Bioinformatic Pipeline for Profiling Foodborne Bacterial Ecology and Resistome from Short-Read Metagenomics.

Next-generation sequencing revolutionized food safety management these last years providing access to a huge quantity of valuable data to identify, characterize, and monitor bacterial pathogens on the food chain. Shotgun metagenomics emerged as a particularly promising approach as it enables in-depth taxonomic profiling and functional investigation of food microbial communities. In this chapter, we provide a comprehensive step-by-step bioinformatical workflow to characterize bacterial ecology and resistome composition from metagenomic short-reads obtained by shotgun sequencing.

See you later: roost fidelity of the "Boomerang Bats",Artibeus lituratus (Olfers, 1818) (Mammalia, Chiroptera) / Até mais tarde: fidelidade de abrigo dos "Morcegos Boomerang", Artibeus lituratus (Olfers, 1818) (Mammalia, Chiroptera)

Animals exhibit sociability behaviors and spatial use patterns that are important for species survival. Bats are animals that exhibit complex patterns of aggregation of individuals, which can vary according to sex and age. Aggregation can be explained by active or passive mechanisms. In this behavioural note, we report a group of female Artibeus lituratus in the reproductive stage that exhibits aggregation behavior supporting the active mechanism hypothesis. The females returned to the same roost, for two reproductive season, maintaining the aggregation with the same individuals with which the social bonds were already established.

Os animais exibem comportamentos de sociabilidade e padrões de uso espacial que são importantes para a sobrevivência das espécies. Os morcegos são animais que apresentam padrões complexos de agregação de indivíduos, que podem variar de acordo com o sexo e a idade. A agregação pode ser explicada por mecanismos ativos ou passivos. Nesta nota comportamental, relatamos um grupo de fêmeas de Artibeus lituratus em fase reprodutiva que exibe comportamento de agregação apoiando a hipótese do mecanismo ativo. As fêmeas retornaram ao mesmo poleiro, por duas estações reprodutivas, mantendo a agregação com os mesmos indivíduos com os quais os laços sociais já foram estabelecidos.

Beyond the here and now: hunter-gatherer socio-spatial complexity and the evolution of language.

Human evolutionary ecology stands to benefit by integrating theory and methods developed in movement ecology, and in turn, to make contributions to the broader field of movement ecology by leveraging our species' distinct attributes. In this paper, we review data and evolutionary models suggesting that major changes in socio-spatial behaviour accompanied the evolution of language. To illustrate and explore these issues, we present a comparison of GPS measures of the socio-spatial behaviour of Hadza hunter-gatherers of northern Tanzania to those of olive baboons (Papio anubis), a comparatively small-brained primate that is also savanna-adapted. While standard spatial metrics show modest differences, measures of spatial diversity, landscape exploration and spatiotemporal displacement between individuals differ markedly. Groups of Hadza foragers rapidly accumulate a vast, diverse knowledge pool about places and things over the horizon, contrasting with the baboon's narrower and more homogeneous pool of ecological information. The larger and more complex socio-spatial world illustrated by the Hadza is one where heightened cognitive abilities for spatial and episodic memory, navigation, perspective taking and communication about things beyond the here and now all have clear value.This article is part of the theme issue 'The spatial-social interface: a theoretical and empirical integration'.

Expanding theory, methodology and empirical systems at the spatial-social interface.

All animals exhibit some combination of spatial and social behaviours. A diversity of interactions occurs between such behaviours, producing emergent phenomena at the spatial-social interface. Untangling and interrogating these complex, intertwined processes can be vital for identifying the mechanisms, causes and consequences of behavioural variation in animal ecology. Nevertheless, the integrated study of the interactions between spatial and social phenotypes and environments (at the spatial-social interface) is in its relative infancy. In this theme issue, we present a collection of papers chosen to expand the spatial-social interface along several theoretical, methodological and empirical dimensions. They detail new perspectives, methods, study systems and more, as well as offering roadmaps for applied outputs and detailing exciting new directions for the field to move in the future. In this Introduction, we outline the contents of these papers, placing them in the context of what comes before, and we synthesize a number of takeaways and future directions for the spatial-social interface. This article is part of the theme issue 'The spatial-social interface: a theoretical and empirical integration'.

Anthropogenic impacts at the interface of animal spatial and social behaviour.

Human disturbance is contributing to widespread, global changes in the distributions and densities of wild animals. These anthropogenic impacts on wildlife arise from multiple bottom-up and top-down pathways, including habitat loss, resource provisioning, climate change, pollution, infrastructure development, hunting and our direct presence. Animal behaviour is an important mechanism linking these disturbances to population outcomes, although these behavioural pathways are often complex and can remain obscured when different aspects of behaviour are studied in isolation from one another. The spatial-social interface provides a lens for understanding how an animal's spatial and social environments interact to determine its spatial and social phenotype (i.e. measurable characteristics of an individual), and how these phenotypes interact and feed back to reshape environments. Here, we review studies of animal behaviour at the spatial-social interface to understand and predict how human disturbance affects animal movement, distribution and intraspecific interactions, with consequences for the conservation of populations and ecosystems. By understanding the spatial-social mechanisms linking human disturbance to conservation outcomes, we can better design management interventions to mitigate undesired consequences of disturbance.This article is part of the theme issue 'The spatial-social interface: a theoretical and empirical integration'.

Toward a comparative framework for studies of altitudinal migration.

The study and importance of altitudinal migration has attracted increasing interest among zoologists. Altitudinal migrants are taxonomically widespread and move across altitudinal gradients as partial or complete migrants, subjecting them to a wide array of environments and ecological interactions. Here, we present a brief synthesis of recent developments in the field and suggest future directions toward a more taxonomically inclusive comparative framework for the study of altitudinal migration. Our framework centers on a working definition of altitudinal migration that hinges on its biological relevance, which is scale-dependent and related to fitness outcomes. We discuss linguistic nuances of altitudinal movements and provide concrete steps to compare altitudinal migration phenomena across traditionally disparate study systems. Together, our comparative framework outlines a "phenotypic space" that contextualizes the biotic and abiotic interactions encountered by altitudinal migrants from divergent lineages and biomes. We also summarize new opportunities, methods, and challenges for the ongoing study of altitudinal migration. A persistent, primary challenge is characterizing the taxonomic extent of altitudinal migration within and among species. Fortunately, a host of new methods have been developed to help researchers assess the taxonomic prevalence of altitudinal migration-each with their own advantages and disadvantages. An improved comparative framework will allow researchers that study disparate disciplines and taxonomic groups to better communicate and to test hypotheses regarding the evolutionary and ecological drivers underlying variation in altitudinal migration among populations and species.

Assessing abundance-suitability models to prioritize conservation areas for the dwarf caimans in South America.

Species-environment relationships have been extensively explored through species distribution models (SDM) and species abundance models (SAM), which have become key components to understand the spatial ecology and population dynamics directed at biodiversity conservation. Nonetheless, within the internal structure of species' ranges, habitat suitability and species abundance do not always show similar patterns, and using information derived from either SDM or SAM could be incomplete and mislead conservation efforts. We gauged support for the abundance-suitability relationship and used the combined information to prioritize the conservation of South American dwarf caimans (Paleosuchus palpebrosus and P. trigonatus). We used 7 environmental predictor sets (surface water, human impact, topography, precipitation, temperature, dynamic habitat indices, soil temperature), 2 regressions methods (Generalized Linear Models-GLM, Generalized Additive Models-GAM), and 4 parametric distributions (Binomial, Poisson, Negative binomial, Gamma) to develop distribution and abundance models. We used the best predictive models to define four categories (low, medium, high, very high) to plan species conservation. The best distribution and abundance models for both Paleosuchus species included a combination of all predictor sets, except for the best abundance model for P. trigonatus which incorporated only temperature, precipitation, surface water, human impact, and topography. We found non-consistent and low explanatory power of environmental suitability to predict abundance which aligns with previous studies relating SDM-SAM. We extracted the most relevant information from each optimal SDM and SAM and created a consensus model (2,790,583 km2) that we categorized as low (39.6%), medium (42.7%), high (14.9%), and very high (2.8%) conservation priorities. We identified 279,338 km2 where conservation must be critically prioritized and only 29% of these areas are under protection. We concluded that optimal models from correlative methods can be used to provide a systematic prioritization scheme to promote conservation and as surrogates to generate insights for quantifying ecological patterns.

36-year study reveals stability of a wild wheat population across microhabitats.

Long-term genetic studies of wild populations are very scarce, but are essential for connecting ecological and population genetics models, and for understanding the dynamics of biodiversity. We present a study of a wild wheat population sampled over a 36-year period at high spatial resolution. We genotyped 832 individuals from regular sampling along transects during the course of the experiment. Genotypes were clustered into ecological microhabitats over scales of tens of metres, and this clustering was remarkably stable over the 36 generations of the study. Simulations show that it is difficult to determine whether this spatial and temporal stability reflects extremely limited dispersal or fine-scale local adaptation to ecological parameters. Using a common-garden experiment, we showed that the genotypes found in distinct microhabitats differ phenotypically. Our results provide a rare insight into the population genetics of a natural population over a long monitoring period.

Evaluating the efficacy of ecological restoration of fish habitat in coastal waters of Lake Ontario.

Ecological restoration is a common strategy applied to degraded wetlands and tributaries in large lakes. As resources are typically limited for restoration, it is essential to ensure that such efforts achieve associated goals. Using both discrete and continuous methods, we evaluated the efficacy of ecological restoration efforts on fish habitat within Canada's largest city, Toronto, (Cell 2 and Embayment D of Tommy Thompson Park) relative to a control site (Toronto Islands). First, we used a long-term electrofishing dataset (i.e., discrete) to examine catch and community composition relative to restoration status. Catch for northern pike (Esox lucius) remained constant at both restoration sites, and catch of invasive common carp (Cyprinus carpio) decreased at Embayment D, indicating that exclusion barriers may be effective. Restoration was less effective for largemouth bass, as catches remained similar after restoration at Cell 2, but decreased within Embayment D. We also found that relative abundance for coldwater species at both restoration sites decreased post-restoration, with increases in warmwater species at Cell 2 and coolwater species at Embayment D. Next, we used a long-term acoustic telemetry dataset (i.e., continuous sampling) with three focal species: largemouth bass, northern pike, and invasive common carp. Based on telemetry, we found that restoration efficacy was species-specific, with largemouth bass present before and after ecological restoration (particularly in spring, which may be associated with spawning), but clear reductions in use of the restored areas for common carp and northern pike. Exclusion barriers, while effective for non-native common carp, appeared to also influence access for northern pike. Using both discrete and continuous methods longitudinally and across both treatment and control sites provided complementary information on the efficacy of restoration works within Toronto Harbour with electrofishing data highlighting changes in fish community composition while acoustic telemetry provided continuous information on timing and duration of habitat use.

Cancer and One Health: tumor-bearing individuals can act as super spreaders of symbionts in communities.

Recent theoretical advances in the One Health approach have suggested that cancer pathologies should be given greater consideration, as cancers often render their hosts more vulnerable to infectious agents, which could turn them into super spreaders within ecosystems. Although biologically plausible, this hypothesis has not yet been validated experimentally. Using a community of cnidarians of the Hydra genus (Hydra oligactis, Hydra viridissima, Hydra vulgaris) and a commensal ciliate species (Kerona pediculus) that colonizes them, we tested whether tumoral polyps of H. oligactis, compared to healthy ones, played an amplifying role in the number of ciliates, potentially resulting in a higher likelihood of infection for other community members through spillovers. Our results indicate that K. pediculus has a higher proliferation rate on tumoral polyps of H. oligactis than on healthy ones, which results in the infestation of other hydras. However, the magnitude of the spillover differed between recipient species. This study provides to our knowledge the first elements of proof of concept that tumoral individuals in communities could act as super spreaders of symbionts within and between species, and thus affect biotic interactions and dynamics in ecosystems.

A study on the diversity of phlebotomine sand flies (Diptera, Psychodidae) in karstic limestone areas in Vientiane Province, Laos, with a description of two new species of Sergentomyia França and & Parrot.

BACKGROUND: Southeast Asia is well known as a hotspot of biodiversity. However, very little is known about cave-dwelling hematophagous insects that are medically important. Taxonomic knowledge and ecology of phlebotomine sand flies are very poorly studied in Laos, as well as in other countries in the region. Herein, we report species diversity data and some notes on the ecology of the detected species from these karstic limestone areas of Laos. METHODS: Phlebotomine sand flies were collected using Centers for Disease Control and Prevention (CDC) light traps from limestone cave locations in three districts of Vientiane Province, Laos. Both morphological and molecular techniques were used for sand fly identification. Species diversity and abundance were analyzed according to sites, locations, collection seasons, and trapping positions. RESULTS: A total of 6564 sand flies, of which 5038 were females and 1526 were males, were morphologically identified into 20 species belonging to five genera (Chinius, Idiophlebotomus, Phlebotomus, Sergentomyia, and Grassomyia). The most abundant species were Chinius eunicegalatiae, Phlebotomus stantoni, Sergentomyia hivernus, Se. siamensis, and Idiophlebotomus longiforceps. Cytochrome b analysis results supported the morphological identification and revealed that Se. siamensis was separated from other members of the Se. barraudi group. Two new species, Se. dvoraki n. sp. and Se. marolii n. sp., were described. Sand fly density was generally high except in a cave in Vangvieng, with species richness ranging from 14 to 18 across different caves. Outside caves had higher species richness (R = 20) and diversity (H = 2.50) than cave entrances (R = 18, H = 2.41) and interiors (R = 16, H = 2.13). Seasonal variations showed high sand fly density in Feung and Hinheup during both dry and rainy seasons, while Vangvieng had a notable decrease in density during the dry season (D = 6.29). CONCLUSIONS: This study revealed that the diversity of phlebotomine sand fly fauna in Laos, particularly in karstic limestone areas, is greater than previously known. However, the taxonomic status of many species in Laos, as well as Southeast Asia, still needs more in-depth study using both morphological characters and molecular methods. Many species could be found from inside, at the entrance, and outside of caves, indicating a wide range of host-seeking behavior or possible natural breeding in the karstic cave areas.

Sod farms drive habitat selection of a migratory grassland shorebird during a critical stopover period.

Migratory shorebirds are one of the fastest declining groups of North American avifauna. Yet, relatively little is known about how these species select habitat during migration. We explored the habitat selection of Buff-breasted Sandpipers (Calidris subruficollis) during spring and fall migration through the Texas Coastal Plain, a major stopover region for this species. Using tracking data from 118 birds compiled over 4 years, we found Buff-breasted Sandpipers selected intensively managed crops such as sod and short-stature crop fields, but generally avoided rangeland and areas near trees and shrubs. This work supports prior studies that also indicate the importance of short-stature vegetation for this species. Use of sod and corn varied by season, with birds preferring sod in spring, and avoiding corn when it is tall, but selecting for corn in fall after harvest. This dependence on cropland in the Texas Coastal Plain is contrary to habitat use observed in other parts of their non-breeding range, where rangelands are used extensively. The species' almost complete reliance on a highly specialized crop, sod, at this critical stopover site raises concerns about potential exposure to contaminants as well as questions about whether current management practices are providing suitable conditions for migratory grassland birds.

Genetic diversity, population structure and ecological niche modeling of Thyrinteina arnobia (Lepidoptera: Geometridae), a native Eucalyptus pest in Brazil.

Thyrinteina arnobia (Lepidoptera: Geometridae) is a native American species. Despite its historical importance as an insect pest in Eucalyptus plantations, more information is needed regarding the population diversity, demography, and climatic variables associated with its distribution in different regions of Brazil. We used a phylogeographic approach to infer the genetic diversity, genetic structure, and demographic parameters of T. arnobia. We also conducted an ecological niche modeling (ENM) to predict suitable areas for T. arnobia occurrence in Brazil and other countries worldwide. Although T. arnobia populations have low genetic diversity in Brazil, we identified mitochondrial haplogroups predominating in different Brazilian regions and high ФST and ФCT values in AMOVA, suggesting a low frequency of insect movement among these regions. These results indicate that outbreaks of T. arnobia in Eucalyptus areas in different regions of Brazil are associated with local or regional populations, with no significant contribution from long-distance dispersal from different regions or biomes, suggesting that pest management strategies would be implemented on a regional scale. In Brazil, the demographic and spatial expansion signals of T. arnobia seem to be associated with the history of geographical expansion of Eucalyptus plantations, a new sustainable host for this species. ENM indicated that isothermality and annual rainfall are critical climatic factors for the occurrence of T. arnobia in tropical and subtropical areas in the Americas. ENM also suggested that T. arnobia is a potential pest in Eucalyptus areas in all Brazilian territory and in regions from Africa, Asia, and Oceania.

Body size modulates the extent of seasonal diet switching by large mammalian herbivores in Yellowstone National Park.

Prevailing theories about animal foraging behaviours and the food webs they occupy offer divergent predictions about whether seasonally limited food availability promotes dietary diversification or specialization. Emphasis on how animals compete for food predominates in work on the foraging ecology of large mammalian herbivores, whereas emphasis on how the diversity of available foods generally constrains dietary opportunity predominates work on entire food webs. Reconciling predictions about what promotes dietary diversification is challenging because species' different body sizes and mobilities modulate how they seek and compete for resources-the mechanistic bases of common predictions may not pertain to all species equally. We evaluated predictions about five large-herbivore species that differ in body size and mobility in Yellowstone National Park using GPS tracking and dietary DNA. The data illuminated remarkably strong and significant correlations between body size and five key indicators of diet seasonality (R 2 = 0.71-0.80). Compared to smaller species, bison and elk showed muted diet seasonality and maintained access to more unique foods when winter conditions constrained food availability. Evidence from GPS collars revealed size-based differences in species' seasonal movements and habitat-use patterns, suggesting that better accounting for the allometry of foraging behaviours may help reconcile disparate ideas about the ecological drivers of seasonal diet switching.

Virulence and transmission biology of the widespread, ecologically important pathogen of zooplankton, Spirobacillus cienkowskii.

Spirobacillus cienkowskii (Spirobacillus, hereafter) is a widely distributed bacterial pathogen that has significant impacts on the population dynamics of zooplankton (Daphnia spp.), particularly in months when Daphnia are asexually reproducing. However, little is known about Spirobacillus' virulence, transmission mode, and dynamics. As a result, we cannot explain the dynamics of Spirobacillus epidemics in nature or use Spirobacillus as a model pathogen, despite Daphnia's tractability as a model host. Here, we work to fill these knowledge gaps experimentally. We found that Spirobacillus is among the most virulent of Daphnia pathogens, killing its host within a week and reducing host fecundity. We further found that Spirobacillus did not transmit horizontally among hosts unless the host died or was destroyed (i.e., it is an "obligate killer"). In experiments aimed at quantifying the dynamics of horizontal transmission among asexually reproducing Daphnia, we demonstrated that Spirobacillus transmits poorly in the laboratory. In mesocosms, Spirobacillus failed to generate epidemics; in experiments wherein individual Daphnia were exposed, Spirobacillus' transmission success was low. In the (limited) set of conditions we considered, Spirobacillus' transmission success did not change with host density or pathogen dose and declined following environmental incubation. Finally, we conducted a field survey of Spirobacillus' prevalence within egg cases (ephippia) made by sexually reproducing Daphnia. We found Spirobacillus DNA in ~40% of ephippia, suggesting that, in addition to transmitting horizontally among asexually reproducing Daphnia, Spirobacillus may transmit vertically from sexually reproducing Daphnia. Our work fills critical gaps in the biology of Spirobacillus and illuminates new hypotheses vis-à-vis its life history. IMPORTANCE: Spirobacillus cienkowskii is a bacterial pathogen of zooplankton, first described in the 19th century and recently placed in a new family of bacteria, the Silvanigrellaceae. Spirobacillus causes large epidemics in lake zooplankton populations and increases the probability that zooplankton will be eaten by predators. However, little is known about how Spirobacillus transmits among hosts, to what extent it reduces host survival and reproduction (i.e., how virulent it is), and what role virulence plays in Spirobacillus' life cycle. Here, we experimentally quantified Spirobacillus' virulence and showed that Spirobacillus must kill its host to transmit horizontally. We also found evidence that Spirobacillus may transmit vertically via Daphnia's seed-like egg sacks. Our work will help scientists to (i) understand Spirobacillus epidemics, (ii) use Spirobacillus as a model pathogen for the study of host-parasite interactions, and (iii) better understand the unusual group of bacteria to which Spirobacillus belongs.

Fine-scale tracking reveals visual field use for predator detection and escape in collective foraging of pigeon flocks.

During collective vigilance, it is commonly assumed that individual animals compromise their feeding time to be vigilant against predators, benefiting the entire group. One notable issue with this assumption concerns the unclear nature of predator 'detection', particularly in terms of vision. It remains uncertain how a vigilant individual utilizes its high-acuity vision (such as the fovea) to detect a predator cue and subsequently guide individual and collective escape responses. Using fine-scale motion-capture technologies, we tracked the head and body orientations of pigeons (hence reconstructed their visual fields and foveal projections) foraging in a flock during simulated predator attacks. Pigeons used their fovea to inspect predator cues. Earlier foveation on a predator cue was linked to preceding behaviors related to vigilance and feeding, such as head-up or down positions, head-scanning, and food-pecking. Moreover, earlier foveation predicted earlier evasion flights at both the individual and collective levels. However, we also found that relatively long delay between their foveation and escape responses in individuals obscured the relationship between these two responses. While our results largely support the existing assumptions about vigilance, they also underscore the importance of considering vision and addressing the disparity between detection and escape responses in future research.

Most animals have to compromise between spending time foraging for food and other resources and keeping careful watch for approaching predators or other threats. Many are thought to address this trade-off by living in a group where they rely on the vigilance of others to free up more time for foraging. If one individual animal detects a threat, they alert the whole group so that every individual can respond. However, it remains unclear how individuals use vision to detect a threat and how they communicate the threat to the rest of the group. Pigeons are a useful animal model to address this question because they tend to live in groups and their vision is well understood. A pit at the back of their eye called the fovea is responsible for building clear, detailed images of the centre of the field of vision. When pigeons attend to something of interest, they typically direct their gaze by moving their whole head instead of moving their eyes, making head orientation a good proxy for researchers to track where they are looking. To better understand how pigeons detect potential threats and communicate them to the rest of the flock, Delacoux and Kano used motion capture technology to track the head movements of groups of pigeons. To encourage the pigeons to forage, grain was scattered in the centre of an enclosed room. A plastic sparrowhawk (representing a potential predator) would then emerge and move across the room before disappearing again. Analysis of the imaging data revealed that pigeons use their fovea to spot predators. Individuals that were looking around before the potential predator emerged directed their fovea towards it more quickly than pigeons that were eating. These pigeons also took flight more quickly, and this likely triggered the rest of the group to follow. Due to improvements in the tracking technologies, these findings may help scientists understand in finer detail how animals in a group detect and respond to threats and other cues in their environment. Therefore, the experimental approach used by Delacoux and Kano could also be used to investigate how information is passed among groups of other animal species.

Exploring and exploiting the rice phytobiome to tackle climate change challenges.

The future of agriculture is uncertain under the current climate change scenario. Climate change directly and indirectly affects the biotic and abiotic elements that control agroecosystems, jeopardizing the safety of the world's food supply. A new area that focuses on characterizing the phytobiome is emerging. The phytobiome comprises plants and their immediate surroundings, involving numerous interdependent microscopic and macroscopic organisms that affect the health and productivity of plants. Phytobiome studies primarily focus on the microbial communities associated with plants, which are referred to as the plant microbiome. The development of high-throughput sequencing technologies over the past ten years has dramatically advanced the understanding of the structure, functionality, and dynamics of the phytobiome; however, comprehensive methods for using this knowledge are lacking, particularly on major crops such as rice. Taking into account the impact of rice production on world food security, gaining fresh perspectives on the interdependent and interrelated components of the rice phytobiome could enhance rice production and crop health, sustain rice ecosystem function, and combat the effects of climate change. Our review re-conceptualizes the complex dynamics of the microscopic and macroscopic components in the rice phytobiome as influenced by human interventions and changing environmental conditions driven by climate change. We also discuss the interdisciplinary and systematic approaches to decipher and reprogram the sophisticated interactions in the rice phytobiome using novel strategies and cutting-edge technology. Converging the gigantic datasets and complex information on the rice phytobiome and its application in the context of regenerative agriculture could lead to sustainable rice farming practices that are resilient to the impacts of climate change.