human built habitats) than urbanization of the broader landscape (city versus rural). The bacterial genera characterizing the microbiomes of built-environment squirrels are thought to specialize on host-derived products and have been linked in previous research to low fibre diets. However, despite an effect of urbanization at fine spatial scales, phylogenetic patterns in the microbiome were coat colour phenotype dependent. City and built-environment agouti squirrels displayed greater phylogenetic beta-dispersion than those in rural or forest environments, and null modelling results indicated that the phylogenetic structure of urban agouti squirrels did not differ greatly from stochastic expectations. Conclusions Squirrel microbiomes differed between city and rural environments, but differences of comparable magnitude were observed between land classes at a within-city scale. We did not observe strong evidence that inter-environmental differences were the result of disparate selective pressures. Rather, our results suggest that microbiota dispersal and ecological drift are integral to shaping the inter-environmental differences we observed. However, these processes were partly mediated by squirrel coat colour phenotype. Given a well-known urban cline in squirrel coat colour melanism, grey squirrels provide a useful free-living system with which to study how host genetics mediate environment x microbiome interactions.

scholarly journals Novel combination of CRISPR-based gene drives eliminates resistance and localises spread

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Nicky R. Faber ◽  
Gus R. McFarlane ◽  
R. Chris Gaynor ◽  
Ivan Pocrnic ◽  
C. Bruce A. Whitelaw ◽  
...  
Keyword(s):  
Driving Forces ◽  
Spatial Models ◽  
Cost Effective ◽  
Biodiversity Loss ◽  
Invasive Pest ◽  
Economic Losses ◽  
Sciurus Carolinensis ◽  
Gene Drive ◽  
Grey Squirrel ◽  
Gene Drives

AbstractInvasive species are among the major driving forces behind biodiversity loss. Gene drive technology may offer a humane, efficient and cost-effective method of control. For safe and effective deployment it is vital that a gene drive is both self-limiting and can overcome evolutionary resistance. We present HD-ClvR in this modelling study, a novel combination of CRISPR-based gene drives that eliminates resistance and localises spread. As a case study, we model HD-ClvR in the grey squirrel (Sciurus carolinensis), which is an invasive pest in the UK and responsible for both biodiversity and economic losses. HD-ClvR combats resistance allele formation by combining a homing gene drive with a cleave-and-rescue gene drive. The inclusion of a self-limiting daisyfield gene drive allows for controllable localisation based on animal supplementation. We use both randomly mating and spatial models to simulate this strategy. Our findings show that HD-ClvR could effectively control a targeted grey squirrel population, with little risk to other populations. HD-ClvR offers an efficient, self-limiting and controllable gene drive for managing invasive pests.

A framework for the Integrated Assessment of SDG trade-offs in the Sundarbans Biosphere Reserve.

2021 ◽  
Author(s):  
Charlotte Marcinko ◽  
Robert Nicholls ◽  
Tim Daw ◽  
Sugata Hazra ◽  
Craig Hutton ◽  
...  
Keyword(s):  
Environmental Change ◽  
Integrated Assessment ◽  
Spatial Scales ◽  
Strong Dependence ◽  
Management Strategies ◽  
Rural Livelihoods ◽  
Biosphere Reserve ◽  
Integrated Analysis ◽  
Trade Offs ◽  
The Sundarbans

<p>The United Nations Sustainable Development Goals (SDGs) and their corresponding targets are significantly interconnected, with many interactions, synergies and trade-offs between individual goals across multiple temporal and spatial scales.  We propose a framework for the Integrated Assessment Modelling (IAM) of a complex deltaic socio-ecological system in order to analyse such SDG interactions. We focus on the Sundarbans Biosphere Reserve (SBR), India within the Ganges-Brahmaputra-Meghna Delta. It is densely populated with 4.4 million people (2011), high levels of poverty and a strong dependence on rural livelihoods. It is only 50 km from the growing megacity of Kolkata (about 15 million people in 2020). The area also includes the Indian portion of the world’s largest mangrove forest – the Sundarbans – hosting the iconic Bengal Tiger. Like all deltaic systems, this area is subject to multiple drivers of environmental change operating across different scales. The IAM framework is designed to investigate current and future trends in socio-environmental change and explore associated policy impacts, considering a broad range of sub-thematic SDG indicators. Integration is achieved through the soft coupling of multiple sub-models, knowledge and data of relevant environmental and socio-economic processes.  The following elements are explicitly considered: (1) agriculture; (2) aquaculture; (3) mangroves; (4) fisheries; and (5) multidimensional poverty. Key questions that can be addressed include the implications of changing monsoon patterns, trade-offs between agriculture and aquaculture, or the future of the Sundarbans mangroves under sea-level rise and different management strategies, including trade-offs with land use to the north.  The novel high-resolution analysis of SDG interactions allowed by the IAM will provide stakeholders and policy makers the opportunity to prioritize and explore the SDG targets that are most relevant to the SBR and provide a foundation for further integrated analysis.</p>

scholarly journals The genome sequence of the eastern grey squirrel, Sciurus carolinensis Gmelin, 1788

2020 ◽  
Vol 5 ◽  
pp. 27
Author(s):  
Dan Mead ◽  
Kathryn Fingland ◽  
Rachel Cripps ◽  
Roberto Portela Miguez ◽  
Michelle Smith ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Sex Chromosomes ◽  
Genome Assembly ◽  
Sciurus Carolinensis ◽  
Grey Squirrel ◽  
Individual Male ◽  
A Genome

We present a genome assembly from an individual male Sciurus carolinensis (the eastern grey squirrel; Vertebrata; Mammalia; Eutheria; Rodentia; Sciuridae). The genome sequence is 2.82 gigabases in span. The majority of the assembly (92.3%) is scaffolded into 21 chromosomal-level scaffolds, with both X and Y sex chromosomes assembled.

scholarly journals Demand for provisioning ecosystem services as a driver of change in the Canadian boreal zone1

2019 ◽  
Vol 27 (2) ◽  
pp. 166-184 ◽  
Author(s):  
Maitane Erdozain ◽  
Erika C. Freeman ◽  
Camille Ouellet Dallaire ◽  
Sonja Teichert ◽  
Harry W. Nelson ◽  
...  
Keyword(s):  
Climate Change ◽  
Ecosystem Services ◽  
Cumulative Effect ◽  
Careful Consideration ◽  
Wood Products ◽  
Boreal Zone ◽  
Drivers Of Change ◽  
Trade Offs ◽  
Provisioning Ecosystem Services ◽  
The Future

The Canadian boreal zone provides extractive goods and services (provisioning ecosystem services (PrES)) to domestic and global markets and makes a significant contribution to the Canadian economy. The intensity and location of these extractive activities, however, may positively or negatively affect the availability of other benefits that the Canadian and global society receive from the boreal. Where PrES compete, managing these activities along with their impacts to boreal ecosystems becomes a balancing act between the need for resource extraction and the continued availability of the other benefits from ecosystems. Management measures and policies are more likely to succeed if they are designed with foresight, which means accounting for how demand, a key driver of change in the boreal, may change in the future. To help this process, we present three divergent, yet plausible future scenarios based on the analysis of: (i) the capacity of the boreal to provide wood products, fossil fuels, metals and minerals, and hydropower and other renewables; (ii) past trends (1985–2015) and key events in the demand for these PrES; (iii) the interaction of demand for PrES with other drivers of change to the boreal zone; and (iv) the synergies and trade-offs between PrES. We find that historically and currently the capacity of the boreal to provide these PrES exceeds the amount currently supplied. However, the capacity of different PrES and location of extractive activities are spatially dispersed creating a spatial and temporal patchwork of associated risks to local ecosystem integrity and the supply of non-PrES. In addition, these scenarios suggest that the future of boreal PrES is very uncertain and highly dependent on how other drivers of change (namely governance and geopolitics, societal values and climate change) play out in the future. Given the spatial complexity, we find that the cumulative effect of these drivers (e.g., climate change) will determine what paths unfold for different areas of the boreal, and we conclude that careful consideration and planning must be given to ensure that the balance between PrES and non-PrES is maintained.

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