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.

Tracking animal movements via collaborative acoustic telemetry networks: Multiscale habitat use, phenology, and management insights.

Estuaries support diverse fish and invertebrate communities, including resident species that rely on estuarine habitats year-round and transient migratory species. The unique movement patterns of these animals connect habitats within and far beyond the estuary and are integrally linked to fisheries management objectives. With a focus on Chesapeake Bay, this study leveraged data from collaborative acoustic telemetry networks in the northwest Atlantic to assess habitat use and phenology of movements for seven species of fish (cownose rays, dusky sharks, smooth dogfish, alewife, striped bass, common carp, and blue catfish) and one invertebrate (horseshoe crabs). A total of 288 acoustically tagged individuals were detected >3.2 million times (6,743 to 2,095,717 detections per species) on receivers across ~20.5 degrees of latitude spanning the North American Atlantic seaboard from Florida, USA, to New Brunswick, Canada. Common metrics of movement and phenology grouped these species as resident (common carp, blue catfish, horseshoe crabs), primarily resident in estuaries (juvenile striped bass), and coastal migrant (cownose rays, dusky sharks, smooth dogfish, alewife); maximum distance traveled varied by three orders of magnitude among these species. Further analysis of phenology for coastal migrants elucidated the timing and duration of these species' use of Chesapeake Bay. Collectively, movements linked habitats within Chesapeake Bay and connected the estuary to coastal ecosystems both to the north (e.g., alewife) and south (e.g., cownose rays), creating networks of fisheries management jurisdictions that varied in complexity and identified opportunities for enhancement to current management or co-management of some species. Our results elucidate the importance of estuaries to species with diverse movement behaviors, identify scales and pathways of habitat connectivity via animal movements, and highlight the utility of collaborative acoustic telemetry networks for quantifying movements relevant to both ecological research and fisheries management.

The ecological and evolutionary dynamics of inselbergs.

Islands are fundamental model systems in ecology, biogeography, and evolutionary biology. However, terrestrial islands, unlike their aquatic counterparts, have received comparatively less attention. Among these land islands, inselbergs (i.e. isolated rock outcrops with diverse lithologies and a modest topographical prominence) stand out as iconic examples distributed worldwide across global biomes. Due to their durable lithology, inselbergs change slowly, persisting for tens of millions of years. In this review, we propose a biological definition for inselbergs that captures three fundamental characteristics of inselbergs from the perspective of biota. These are old age, isolation and the presence of unique microhabitats that are rare or absent in the surrounding matrix, fostering distinct communities often with unique and endemic biota. We synthesise the state of the art and formulate a set of testable hypotheses to deepen our understanding of the origins and maintenance of diversity on inselbergs, which are increasingly exposed to anthropogenic threats. By offering different habitats compared to the surrounding habitat matrix (e.g. moist microhabitats in dryland landscapes and xeric environments in humid tropical landscapes), inselbergs may allow specific lineages to thrive beyond their typical geographical limits. Particularly in drylands and degraded landscapes, inselbergs may not just provide different habitats but also act as ecological refuges or evolutionary refugia by providing a wider range of potential microhabitats than the surrounding matrix, enhancing resilience and promoting regional biodiversity. The central role of the matrix ensures that the ecological and evolutionary dynamics of inselbergs differ from those of true islands such as oceanic islands. Given that inselberg biota coexist within a terrestrial matrix, interactions between inselberg and matrix populations impact each other significantly. Over evolutionary timescales, matrix species may contract to inselberg refugia, preserving lineages while cycles of isolation and reconnection may drive speciation via a species pump. Although inselberg biodiversity has been studied predominantly from an island biogeography perspective, we argue that depending on the spatial scale, habitat specificity and mobility of the organisms considered, a range of different theories and paradigms can help explain the biogeography and local distribution patterns of different taxonomic and functional groups of inselberg species.

Spatial ecology, biodiversity, and abiotic determinants of Congo's bai ecosystem.

Canopy gaps are foundational features of rainforest biodiversity and successional processes. The bais of Central Africa are among the world's largest natural forest clearings and thought to be critically important islands of open-canopy habitat in an ocean of closed-canopy rainforest. However, while frequently denoted as a conservation priority, there are no published studies on the abundance or distribution of bais across the landscape, nor on their biodiversity patterns, limiting our understanding of their ecological contribution to Congolese rainforests. We combined remote sensing and field surveys to quantify the abundance, spatial distribution, shape, size, biodiversity, and soil properties of bais in Odzala-Kokoua National Park (OKNP), Republic of the Congo (hereafter, Congo). We related bai spatial distribution to variation in hydrology and topography, compared plant community composition and 3D structure between bais and other open ecosystems, quantified animal diversity from camera traps, and measured soil moisture content in different bai types. We found bais to be more numerous than previously thought (we mapped 2176 bais in OKNP), but their predominantly small size (80.7% of bais were <1 ha), highly clustered distribution, and restriction to areas of low topographic position make them a rare riparian habitat type. We documented low plant community and structural similarity between bai types and with other open ecosystems, and identified significant differences in soil moisture between bai and open ecosystem types. Our results demonstrate that two distinct bai types can be differentiated based on their plant and animal communities, soil properties, and vegetation structure. Taken together, our findings provide insights into how bais relate to other types of forest clearings and on their overall importance to Congolese rainforest ecosystems.

Ecological implications of chromium-contaminated effluents from Indian tanneries and their phytoremediation: a sustainable approach.

Industrial activities are paramount to sustaining the economy in a rapidly developing nation and global powerhouse like India. Leather industries are important in the country's economic map due to the high revenue and employment generation opportunities. Several of these industries contribute largely to environmental pollution. The pollution of the environment is mainly caused by improper disposal of the tannery effluents that are highly rich in hexavalent chromium, a potent human carcinogen. Hexavalent chromium imparts toxic effects on the biotic components, which include plants, animals, and humans. The review portrays the current status of the Indian leather tanning sector and its impact on the Indian economy. The process of chromium tanning and its adverse effects on the environmental biotic components have been briefly discussed. Phytoremediation of these effluents using suitable hyperaccumulating plants has been suggested as an eco-friendly and cost-effective approach for the sustainable restoration of the polluted environment. The mechanism behind the remediation approach and the factors influencing it have been detailed. The manuscript briefly discusses some important advancements in the field of phytoremediation and emerging technologies and concludes by emphasizing further research for sustainable management of tannery wastes.

Asymmetric Biotic Interactions Cannot Be Inferred Without Accounting for Priority Effects.

Understanding biotic interactions is a crucial goal in community ecology and species distribution modelling, and large strides have been made towards improving multivariate computational methods with the aim of quantifying biotic interactions and improving predictions of species occurrence. Yet, while considerable attention has been given to computational approaches and the interpretation of these quantitative tools, the importance of sampling design to reveal these biotic interactions has received little consideration. This study explores the influential role of priority effects, that is, the order of habitat colonisation, in shaping our ability to detect biotic interactions. Using a simple set of simulations, we demonstrate that commonly used cross-sectional co-occurrence data alone cannot be used to make reliable inferences on asymmetric biotic interactions, even if they perform well in predicting the occurrence of species. We then show how sampling designs that consider priority effects can recover the asymmetric effects that are lost when priority effects are ignored. Based on these findings, we urge for caution when drawing inferences on biotic interactions from cross-sectional binary co-occurrence data, and provide guidance on sampling designs that may provide the necessary data to tackle this longstanding challenge.

Consequences of Local Conspecific Density Effects for Plant Diversity and Community Dynamics.

Conspecific density dependence (CDD) in plant populations is widespread, most likely caused by local-scale biotic interactions, and has potentially important implications for biodiversity, community composition, and ecosystem processes. However, progress in this important area of ecology has been hindered by differing viewpoints on CDD across subfields in ecology, lack of synthesis across CDD-related frameworks, and misunderstandings about how empirical measurements of local CDD fit within the context of broader ecological theories on community assembly and diversity maintenance. Here, we propose a conceptual synthesis of local-scale CDD and its causes, including species-specific antagonistic and mutualistic interactions. First, we compare and clarify different uses of CDD and related concepts across subfields within ecology. We suggest the use of local stabilizing/destabilizing CDD to refer to the scenario where local conspecific density effects are more negative/positive than heterospecific effects. Second, we discuss different mechanisms for local stabilizing and destabilizing CDD, how those mechanisms are interrelated, and how they cut across several fields of study within ecology. Third, we place local stabilizing/destabilizing CDD within the context of broader ecological theories and discuss implications and challenges related to scaling up the effects of local CDD on populations, communities, and metacommunities. The ultimate goal of this synthesis is to provide a conceptual roadmap for researchers studying local CDD and its implications for population and community dynamics.

Coral responses to a catastrophic marine heatwave are decoupled from changes in total coral cover at a continental scale.

The services provided by the world's coral reefs are threatened by increasingly frequent and severe marine heatwaves. Heatwave-induced degradation of reefs has often been inferred from the extent of the decline in total coral cover, which overlooks extreme variation among coral taxa in their susceptibility and responses to thermal stress. Here, we provide a continental-scale assessment of coral cover changes at 262 shallow tropical reef sites around Australia, using ecological survey data on 404 coral taxa before and after the 2016 mass bleaching event. A strong spatial structure in coral community composition along large-scale environmental gradients largely dictated how coral communities responded to heat stress. While heat stress variables were the best predictors of change in total coral cover, the pre-heatwave community composition best predicted the temporal beta-diversity index (an indicator of change in community composition over time). Indicator taxa in each coral community differed before and after the heatwave, highlighting potential winners and losers of climate-driven coral bleaching. Our results demonstrate how assessment of change in total cover alone may conceal very different responses in community structure, some of which showed strong regional consistency, and may provide a telling outlook of how coral reefs may reorganize in a warmer future.

Trade-Offs Between Forage Availability, Accessibility, and Predation Risk on Winter Foraging Strategies of Wood Bison (Bison bison athabascae).

Optimal foraging theory (OFT) and the energy maximization hypothesis (EMH) have long been essential when examining wildlife habitat selection. At high latitudes and altitudes, animals in winter face greater limitations in availability and accessibility of forage. Here we explore the foraging behavior of wood bison (Bison bison athabascae) during winter within the Ronald Lake bison herd in northeastern Alberta, Canada, and examine the trade-offs they face due to limitations in forage abundance and availability (snow conditions), as well as the need to minimize predation risk. We used Global Positioning System (GPS) location data collected from 70 female wood bison to identify winter foraging sites and craters selected by bison to access forage beneath the snow. Within wetlands used by bison we selected 190 pairs of used (foraged) and random (available) sites to test eight a priori hypotheses explaining how bison traded-off between forage availability, accessibility, and minimizing predation risk. We found with matched-paired logistic regression that Carex atherodes was 1.21-times more likely to be selected per unit increase in ground cover, compared to 1.17-times per unit ground cover for C. aquatilis and C. utriculata. However, all Carex species showed an increase in selection when cover was > 50% cover within individual craters. While the importance of Carex was clear, forage site selection was still inversely related to snow depth. There is also a neutralizing combined effect of snow depth and Carex species ground cover which suggests that bison maximized their energy return by avoiding areas with deep snow (> 30 cm) that demanded intensive cratering, even when highly selected forage was accessible beneath. Avoidance of forage areas with deep snow demonstrates that wood bison employed a foraging strategy that considers both forage availability and environmental conditions, with snow depth being a limiting factor. We highlight the relationship between optimal foraging based on food availability and the trade-offs within an energy restrictive winter season, furthering the understanding of how large herbivores forage strategically to maximize energy intake in northern environments.

Assessing stakeholder perceptions to guide social and ecological fit of marine protected areas.

Effective social and ecological interventions that can benefit both nature and people are needed to halt the degradation of ecosystems and subsequent negative impacts on human well-being. Marine protected areas (MPAs) are commonly used to foster the sustainability of coastal social-ecological systems. However, because MPAs are often proposed and implemented by external actors, ensuring they are fit to the local social and ecological context remains a challenge. Here, we introduce a framework to identify the place-based social and ecological goals for an MPA. We use a marine conservation project in the Philippines as a case study. We assess the perceptions of local communities and decision-makers across four categories: (i) marine importance, (ii) environmental stressors, (iii) proposed management options, and (iv) MPA goals and needs. Assessing these is a way to refine marine conservation goals locally, adapt the implementation of planned interventions, and monitor their future outcomes.

Emergent ecology in a microscale model of the surface ocean.

Microbial processes operate at the microscale, which is not resolved by existing ecosystem models. Here, we present a novel model that simulates a 1 mL three-dimensional cube using a hybrid Lagrangian-Eulerian approach, at ecologically relevant timescales. The model simulates individual microbes, including three phytoplankton size classes with healthy, senescent, and dead lifecycle stages; copiotrophic and oligotrophic heterotrophic bacteria; and dissolved organic matter at 50 µm resolution. Diffusion, shear, sedimentation, chemotaxis, and attachment processes are explicitly resolved. The emerging quantitative representation of the ecosystem shows that (1) copiotrophs grow mostly attached to eukaryotic phytoplankters and get almost all of their carbon from them vs. oligotrophs that grow on exudates and lysates of cyanobacteria; (2) contrasting diel patterns in substrate appearance in the phycosphere vs. ambient water and growth of particle-associated copiotrophs vs. free-living oligotrophs; (3) attached bacteria reduce carbon flux from the phycosphere, lowering chemotactic efficiency toward eukaryotes below that toward cyanobacteria; (4) shear reduces chemotactic efficiency and fitness of the copiotroph; and (5) the main benefit of chemotaxis is to locate attachment partners. These patterns are consistent with available observations. Our study provides insights into the microscale ecology of marine bacteria, and the open-source code is a tool for further research in this area.IMPORTANCEA large amount of global CO2 fixation is performed by marine phytoplankton, and a substantial fraction of that is released as dissolved organic carbon and further processed by heterotrophic bacteria. The interaction between phytoplankton and bacteria, i.e., the carbon flux between them, is therefore an important process in the global carbon and climate system. Some bacteria have developed specialized behavioral traits, like swimming and attachment, to increase their carbon acquisition. These interactions occur at the micrometer scale, for example, the immediate vicinity of phytoplankters (the phycosphere), but existing biogeochemical models typically only simulate down to the 1 meter vertical or ~100 kilometer horizontal scale. We present a new microscale model and use it to predict fluxes and other features in the surface ocean. The model makes important predictions about the fluxes between various types of phytoplankton and bacteria and the role of behavioral traits, and it provides a basis and tool for further research in this area.

Coevolution promotes the coexistence of Tasmanian devils and a fatal, transmissible cancer.

Emerging infectious diseases threaten natural populations, and data-driven modeling is critical for predicting population dynamics. Despite the importance of integrating ecology and evolution in models of host-pathogen dynamics, there are few wild populations for which long-term ecological datasets have been coupled with genome-scale data. Tasmanian devil (Sarcophilus harrisii ) populations have declined range-wide due to devil facial tumor disease (DFTD), a fatal transmissible cancer. Although early ecological models predicted imminent devil extinction, diseased devil populations persist at low densities, and recent ecological models predict long-term devil persistence. Substantial evidence supports evolution of both devils and DFTD, suggesting coevolution may also influence continued devil persistence. Thus, we developed an individual-based, eco-evolutionary model of devil-DFTD coevolution parameterized with nearly two decades of devil demography, DFTD epidemiology, and genome-wide association studies. We characterized potential devil-DFTD coevolutionary outcomes and predicted the effects of coevolution on devil persistence and devil-DFTD coexistence. We found a high probability of devil persistence over 50 devil generations (100 years) and a higher likelihood of devil-DFTD coexistence, with greater devil recovery, than predicted by previous ecological models. These novel results add to growing evidence for long-term devil persistence and highlight the importance of eco-evolutionary modeling for emerging infectious diseases.

Effects of a large-scale bioretention installation on the species composition of an urban bird community as determined by passive acoustic monitoring.

As urbanization accelerates worldwide, municipalities are attempting to construct new green spaces within their borders. The perceived ecological value of these places is frequently tied to their ability to attract urban wildlife, such as birds, which can easily be observed and enjoyed. As one strategy, stormwater is now frequently managed with green infrastructure: planted areas that retain and treat stormwater rather than merely directing it to surface waters. While these practices have the potential to provide habitat for urban wildlife, the ecological effects of these systems are largely unknown. To assess whether one green infrastructure project increases habitat value, we used passive acoustic monitoring to survey urban bird communities in and near a large green infrastructure project in Columbus, Ohio (USA). Bird communities near bioretention cells (rain gardens) were compared to those at nearby lawns and remnant or restored natural areas. We found that recently installed bioretention cells tended to support more omnivores, lower-canopy foraging species, and species from a higher diversity of feeding guilds than did nearby lawn control sites. We were unable to detect effects of nearby bioretention installations on bird species richness at other sites. The observed differences in species richness were fairly small, and we urge caution when anticipating the habitat value of bioretention cells, at least for bird species. However, the results that we observed suggest that bioretention cells could have a more positive impact on bird communities in different contexts or using different design strategies. The bioretention cells surveyed in this study were small and only planted in grasses and forbs, potentially limiting their ability to offer complex habitat. They were also relatively young, and future work is needed to determine their long-term effect on avian communities and biodiversity of other taxa.

A systematic review and guide for using multi-response statistical models in co-infection research.

The simultaneous infection of organisms with two or more co-occurring pathogens, otherwise known as co-infections, concomitant infections or multiple infections, plays a significant role in the dynamics and consequences of infectious diseases in both humans and animals. To understand co-infections, ecologists and epidemiologists rely on models capable of accommodating multiple response variables. However, given the diversity of available approaches, choosing a model that is suitable for drawing meaningful conclusions from observational data is not a straightforward task. To provide clearer guidance for statistical model use in co-infection research, we conducted a systematic review to (i) understand the breadth of study goals and host-pathogen systems being pursued with multi-response models and (ii) determine the degree of crossover of knowledge among disciplines. In total, we identified 69 peer-reviewed primary studies that jointly measured infection patterns with two or more pathogens of humans or animals in natural environments. We found stark divisions in research objectives and methods among different disciplines, suggesting that cross-disciplinary insights into co-infection patterns and processes for different human and animal contexts are currently limited. Citation network analysis also revealed limited knowledge exchange between ecology and epidemiology. These findings collectively highlight the need for greater interdisciplinary collaboration for improving disease management.

Navigating the archaeal frontier: insights and projections from bioinformatic pipelines.

Archaea continues to be one of the least investigated domains of life, and in recent years, the advent of metagenomics has led to the discovery of many new lineages at the phylum level. For the majority, only automatic genomic annotations can provide information regarding their metabolic potential and role in the environment. Here, genomic data from 2,978 archaeal genomes was used to perform automatic annotations using bioinformatics tools, alongside synteny analysis. These automatic classifications were done to assess how good these different tools perform in relation to archaeal data. Our study revealed that even with lowered cutoffs, several functional models do not capture the recently discovered archaeal diversity. Moreover, our investigation revealed that a significant portion of archaeal genomes, approximately 42%, remain uncharacterized. In comparison, within 3,235 bacterial genomes, a diverse range of unclassified proteins is obtained, with well-studied organisms like Escherichia coli having a substantially lower proportion of uncharacterized regions, ranging from <5 to 25%, and less studied lineages being comparable to archaea with the range of 35-40% of unclassified regions. Leveraging this analysis, we were able to identify metabolic protein markers, thereby providing insights into the metabolism of the archaea in our dataset. Our findings underscore a substantial gap between automatic classification tools and the comprehensive mapping of archaeal metabolism. Despite advances in computational approaches, a significant portion of archaeal genomes remains unexplored, highlighting the need for extensive experimental validation in this domain, as well as more refined annotation methods. This study contributes to a better understanding of archaeal metabolism and underscores the importance of further research in elucidating the functional potential of archaeal genomes.