Ecological Insights Research Articles

Mindset × Context: Schools, Classrooms, and the Unequal Translation of Expectations into Math Achievement.

Mindset × Context: Schools, Classrooms, and the Unequal Translation of Expectations into Math Achievement.

Ecological and Evolutionary Insights About Emerging Infectious Diseases from the COVID-19 Pandemic

The coronavirus disease 2019 (COVID-19) pandemic challenged the workings of human society, but in doing so, it advanced our understanding of the ecology and evolution of infectious diseases. Fluctuating transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) demonstrated the highly dynamic nature of human social behavior, often without government intervention. Evolution of SARS-CoV-2 in the first two years following spillover resulted primarily in increased transmissibility, while in the third year, the globally dominant virus variants had all evolved substantial immune evasion. The combination of viral evolution and the buildup of host immunity through vaccination and infection greatly decreased the realized virulence of SARS-CoV-2 due to the age dependence of disease severity. The COVID-19 pandemic was exacerbated by presymptomatic, asymptomatic, and highly heterogeneous transmission, as well as highly variable disease severity and the broad host range of SARS-CoV-2. Insights and tools developed during the COVID-19 pandemic could provide a stronger scientific basis for preventing, mitigating, and controlling future pandemics.

Not up in smoke: Lipid and phytolith evidence for the function of combustion features at CA-ALA-11, a San Francisco Bay area shellmound

Ash and black char samples from seven combustion features at CA-ALA-11, an Early to Middle Period (ca. 2500 cal BCE to 585 cal CE) shellmound site on the San Francisco Bay shoreline, were analyzed for lipid, isotope, and phytolith content. Three features were intermingled with human burials and four were from nearby contexts not directly associated with human remains. Unlike more fragile biomolecules and floral remains, lipids and phytoliths can survive exposure to high temperatures. Together, these techniques supply independent and complementary lines of data for considering past cultural practices, local ecology, and post-depositional contributions. Our results shed light on the function and content of several combustion features, highlighting the untapped potential of such applications in the archaeology of California and elsewhere in North America. We focus on two combustion features with very different purposes. One appears to be the burnt remains of a basket (or possibly, a woven mat) coated with bitumen. This feature was associated with a burial and the basket or other woven object may have been burned as part of the funerary ceremony. Another feature, not directly associated with a burial, was composed of burned oyster shells and layered with leaves from a broadleaf tree—seemingly the remains of an ancient cooking feature for baking/steaming shellfish. Though small, this study demonstrates that analysis of sediments from combustion features can provide behavioral and ecological insights while avoiding destructive analysis of artifacts or human remains. We conclude with simple recommendations for integrating phytolith and lipid analysis of combustion features in future archaeological projects.

In search of relevant contemporary ecological insights from John Calvin (1509-1564): the case of CCAP Blantyre Synod in Malawi

Ecology and ecological destruction have become significant multi-sectorial subjects for worldwide conversation in recent decades (Foster, 2005:4-5). Many ecological problems stem from human activity which suggests that Christian contextual theology might also have some solutions to mitigate destructive patterns of survival. The ecological damage that is perpetrated affects not only the health of population, but also the natural species that live in particular areas (WWF Global, 2019). John Calvin (1509-1564) believed that God commissions humans to rule over the whole creation in a way that sustains, protects, and enhances His works so that all creation may fulfil the purposes of God. Human beings are responsible for taking care of the creation, and sharing all the wonders and resources to the glory of God (Forster, 2005:1). The aim of this study is to understand some aspects of ecology, causes and impacts of ecological destruction and review relevant contemporary ecological insights from John Calvin (1509-1564), redefine interdisciplinary ecological approaches, and to consider how to apply the interdisciplinary contemporary approaches to the ecological destruction in the Blantyre Synod in Malawi and elsewhere.

Characterization of fish assemblages in eleven multi-use reservoirs from North Carolina, USA

Managing impounded river systems is a recurring challenge for aquatic resource professionals because reservoirs serve multiple functions with different ecological and socioeconomic outcomes. However, research on fishes in reservoirs has disproportionally focused on recreationally and economically important species, with less attention directed toward fish assemblages despite the potential for management at the assemblage level. As such, evaluation of relationships between reservoir fish assemblages and biotic and abiotic factors and testing whether assemblage structure is affected by changing environmental conditions may deepen ecological understanding and provide insights for reservoir fisheries management. Our overall objective was to assess these relationships in 11 reservoirs from North Carolina, USA. We sampled fish assemblages in the reservoirs, which spanned five river basins representing a range of habitat conditions, using experimental gillnets and pulsed DC nighttime electrofishing. Multivariate statistical analyses indicated that taxonomic differences in fish assemblage composition among river basins followed a gradient of productivity. The top contributing species to reservoir dissimilarity were bluegill (Lepomis macrochirus), gizzard shad (Dorosoma cepedianum), black crappie (Pomoxis nigromaculatus), and white perch (Morone americana). These four species were positively associated with factors that reflect increasing eutrophic conditions in the 11 reservoirs and could, therefore, serve as indicators of reservoir productivity, anthropogenic influence, and fish assemblage structure, in addition to their key role in reservoir fisheries management. Whereas ­fisheries research has historically focused on assessing fish ­populations, our results illustrate the ecological and management insights derived from simultaneously collecting assemblage- and population-level data. Research on reservoir fish assemblages in relation to biotic and abiotic conditions may help advance fish ecology and management alike.

A discrete, stochastic model of colonial phytoplankton population size structure: Development and application to in situ imaging-in-flow cytometer observations of Dinobryon.

The scientific community lacks models for the dynamic changes in population size structure that occur in colonial phytoplankton. This is surprising, as size is a key trait affecting many aspects of phytoplankton ecology, and colonial forms are very common. We aim to fill this gap with a new discrete, stochastic model of dynamic changes in phytoplankton colonies' population size structure. We use the colonial phytoplankton Dinobryon as a proof-of-concept organism. The model includes four stochastic functions-division, stomatocyst production, colony breakage, and colony loss-to determine Dinobryon population size structure and populations counts. Although the functions presented here are tailored to Dinobryon, the model is readily adaptable to represent other colonial taxa. We demonstrate how fitting our model to in situ observations of colony population size structure can provide a powerful approach to explore colony size dynamics. Here, we have (1) collected high-frequency in situ observations of Dinobryon in Lac (Lake) Montjoie (Quebec, Canada) in 2013 with a moored Imaging FlowCytobot (IFCB) and (2) fit the model to those observations with a genetic algorithm solver that extracts parameter estimates for each of the four stochastic functions. As an example of the power of this model-data integration, we also highlight ecological insights into Dinobryon colony size and stomatocyst production. The Dinobryon population was enriched in larger, flagellate-rich colonies near bloom initiation and shifted to smaller and emptier colonies toward bloom decline.

Jaws from the deep: biological and ecological insights on the kitefin shark Dalatias licha from the Mediterranean Sea

Due to their late maturation, extreme longevity, low fecundity and slow growth rates, deep-sea Chondrichthyes are extremely vulnerable to human impacts. Moreover, assessing the impact of deep-sea fisheries is difficult, as many species (including sharks) are part of the bycatch and are often discarded at sea, and/or landed under generic commercial-species codes. The lack of this information on fishery data sets and the limited availability of species-specific life history data make challenging the management of deep-sea Chondrichthyes. The kitefin shark Dalatias licha is a cosmopolitan elasmobranch, mainly found on continental and insular shelf-breaks and slopes in warm-temperate and tropical waters. This species is a common by-catch of the deep-sea trawling, considered as “Endangered” by the IUCN Red List for all European waters, Mediterranean Sea included. Here we present the results of a study based on a total of 78 specimens of kitefin shark collected over 3 years in the Ligurian Sea (NW Mediterranean) as by-catch from deep-water fisheries. Total length ranged from 380 to 1164 mm, and individual weight ranged from 198 to 8000 g. Immature and mature individuals showed a sex ratio dominated by males. Adult males were observed throughout the year, while mature females were observed only in spring-summer. These data lead to hypothesise a spatial segregation between genders. The kitefin shark diet was dominated by bony fish (mainly Macrouridae) and other small sharks (e.g., Galeus melastomus and Etmopterus spinax), but their gut included plastic items and parasites. Data reported here underline the rarity, complex ecology and the threat for this shark species and support the urgency of promoting initiatives for their monitoring and conservation.

Enhancing mango disease diagnosis through eco-informatics: A deep learning approach

The mango is one of the most popular and economically important fruits in the world, but it is vulnerable to various diseases that can significantly reduce the quality and yield of the fruit. In the field of ecological informatics, tackling these challenges usually necessitate integrating cutting-edge technologies and ecological insights for effective disease management. Deep learning (DL) has been showing great promise in developing automated systems for leaf disease detection. This work proposes a novel DL approach that integrates the power of DL with ecological information management for the automated detection of mango leaf diseases. Our methodology introduces a visual modulation network that can innovatively learn the visual representations of leaf diseases along spatial and channel dimensions through simple but effective linear layers. An overlapped patching embedding is presented to tackle the discontinuity of non-overlapped patching in vision transformers (ViTs). Then, a succession of visual modulator blocks is presented to learn compact and long-term representations of disease in mango leaves without the inclusion of attention operation. Experimental results on the MangoLeafDB dataset show that the proposed visual modulation network can accurately detect various mango leaf diseases, demonstrating its potential as a cost-effective and efficient tool for disease management in mango cultivation.

Quantifying vegetation indices using terrestrial laser scanning: methodological complexities and ecological insights from a Mediterranean forest

Abstract. Accurate measurement of vegetation density metrics including plant, wood and leaf area indices (PAI, WAI and LAI) is key to monitoring and modelling carbon storage and uptake in forests. Traditional passive sensor approaches, such as digital hemispherical photography (DHP), cannot separate leaf and wood material, nor individual trees, and require many assumptions in processing. Terrestrial laser scanning (TLS) data offer new opportunities to improve understanding of tree and canopy structure. Multiple methods have been developed to derive PAI and LAI from TLS data, but there is little consensus on the best approach, nor are methods benchmarked as standard. Using TLS data collected in 33 plots containing 2472 trees of 5 species in Mediterranean forests, we compare three TLS methods (lidar pulse, 2D intensity image and voxel-based) to derive PAI and compare with co-located DHP. We then separate leaf and wood in individual tree point clouds to calculate the ratio of wood to total plant area (α), a metric to correct for non-photosynthetic material in LAI estimates. We use individual tree TLS point clouds to estimate how α varies with species, tree height and stand density. We find the lidar pulse method agrees most closely with DHP, but it is limited to single-scan data, so it cannot determine individual tree properties, including α. The voxel-based method shows promise for ecological studies as it can be applied to individual tree point clouds. Using the voxel-based method, we show that species explain some variation in α; however, height and plot density were better predictors. Our findings highlight the value of TLS data to improve fundamental understanding of tree form and function as well as the importance of rigorous testing of TLS data processing methods at a time when new approaches are being rapidly developed. New algorithms need to be compared against traditional methods and existing algorithms, using common reference data. Whilst promising, our results show that metrics derived from TLS data are not yet reliably calibrated and validated to the extent they are ready to replace traditional approaches for large-scale monitoring of PAI and LAI.

Large-scale exploration of nitrogen utilization efficiency in Asia region for rice crop: Variation patterns and determinants.

Improving rice nitrogen utilization efficiency (NUtE) is imperative to maximizing future food productivity while minimizing environmental threats, yet knowledge of its variation and the underlying regulatory factors is still lacking. Here, we integrated a dataset with 21,571 data compiled by available data from peer-reviewed literature and a large-scale field survey to address this knowledge gap. The overall results revealed great variations in rice NUtE, which were mainly associated with human activities, climate conditions, and rice variety. Specifically, N supply rate, temperature, and precipitation were the foremost determinants of rice NUtE, and NUtE responses to climatic change differed among rice varieties. Further prediction highlighted the improved rice NUtE with the increasing latitude or longitude. The indica and hybrid rice exhibited higher NUtE in low latitude regions compared to japonica and inbred rice, respectively. Collectively, our results evaluated the primary drivers of rice NUtE variations and predicted the geographic responses of NUtE in different varieties. Linking the global variations in rice NUtE with environmental factors and geographic adaptability provides valuable agronomic and ecological insights into the regulation of rice NUtE.

Evolutionary and ecological insights from Cytinus: A plant within a plant

Evolutionary and ecological insights from <i>Cytinus</i>: A plant within a plant

Meta-analysis of microbiomes reveals metagenomic features of fermented vegetables

An insightful exploration of the fermented vegetable microbiome is the key to improving food quality and sustainability. Based on 57 fermented vegetable samples from China, Ireland, the UK, and Germany retrieved from public genome databases, we conducted a high-resolution meta-analysis of the fermented vegetable microbiomes. There were significant differences in the microbiota composition and functional pathway diversity of the tested samples, as reflected by the differences in their geographical origins. Metagenomic analysis also revealed the metagenomic features of carbohydrate-active enzymes and antibiotic resistance genes in the fermented vegetable metagenomes. Five putative new species were detected by recovering 221 metagenome-assembled genomes belonging to the genera Rubrobacteraceae, Bifidobacteriaceae, and Ruminococcaceae. Our results provide new ecological insights into the implications of fermented vegetable microbiota composition and functional potential and highlight the importance of high-resolution metagenomic analysis to further investigate the fermented food microbiome.

Chemotaxis mediates nitrogen acquisition of maize under long-term nitrogen input

Chemotaxis is a process that enables motile bacteria to move along nutrient gradients, thereby exploring nutrient hotspots, and potentially playing important biogeochemical roles in agricultural ecosystems. In this study, a 36-year field experiment of nitrogen (N) input was conducted, along with the use of a synthetic community (SynCom) inoculation, to confirm the role of chemotaxis in the cycling of N. The chemotaxis genes abundances of N+ treatments were 97.2% and 95.3% higher than that of N- treatments in bulk soil and rhizosphere, respectively, indicating a significant increase in chemotaxis genes under long-term N input. Positive correlations between chemotaxis genes and N metabolism genes in N+ treatments suggested an important role of chemotaxis in N cycling. The chemotaxis genes abundance was 3.6 times higher in rhizosphere than in bulk soil, and chemotaxis genes showed the most complex correlations with N metabolism genes in rhizosphere under N input, suggesting a key role of chemotaxis in plant N uptake. To assess the potential function of chemotactic bacteria, a SynCom consisting of 10 bacterial strains isolated from in situ N-input soils and capable of chemotaxis, was applied to the maize rhizosphere. The promotion of N acquisition in maize plants through inoculation was confirmed by about 30% greater N content in the shoots of SynCom inoculated soil than in the control. Long-term N input enhanced the functions related to metabolite transport and energy metabolism in the bacterial community, particularly in the rhizosphere. Thus, plants may provide bacteria that migrate to the rhizosphere via chemotaxis with more root metabolites as nutrients. In summary, this study provides novel ecological and molecular insights into chemotaxis-mediated biogeochemical cycling in agricultural ecosystems.

When does a Lotka-Volterra model represent microbial interactions? Insights from in vitro nasal bacterial communities.

To alter microbial community composition for therapeutic purposes, an accurate and reliable modeling framework capable of predicting microbial community outcomes is required. Lotka-Volterra (LV) equations have been utilized to describe a breadth of microbial communities, yet, the conditions in which this modeling framework is successful remain unclear. Here, we propose that a set of simple in vitro experiments-growing each member in cell-free spent medium obtained from other members-can be used as a test to decide whether an LV model is appropriate for describing microbial interactions of interest. We show that for LV to be a good candidate, the ratio of growth rate to carrying capacity of each isolate when grown in the cell-free spent media of other isolates should remain constant. Using an in vitro community of human nasal bacteria as a tractable system, we find that LV can be a good approximation when the environment is low-nutrient (i.e., when growth is limited by the availability of nutrients) and complex (i.e., when multiple resources, rather than a few, determine growth). These findings can help clarify the range of applicability of LV models and reveal when a more complex model may be necessary for predictive modeling of microbial communities. IMPORTANCE Although mathematical modeling can be a powerful tool to draw useful insights in microbial ecology, it is crucial to know when a simplified model adequately represents the interactions of interest. Here, we take advantage of bacterial isolates from the human nasal passages as a tractable model system and conclude that the commonly used Lotka-Volterra model can represent interactions among microbes well when the environment is complex (with many interaction mediators) and low-nutrient. Our work highlights the importance of considering both realism and simplicity when choosing a model to represent microbial interactions.

Roof of the world: Home and border in the genomic era

Himalaya and the Tibetan Plateau, known as the ‘land of snow’ and the ‘roof of the world’, is home to tens of millions of indigenous people who live with a staggering amount of biological diversity. In the past decade scientists have applied genomic tools and methods to substantially advance the understanding of phylogeography and genetic mechanisms behind high‐elevation adaptation of local biota. However, contributions from indigenous researchers and native institutions are underrepresented in this scientific endeavour. We point to the higher degree of indigenous contribution within the discipline of conservation biology and how recognizing the prominence of traditional ecological knowledge (TEK) could deliver keen molecular ecological insights. Since the Himalaya‐Tibet ecological interface spans five countries, comprehensive biogeographical and phylogeographical taxon sampling in the region requires multi‐national collaborations across indigenous lands as well as indigenous community participation at both national and international levels. For the next generation of indigenous molecular ecologists, researching and cataloguing the evolutionary history and genetic information of the Tibetan and Himalayan landscape is a race against the melting glacier. At the roof of the world, their scientific judgement and stewardship will have environmental impacts that percolate far beyond indigenous lands.

Mechanistic Insight into the Inhibitory Activity of Elasnin-Based Coating against Early Marine Biofilms.

Marine biofilms are multispecies microbial communities on surfaces that are crucial to the marine environment. They cause marine corrosion, biofouling, and transmission of marine pathogens and thus pose a great threat to public health and the maritime industry. To control marine biofilms, effective and environmentally friendly antibiofilm compounds are highly needed. Elasnin is a potent antibiofilm compound that exhibits high efficiency in inhibiting marine biofilms and biofouling, but its mode of action remains unclear. In the present study, multiomic analysis combined with quorum-sensing assays and in silico study revealed that elasnin acted as a signaling molecule in the microbial community. Elasnin promoted the growth of dominant species in the biofilm but deprived their ability of sensing and responding to environmental changes by disturbing their regulations of the two-component system, i.e., the ATP-binding cassette transport system and the bacterial secretion system. Consequently, biofilm maturation and subsequent biofouler settlement were inhibited. Elasnin also exhibited higher antibiofilm efficiency than dichlorooctylisothiazolinone and had low toxicity potential on the embryos and adults of marine medaka fish. Overall, this study provided molecular and ecological insights into elasnin's mode of action, highlighting its application potential in controlling marine biofilms and the feasibility and advantages of using signal molecules to develop eco-friendly technologies.

Habitat suitability models of elkhorn coral provide ecological insight to support coral reef restoration

Coral reefs are experiencing unprecedented levels of stress from global warming, ocean acidification, fishing, and water pollution. In the Caribbean and Western Atlantic, multiple stressors have resulted in widespread losses of the dominant reef‐building Acroporid corals, two of which are listed as threatened species under the 1973 U.S. Endangered Species Act. In response, active coral reef restoration through the outplanting of live corals has become a widespread intervention technique. To increase restoration success, active coral reef restoration requires significant investment and careful planning, and selection of suitable sites for coral outplanting is an essential early step with considerable influence on restoration outcomes. We applied a maximum entropy model to predict and map habitat suitability for the reef‐building coral species,Acropora palmata, around the island of St. Croix in the U.S. Virgin Islands. Based mostly on bathymetry and benthic habitat type, the highest performing model predicted approximately 21.75 km2of the highest probability of suitable habitat, of which over half occurred within existing marine protected areas (MPAs). Outplanted coral at 60% of sites coincided with predicted maximum habitat suitability index values greater than 0.75 and 35% with values greater than 0.90. The model reveals that all three statutory MPAs with shallow water coral reefs have a considerable area (13.24 km2) of predicted high suitability seabed with potential for activeA. palmatarestoration efforts. The predictive spatial modeling approach provides a cost‐effective tool to inform future coral restoration design and to evaluate the habitat suitability of coral outplanting sites.

Unpacking the ‘black box’: Improving ecological interpretation of regression‐based models

AbstractAimMany tree species distribution models use black‐box machine learning techniques that often neglect interpretative aspects and instead focus mainly on maximizing predictive accuracy. In this study, we outline an interpretative modelling framework to gain better ecological insights while mapping abundance patterns of six North American species.LocationContinental United States and Canada.MethodsWe develop an innovative procedure using regression trees by stabilizing variance, and mapping dominant rules which we term ‘optimized regression tree bagging for interpretation and mapping’ (ORTBIM). We apply this technique to understand ecological features influencing the abundance patterns of three eastern (Pinus strobus, Acer saccharum and Quercus montana), and three western (Picea engelmannii, Pinus ponderosa and Pseudotsuga menziesii) tree species in North America. For these species, we assess and map the dominant climate–terrain interactions that partly determine abundance patterns in the eastern and western regions. In the process, we examine the role of varying responses and scales and explore finer‐scale species climate–terrain niches and non‐linear relationships.ResultsOur study emphasizes the prominent role of elevation and heat–moisture variables in the west and the greater importance of seasonal precipitation and seasonal temperature in the east. The abundance patterns under future climate (SSP5‐8.5) show climate–terrain habitats shifting northward and westward into Canada and Alaska for the eastern species, and predominantly north‐westward for the western species.ConclusionOur interpretative modelling framework can be used to gain a more comprehensive understanding of the abundance patterns across the full species range, formulate better predictive models and facilitate improved management practices under climate change.

Spatial patterns in host-associated and free-living bacterial communities across six temperate estuaries.

A major goal of microbial ecology is to establish the importance of spatial and environmental factors in driving community variation. Their relative importance likely varies across spatial scales, but focus has primarily been on free-living communities within well-connected aquatic environments rather than less connected island-like habitats such as estuaries, and key host-associated communities within these systems. Here we sampled both free-living (seawater and sediment) and host-associated (estuarine fish hindgut microbiome, Pelates sexlineatus) communities across six temperate Australian estuaries spanning ∼500km. We find that spatial and environmental factors have different influences on these communities, with seawater demonstrating strong distance-decay relationships (R = -0.69) and significant associations with a range of environmental variables. Distance-decay relationships were weak for sediment communities but became stronger over smaller spatial scales (within estuaries, R = -0.5), potentially reflecting environmental filtering across biogeochemical gradients or stochastic processes within estuary sediments. Finally, P. sexlineatus hindgut microbiome communities displayed weak distance-decay relationships (R = -0.36), and limited variation explained by environmental variables, indicating the significance of host-related factors in driving community variation. Our findings provide important ecological insights into the spatial distributions and driving forces of both free-living and host-associated bacterial patterns across temperate estuarine systems.

Ecological insights and conservation imperatives for Laurus azorica in Morocco

The Azores laurel Laurus azorica (Seub.) Franco is a highly esteemed forest species in Morocco due to its medicinal and aromatic properties. However, the natural habitats of this species are increasingly scarce, resulting in its classification as a rare species. This study comprehensively investigates the autoecology, plant communities, and distribution patterns of L. azorica, aiming to discern the crucial ecological factors underpinning its survival and shed light on its conservation status. Field surveys, including floristic relevés and environmental characterization, were conducted to identify the primary plant communities hosting remnants of L. azorica. Fieldwork and ecological analysis reveal five distinct plant communities associated with L. azorica: low elevation thermophilic holm oak woodland, mesophilic mid-altitude holm oak woodland, Quercus faginea, deciduous broadleaf mountain and Cytisus balansae plant communities. The study emphasizes the importance of ecological requirements such as oceanic exposure, rainfall, temperature, and forest mull soils in creating suitable habitats for L. azorica populations. Currently, L. azorica populations in Morocco are represented by small trees, shrubs, or bushes, often exhibiting distorted and damaged structures due to unregulated pruning. Natural regeneration of the species is completely absent. The value chain associated with L. azorica is limited, involving informal harvesters, intermediary herbalist grocers, and final consumers, due to the lack of a legal framework for resource evaluation caused by its severe depletion. To secure the survival of L. azorica in Morocco, it is crucial to address gaps in legislation, intensify conservation efforts, and promote sustainable development practices. Protecting and restoring the natural habitats of the species, along with implementing responsible harvesting practices, are essential steps towards conserving this valuable forest species.