Ecological Questions Research Articles

The zoonotic potential of mink farming

Minks can be infected and serve as a source of several zoonotic diseases, among which the recently gaining popularity SARS-CoV-2 and Highly Pathogenic Avian Influenza (HPAI). However, many others can be potentially dangerous to humans and other animals but have been neglected as rare. Nowadays mink farming has been widen its influence beyond the bars of cages and has become both an economical, ecological and ethical question. Economy lies in the heavy losses of many countries with developed mink industry during the COVID crisis and the need for welfare improvement in the sector. Ecology calls for attention on the invasive nature of the species and the effect of feral populations on native fauna. It is also ethical to ask do we really need to breed minks for their fur especially under conditions that do not answer their behavioral needs, definitely unsanitary and cruel, as well as being the cause of unprecedented exchange of pathogens between humans and a naturally solitary creature? This article is dedicated to the zoonotic potential of minks as a part of a wider problem that can shake the One Health concept.

When and where? Day-night alterations in wild boar space use captured by a generalized additive mixed model.

Wild boar (Sus scrofa), an abundant species across Europe, is often subjected to management in agro-ecosystems in order to control population size, or to scare them away from agricultural fields to safeguard crop yields. Wild boar management can benefit from a better understanding on changes in its space use across the diel cycle (i.e., diel space use) in relation to variable hunting pressures or other factors. Here, we estimate wild boar diel space use in an agro-ecosystem in central Belgium during four consecutive "growing seasons" (i.e., April-September). To achieve this, we fit generalized additive mixed models (GAMMs) to camera trap data of wild boar aggregated over 1-h periods. Our results reveal that wild boar are predominantly nocturnal in all of the hunting management zones in Meerdaal, with activity peaks around sunrise and sunset. Hunting events in our study area tend to take place around sunrise and sunset, while non-lethal human activities occur during sunlight hours. Our GAMM reveals that wild boar use different areas throughout the diel cycle. During the day, wild boar utilized areas in the centre of the forest, possibly to avoid human activities during daytime. During the night, they foraged near (or in) agricultural fields. A post hoc comparison of space use maps of wild boar in Meerdaal revealed that their diurnal and nocturnal space use were uncorrelated. We did not find sufficient evidence to prove that wild boar spatiotemporally avoid hunters. Finally, our work reveals the potential of GAMMs to model variation in space across 24-h periods from camera trap data, an application that will be useful to address a range of ecological questions. However, to test the robustness of this approach we advise that it should be compared against telemetry-based methods to derive diel space use.

Linking microbial population dynamics in anaerobic bioreactors to food waste type and decomposition stage

A key question in anaerobic microbial ecology is how microbial communities develop over different stages of waste decomposition and whether these changes are specific to waste types. We destructively sampled over time 26 replicate bioreactors cultivated on fruit/vegetable waste (FVW) and meat waste (MW) based on pre-defined waste components and composition. To characterize community shifts, we examined 16S rRNA genes from both the leachate and solid fractions of the waste. Waste decomposition occurred faster in FVW than MW, as accumulation of ammonia in MW reactors led to inhibition of methanogenesis. We identified population succession during different stages of waste decomposition and linked specific populations to different waste types. Community analyses revealed underrepresentation of methanogens in the leachate fractions, emphasizing the importance of consistent and representative sampling when characterizing microbial communities in solid waste.

From whole bodies to single cells: A guide to transcriptomic approaches for ecology and evolutionary biology

AbstractRNA sequencing (RNAseq) methodology has experienced a burst of technological developments in the last decade, which has opened up opportunities for studying the mechanisms of adaptation to environmental factors at both the organismal and cellular level. Selecting the most suitable experimental approach for specific research questions and model systems can, however, be a challenge and researchers in ecology and evolution are commonly faced with the choice of whether to study gene expression variation in whole bodies, specific tissues, and/or single cells. A wide range of sometimes polarised opinions exists over which approach is best. Here, we highlight the advantages and disadvantages of each of these approaches to provide a guide to help researchers make informed decisions and maximise the power of their study. Using illustrative examples of various ecological and evolutionary research questions, we guide the readers through the different RNAseq approaches and help them identify the most suitable design for their own projects.

Consideration of the Disease Complexes, the Missing Link to Correctly Analyze the Impact of Intercropping on Disease Development

Diversification at the plot level, through the use of intercropping (mixtures of crops), is an alternative to the conventional system of intensive agriculture, based on monospecific, usually single-variety canopies. Intercropping has been shown to provide benefits in terms of disease control. However, competition phenomena and the heterogeneity of the associated crops raise new ecological questions, particularly with regard to the dynamics and evolution of parasite populations. No study has assessed the potential impact of these associations on the dynamics of pathogenic species complexes. Changes in the nutritional status of plants and therefore in their physiological susceptibility to infection within intercropping systems could contribute to an increased diversity of ecological niches and thus affect the composition of the parasitic complex and its spatiotemporal dynamics. In this review, focusing on foliar diseases of fungal origin, and after outlining some elements of the biology and epidemiology of these fungal diseases, we will (i) describe the mechanisms that contribute to the composition of disease clusters and that drive interactions, but we will also review the strategies that these foliar diseases have adopted to deal with these co-infections; (ii) define how intercropping can lead to changes in epidemic dynamics, in particular by presenting the mechanisms that have a direct and indirect effect on disease evolution; and (iii) present the approach that should be adopted to properly study intercropping correctly in a multi-infection situation.

Invertebrate responses to rewilding: a monitoring framework for practitioners

Rewilding presents a unique opportunity to better understand the processes influencing ecological communities and how they function. Although empirical evidence on the effects of rewilding is growing rapidly, knowledge gain is unbalanced, particularly for invertebrates, despite this group representing a large proportion of biodiversity and being fundamental to key ecosystem processes. Here, we advocate for more targeted systematic monitoring and experimental research, providing a site‐based framework for practitioners to evaluate project effects on invertebrate biodiversity. This framework utilizes taxonomic indicators of change, representative of processes important to ecosystem functioning. Implementation of this framework and the associated opportunities and challenges for practitioners are discussed. Adopting this framework would broaden the taxonomic groups and ecosystem processes evaluated by rewilding projects, transform the sector from opinion‐based to evidence‐based, and help address some of the most pressing ecological and conservation questions of the twenty‐first century.

The atmosphere: a transport medium or an active microbial ecosystem?

The atmosphere may be Earth's largest microbial ecosystem. It is connected to all of Earth's surface ecosystems and plays an important role in microbial dispersal on local to global scales. Despite this grand scale, surprisingly little is understood about the atmosphere itself as a habitat. A key question remains unresolved: does the atmosphere simply transport microorganisms from one location to another, or does it harbour adapted, resident, and active microbial communities that overcome the physiological stressors and selection pressures the atmosphere poses to life? Advances in extreme microbiology and astrobiology continue to push our understanding of the limits of life towards ever greater extremes of temperature, pressure, salinity, irradiance, pH, and water availability. Earth's atmosphere stands as a challenging, but potentially surmountable, extreme environment to harbour living, active, resident microorganisms. Here, we confront the current understanding of the atmosphere as a microbial habitat, highlighting key advances and limitations. We pose major ecological and mechanistic questions about microbial life in the atmosphere that remain unresolved and frame the problems and technical pitfalls that have largely hindered recent developments in this space, providing evidence-based insights to drive future research in this field. New innovations supported by rigorous technical standards are needed to enable progress in understanding atmospheric microorganisms and their influence on global processes of weather, climate, nutrient cycling, biodiversity, and microbial connectivity, especially in the context of rapid global change.

The temporal order of emotional, cognitive, and behavioral gains in daily life during treatment of depression.

Despite the importance for understanding mechanisms of change, little is known about the order of change in daily life emotions, cognitions, and behaviors during treatment of depression. This study examined the within-person temporal order of emotional, cognitive, and behavioral improvements using ecological momentary assessment data. Thirty-two individuals with diagnosed depression completed ecological momentary assessment questions on emotions (sad mood, happy mood), behaviors (social interaction, number of activities), and cognitive variables (worrying, negative self-thoughts) 5 times a day during a 4-month period in which they underwent psychotherapy for depression. Nonparametric change-point analyses were used to determine the timing of gains (i.e., improvements in the mean of each variable) for each individual. We then established whether the first (i.e., earliest) gains in emotions preceded, followed, or occurred in the same week as cognitive and behavioral gains for each individual. Contrary to our hypotheses, first gains in behaviors did not precede first emotional gains (3 times, 8%) more often than they followed them (26 times, 70%). Cognitive gains often occurred in the same week as first emotional gains (43 times, 58%) and less often preceded (13 times, 18%) or followed emotional gains (18 times, 24%). The first improvements in behaviors did not tend to precede the first improvements in emotions likely because fewer behavioral gains were found. The finding that cognitive variables tend to improve around the same time as sad mood may explain why many studies failed to find that cognitive change predicts later change in depressive symptoms. (PsycInfo Database Record (c) 2024 APA, all rights reserved).

The Agrarian Question as an Ecological Question: An Introduction

The Agrarian Question as an Ecological Question: An Introduction

A Specific Resistance Gene to Leptosphaeria maculans, Rlm11, Has a Limited Impact on Brassica napus Mycobiota Compared with Plant Compartment or Cropping Season Effects

One important ecological question regarding the use of plant resistance genes against fungal pathogens concerns whether and how such resistance genes may modify pathogenic or beneficial members of the plant-associated microbiota. We studied the impact of a plant resistance gene by analyzing the mycobiota associated with Brassica napus organs over two cropping seasons. Sampling dates coincided with key stages of the life cycle of the B. napus pathogen Leptosphaeria maculans. Leaf samples were collected at three time points in autumn and spring, and stem base samples were collected at two time points a few weeks before and at harvest. Stem residues, where L. maculans survives in the intercropping season and develops sexual reproduction, were also analyzed at four time points between the two cropping seasons. The sampling was performed on two plant genotypes, Darmor and Darmor- Rlm11, only differing by the effective resistance gene against L. maculans, Rlm11. Altogether, 419 samples were analyzed using two barcode: internal transcribed spacer (ITS) and Actin. The plant organ was shown to be the main mycobiota structuring factor, as clear-cut alternation of the species suggested that each plant organ represented a specific ecological niche. The cropping season and plant genotype also significantly influenced the community structure in lower proportions. The resistance gene contributed differently to the community structure depending on the year and the organ concerned. A significant but low impact of Rlm11 on other B. napus fungal pathogens was detected. The ITS and Actin barcodes showed similar results, but the species assignation was limited for the latter.

Modeling the larval growth and survival of Pacific cod (Gadus macrocephalus) in the eastern Bering Sea

The eastern Bering Sea (EBS) is a highly productive ecosystem that supports several important commercial species such as the Pacific cod (Gadus macrocephalus). Climate variability affects the population dynamics of this stock throughout its life stages, especially early life stages, since they are particularly susceptible to environmental changes. In recent decades, warm and cold stanzas (i.e., 3–5 year periods) have been observed in the EBS, and there is evidence that they can modulate the recruitment of this stock, causing important socioeconomic impacts. Using a mechanistic individual-based model, this study investigates the spatial and temporal variability of growth and survival of Pacific cod's early life stages during 2000–2020. We examined changes by year and over space and compared our results with published literature to validate our model. We found that temperature played a key role in modulating the survival of fish larvae, observing an increase in starvation events in warmer years or locations. Periods or areas with low prey density, especially small-bodied copepods, also contributed to increased starvation. The average temperature in the fish habitat was negatively correlated with recruitment estimates from the stock assessment model. Growth was primarily temperature-driven; however, food-limited growth became more frequent when larvae were smaller during cold years. Spatially, we found that the environmental conditions in the southeastern Bering Sea may favor larval survival but reduce growth, and higher mortality may be persistent on the middle and outer shelf. Our model produces results that agree with previous field studies, and it offers a valuable tool to investigate other ecological questions on the impact of the environment on early life stages of fishes.

Biodiversity is enhanced by sequential resource utilization and environmental fluctuations via emergent temporal niches.

How natural communities maintain their remarkable biodiversity and which species survive in complex communities are central questions in ecology. Resource competition models successfully explain many phenomena but typically predict only as many species as resources can coexist. Here, we demonstrate that sequential resource utilization, or diauxie, with periodic growth cycles can support many more species than resources. We explore how communities modify their own environments by sequentially depleting resources to form sequences of temporal niches, or intermediately depleted environments. Biodiversity is enhanced when community-driven or environmental fluctuations modulate the resource depletion order and produce different temporal niches on each growth cycle. Community-driven fluctuations under constant environmental conditions are rare, but exploring them illuminates the temporal niche structure that emerges from sequential resource utilization. With environmental fluctuations, we find most communities have more stably coexisting species than resources with survivors accurately predicted by the same temporal niche structure and each following a distinct optimal strategy. Our results thus present a new niche-based approach to understanding highly diverse fluctuating communities.

Multi-year soundscape recordings and automated call detection reveals varied impact of moonlight on calling activity of neotropical forest katydids.

Night-time light can have profound ecological effects, even when the source is natural moonlight. The impacts of light can, however, vary substantially by taxon, habitat and geographical region. We used a custom machine learning model built with the Python package Koogu to investigate the in situ effects of moonlight on the calling activity of neotropical forest katydids over multiple years. We prioritised species with calls that were commonly detected in human annotated data, enabling us to evaluate model performance. We focused on eight species of katydids that the model identified with high precision (generally greater than 0.90) and moderate-to-high recall (minimum 0.35), ensuring that detections were generally correct and that many calls were detected. These results suggest that moonlight has modest effects on the amount of calling, with the magnitude and direction of effect varying by species: half of the species showed positive effects of light and half showed negative. These findings emphasize the importance of understanding natural history for anticipating how biological communities respond to moonlight. The methods applied in this project highlight the emerging opportunities for evaluating large quantities of data with machine learning models to address ecological questions over space and time. This article is part of the theme issue 'Towards a toolkit for global insect biodiversity monitoring'.

Comparing long-term patterns of spread of native and invasive plants in a successional forest.

A fundamental question in invasive plant ecology is whether invasive and native plants have different ecological roles. Differences in functional traits have been explored, but we lack a comparison of the factors affecting the spread of co-occurring natives and invasives. Some have proposed that to succeed, invasives would colonize a wider variety of sites, would disperse farther, or would be better at colonizing sites with more available light and soil nutrients than natives. We examined patterns of spread over 70years in a regenerating forest in Connecticut, USA, where both native and invasive species acted as colonizers. We compared seven invasive and 19 native species in the characteristics of colonized plots, variation in these characteristics, and the importance of site variables for colonization. We found little support for the hypotheses that invasive plants succeed by dispersing farther than native plants or by having a broader range of site tolerances. Colonization by invasives was also not more dependent on light than colonization by natives. Like native understory species, invasive plants spread into closed-canopy forest and species-rich communities despite earlier predictions that these communities would resist invasion. The biggest differences were that soil nitrate and the initial land cover being open field increased the odds of colonization for most invasives but only for some natives. In large part, though, the spread of native and invasive plants was affected by similar factors.

Explaining empirical dynamic modelling using verbal, graphical and mathematical approaches.

Empirical dynamic modelling (EDM) is becoming an increasingly popular method for understanding the dynamics of ecosystems. It has been applied to laboratory, terrestrial, freshwater and marine systems, used to forecast natural populations and has addressed fundamental ecological questions. Despite its increasing use, we have not found full explanations of EDM in the ecological literature, limiting understanding and reproducibility. Here we expand upon existing work by providing a detailed introduction to EDM. We use three progressively more complex approaches. A short verbal explanation of EDM is then explicitly demonstrated by graphically working through a simple example. We then introduce a full mathematical description of the steps involved. Conceptually, EDM translates a time series of data into a path through a multi-dimensional space, whose axes are lagged values of the time series. A time step is chosen from which to make a prediction. The state of the system at that time step corresponds to a 'focal point' in the multi-dimensional space. The set (called the library) of candidate nearest neighbours to the focal point is constructed, to determine the nearest neighbours that are then used to make the prediction. Our mathematical explanation explicitly documents which points in the multi-dimensional space should not be considered as focal points. We suggest a new option for excluding points from the library that may be useful for short-term time series that are often found in ecology. We focus on the core simplex and S-map algorithms of EDM. Our new R package, pbsEDM, enhances understanding (by outputting intermediate calculations), reproduces our results and can be applied to new data. Our work improves the clarity of the inner workings of EDM, a prerequisite for EDM to reach its full potential in ecology and have wide uptake in the provision of advice to managers of natural resources.

Host influence on the eukaryotic virome of sympatric mosquitoes and abundance of diverse viruses with a broad host range.

Mosquitoes harbor a large diversity of eukaryotic viruses. Those viromes probably influence mosquito physiology and the transmission of human pathogens. Nevertheless, their ecology remains largely unstudied. Here, we address two key questions in virome ecology. First, we assessed the influence of mosquito species on virome taxonomic diversity and relative abundance. Contrary to most previous studies, the potential effect of the habitat was explicitly included. Thousands of individuals of Culex poicilipes and Culex tritaeniorhynchus, two vectors of viral diseases, were concomitantly sampled in three habitats over two years. A total of 95 viral taxa from 25 families were identified with meta-transcriptomics, with 75% of taxa shared by both mosquitoes. Viromes significantly differed by mosquito species but not by habitat. Differences were largely due to changes in relative abundance of shared taxa. Then, we studied the diversity of viruses with a broad host range. We searched for viral taxa shared by the two Culex species and Aedes vexans, another disease vector, present in one of the habitats. Twenty-six out of the 163 viral taxa were found in the three mosquitoes. These taxa encompassed 14 families. A database analysis supported broad host ranges for many of those viruses, as well as a widespread geographical distribution. Thus, the viromes of mosquitoes from the same genera mainly differed in the relative abundance of shared taxa, whereas differences in viral diversity dominated between mosquito genera. Whether this new model of virome diversity and structure applies to other mosquito communities remains to be determined.

A model to follow? The EU and global eco-social policy

In this article, we study the political project promoted by the European Commission (EC) for tackling simultaneously socioeconomic and environmental issues. Based on a detailed analysis of the most relevant EC policy documents (adopted between 2000 and 2020) that explicitly articulate ecological and socioeconomic questions, we offer two contributions to the literature on eco-social policy. First, we identify the nature of what we call the ‘European Eco-Social Model’. This political project subordinates social-ecological goals to the economic rationality of growth, competitiveness and profits and de-politicizes the efforts to promote more sustainable societies and economies. Second, we show how the Commission is repositioning itself as a global leader in the transformation to sustainability, attempting to extend its particular eco-social model to the whole world. Overall, we argue that this ‘model’ is based on self-contradictory assumptions and cannot demonstrate how it should be able to solve problems of social inequality and climate change on a global level.

Male genital system of Ameiva ameiva (Squamata: Teiidae).

Understanding squamate reproductive morphology is crucial for investigating ecological, behavioral, and evolutionary questions. Here, we describe the anatomy and histology of the male genital system of Ameiva ameiva from southeastern Brazil. Ten adult males were dissected to characterize genital macroscopy and collect fragments of the testes, gonadoducts, and kidneys for histological examination. We examined 10 transverse histological sections per individual and measured the epithelial height of the epididymis and ductus deferens. The male reproductive system consists of a pair of yellowish oval testes, the rete testis, ductuli efferentes, epididymis, ductus deferens, ampulla ductus deferentis, sexual segment of the kidney (SSK), cloaca, and hemipenis. The hemipenis is elongated, cylindrical, and unilobed, with a sulcate face and an asulcate face, which has continuous fringes throughout its length. Seminiferous tubules exhibited germ cells at various stages. The epididymis is wider and more coiled than the ductus deferens. The rete testis has a simple squamous epithelium with long stereocilia, while the narrower ductuli efferentes are lined by a simple ciliated cuboidal epithelium. The epididymal epithelium is pseudostratified columnar, with basal and ciliated principal cells, whereas the ductus deferens epithelium is pseudostratified to simple cuboidal. The epididymal epithelium is 1.5 times taller than the ductus deferens epithelium. Here, we observed the SSK present in the cortex of the ventral region of the kidneys due to the hypertrophy of the distal convoluted tubules, as well as its secretory activity. Our findings will contribute to future research into the evolution of squamate reproductive morphology.

From little things big things grow: enhancement of an acoustic telemetry network to monitor broad-scale movements of marine species along Australia’s east coast

BackgroundAcoustic telemetry has become a fundamental tool to monitor the movement of aquatic species. Advances in technology, in particular the development of batteries with lives of > 10 years, have increased our ability to track the long-term movement patterns of many species. However, logistics and financial constraints often dictate the locations and deployment duration of acoustic receivers. Consequently, there is often a compromise between optimal array design and affordability. Such constraints can hinder the ability to track marine animals over large spatial and temporal scales. Continental-scale receiver networks have increased the ability to study large-scale movements, but significant gaps in coverage often remain.MethodsSince 2007, the Integrated Marine Observing System’s Animal Tracking Facility (IMOS ATF) has maintained permanent receiver installations on the eastern Australian seaboard. In this study, we present the recent enhancement of the IMOS ATF acoustic tracking infrastructure in Queensland to collect data on large-scale movements of marine species in the northeast extent of the national array. Securing a relatively small initial investment for expanding receiver deployment and tagging activities in Queensland served as a catalyst, bringing together a diverse group of stakeholders (research institutes, universities, government departments, port corporations, industries, Indigenous ranger groups and tourism operators) to create an extensive collaborative network that could sustain the extended receiver coverage into the future. To fill gaps between existing installations and maximise the monitoring footprint, the new initiative has an atypical design, deploying many single receivers spread across 2,100 km of Queensland waters.ResultsThe approach revealed previously unknown broad-scale movements for some species and highlights that clusters of receivers are not always required to enhance data collection. However, array designs using predominantly single receiver deployments are more vulnerable to data gaps when receivers are lost or fail, and therefore “redundancy” is a critical consideration when designing this type of array.ConclusionInitial results suggest that our array enhancement, if sustained over many years, will uncover a range of previously unknown movements that will assist in addressing ecological, fisheries, and conservation questions for multiple species.

Social interactions and habitat structure in understanding the dynamic space use of invasive wild pigs

Untangling the abiotic and biotic feedback mechanisms driving animal movements and ranges is a core question in ecology, yet progress is hampered by inadequate modelling procedures. Here we show how a recently developed process‐based modelling approach, combining step‐selection functions and individual‐based models, enables a flexible method to infer movement drivers and multi‐scale emergent space use patterns. As a case study, we examine the movement behaviours of a highly invasive social generalist (wild pigs, Sus scrofa) in relation to conspecific space use and multiple land cover types in a complex agricultural landscape, showing that social interactions are predominantly more important to this species than selection for land cover. Thus, animal movement studies should not neglect the effects of sociality when inferring resource driven movements and, crucially, use multi‐scale techniques that incorporate movement processes to untangle drivers of animal space use.