bioRxiv - Ecology最新文献

{"title":"Diet driven differences in host tolerance are linked to shifts in global gene expression in a common avian host-pathogen system","authors":"Erin L Sauer, Carson Stacy, Weston Perrine, Ashley C Love, Jeffrey A Lewis, Sarah E DuRant","doi":"10.1101/2024.08.07.607042","DOIUrl":"https://doi.org/10.1101/2024.08.07.607042","url":null,"abstract":"As humans alter the landscape, wildlife have become increasingly dependent on anthropogenic resources, altering interactions between individuals and subsequently disease transmission dynamics. Further, nutritional quantity and quality greatly impact an individual hosts immune capacity and ability to mitigate damage caused by infectious disease. Thus, understanding the impact of dietary nutrition on immune function is critical for predicting disease severity and transmission as human activity both facilitates the dispersal of pathogens and alters dietary options for wildlife. Here, we use transcriptomics to explore the previously unstudied molecular mechanisms underpinning diet-driven differences in pathogen tolerance using a widespread avian bacterial pathogen, Mycoplasma gallisepticum (MG). MG is an ideal model for understanding the dietary drivers of disease as the human supplementation that wild birds commonly rely on, bird feeders, are also an important source for MG transmission. Significant diet-driven differences in the expression of many genes encoding immune response and translational machinery proteins are seen both in the absence of MG and during the recovery period. Prior to infection, protein-fed birds are more transcriptionally primed for infection than lipid-fed birds which translates to greater tolerance in protein-fed birds during the recovery period. Given the significant importance of human supplemented food in wildlife disease systems, the molecular mechanisms by which interactions between diet and infection emerge provide insight into the ecological and immunological consequences of human behavior and wildlife disease.","PeriodicalId":501320,"journal":{"name":"bioRxiv - Ecology","volume":"56 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-08-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141930819","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Rapid GIT transit time in volant vertebrates, with implications for convergence in microbiome composition","authors":"Emily Cornelius Ruhs, Katherine McFerrin, Devin N Jones, Natalia Cortes-Delgado, Ny Anjara Fifi Ravelomanantsoa, Carl J Yeoman, Raina K Plowright, Cara E Brook","doi":"10.1101/2024.08.09.607319","DOIUrl":"https://doi.org/10.1101/2024.08.09.607319","url":null,"abstract":"Flying birds and bats have simplified gastrointestinal tracts (GITs) and low intestinal mass to facilitate flight. Previous work showed reduced GIT transit times in birds relative to other vertebrates, but GIT transit has never been collectively quantified for bats. Unique among mammals, bat GIT microbiomes are dominated by Pseudomonadota bacteria (previously Proteobacteria), which also dominate the microbiomes of flying birds; we hypothesized this convergence to result from rapid GIT transit times for both volant taxa. We conducted a meta-analysis of vertebrate GIT transit times which showed that bats and flying birds have significantly faster transit times relative to nonvolant vertebrates. Additionally, within the bat order (Chiroptera), we demonstrated decreasing transit times associated with increasing body mass, a pattern contrasting other vertebrates (including volant birds) and possibly influencing GIT microbiome composition. This inverted mass-transit association is likely driven by diet as fruit- and nectar-consuming Pteropodids are the largest of all bats.","PeriodicalId":501320,"journal":{"name":"bioRxiv - Ecology","volume":"30 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-08-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141930769","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Forecasting hotspots of grassland suitability under climate change for restoration","authors":"Santosh Kumar Rana, Jessica Lindstrom, Melissa A Lehrer, Marissa Ahlering, Jill Hamilton","doi":"10.1101/2024.08.08.607270","DOIUrl":"https://doi.org/10.1101/2024.08.08.607270","url":null,"abstract":"Abstract ●Local species-climate relationships are often considered in restoration management. However, as climate change disrupts species-climate relationships, identifying factors that influence habitat suitability now and into the future for individual species, functional groups, and communities will be increasingly important for restoration. This involves identifying hotspots of community suitability to target seed sourcing and restoration efforts.\u0000●Using ensemble species distribution modeling (eSDM), we analyzed 26 grassland species commonly used in restoration to identify bioclimatic variables influencing their distributions. We predicted habitat suitability under current and future (2050) climates and identified hotspots where diverse species and functional group suitability was greatest. These hotspots of habitat suitability were then overlaid with estimates of landscape connectivity and protected status to quantify potential suitability for restoration now and into the future. ●Temperature and precipitation during warmer quarters largely influenced grassland species habitat suitability. Hotspots of grassland habitat suitability were identified in Minnesota, North Dakota, and South Dakota, with projected northward shifts under future climate scenarios. Overlaying these hotspots with estimates of landscape connectivity and protected status revealed limited connectivity and protection, highlighting regions to prioritize for restoration and conservation efforts.\u0000●Leveraging an understanding of species relationship with climate, this research emphasizes the importance of quantifying connectivity and protected status across aggregated hotspots of species suitability for conservation and restoration. Identifying these hotspots now and into the future can be used to prioritize regions for seed sourcing and restoration, ensuring long-term maintenance of functional ecosystems across grassland communities.","PeriodicalId":501320,"journal":{"name":"bioRxiv - Ecology","volume":"24 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-08-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141968639","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Divergence of discrete- versus continuous-time calculations of the temperature dependence of maximum population growth rate in a disease vector","authors":"Paul J Huxley, Leah R Johnson, Lauren Cator, Samraat Pawar","doi":"10.1101/2024.08.09.607340","DOIUrl":"https://doi.org/10.1101/2024.08.09.607340","url":null,"abstract":"The temperature dependence of maximal population growth rate (<em>r</em>_m) is key to predicting how organisms respond and adapt to natural and anthropogenic changes in climate. For organisms with complex life histories, discrete-time matrix projection models (MPMs) can be used to calculate temperature-dependent <em>r</em>_m because they directly capture variation in empirically-observed life-history trait values as well as the time delays inherent in those traits. However, MPM calculations can be laborious and do not capture the continuous nature of time. Temperature-dependent <em>r</em>_m calculated from more complex approaches based on delay-differential equation and integral projection models are more accurate but are notoriously difficult to parameterise. Ordinary differential equation-based models (ODEMs) offer a relatively tractable alternative of intermediate complexity but it is largely unknown whether ODEM-based calculations and MPMs broadly agree when the effects of time delays and altered juvenile survival trajectories on temperature-dependent <em>r</em>_m are introduced by environmental variation. Here we investigate differences in the predicted temperature dependence of <em>r</em>_m obtained from an ODE-based model with those calculated from MPMs using high-resolution temperature- and resource dependent life-history trait data for the globally-distributed disease vector, <em>Aedes aegypti</em>. We show that the level of agreement between discrete- and continuous-time representations of temperature-dependent <em>r</em>_m can vary with resource availability, and is extremely sensitive to how juvenile survival is characterised. This finding suggests that analytic <em>r</em>_m models can consistently provide comparable <em>r</em>_m predictions to standard methods except for under severe resource constraints. Our study also suggests that all formulations of the intrinsic growth rate of a population may not be equally accurate for all types of organisms in all situations. Furthermore, this study's findings raise questions relating to whether existing mathematical models can be used to predict and understand population-level effects of environmental change.","PeriodicalId":501320,"journal":{"name":"bioRxiv - Ecology","volume":"57 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-08-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141930770","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Niche and spatial partitioning restrain ecological equivalence among microbes along aquatic redox gradient","authors":"Katarina Kajan, Rasmus Kirkegaard, Petra Pjevac, Sandi Orlic, Maliheh Mehrshad","doi":"10.1101/2024.08.09.607300","DOIUrl":"https://doi.org/10.1101/2024.08.09.607300","url":null,"abstract":"Microbial metabolic capabilities and interactions shape their niche hypervolume that in turn governs their ecological strategies and ecosystem services. In the context of functional redundancy or ecological equivalence, the focus has been on functional guilds in order to bypass the complex challenge faced by niche theory for disentangling the niche hypervolume. However, in some cases this simplification has been at the expense of ignoring the role of individual genotype of each microbe within a functional guild and fails to explain how the diversity within each functional guild is maintained. In this study, we inspect the metabolic profile of metagenome-assembled genomes along the pronounced redox gradient of the water column in an anchialine cave. Bridging neutral theory of biodiversity and biogeography and niche theory, our analysis uses focal metabolic capabilities while also incorporating individuality by looking into background metabolic capabilities of each individual and further includes spatial distribution of microbes to delineate their niche space. Our results emphasize that differences in background metabolic capabilities are critical for furnishing the niche hypervolume of microbes carrying the same focal metabolic capability and refute their ecological equivalence with their spatial distribution further enables niche partitioning among them.","PeriodicalId":501320,"journal":{"name":"bioRxiv - Ecology","volume":"84 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-08-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141930768","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The Performance and Potential of Deep Learning for Predicting Species Distributions","authors":"Benjamin A Kellenberger, Kevin Winner, Walter Jetz","doi":"10.1101/2024.08.09.607358","DOIUrl":"https://doi.org/10.1101/2024.08.09.607358","url":null,"abstract":"Species distribution models (SDMs) address the whereabouts of species and are central to ecology. Deep learning (DL) is poised to further elevate the already significant role of SDMs in ecology and conservation, but the potential and limitations of this transformation are still largely unassessed. We evaluate DL SDMs for 2,299 terrestrial vertebrate and invertebrate species at continental scale and 1km resolution in a like-for-like comparison with latest implementation of classic SDMs. We compare two DL methods (a multi-layer perceptron (MLP) on point covariates and a convolutional neural network (CNN) on geospatial patches) against existing SDMs (Maxent and Random Forest). On average, DL models match, but do not surpass, the performance of existing methods. DL performance is substantially weaker for species with narrow geographic ranges, fewer data points, and those assessed as threatened and hence often of greatest conservation concern. Furthermore, information leakage across dataset splits substantially inflates performance metrics, especially of CNNs. We find current DL SDMs to not provide significant gains, instead requiring careful experimental design to avoid biases. However, future advances in DL-supported use of ancillary ecological information have the potential to make DL a viable instrument in the larger SDM toolbox. Realising this opportunity will require a close collaboration between ecology and machine learning disciplines.","PeriodicalId":501320,"journal":{"name":"bioRxiv - Ecology","volume":"192 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-08-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141930816","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Trophic transfer and bioaccumulation of nanoplastics in Coryphaena hippurus (Mahi-mahi) and effect of depuration","authors":"Preyojon Dey, Terence M. Bradley, Alicia Boymelgreen","doi":"10.1101/2024.08.05.606698","DOIUrl":"https://doi.org/10.1101/2024.08.05.606698","url":null,"abstract":"Ocean plastic pollution is a global concern, exacerbated by the distinctive physiochemical characteristics of nanoplastics (NPs), making it crucial to study the impacts on marine animals. While most studies focus on the impacts of waterborne NP exposure, trophic transfer is another key transport mechanism that may also provide insight into the potential transfer of NPs to humans through the food chain. This study investigates polystyrene NP transfer to <em>Coryphaena hippurus</em> (mahi-mahi) larvae, a widely consumed fish and significant marine predator, during the early life stage. Using a two-step food chain, <em>Brachionus plicatilis</em> (rotifers) were exposed to NPs, and subsequently fed to <em>C. hippurus</em> larvae, with exposure durations ranging from 24 to 96 h. Significant NP transfer was observed via the food chain, varying with exposure duration. A depuration study over 72 h, simulating environmental intermittent NP exposure, revealed substantial NP excretion but also notable retention in the larvae. Biodistribution analysis indicated that most NPs accumulated in the gut, with a significant portion remaining post-depuration and some translocating to other body parts. Despite no significant effects on body length and eye diameter during this short study period, histopathological analysis revealed intestinal tissue damage in the larvae.","PeriodicalId":501320,"journal":{"name":"bioRxiv - Ecology","volume":"18 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-08-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141930824","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Quantifying irreversibility of ecological systems","authors":"Junang Li, Stephan B. Munch, Tzer Han Tan, Chuliang Song","doi":"10.1101/2024.08.04.606544","DOIUrl":"https://doi.org/10.1101/2024.08.04.606544","url":null,"abstract":"Irreversibility—the asymmetry of population dynamics when played forward versus backward in time—is a fundamental property of ecological dynamics. Despite its early recognition in ecology, irreversibility has remained a high-level and unquantifiable concept. Here, we introduce a quantitative framework rooted in non-equilibrium statistical physics to measure irreversibility in general ecological systems. Through theoretical analyses, we demonstrate that irreversibility quantifies the degree to which a system is out of equilibrium, a property not captured by traditional ecological metrics. We validate this prediction empirically across diverse ecological systems structured by different forces, such as rapid evolution, nutrient availability, and temperature. In sum, our study provides a rigorous formalism for quantifying irreversibility in ecological systems, with the potential to integrate dynamical, energetic, and informational perspectives in ecology.","PeriodicalId":501320,"journal":{"name":"bioRxiv - Ecology","volume":"11 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-08-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141930882","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Connectivity loss in experimental pond networks leads to biodiversity loss in microbial communities","authors":"Beáta Szabó, Máté Váczy-Földi, Csaba F. Vad, Károly Pálffy, Thu-Hương Huỳnh, Péter Dobosy, Ádám Fierpasz, Zsuzsanna Márton, Tamás Felföldi, Zsófia Horváth","doi":"10.1101/2024.08.05.606584","DOIUrl":"https://doi.org/10.1101/2024.08.05.606584","url":null,"abstract":"Habitat fragmentation is among the most important global threats to biodiversity, however, the direct effects of its components including connectivity loss are still lesser known. Our understanding of these drivers is especially limited in microbial communities. Here, by conducting a four-month outdoor experiment with artificial pond (mesocosm) metacommunities, we studied the effects of connectivity loss on planktonic prokaryote and microeukaryote communities. Connectivity loss was simulated by stopping the dispersal among local habitats while keeping the habitat amount constant and the abiotic environment homogeneous. We found that connectivity loss led to higher levels of extinction and a decrease in both local and regional diversity in microeukaryotes. In contrast, diversity patterns of prokaryotes remained largely unaffected, with some indications of extinction debt. Connectivity loss also led to lower evenness in microeukaryotes, likely through changes in biotic interactions with zooplankton grazers. Our results imply that connectivity loss can directly translate into species losses in communities and highlight the importance of conserving habitat networks with sufficient dispersal among local habitats.","PeriodicalId":501320,"journal":{"name":"bioRxiv - Ecology","volume":"46 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-08-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141930712","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Resource-use plasticity governs the causal relationship between traits and community structure in model microbial communities","authors":"Brendon McGuinness, Stephanie C. Weber, Frédéric Guichard","doi":"10.1101/2024.08.06.606555","DOIUrl":"https://doi.org/10.1101/2024.08.06.606555","url":null,"abstract":"Resolving the relationship between species’ traits and their relative abundance is a central challenge in ecology. Current hypotheses assume relative abundances either result from or are independent of traits. However, despite some success, these hypotheses do not integrate the reciprocal and feedback interactions between traits and abundances to predictions of community structure such as relative abundance distributions. Here we study how plasticity in resource-use traits govern the causal relationship between traits and relative abundances. We adopt a consumer-resource model that incorporates resource-use plasticity that operates to optimize organism growth, underpinned by investment constraints in physiological machinery for acquisition of resources. We demonstrate that the rate of plasticity controls the coupling strength between trait and abundance dynamics, predicting species’ relative abundance variation. We first show how plasticity in a single species in a community allows all other non-plastic species to coexist, a case of facilitation emerging from competitive interactions where a plastic species minimizes its similarity with competitors and maximizes resource-use efficiency in its environment. We apply this environment-competition trade-off to predict trait-abundance relationships and reveal that initial traits are better predictors of equilibrium abundances than final trait values. This result highlights the importance of transient dynamics that drive species sorting. The temporal scale of transients determines the strength of species sorting due to the emergence of ‘ecological equivalence’ at equilibrium. We propose trait-abundance feedback as an eco-evolutionary mechanism linking community structure and assembly, highlighting trait plasticity’s role in community dynamics.","PeriodicalId":501320,"journal":{"name":"bioRxiv - Ecology","volume":"15 Suppl 1 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-08-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141930822","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}