Biology subjects

Stewart, P. S.

Publications and source records attributed to Stewart, P. S..

6 recordsLinked to original sources

bioRxiv2024

Contrasting impacts of invasive Opuntia cacti on mammal habitat use

Biological invasions impact ecosystems worldwide, including through changing the behaviour of native species. Here, we used camera traps to investigate the effects of invasive Opuntia cacti on the habitat use of twelve mammal species in Laikipia County, Kenya, an internationally important region of mammalian biodiversity. We found that Opuntia impacted mammal occupancy and activity, but the strength and direction of the effects varied among species and between seasons, and depended on the spatial scale at which Opuntia was considered. Notably, we observed consistent positive effects for olive baboons and elephants, two major consumers of Opuntia fruit. We also observed seasonally varying effects on the occupancy of two key grazers: Grevys zebra and plains zebra. As well as having important implications for mammal conservation, ecosystem functioning, and the future spread of Opuntia, our findings highlight behavioural changes in large mammals as a potentially important pathway through which invasive species impact ecosystems.

ecology↗

bioRxiv2022

Model selection in occupancy models: inference versus prediction

Occupancy models are a vital tool for applied ecologists studying the patterns and drivers of species occurrence, but their use requires a method for selecting between models with different sets of occupancy and detection covariates. The information-theoretic approach, which employs information criteria such as Akaikes Information Criterion (AIC) is arguably the most popular approach for model selection in ecology and is often used for selecting occupancy models. However, the information-theoretic approach risks selecting models which produce inaccurate parameter estimates, due to a phenomenon called collider bias. Using simulations, we investigated the consequences of collider bias (using an illustrative example called M-bias) in the occupancy and detection processes of an occupancy model, and explored the implications for model selection using AIC and a common alternative, the Schwarz Criterion (or Bayesian Information Criterion, BIC). We found that when M-bias was present in the occupancy process, AIC and BIC selected models which inaccurately estimated the effect of the focal occupancy covariate, while simultaneously producing more accurate predictions of the site-level occupancy probability. In contrast, M-bias in the detection process did not impact the focal estimate; all models made accurate inferences, while the site-level predictions of the AIC/BIC-best model were slightly more accurate. Our results demonstrate that information criteria can be used to select occupancy covariates if the sole purpose of the model is prediction, but must be treated with more caution if the purpose is to understand how environmental variables affect occupancy. By contrast, detection covariates can usually be selected using information criteria regardless of the models purpose. These findings illustrate the importance of distinguishing between the tasks of parameter inference and prediction in ecological modelling. Furthermore, our results underline concerns about the use of information criteria to compare different biological hypotheses in observational studies. Open Research StatementCode to fully reproduce our simulations and analyses is available at: https://zenodo.org/badge/latestdoi/462801230

ecology↗

bioRxiv2020

Global impacts of climate change on avian functional diversity

Climate change is predicted to drive geographical range shifts in many taxa, leading to the formation of novel species assemblages and fluctuations in species richness worldwide. However, the effect of these changes on functional diversity is not yet fully understood, in part because comprehensive species-level trait data are generally lacking at global scales. Here we use morphometric and ecological trait data for 8269 terrestrial bird species to compare functional diversity (FD) of current and future bird assemblages under a medium emissions scenario. We show that future assemblages are likely to undergo substantial shifts in trait structure, with the direction and magnitude of these shifts varying with geographical location and trophic guild. Specifically, invertivore FD is projected to increase at higher latitudes with concurrent losses at mid-latitudes, reflecting poleward shifts in range, whereas frugivore FD is projected to fluctuate in many tropical regions with major declines in much of South America and New Guinea. We show that these projected changes in FD are generally greater than expected from changing species richness alone, indicating that projected FD changes are primarily driven by the loss or gain of functionally distinct species. Our findings suggest that climate change will drive continental-scale shifts in avian functional diversity, with potentially far-reaching implications for ecosystem functions and resilience.

ecology↗

bioRxiv2019

The origin of extracellular DNA in bacterial biofilm infections in vivo

Extracellular DNA (eDNA) plays an important role in both the aggregation of bacteria and in the interaction of the resulting biofilms with polymorphonuclear leukocytes (PMNs) during an inflammatory response. Here, transmission electron and confocal scanning laser microscopy were used to examine the interaction between biofilms of Pseudomonas aeruginosa and PMNs in a murine implant model and in lung tissue from chronically infected cystic fibrosis patients. PNA FISH, DNA staining, labeling of PMN DNA with a thymidine analogue, and immunohistochemistry were applied to localize bacteria, eDNA, PMN-derived eDNA, PMN-derived histone H3 (H3), neutrophil elastase (NE), and citrullinated H3 (citH3). Host-derived eDNA was observed surrounding bacterial aggregates but not within the biofilms. H3 localized to the lining of biofilms while NE was found throughout biofilms. CitH3, a marker for neutrophil extracellular traps (NETs) was detected only sporadically indicating that most host-derived eDNA in vivo was not a result of NETosis. Together these observations show that, in these in vivo biofilm infections with P. aeruginosa, the majority of eDNA is found external to the biofilm and derives from the host.\n\nAuthor summaryThe role of extracellular DNA (eDNA) has been described in vitro to play a major role in biofilm formation and antibiotic tolerance, but never for biofilm infections in vivo.\n\nTwo important characteristics of human chronic bacterial infections are aggregated bacteria and white blood cells (WBC). Bacteria use eDNA to stabilize biofilms and WBC use eDNA to trap bacteria. Given the importance of eDNA for both bacteria and WBC we show here for the first time that bacterial biofilms do not co-localize with either bacterial or WBC-derived eDNA during chronic infections. Our in vivo findings show eDNA is located outside biofilms as opposed to incorporated within the biofilm as commonly observed in vitro.\n\nWe believe that understanding the interplay between biofilms and WBC during chronic infection is essential if we are to elucidate the mechanisms underlying persistent infection and ascertain why WBC fail to eradicate bacteria; this will enable us to develop new treatment strategies.

microbiology↗

bioRxiv2018

Flux-Balance Based Modeling of Biofilm Communities

Models of microbial community dynamics generally rely on a sub-scale model for microbial metabolisms. In systems such as distributed multispecies communities like biofilms, where it is not reasonable to simplify to a small number of limiting substrates, tracking the large number of active metabolites likely requires measurement or estimation of large numbers of kinetic and regulatory parameters. Alternatively, a largely kinetics-free methodology is proposed combining cellular level constrained, steady state metabolic flux analysis with macro scale microbial community models. The methodology easily allows coupling of macroscale information, including measurement data, with cell-scale metabolism. Illustrative examples are included.

microbiology↗

bioRxiv2018

Nisin penetrates Staphylococcus aureus biofilms but shows differences in killing effects against sessile and planktonic cells.

Biofilms may restrict antimicrobial penetration and contribute to the recalcitrance of bacterial infections. In this work, we investigated the penetration of nisin into S. aureus biofilms and compared the susceptibility of S. aureus planktonic and sessile cells to this lantibiotic. Biofilms were grown under continuous flow in CDC reactors and calcein fluorescence was used to monitor the effect of nisin on the cytoplasmic membrane of S. aureus cells. Confocal scanning laser microscopy (CLSM) showed that calcein was lost within approximately 20 min in CDC biofilms, demonstrating that nisin penetrated to the bottom of the biofilm and caused membrane permeabilization. Viability analysis using PI staining showed that nisin was bactericidal against S. aureus sessile cells. Time-kill assays were performed against S. aureus in the following conditions: homogenized exponential planktonic (HEP), homogenized stationary planktonic (HSP), homogenized CDC biofilm (HB) and intact CDC biofilm (IB). The mean viability reduction of HEP and HSP were 6.71 and 1.64 log CFU.ml-1, respectively, confirming that stationary S. aureus cells were much less susceptible than exponential cells. The HB and IB treatments showed mean viability reductions of 1.25 and 0.50 log CFU.ml-1, respectively. Nisin activity against S. aureus was not limited by its ability to penetrate the bacterial biofilm, but the killing efficacy of the antimicrobial peptide was reduced by the physiological status of the biofilm-grown cells.\n\nImportanceBiofilms represent a major problem to control microorganisms in industrial environments and medical devices. We developed a direct real-time microscopic visualization technique to demonstrate experimentally that the antimicrobial peptide nisin is able to penetrate S. aureus biofilms. Our results confirmed that nisin caused membrane permeabilization of sessile bacteria and revealed qualitative agreement between viability loss and membrane integrity loss. This approach could improve the evaluation of antibacterial susceptibility breakpoints when testing the efficacy of standard and novel antimicrobials.

microbiology↗