Back

Journal of Applied Ecology

Wiley

Preprints posted in the last 30 days, ranked by how well they match Journal of Applied Ecology's content profile, based on 39 papers previously published here. The average preprint has a 0.04% match score for this journal, so anything above that is already an above-average fit.

1
Small stream restoration increases habitat and plant diversity across scales

Lerbs, L.; Singer, A.; Dotzert, A.; Grunwald, L.; Lampe, J.; Farwig, N.; Liepelt, S.; Willems, F. M.; Pinkert, S.; Bucharova, A.

2026-06-24 ecology 10.64898/2026.06.23.733988 medRxiv
Top 0.1%
22.0%
Show abstract

A majority of stream restoration efforts in central Europe focus on streams that are less than five meters wide. Restoration aims to increase structural complexity, thereby enhancing habitat heterogeneity, promoting biodiversity, and reestablishing aquatic-terrestrial linkages that can drive responses in adjacent terrestrial communities. However, the effects of small stream restoration on terrestrial biodiversity remain poorly understood because research focuses mainly on large rivers. Here, we investigated the effects of restoration on the structural complexity of the stream channel as well as the terrestrial habitat and plant diversity on a local and landscape scale across 55 small streams in an agricultural landscape. We compared restored stream sections with non-restored ones that were similar to the conditions before restoration. We also assessed how restored sections changed over time since restoration. Restored stream sections showed a higher stream structural complexity and habitat diversity, both of which are targets of active restoration measures. Restoration also increased riparian plant diversity, both directly and indirectly through structural complexity and habitat diversity. Although time since restoration did not influence structural complexity, it drove successional changes in plant communities that became increasingly associated with wetland habitat conditions. Our results demonstrate that small stream restoration effectively increases floodplain habitat and plant diversity in agricultural landscapes, primarily by enhancing water availability in the floodplain. Restoration actions on small streams support biodiversity if they improve stream channel complexity, connect the stream with its floodplain, and create floodplain habitats.

2
Small scale habitat components as key drivers of biodiversity in urban park design

Trigos-Peral, G.; Reyes Lopez, J. L.

2026-07-01 ecology 10.64898/2026.06.30.735471 medRxiv
Top 0.1%
18.2%
Show abstract

Urban green spaces are increasingly recognised as important refuges for biodiversity, yet their ecological value depends strongly on design and management. Here, we investigate how fine-scale structural and microhabitat components shape urban ant assemblages, using ants as indicators of broader arthropod responses to urbanisation. Ant communities were sampled in twelve urban green spaces in Cordoba (southern Spain) over a ten-year period (2004 to 2013) using pitfall traps, alongside detailed characterisation of vegetation structure and ground-layer microhabitats. In total, 38 species and 25,578 individuals were recorded. Microhabitat variables explained 58% of the variation in species occurrence. Community differences among microhabitats were driven primarily by nestedness, with dense herbaceous cover acting as a core habitat and edge-related components contributing disproportionately to beta diversity. Tree abundance showed a unimodal relationship with species richness, with maximum diversity at intermediate densities, while shrub and lawn cover had weak or inconsistent effects. Fine-scale elements such as leaf litter, stones, woody debris, and small bare-ground patches strongly influenced species occurrence by providing thermal refugia, nesting substrates, and foraging opportunities. The invasive Argentine ant (Linepithema humile) exhibited strong but spatially restricted dominance and species-specific negative effects on native ants, emphasising the role of habitat context in mediating invasion impacts. Our results demonstrate that urban biodiversity is maximised by enhancing fine-scale habitat heterogeneity rather than increasing green cover alone. We highlight practical design principles for urban green infrastructure that prioritise structural diversity and ground-layer complexity to support resilient arthropod communities.

3
'Who Goes There?' Quantifying Scavenger-Carcass Activity at Mass Mortality Events

Barton, K. A.; Finnerty, P. B.; Bonat, S. J.; Martinez-Lopez, B.; Meisuria, N. Y.; Newsome, T. M.; Peel, A. J.; Smith, J. A.; Brookes, V. J.

2026-07-06 ecology 10.64898/2026.07.03.735954 medRxiv
Top 0.1%
18.0%
Show abstract

Mass mortality events (MMEs) create sudden pulses of carrion that can alter how vertebrate scavengers use carcass resources, including the frequency, duration, and timing of species-carcass contacts. These changes could have implications for pathogen transmission at the scavenger-carcass interface. We aimed to develop and apply a reproducible analytical framework for using camera-trap data to quantify transmission-relevant vertebrate activity at carcass sites under differing carrion biomass scenarios. We studied experimental carcass plots (single carcass ~43 kg; 'mass mortality' plots [10 carcasses, >350 kg total]; 6 of each) in Australia's alpine ecosystem. The framework integrated descriptive summaries (bipartite network analysis, Kaplan-Meier curves) and marked temporal point-process models to characterise structural and temporal dimensions of species-carcass activity. Mass mortality plots had greater overall visitation duration, occurring as sustained activity (50% of visitation event volume by day 17), compared with intense then rapidly declining activity at single carcasses (50% by day 8). Mass mortality plots also had higher predicted daily arrival probability and contact hours across most species, indicating an extended window for pathogen transmission. This framework provides empirically derived contact parameters for MME-related disease spread models using camera-trap data to identify potential transmission pathways at the scavenger-carcass interface.

4
One scale does not fit all: invasive predator identity determines the impact on native prey

Bonet Bigata, A.; Sutherland, C.; Lambin, X.

2026-06-27 ecology 10.64898/2026.06.26.734748 medRxiv
Top 0.1%
14.5%
Show abstract

O_LIWhen eradication is unfeasible, invasive predator control should evaluate how removal affects ecological responses by native species. Assessments often use total invasive predator abundance to evaluate prey responses, yet intraspecific variation in diet and space use means that some subgroups cause disproportionate impacts. Identifying these problem individuals, and the spatial scales over which their impacts operate, can enable targeted spatially explicit removal to maximise impact reduction. However, despite individual-level information is often already collected during trapping operations it is seldom included when analysing predator impacts, potentially biasing the conservation outcomes expected under blanket removal. C_LIO_LIWe use a novel framework and two decades of invasive predator control data to estimate how individual variation in residency status influences the distance-dependent impacts of invasive American mink Neogale vison on water vole Arvicola amphibius occupancy across two prey surveys. We also develop a sub-model to predict mink residency status for individuals with missing age data. C_LIO_LIThe probability of capturing adult mink decreased with elevation and years of control, indicating that long-term control altered the resident population and demographic composition of mink around water vole sites. C_LIO_LIDistance-dependent negative impacts of mink varied by residency status, becoming negligible at approximately 20 km from water vole sites for resident mink and 2 km for transient. The spatial scale of mink impacts was largest during the first vole survey when resident mink were more abundant, and declined rapidly for the second survey, when mink were less abundant and spatially clustered. Our results suggest that water voles have benefited mostly from reducing resident mink rather than the total population, especially in early control phases. C_LIO_LIManagers can use our framework to develop spatially explicit and impact-based strategies, not restricted to invasive species control, to construct empirically informed management buffers around populations of conservation concern. Long-term efforts will change the landscape and invasive predator contexts, and thus we recommend iteratively updating and re-evaluating management outcome evaluations. We argue that incorporating individual heterogeneity improves our understanding of ecological mechanisms influencing management success but that the suitability of targeted strategies should be evaluated for target socioecological contexts. C_LI

5
Where species distribution models fail under occurrence-data contamination: calibration error concentrates at stream-network headwaters

Miok, K.; Laza, A. V.; Skrlj, B.; Robnik-Sikonja, M.; Parvulescu, L.

2026-07-15 ecology 10.64898/2026.07.14.738364 medRxiv
Top 0.1%
12.7%
Show abstract

Species distribution models (SDMs) increasingly inform conservation and biosecurity decisions in freshwater systems, where the reliability of its uncertainty estimates matters as much as its point predictions. Ensemble SDMs derive prediction intervals from across-replicate variance, but this variance captures systematic error only when replicates disagree about it, an assumption that fails when training data are contaminated with low-accuracy records, the norm in citizen-science datasets. Whether this failure is spatially uniform or concentrates in identifiable parts of a range is unknown. Using a panel of European freshwater crayfish spanning native headwater-associated species and invasive lowland colonizers, we show that contamination-induced calibration failure is strongly spatially structured: it concentrates at stream-network headwaters, the topological tops of the network, where upstream-aggregated predictors are structurally undefined, and scales with contamination severity, replicated across four species and both dominant ensemble protocols (replicate and consensus). The failure is driven by upward prediction bias, not by intervals failing to widen: contaminated ensembles overpredict suitability in headwaters, and because the bias is shared across ensemble members, the intervals do not flag it. This is a conservation-relevant blind spot, because headwaters are both refugia for threatened native crayfish and front lines for invasion; an SDM that silently overpredicts suitability there misdirects survey and management effort toward the segments where its predictions are least trustworthy. Standard leave-one-basin-out conformal calibration, the recommended panel-wide remedy, repairs marginal coverage but leaves headwaters undercovered, because a single calibration threshold is dominated by the abundant non-headwater segments. A group-conditional (Mondrian) variant, calibrating the two populations separately, restores reliable coverage in both at no extra cost and reallocates width where it is needed. We recommend network-position-stratified calibration as a default for ensemble SDMs in dendritic freshwater systems.

6
There is no silver bullet: Tiger corridors do not ensure multispecies carnivore connectivity

Rana, D.; Ramakrishnan, U.

2026-07-06 ecology 10.64898/2026.07.05.736645 medRxiv
Top 0.1%
10.7%
Show abstract

Connectivity is critical to sustaining endangered carnivores in speciose yet fragmented landscapes such as in the global south. Corridors to mitigate fragmentation are designed based on charismatic species or habitat-based approaches, but their multispecies effectiveness for maintaining functional connectivity remains poorly tested. We combined landscape genetic analyses across five sympatric carnivores - Panthera tigris, Panthera pardus, Prionailurus viverrinus, Felis chaus, and Melursus ursinus, to evaluate how landscape features shape functional connectivity in a globally important felid landscape. We then assessed the efficiency of existing tiger corridors and single-species surrogates for maintaining multispecies functional connectivity. Species exhibited contrasting responses to landscape variables, producing distinct resistance surfaces and connectivity corridors. Spatial similarity of connectivity between species pairs was highly variable (r = 0.14-0.93), but no single species effectively captured connectivity patterns of the broader carnivore community (maximum mean overlap of <0.7 across species). Moreover, genetically optimized corridors were at least 70% more efficient in capturing connectivity compared to existing tiger corridors, demonstrating mismatches between structural and functional connectivity. Our results highlight limitations of surrogate-based corridor planning and demonstrate that integrating multispecies functional connectivity can substantially improve conservation planning in human-dominated landscapes.

7
Ecosystem service gradients at protected area borders reveal multiple patterns and prevalent management conflicts

Gonzalez-Garcia, A.; Neyret, M.; Lopez-Tejedor, A.; Prima, M. C.; Si-Moussi, S.; Renaud, J.; Gueguen, M.; Lavorel, S.

2026-07-01 ecology 10.64898/2026.06.30.735453 medRxiv
Top 0.1%
10.6%
Show abstract

Protected areas cannot halt biodiversity loss in isolation; integrating them with surrounding human-dominated landscapes is critical. However, this integration is challenged by substantial landscape heterogeneity at their borders, hindering our understanding of cross-border changes in ecosystem service provision. We introduce a novel framework for characterizing these dynamics by analyzing ecosystem service gradients along protected area borders. For 16 protected areas in the French Alps, we assessed 12 ecosystem services using a mix of established biophysical models and novel connectivity-based models for mobile species. These were aggregated into three stakeholder-driven domains reflecting respectively rural, cultural, and urban management priorities. Automated polynomial regression analysis classified borders into five gradient types. The most common were 'Decreasing Gradients', representing a decline in ecosystem services outside the protected area, and 'Increasing Gradients', with the opposite pattern. Our analysis reveals these patterns are driven by specific landscape configurations, uncovering frequent trade-offs between the three management priorities, where, for instance, landscapes supporting rural priorities often degrade cultural and urban ones. We also identify key opportunities for synergies, by identifying areas where ecosystem services for all three priority domains increase simultaneously outside the protected area. This spatially explicit typology provides a powerful diagnostic tool for designing targeted interventions, such as prioritizing habitat restoration where ecosystem services decline or managing agricultural landscapes to mitigate conflicts across management priorities, supporting a more effective integration of protected areas into the wider landscape.

8
From strandline vegetation to embryo dunes: natural sand retention along a heavily urbanized coast

Taelman, C.; Provoost, S.; Batsleer, F.; Bonte, D.; Van Uytvanck, J.

2026-07-15 ecology 10.64898/2026.07.14.738448 medRxiv
Top 0.1%
7.7%
Show abstract

1. Sandy beaches along urbanized coasts are increasingly managed through beach nourishment and hard infrastructure, yet these interventions often constrain natural dune-building processes. Along the Belgian coast, where much of the beach-dune interface is bordered by dikes, promenades and intensive recreation, strandline vegetation may provide an overlooked mechanism for retaining sand and initiating embryo dune development. 2. We assessed the potential for four pioneer dune plant species (Cakile maritima, Calamagrostis arenaria, Elymus farctus and Salsola kali) to establish, develop vegetation cover and contribute to sand accumulation along the Belgian coast. Using field surveys from 2017-2023, LiDAR-derived beach elevation and annual sediment dynamics, we modelled species occurrence and abundance/cover in low-disturbance reference zones and projected these relationships across the wider coastline. 3. Occurrence models identified where abiotic conditions allow plants to establish and persist until the late growing season, whereas zero-inflated abundance/cover models estimated expected vegetation development across environmental gradients. Predicted occurrence was widespread for several species, suggesting that the abiotic gradients modelled here are not the primary constraints on potential establishment across large parts of the coast. In contrast, expected abundance/cover showed stronger species-specific responses, particularly to sand accretion, indicating that sediment dynamics mainly affect post-establishment vegetation development rather than occurrence alone. 4. Independent field measurements of embryo dunes showed positive relationships between vegetation cover and local sand accumulation for all four species. When scaled using spatial predictions of potential abundance/cover, pioneer vegetation could retain substantial volumes of sand, with Cakile maritima contributing the largest share, followed by Salsola kali, Elymus farctus and Calamagrostis arenaria. Estimated volumes depended on assumptions about whether vegetation occurs as dispersed units or aggregated patches. 5. Synthesis and applications. Our results show that, even along a heavily urbanized and nourished coastline, abiotic conditions can support strandline vegetation and embryo dune initiation where disturbance is reduced. Management actions such as limiting trampling, adapting beach cleaning and protecting strandline vegetation could enhance the retention of nourished sand and support nature-based coastal defense. Rather than replacing engineered interventions, strandline vegetation may increase the efficiency with which available sediment is retained within the beach-dune system.

9
Assessing the influence of edge effects on macrofaunal contributions to decomposition rates across forest-field ecotones.

Niles, T. E.; Taheri, C.; Buchkowski, R. W.

2026-06-25 ecology 10.64898/2026.06.24.734239 medRxiv
Top 0.1%
6.2%
Show abstract

Understanding the relationships between soil macrofauna and decomposition is crucial for predicting how land-use change impacts ecosystem function in fragmented systems. This is because soil macrofauna affect decomposition and also respond to the changes in abiotic conditions across habitat gradients. This study investigates edge effects on the macrofauna contributions to decomposition across forest-field ecotones. We used bait lamina assay to quantify aboveground and belowground feeding activity of soil macrofauna in Autumn 2025 in three deciduous forest-old field ecotones and one coniferous forest-old field ecotone, in Southwestern Ontario, Canada. Vegetation diversity and composition, LAI and soil characteristics (i.e., soil organic matter, pH, temperature and moisture) were measured at each plot along the ecotone. Pitfall trap data collected in Summer 2025 at the same sites were used to characterize macrofauna communities. We used generalized linear mixed effects models to estimate the effect of distance to edge, site, and depth into the soil on bait lamina consumption and soil macrofauna, with transect nested within site as random effects. Consumption activity increased with distance into the forest from the field, with the edge representing an intermediate; and, decreased with increasing depth into the soil. In contrast, soil macrofauna abundance, especially isopods, decrease with distance into the forest from the field. These trends varied significantly across sites, so that consumption activity and abundance sometimes remained constant across the ecotone (i.e., site x distance interaction). The results demonstrate that macrofaunal contributions to bait consumption varied along the ecotone, shaped by interacting environmental gradients and shifts in community composition unique to each site.

10
Coral settlement module designs for scalable reef restoration

Reichert, J.; Asbury, M.; Argall, R.; Chen, G. K.; Ehrenberg, J.; Huang, Z.; Jones, B.; Jorissen, H.; Levy, J.; Nims, A. D.; Rottmueller, M. E.; Rova, L. H.; Thode, A.; Wangpraseurt, D.; The R3D Consortium, ; Madin, J. S.

2026-06-25 ecology 10.64898/2026.06.24.733534 medRxiv
Top 0.2%
5.4%
Show abstract

The global coral reef crisis has prompted restoration initiatives worldwide. Targeting the coral larval stage is among the most scalable approaches as recruitment operates over large spatial scales. It thus represents one of the best levers for coral population recovery. Active coral larval seeding has shown considerable success, and passive substrate engineering has emerged as a promising complementary strategy. Coral settlement modules featuring helix recesses have increased settlement and survival by up to 80-fold on small experimental units, but whether these results translate to tools deployable at the scale of thousands of units, remains yet an open question. Here, we transferred structural features from successful experimental coral settlement designs into production-ready concrete modules to (i) evaluate coral recruitment on five designs at four reef sites differing in flow regime and coral cover over one year; (ii) compare production-scale performance against experimental clay modules and natural reef substrate; and (iii) identify key parameters for large-scale production. The helix recess geometry of coral settlement modules outperformed the featureless control design approximately 20-fold and exceeded natural reef recruitment at least 3- to 32-fold. The helix features were successfully transferred from experimental clay to production-scale concrete modules, yielding comparable settlement densities when standardized to crevice length, which proved to be the biologically relevant unit of available habitat. Production feasibility was demonstrated by producing 690 modules for deployment on a hybrid reef on the west side of Oahu, Hawaii. The passive coral larval recruitment approach presented here could substantially improve the logistical and economic feasibility of large-scale coral reef restoration. This approach requires neither coral larval rearing, handling, nor coral fragmenting, and is compatible with active larval seeding where genetic diversity or larvae supply are limiting factors. The coral settlement modules can be cast in standardized concrete molds at precast facilities. Modules have demonstrated consistent coral recruitment enhancement across reef environments with contrasting flow and coral cover. Deploying mixed arrays of helix-recess structures with designs offering multi-level complexity and three-dimensional rugosity maximizes outcomes for coral, fish, and invertebrate communities simultaneously. Site selection is the most critical deployment decision and should consider larval supply, hydrodynamics, and substrate stability which drive recruitment outcomes more than design choice alone. The modules offer a range of application potential, ranging from integration into existing coastal infrastructure over stand-alone reef restoration approaches, to substrate-consolidating interconnected arrangements.

11
Testing the waters of macrophyte biodiversity with multiscale spatial analysis of public lake monitoring data

Tseitlin, M.; Garcia-Giron, J.; Crabot, J.; Jiang, X.; Larkin, D. J.

2026-06-23 ecology 10.64898/2026.06.22.733670 medRxiv
Top 0.2%
5.4%
Show abstract

Freshwater monitoring programmes like the European Unions Water Framework Directive (WFD) provide a wealth of data on European lake status, including water quality and macrophytes (aquatic plants) as critical habitat features that support health of humans and wildlife. Easier WFD data access can enable external management and research to better safeguard human and natural freshwater use. We demonstrate a replicable workflow to easily download and process multi-year (2007-2024) observations of lake macrophytes (425 sites) and complementary water quality variables (202 sites) from Swedish WFD data. Then, we illustrate the value of improved data access to address ecological questions that drive conservation, investigating how spatial scales influence macrophyte richness and associated water quality relationships using a spatial random intercept model. Decomposing the spatial intercept links small scales (<10 km) to site-level gradients and large scales (>100 km) to biogeographical drivers. Stochastic and environmentally-structured processes coexisted at intermediate scales (10-100 km). Adding water quality rarely improved overall predictive performance of macrophyte diversity models but consistently influences the role of different spatial scales. Water quality variables showed consistent spatially structured variation at intermediate scales and unique spatial patterns in tandem, overlapping with large-scale biogeographical influences. Altogether, we show context-dependencies for spatial model interpretation and provide guidance in accounting for spatial confounding to improve inferential and predictive performance. Our workflow and results show a clear way forward for accessing high-quality macrophyte and water quality data sets and their utility for addressing ecological questions that guide macrophyte protection under the WFD. HighlightsO_LIyears Swedish of macrophyte and water quality monitoring data were extracted. C_LIO_LIrichness showed scale-specific patterns linked to geographic gradients. C_LIO_LIbest predictive models for richness had no water quality at all. C_LIO_LIoverlap in their spatial scales and must be carefully separated. C_LIO_LIpen access data and multiscale analysis can apply to many ecological questions. C_LI

12
West Nile virus response to mosquito and avian biodiversity in rural environments

Marcolin, L.; Ceci, N.; Gobbo, F.; Montarsi, F.; Chiarello, G.; Dorigatti, I.; Di Marco, M.

2026-06-27 ecology 10.64898/2026.06.26.734801 medRxiv
Top 0.2%
5.3%
Show abstract

Context. The relationship between biodiversity and zoonotic disease risk is a central topic in community ecology, yet empirical evidence in Europe remains scarce and often contradictory compared to North American studies. Addressing this gap is fundamental to better anticipate zoonotic disease dynamics. Objectives. We investigated the transmission dynamics of West Nile virus (WNV) in Veneto (Italy), a major European hotspot. Because this vector-borne pathogen is primarily transmitted by Culex mosquitoes and maintained by several avian hosts, we analysed how multiple facets of both avian and mosquito biodiversity influence its transmission. Methods. Using Generalized Additive Models (GAMs) trained on longitudinal entomological and ornithological surveillance data, we modelled the probability of WNV presence in mosquito pools as a function of host and vector community structure. To isolate the effects of biodiversity, we explicitly controlled for climatic and landscape covariates. Results. In agricultural landscapes, we found that higher avian diversity leads to higher viral presence, driven by the dominance of highly competent synanthropic hosts. Conversely, a dilution effect emerges across the broader regional landscape where areas of higher ecological integrity allow for more complex and functionally diverse avian communities. Furthermore, we identified significant vector-mediated regulation, where high abundances of mammophilic vectors effectively suppress viral prevalence through larval competition. Conclusions. Our findings suggest that the dilution effect is a property of intact ecosystems which can be lost, or even locally reversed, in anthropogenically altered environments. Because such habitat degradation fundamentally alters zoonotic transmission dynamics, landscape planning must prioritize ecological restoration. Ultimately, embedding these practices into One Health strategies represents a proactive approach to mitigating disease emergence.

13
The illusion of diversity: sampling design drives conflicting estimates of soil bacterial richness

Kostakou, M.; Neisse, N.; Goldmann, K.; Chatzinotas, A.; Jurburg, S. D.

2026-07-03 ecology 10.64898/2026.07.03.736139 medRxiv
Top 0.2%
5.3%
Show abstract

Soil microbial diversity is shaped by the spatial scale at which communities are sampled, yet standard sampling practices often homogenize samples, obscuring fine-scale spatial structure and diversity patterns. To better understand how sampling effort, spatial extent, and physical homogenization influence plot-level microbial richness estimates, we sampled 57 forest and grassland sites across three regions in Germany using a 14-core cross-transect design and performed 16S rRNA gene metabarcoding. We simulated sampling efforts and a range of spatial extents and compared diversity estimates to those from physically homogenized composite samples. Plot-level richness increased continuously with sampling effort and spatial extent, with no evidence of saturation. However, when sequencing depth was held constant, sampling completeness declined with increasing sampling effort, meaning that more diversity is not captured. Composite samples substantially underestimated plot-level richness and altered apparent diversity relationships between ecosystems; individual cores identified forests as richer than grasslands, whereas homogenized samples suggested the opposite relationship. These results demonstrate that sampling effort, spatial extent, and homogenization fundamentally shape soil microbial diversity estimates. Homogenized composite samples cannot substitute for individual cores when the goal is to reliably quantify plot-level richness or compare diversity across ecosystems.

14
Microbial, dietary insect, and pathogen communities in fresh and decomposing guano of anthropic little brown bat (Myotis lucifugus) maternity colonies

Defenza, J.; Eddins, L.; Gauvin, A.; Heaney, D. J.; Lewis, D.; Lin, R.; Martinez, R.; Schilace, K.; Stover, K. A.; Taormina, J.; Vargas, S. C.; Paist, K.; Maas, K.; Askew, D. J.; Castellano, K.; Rutter, M.; Rork, A.; Pauloski, N.; O'Neill, R. J.; King, T.; Jockusch, E. L.; Wegrzyn, J. L.; Fischer, J.; McGuire, A.; Fraser, D.; Reynolds, H.

2026-07-03 ecology 10.64898/2026.07.02.734860 medRxiv
Top 0.2%
5.3%
Show abstract

The guano of insectivorous bats holds ecological information that can be assessed non-invasively to characterize the gut microbiome and diet, alongside environmental microbes and pathogens of conservation concern. Despite this potential, how guano communities change during decomposition remains understudied, particularly inside anthropic roosts rather than caves. In this study, guano from little brown bat (Myotis lucifugus) colonies was sampled monthly across the summer maternity season from three sites across two locations in Connecticut, USA, at fresh deposition and at 4, 8, and 12 weeks following deposition. Resolving these cross-kingdom signals required five workflows: short-read 16S and ITS2 amplicon sequencing (Illumina) for bacterial and fungal profiling, long-read CO1 metabarcoding (Oxford Nanopore) for arthropod diet in fresh samples, long-read shotgun metagenomics for viral identification in aged samples, and targeted qPCR for organisms of bat, human, and forest-health concern. Fresh guano generated a consistent bacterial signal across sites, whereas fresh fungal communities differed by site. Responses to decomposition depended on roost setting: exterior sites lost fungal diversity and shifted toward environmental aerobes over time, while the interior roost retained the fresh sample profile. Dietary composition varied temporally, was dominated by Diptera, and included the invasive emerald ash borer (Agrilus planipennis). Pseudogymnoascus destructans, the causal agent of white-nose syndrome, occurred in fresh and aged samples at all three sites but persisted for 12 weeks only at the interior roost, where antifungal bacterial taxa were depleted. Long-read shotgun metagenomics of aged guano recovered roughly 100 viral species, predominantly bacteriophages, alongside non-bacteriophage mastadenoviruses associated with humans, bats, and other mammals. These results show that anthropic structures influence the trajectory of guano microbiome succession, and that maternity colony guano enables non-invasive assessment of environmental pathogens, bat diet, and bacterial and fungal communities.

15
Temporal variability and its effects on diversity maintenance in an agroecological matrix

Zepeda, V.; Garcia Jacome, L. G.; Azpeitia, E.; Abrica-Jacinto, N. L.; Benitez, M.

2026-07-13 ecology 10.64898/2026.07.10.737830 medRxiv
Top 0.2%
4.3%
Show abstract

Agroecosystems are dynamic ecosystems, constituted by patches of vegetation and agricultural use, where biodiversity is shaped by spatial and temporal variability. While most studies have focused on spatial composition and configuration, the role of temporal variability remains poorly understood. Yet, temporal dynamics can strongly modify species composition, abundance, and persistence in ecological communities. Temporal variability is particularly relevant in agroecosystems with rainfed agriculture where environmental conditions shift dramatically between rainy and dry seasons. In this paper, we assess the role of temporal variability on biodiversity maintenance in an agricultural matrix using a metacommunity model that simulates an agricultural landscape under rainfed conditions, that is, with abrupt seasonal changes in the agricultural patches. This model couples a local community network dynamic with a migration dynamic and is based on empirically documented features of rainfed agricultural matrices. Our results show that temporal variability provides new opportunities for species to recover from low densities. However, the effect of temporal variability is not straightforward. It depends on the initial and final conditions, the migration and mortality rates and the intensity of temporal variability. Overall, our findings highlight the need to further investigate temporal variability to better understand its role in shaping biodiversity in agricultural landscapes.

16
Spatiotemporal differences in salmon nutrient inputs restructure functional and taxonomic fungal communities in riparian system

Polyakov, A. Y.; Larocque, A.; Lilleskov, E.; Mafune, K.; Vogt, K.; Vogt, D.; Berdahl, A.

2026-06-25 ecology 10.64898/2026.06.23.734103 medRxiv
Top 0.2%
4.3%
Show abstract

O_LISpawning salmon transport marine-derived nutrients (MDN) into riparian forests, influencing soil, plant, and animal communities, yet their effects on fungal communities remain poorly understood. C_LIO_LIWe used DNA metabarcoding to examine fungal responses to three spatial patterns of salmon-derived nitrogen (N) in southwest Alaska: (i) patchy inputs from wildlife-deposited carcasses, (ii) a 21-year carcass relocation experiment, and (iii) natural N gradients with distance from streams. C_LIO_LIDecomposing carcasses increased saprotrophic fungal diversity, identifying taxa responsible for salmon carcass decomposition. Long-term carcass relocation reduced diversity of medium-distance fringe ectomycorrhizal fungi (EMF), whereas recent, patchy carcass inputs increased diversity of both medium-distance fringe and long-distance EMF--guilds often associated with low-nutrient environments. Along natural stream N gradients, EMF responses varied markedly within functional guilds and genera, revealing unexpected variation in N sensitivity among closely related taxa. C_LIO_LIPulsed, spatially heterogeneous nutrient inputs enhanced diversity of typically nitrophobic EMF, likely reflecting their capacity to maintain extensive mycelial networks, exploit nutrient hotspots, and mobilize organic N and phosphorus. The diversity of responses along natural N gradients suggests that mechanisms linking EMF traits to nutrient acquisition and tolerance remain unresolved. Our findings emphasize the importance of linking fungal community composition with functional attributes and nutrient dynamics. C_LI

17
Large parks and city-wide tree cover boost butterfly diversity across 22 major U.S. cities

Ulrich, J.; Cheung, Y. Y. J.; Cosma, C. T.; Kharouba, H.; Guzman, L. M.

2026-07-03 ecology 10.64898/2026.07.02.736135 medRxiv
Top 0.3%
4.2%
Show abstract

Accelerating global urbanization necessitates a better understanding of how to manage cities that promote biodiversity. However, we currently lack multi-year, multi-city studies, which limits a generalizable understanding of how both within and between city differences impact the spatial and temporal dynamics of urban biodiversity. Here, we tested hypotheses about the drivers of butterfly diversity within and across urban parks by applying Bayesian occupancy models to five years of iNaturalist community science data from 2,550 parks in 22 major U.S. cities. We found that cities with bigger parks supported more species per park, including more disturbance- and edge-avoidant species. This was driven by a positive effect of park size on butterfly species colonization rates. We also found that attributes of habitat quality (plant diversity within parks and tree cover surrounding parks) contributed to butterfly species occupancy. Park connectivity increased species persistence, but the overall effects on butterfly species occupancy varied across cities. Finally, we found that the total area of tree cover throughout a city, rather than the size or connectivity of individual parks, was the primary determinant of city-wide diversity: Increasing total tree canopy cover from below-average (~6%) to above-average (~22%) increased city-wide species richness by ~10%. These findings highlight the need for cities to maintain large parks while also increasing city-wide tree cover to support biodiversity across local to regional scales. By integrating high-resolution community science data across the continental U.S., this study provides mechanistic insight into how cross-scale processes shape urban biodiversity dynamics and identifies generalizable recommendations for improving urban conservation management.

18
Pretty Good Yields allow the spatial management of multiple objectives in agricultural landscapes

Kubasch, M.; Costa, M.; Loeuille, N.

2026-07-09 ecology 10.64898/2026.07.06.736684 medRxiv
Top 0.3%
3.5%
Show abstract

In order to feed a growing global population without silencing nature, conceiving agricultural management strategies reconciling yield and conservation goals is key. Using numerical simulations of a metacommunity model, we explore the possibilities for compromise offered by spatial management strategies of farmed areas. Each strategy is characterized by its farming intensity, the proportion of farmed lands and their spatial aggregation. We show that achieving equitable yield-biodiversity compromise is difficult. While conciliatory strategies offering top yield and biodiversity are typically not possible, accepting slightly lower yields (ie, "Pretty Good Yield strategies") allows to recover substantial biodiversity. Such reconciliation possibilities are limited for species with small dispersal. Yield increases mainly through farmland expansion, whereas farming intensity strongly influences biodiversity, increasing it at low intensity before decreasing with further intensification. Finally, we demonstrate that reconciliation is easier if agricultural production relies on biodiversity through ecosystem services.

19
200 years of river engineering: changes in meta-ecosystem resilience and connectivity

Kowal, J. L.; Gross, S.; Haidvogl, G.; Hein, T.; Hohensinner, S.; Funk, A.

2026-07-03 ecology 10.64898/2026.07.03.736339 medRxiv
Top 0.3%
3.2%
Show abstract

This study investigates changes in habitat connectivity and meta-ecosystem resilience between 1817 and 2022 along a 150 km section of a large European river (Danube) and its adjacent floodplains. The analysis was based on a time series of functional habitat networks (graphs) constructed from historical records and remote sensing data, integrating habitat suitability and dispersal modes of functional organism groups. The results indicate that overall habitat availability declined by about 50% since 1817, leading to the near-complete loss of functional connectivity among dynamic habitats by 1910. Less dynamic habitats persisted or expanded but became functionally less connected. Connectivity-based habitat classification further revealed four distinct functional connectivity clusters and the near-complete loss of an originally dominant, dynamic, and highly connected habitat type. Furthermore, the results indicated a fundamental loss of meta-ecosystem resilience. This development was reflected by increased spatial modularity among functionally similar habitats and by reduced layer dissimilarity and structural robustness in multilayer networks representing the spatial habitat structure and functional habitat connectivity across different functional organism groups.

20
Emerging Beetle-Pathogen Symbioses and Their Consequences for Forest Health: Lessons from Rapid 'Ohi'a Death in Hawai'i

Boren, A.; Weber, S.; Keith, L. M.; Gillespie, R.; Roderick, G.; Roy, K.

2026-06-25 ecology 10.64898/2026.06.24.732210 medRxiv
Top 0.3%
3.2%
Show abstract

Invasive ambrosia beetles and fungal pathogens threaten forest ecosystems worldwide, exemplified in Hawaii by the widespread loss of keystone species [o]hia (Metrosideros polymorpha), due to Rapid [O]hia Death (ROD). A unique occurrence of five ambrosia beetle species (one native, four introduced) that vary in their symbiotic relationships with two introduced fungal pathogens provide an opportunity to test hypotheses of how opportunistic symbioses facilitate disease dynamics involving dominant forest trees. ROD is caused by two novel Ceratocystis fungal pathogens whose spores can spread via association with ambrosia beetles as they bore into [o]hia trees. We examined beetle-pathogen interactions of all five ambrosia beetle species in three ROD-affected regions on Hawaii Island, and used quantitative PCR (qPCR) to provide the first molecular confirmation of the two ROD pathogens associated with the exterior, mycangia, and gut of each beetle species. Results from generalized linear models and correlation networks show that pathogen acquisition and transport, including the potential for consumption and the presence of the pathogens, are determined by beetle invasion status and mycangia morphology. A niche construction framework suggests that both varying symbioses and opportunism facilitate disease spread, with the three invasive Xyleborus species emerging as key disease vectors. Identifying the beetle species that are more likely to contribute to disease spread, and understanding their biology as vectors, can inform targeted conservation strategies for [o]hia and for insect-pathogen threats in forests worldwide, and illustrates the potential ecosystem-level impacts of novel and opportunistic symbioses between globally distributed invasive vectors and pathogens.