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ANIMAL TRAFFIC: Lively Capital in the Global Exotic Pet Trade: By Rosemary-Claire Collard. First is the erasure of social relations that occurs in the commodity fetishism explained by traditional Marxian analyses, and second is Collard's assertion of the erasure of the animals' socio-ecological relations in their (former) biotic communities. These traits are what provide "use value" for humans, and Collard explains that for the commodity transformation to happen, exotic animals "are subject to a double fetishism" (p. 18). [Extracted from the article]

Knowing what the highest-level mammalian carnivores and intermediate levels eat throughout the geography and how human activities may affect their community dynamics is relevant information to focusing and deciding on conservation efforts within a territory. In this review, we characterize geographically the accumulated knowledge about the trophic niche of terrestrial mammalian carnivore species and evaluate the spatial relationship between the species richness distribution and the geographical distribution of their trophic knowledge in Chile. We found 88 peer-reviewed papers that include trophic studies per se, theses, and short notes carried out in Chile, where at least one trophic element was reported for terrestrial mammalian carnivore species. We found a positive relationship between the species richness distribution pattern and the spatial distribution of accumulated trophic knowledge, i.e., most of the papers have been conducted in Central-southern Chile (Central Chile and Temperate Forest ecoregions) responding to the highest co-occurrence of carnivore species within the limits of the biodiversity hotspot, the most threatened area in the country. Despite this general relationship, we recognize gaps in knowledge regarding regions of the country that require more research effort, such as O'Higgins, Maule, and Ñuble regions, as well as focus efforts on certain species with no or almost no knowledge of their trophic ecology, such as Leopardus colocola, Lyncodon patagonicus and Conepatus chinga. Except for the northern Chilean ecosystems, there is a generalized report of high consumption of exotic mammals in the diet of carnivores in the center and south of the country. However, of the 98 localities recognized in the 88 papers, 20.4% correspond to an anthropized environment, while most (79.6%) correspond to a "non-anthropized" environment or protected area. We hope this review allows researchers and decision-makers to consider the knowledge and lack thereof of carnivore trophic interactions as an opportunity to conserve entire natural communities throughout the Chilean territory. [ABSTRACT FROM AUTHOR]

We respond to comments made in the opinion paper by Ainley et al. (Hydrobiologia, 10.1007/s10750-015-2607-4, ) regarding our recent publication on the biology, ecology and life history of Antarctic toothfish ( Dissostichus mawsoni) in the Ross Sea region. We focus in particular on the spatial and temporal extent of data collected from the fishery; results of research to date on changes in abundance and size of Antarctic toothfish at McMurdo Sound; and the subject of neutral buoyancy and inferences about vertical distribution. We conclude by re-iterating the need for well-designed, standardised research programmes to address remaining uncertainties in its life history. [ABSTRACT FROM AUTHOR]

Background: The National Cancer Institute Informatics Technology for Cancer Research (ITCR) program provides a series of funding mechanisms to create an ecosystem of open-source software (OSS) that serves the needs of cancer research. As the ITCR ecosystem substantially grows, it faces the challenge of the long-term sustainability of the software being developed by ITCR grantees. To address this challenge, the ITCR sustainability and industry partnership working group (SIP-WG) was convened in 2019.Objective: The charter of the SIP-WG is to investigate options to enhance the long-term sustainability of the OSS being developed by ITCR, in part by developing a collection of business model archetypes that can serve as sustainability plans for ITCR OSS development initiatives. The working group assembled models from the ITCR program, from other studies, and from the engagement of its extensive network of relationships with other organizations (eg, Chan Zuckerberg Initiative, Open Source Initiative, and Software Sustainability Institute) in support of this objective.Methods: This paper reviews the existing sustainability models and describes 10 OSS use cases disseminated by the SIP-WG and others, including 3D Slicer, Bioconductor, Cytoscape, Globus, i2b2 (Informatics for Integrating Biology and the Bedside) and tranSMART, Insight Toolkit, Linux, Observational Health Data Sciences and Informatics tools, R, and REDCap (Research Electronic Data Capture), in 10 sustainability aspects: governance, documentation, code quality, support, ecosystem collaboration, security, legal, finance, marketing, and dependency hygiene.Results: Information available to the public reveals that all 10 OSS have effective governance, comprehensive documentation, high code quality, reliable dependency hygiene, strong user and developer support, and active marketing. These OSS include a variety of licensing models (eg, general public license version 2, general public license version 3, Berkeley Software Distribution, and Apache 3) and financial models (eg, federal research funding, industry and membership support, and commercial support). However, detailed information on ecosystem collaboration and security is not publicly provided by most OSS.Conclusions: We recommend 6 essential attributes for research software: alignment with unmet scientific needs, a dedicated development team, a vibrant user community, a feasible licensing model, a sustainable financial model, and effective product management. We also stress important actions to be considered in future ITCR activities that involve the discussion of the sustainability and licensing models for ITCR OSS, the establishment of a central library, the allocation of consulting resources to code quality control, ecosystem collaboration, security, and dependency hygiene. [ABSTRACT FROM AUTHOR]

This document is a special issue of the journal "Plants" that focuses on the soil-plant-water system and its interactions. The articles in this issue cover a wide range of topics, including climate change and soil water deficits, forest and woody plant ecosystems, and alternative crop production methods. The studies explore the effects of drought on plant growth and development, the impact of different inter-row soil management techniques on soil water content, and the response of plants to phosphorus addition. The issue also includes research on zero discharge cultivation of cucumbers and indoor vegetable production methods. The authors highlight the importance of studying the soil-plant-water system as an interconnected system and identify areas for further research. [Extracted from the article]

Network analysis provides a powerful framework to study the complexity underlying the structure, dynamics and function of ecological systems. By now, analysing single‐layered networks is a common practice with clear guidelines and well‐established computational tools. Nevertheless, ecological communities are multilayered because they vary over space and time and contain multiple types of interactions. In recent years, the analysis of ecological multilayer networks (EMLNs) has allowed researchers to include such multilayered complexity. However, there is a paucity of practical guidelines and standardised tools to handle EMLN data, even before downstream analysis.In this article, we accomplish three objectives: (1) We provide practical guidelines for handling EMLN data. (2) We developed the EMLN R package to standardise the workflow of creating, storing and working with EMLN objects. The package also enables conversion between multiple formats for downstream analysis with other standard packages. (3) We provide EMLN data sets for research and training purposes.A dedicated website with explanations, detailed examples and code accompanies our paper. This website is a gateway for novice and experienced network ecologists who want to include EMLNs in their research.By simplifying the analysis of multilayer networks and promoting standardised approaches, we facilitate the analysis of EMLNs. This paves the road towards gaining deeper insights into functioning and resilience of natural ecosystems. [ABSTRACT FROM AUTHOR]

Background: Using next-generation sequencing technologies, scientists can sequence complex microbial communities directly from the environment. Significant insights into the structure, diversity, and ecology of microbial communities have resulted from the study of metagenomics. The assembly of reads into longer contigs, which are then binned into groups of contigs that correspond to different species in the metagenomic sample, is a crucial step in the analysis of metagenomics. It is necessary to organize these contigs into operational taxonomic units (OTUs) for further taxonomic profiling and functional analysis. For binning, which is synonymous with the clustering of OTUs, the tetra-nucleotide frequency (TNF) is typically utilized as a compositional feature for each OTU. Results: In this paper, we present AFIT, a new l-mer statistic vector for each contig, and AFITBin, a novel method for metagenomic binning based on AFIT and a matrix factorization method. To evaluate the performance of the AFIT vector, the t-SNE algorithm is used to compare species clustering based on AFIT and TNF information. In addition, the efficacy of AFITBin is demonstrated on both simulated and real datasets in comparison to state-of-the-art binning methods such as MetaBAT 2, MaxBin 2.0, CONCOT, MetaCon, SolidBin, BusyBee Web, and MetaBinner. To further analyze the performance of the purposed AFIT vector, we compare the barcodes of the AFIT vector and the TNF vector. Conclusion: The results demonstrate that AFITBin shows superior performance in taxonomic identification compared to existing methods, leveraging the AFIT vector for improved results in metagenomic binning. This approach holds promise for advancing the analysis of metagenomic data, providing more reliable insights into microbial community composition and function. Availability: A python package is available at: https://github.com/SayehSobhani/AFITBin. [ABSTRACT FROM AUTHOR]

To explore complex biological questions, it is often necessary to access various data types from public data repositories. As the volume and complexity of biological sequence data grow, public repositories face significant challenges in ensuring that the data is easily discoverable and usable by the biological research community. To address these challenges, the National Center for Biotechnology Information (NCBI) has created NCBI Datasets. This resource provides straightforward, comprehensive, and scalable access to biological sequences, annotations, and metadata for a wide range of taxa. Following the FAIR (Findable, Accessible, Interoperable, and Reusable) data management principles, NCBI Datasets offers user-friendly web interfaces, command-line tools, and documented APIs, empowering researchers to access NCBI data seamlessly. The data is delivered as packages of sequences and metadata, thus facilitating improved data retrieval, sharing, and usability in research. Moreover, this data delivery method fosters effective data attribution and promotes its further reuse. This paper outlines the current scope of data accessible through NCBI Datasets and explains various options for exploring and downloading the data. [ABSTRACT FROM AUTHOR]

Heavy metals (HMs) in aquatic environments are characterized by high toxicity, a propensity for bioaccumulation, and non-degradability, and pose significant risks to biological communities. Previous studies of HMs in lakes have shown that the physical and chemical characteristics of the lake water may control both the migration of HMs in the sediments and the concentration of heavy metals in the lake water. In fact, the change in aquatic environments changes the heavy metal fraction in the sediment, which controls the release of HMs. In this paper, we investigated the effects of the pH, temperature, and salinity levels of overlying water on the chemical fraction of Cu and Zn in Wuliangsuhai Lake surface sediments. The results show that lower water pH and higher water salinity and temperature could increase Cu and Zn release from the sediment. An increase in pH led to changes in the speciation of solid fractions of Zn, namely increases in the residual fraction and decreases in the organic matter and sulfide, whereas acid-extractable and Fe-Mn oxide fractions remained largely the same. Increases in temperature and salinity led to opposite changes in the speciation of solid fractions, namely decreases in the residual fraction and increases in the organic matter and sulfide and Fe-Mn oxide fractions, whereas acid-extractable fractions remained largely the same. The effect of pH, temperature, and salinity on Cu fractions in the solids was much smaller. According to the ratio of the secondary phase to the primary phase (RSP), acidic, high-temperature, and high-salt conditions increase the release risks of Zn. Changes in water temperature have the greatest influence on the risk of Zn and Cu release from sediments, followed by the influence of salinity changes. [ABSTRACT FROM AUTHOR]

The stochastic nature of ecological systems is fundamental to their modeling and understanding. In this paper, we introduce a comprehensive algae-zooplankton model that incorporates general interaction rate and second-order independent stochastic components. Our model’s perturbation component encompasses both white noise and jump processes, enabling us to account for various sources of variability and capture a wide range of potential fluctuations in the system. By utilizing an auxiliary equation, we establish a global threshold for the stochastic system, distinguishing between scenarios of extinction and ergodicity. This threshold serves as a critical determinant of the system’s long-term behavior and sheds light on the delicate balance between population persistence and decline in ecological communities. To elucidate the impact of noise on the dynamics of algae and zooplankton, we present a series of numerical illustrations. Through these simulations, we highlight how noise influences not only the extinction time but also the shape of the stationary distribution. Our findings underscore the significant role of stochasticity in shaping ecological dynamics and emphasize the importance of considering noise effects in ecological modeling and management practices. [ABSTRACT FROM AUTHOR]

Degradation of coastal ecosystems by eutrophication is largely defined by nitrogen loading from land via surface and groundwater flows. However, indicators of water quality are highly variable due to a myriad of other drivers, including temperature and precipitation. To evaluate these drivers, we examined spatial and temporal trends in a 22 year record of summer water quality data from 122 stations in 17 embayments within Buzzards Bay, MA (USA), collected through a citizen science monitoring program managed by Buzzards Bay Coalition. To identify spatial patterns across Buzzards Bay's embayments, we used a principle component and factor analysis and found that rotated factor loadings indicated little correlation between inorganic nutrients and organic matter and chlorophyll a (Chl a) concentration. Factor scores showed that embayment geomorphology in addition to nutrient loading was a strong driver of water quality, where embayments with surface water inputs showed larger biological impacts than embayments dominated by groundwater influx. A linear regression analysis of annual summertime water quality indicators over time revealed that from 1992 to 2013, most embayments (15 of 17) exhibited an increase in temperature (mean rate of 0.082 ± 0.025 (SD) °C yr-1) and Chl a (mean rate of 0.0171 ± 0.0088 log10 (Chl a; mgm-3)yr-1, equivalent to a 4.0% increase per year). However, only 7 embayments exhibited an increase in total nitrogen (TN) concentration (mean rate 0.32 ± 0.47 (SD)μM yr-1). Average summertime log10 (TN) and log10 (Chl a) were correlated with an indication that yield of Chl a per unit total nitrogen increased with time suggesting the estuarine response to TN may have changed because of other stressors such as warming, altered precipitation patterns, or changing light levels. These findings affirm that nitrogen loading and physical aspects of embayments are essential in explaining observed ecosystem response. However, climate-related stressors may also need to be considered by managers because increased temperature and precipitation may worsen water quality and partially offset benefits achieved by reducing nitrogen loading. [ABSTRACT FROM AUTHOR]

Oceanic upwelling velocities are too small to be measured directly. The surface disequilibrium of the ³He/4He ratio provides an indirect method to infer vertical velocities at the base of the mixed layer. Samples of helium isotopes were taken from two coastal upwelling regions, off Peru on cruise M91, and off Mauritania on 3 cruises. The helium- 3 flux into the mixed layer also depends on the diapycnal mixing. Direct observations of the vertical diffusivity have been performed on all 4 cruises and are also used in this study. The resulting upwelling velocities in the coastal regions vary between 1.1x10-5 and 2.8x10-5ms-1 for all cruises. Vertical velocities off the equator can also be inferred from the divergence of the wind driven Ekman transport. In the coastal regimes, the agreement between wind and helium derived upwelling is fairly good at least for the mean values. Further offshore, the helium derived upwelling still reaches 1x10-5ms-1, whereas the wind driven upwelling from Ekman suction is smaller by at least one order of magnitude. One reason for this difference might be eddy induced upwelling. Both advective and diffusive nutrient fluxes into the mixed layer are calculated based on the helium derived vertical velocities and the measured vertical diffusivities. The advective part of these fluxes makes up at least 50% of the total. The nutrient flux into the mixed layer in the coastal upwelling regimes is equivalent to a net community production (NCP) of 1.3gCm² d-1 off Peru and 1.6-1.9 gCm² d-1 off Mauritania. [ABSTRACT FROM AUTHOR]

The successful movement of individuals is fundamental to life. Facilitating these movements by promoting ecological connectivity has become a central theme in ecology and conservation. Urban areas contain more than half of the world's human population, and their potential to support biodiversity and to connect their citizens to nature is increasingly recognized. Promoting ecological connectivity within these areas is essential to reaching this potential. However, our current understanding of ecological connectivity within urban areas appears limited., We reviewed the published scientific literature to assess the state-of-the-art of ecological connectivity research in urban areas, summarized trends in study attributes and highlighted knowledge gaps., We found 174 papers that investigated ecological connectivity within urban areas. These papers addressed either structural (48) or functional connectivity (111), and some addressed both (15), but contained substantial geographic and taxonomic biases. These papers rarely defined the aspect of connectivity they were investigating and objective descriptions of the local urban context were uncommon. Formulated hypotheses or a priori predictions were typically unstated and many papers used suboptimal study designs and methods., We suggest future studies explicitly consider and quantify the landscape within their analyses and make greater use of available and rapidly developing tools and methods for measuring functional connectivity (e.g. biotelemetry or landscape genetics). We also highlight the need for studies to clearly define how the terms ' urban' and ' connectivity' have been applied., Knowledge gaps in ecological connectivity in urban areas remain, partly because the field is still in its infancy and partly because we must better capitalize on the state-of-the-art technological and analytical techniques that are increasingly available. Well-designed studies that employed high-resolution data and powerful analytical techniques highlight our abilities to quantify ecological connectivity in urban areas. These studies are exemplary, setting the standards for future research to facilitate data-driven and evidence-based biodiversity-friendly infrastructure planning in urban areas. [ABSTRACT FROM AUTHOR]

Cities are critical to a sustainable future for our planet; still, the construction and operation of cities rely on intensive resource and energy use and transformation, leading to the generation of waste, effluents, and pollution, representing negative externalities outside and inside the city. Within every process, transformation implies the use of energy and the increase of entropy. In an urban system, the transformation of energy and materials will trigger the creation of entropic landscapes, mainly in the informal city and in unguarded natural landscapes, even hundreds of kilometers away, which generates substantial economic, social, and environmental impacts. In this sense, cities are significant contributors to the environmental crisis. Upstream, degradation of landscapes and ecosystems is frequent. Cities' externalities and exogenous consumptions are directly linked with entropy and entropic landscapes, which are recognized as pollution (in the air, water, and land) or waste and in the degradation of natural ecosystems and communities. Through a systematic review of existing literature, this paper first outlines briefly how entropy has been applied in different disciplines and then focuses on presenting recent developments of how entropy has been defined, used, and characterized in urban studies concerning sustainability in cities and architecture, and presents a definition of the concept in relation to urban systems and key aspects to consider. [ABSTRACT FROM AUTHOR]

This Special Issue intended to collect articles focusing on the assessment of the possible effects of climate changes on aquatic species inhabiting inland waters all over the world, including the possible synergistic effects in combination with other anthropogenic stressors. A total of six original articles were published that report on investigations of different freshwater ecosystems across the world, including the mountain streams of the Western United States and Northwest Italy, river basins of Northwest China and Central Italy, a larger lowland river in north Italy, and a high-elevation temporary pond in Central Italy. In most of these papers, special attention was devoted to the repercussions of the climate change and its effects on three important components of the biotic community: the fish, benthic macroinvertebrates, and zooplankton. According to the aims of this Special Issue, three of the articles offer new insight into the synergistic effects of global warming together with other anthropogenic stressors, including water exploitation and alien species invasions. In light of the studies' aim to highlight the effects of climate change, three papers provided analyses of environmental data collected through long-term monitoring. The scientific findings provided by these studies could help to create sound management strategies for freshwater biodiversity conservation. [ABSTRACT FROM AUTHOR]

The ecological niche is a fundamental concept in ecology that can be used in order better understand species relationships. The overlap in species niches provides a measure of the likelihood for species to co‐occur. Most approaches that quantify niche overlap have been based on distance and similarity indices, for pairwise combinations of species. In this paper, we suggest that niche overlap can be calculated from the predictions of a model. Using a statistical model to predict niche overlap provides various benefits, includes the possibility to adjust the model to properties of the data. We demonstrate this using an example dataset of an ecological community of Foraminifera species, to which we fit a generalized linear latent variable model (GLLVM). GLLVMs are a flexible class of models that allow to estimate the distribution of species using both measured environmental predictors and residual covariation between species. We demonstrate how to calculate niche overlap from GLLVMs for any combination of species, and separately for different environments. Predicting niche overlap from a model further expands the toolset available to ecologists for the exploration of species co‐occurrence patterns. [ABSTRACT FROM AUTHOR]

Analyzing the spatio-temporal relationship between socio-economics and land-use structure at the micro-scale is crucial for effective spatial governance in large cities. This paper focuses on Beijing, utilizing long time-series remote sensing images and multi-source data spanning 30 years. We employ spatio-temporal clustering based on kilometer grid cells and a community-scale multi-factor aggregation method to categorize the linkages and spatio-temporal matching of population, GDP, land development, and ecological protection at the community level in a problem-oriented approach. Results indicate significant changes in Beijing's population, GDP, and land use, with a 11.53% increase in land development intensity. We identify significant temporal and spatial disparities between population–GDP dynamics, population–land development trends, and GDP–land development patterns, underscoring the multifaceted challenges inherent in urban governance. Areas characterized by lagging population concentration, sluggish economic growth, rampant land development, and ecological fragility collectively encapsulate notable portions of Beijing's expansive urban terrain. Mismatches pose governance risks, with medium to high-risk communities comprising 18.08% of community units and high-risk types representing 4.27% in Beijing. These discrepancies pose formidable governance risks, with communities ranging from moderate to high-risk categories, necessitating tailored interventions to address their unique challenges. This systematic exploration of comprehensive governance issues within mega-cities promises to furnish decision-makers with invaluable insights, facilitating nuanced and strategic urban governance approaches tailored to the intricacies of urban dynamics and challenges. [ABSTRACT FROM AUTHOR]

This article discusses the spatial constraints on multiple dimensions of biodiversity. It explores how different measures of biodiversity, such as species richness, compositional dissimilarity, and food-web complexity, change in response to environmental gradients, disturbances, and climatic shifts. The article highlights recent advances in ecological analyses, including virtual simulations and habitat suitability models, that help researchers understand the drivers behind biodiversity patterns. The research papers included in this article cover a range of ecosystems, including virtual landscapes, riverine networks, groundwater caves, and terrestrial habitats. Overall, the article expands our understanding of the spatial and environmental factors that shape biodiversity and emphasizes the importance of protecting biodiversity based on ecological knowledge. [Extracted from the article]

Information on tropical Asian vertebrates has traditionally been sparse, particularly when it comes to cryptic species inhabiting the dense forests of the region. Vertebrate populations are declining globally due to land‐use change and hunting, the latter frequently referred as "defaunation." This is especially true in tropical Asia where there is extensive land‐use change and high human densities. Robust monitoring requires that large volumes of vertebrate population data be made available for use by the scientific and applied communities. Camera traps have emerged as an effective, non‐invasive, widespread, and common approach to surveying vertebrates in their natural habitats. However, camera‐derived datasets remain scattered across a wide array of sources, including published scientific literature, gray literature, and unpublished works, making it challenging for researchers to harness the full potential of cameras for ecology, conservation, and management. In response, we collated and standardized observations from 239 camera trap studies conducted in tropical Asia. There were 278,260 independent records of 371 distinct species, comprising 232 mammals, 132 birds, and seven reptiles. The total trapping effort accumulated in this data paper consisted of 876,606 trap nights, distributed among Indonesia, Singapore, Malaysia, Bhutan, Thailand, Myanmar, Cambodia, Laos, Vietnam, Nepal, and far eastern India. The relatively standardized deployment methods in the region provide a consistent, reliable, and rich count data set relative to other large‐scale pressence‐only data sets, such as the Global Biodiversity Information Facility (GBIF) or citizen science repositories (e.g., iNaturalist), and is thus most similar to eBird. To facilitate the use of these data, we also provide mammalian species trait information and 13 environmental covariates calculated at three spatial scales around the camera survey centroids (within 10‐, 20‐, and 30‐km buffers). We will update the dataset to include broader coverage of temperate Asia and add newer surveys and covariates as they become available. This dataset unlocks immense opportunities for single‐species ecological or conservation studies as well as applied ecology, community ecology, and macroecology investigations. The data are fully available to the public for utilization and research. Please cite this data paper when utilizing the data. [ABSTRACT FROM AUTHOR]

The bacterial and archaeal community composition and the possible carbon assimilation processes and energy sources of microbial communities in oligotrophic, deep, crystalline bedrock fractures is yet to be resolved. In this study, intrinsic microbial communities from six fracture zones from 180-2300 m depths in Outokumpu bedrock were characterized using high-throughput amplicon sequencing and metagenomic prediction. Comamonadaceae-, Anaerobrancaceae- and Pseudomonadaceae-related OTUs form the core community in deep crystalline bedrock fractures in Outokumpu. Archaeal communities were mainly composed of Methanobacteraceae-affiliating OTUs. The predicted bacterial metagenomes showed that pathways involved in fatty acid and amino sugar metabolism were common. In addition, relative abundance of genes coding the enzymes of autotrophic carbon fixation pathways in predicted metagenomes was low. This indicates that heterotrophic carbon assimilation is more important for microbial communities of the fracture zones. Network analysis based on co-occurrence of OTUs revealed the keystone genera of the microbial communities belonging to Burkholderiales and Clostridiales. Bacterial communities in fractures resemble those found from oligotrophic, hydrogen-enriched environments. Serpentinization reactions of ophiolitic rocks in Outokumpu assemblage may provide a source of energy and organic carbon compounds for the microbial communities in the fractures. Sulfate reducers and methanogens form a minority of the total microbial communities, but OTUs forming these minor groups are similar to those found from other deep Precambrian terrestrial bedrock environments. [ABSTRACT FROM AUTHOR]

Nitrogen fixation by filamentous cyanobacteria supplies significant amounts of new nitrogen (N) to the Baltic Sea. This balances N loss processes such as denitrification and anammox and forms an important N source supporting primary and secondary production in N-limited post-spring bloom plankton communities. Laboratory studies suggest that filamentous diazotrophic cyanobacteria growth and N2-fixation rates are sensitive to ocean acidification with potential implications for new N supply to the Baltic Sea. In this study, our aim was to assess the effect of ocean acidification on diazotroph growth and activity as well as the contribution of diazotrophically-fixed N to N supply in a natural plankton assemblage. We enclosed a natural plankton community in a summer season in the Baltic Sea near the entrance to the Gulf of Finland in six large-scale mesocosms (volume ~ 55 m3) and manipulated fCO2 over a range relevant for projected ocean acidification by the end of this century (average treatment fCO2: 365-1231 µatm). The direct response of diazotroph growth and activity was followed in the mesocosms over a 47 day study period during N-limited growth in the summer plankton community. Diazotrophic filamentous cyanobacteria abundance throughout the study period and N2-fixation rates (determined only until day 21 due to subsequent use of contaminated commercial 15N-N2 gas stocks) remained low. Thus estimated new N inputs from diazotrophy were too low to relieve N limitation and stimulate a summer phytoplankton bloom. Instead regeneration of organic N sources likely sustained growth in the plankton community. We could not detect significant CO2-related differences in inorganic or organic N pools sizes, or particulate matter N : P stoichiometry. Additionally, no significant effect of elevated CO2 on diazotroph activity was observed. Therefore, ocean acidification had no observable impact on N cycling or biogeochemistry in this N-limited, post-spring bloom plankton assemblage in the Baltic Sea. [ABSTRACT FROM AUTHOR]

The ecofeminist epistemologies recognize the ecological and social interdependencies in the planetary system. Carolyn Merchant’s (2014) concept of partnership ethics is grounded on the interdependencies between the biotic and abiotic communities: “A partnership ethic holds that the greatest good for the human and nonhuman communities is in their mutual living interdependence” (83). Following this line of thought, this paper studies Barbara Kingsolver’s fiction and nonfiction, namely, High Tide in Tucson (1995), Small Wonder (2003), Prodigal Summer (2000), Flight Behaviour (2012), and Animal Dreams (1990) through the lens of Ecofeminist Partnership Ethics (Carolyn Merchant 2014) and foregrounds the interrelationship between women, women-nature, and human-nature. This paper also analyses the ecofeminist thoughts of Karren Warren, Val Plumwood, and Carolyn Merchant and how Kingsolver’s works repudiate the limitations of dualistic thinking (culture/nature, man/woman) and the subordination of nature and women. [ABSTRACT FROM AUTHOR]

He also wrote about male-male combat and morphology in the Caprinidae (sheep and goats) alone and with his advisor (Schaffer 1968, Reed and Schaffer 1972a, Schaffer and Reed 1972b). Bill moved on to work on nonlinear dynamics in disease systems with his Danish collaborator Lars Olsen for many years (Olsen et al. 1988, Olsen and Schaffer 1990). In their 1986 TREE paper, Bill and his then-student Mark Kot argued that chaotic dynamics were likely widespread in ecology, and that this might necessitate a fundamental reappraisal of many ideas in population and community ecology (Schaffer and Kot 1986). Ecologist William (Bill) M. Schaffer died on 16 January 2021, in Tucson, Arizona, USA. [Extracted from the article]

The topic of health has gained importance in today's society in the context of a healthy China. The success of community environmental design is intimately correlated with everyone's physical and mental health since it is the setting for people's daily lives. At present, although the facilities and equipment of the community environment in our country are improving day by day, the important role of color psychology in the community environment has been neglected. Color has always been a part of human life and a very important component of the community environment. When it comes to the design of communal environments, the color design of various areas will have variable degrees of influence on the psychological space and perspective of individuals. Therefore, the purpose of this paper is to investigate the application value of color psychology in the design of community health environments using color psychology as a scientific foundation. Additionally, the paper attempts to use color psychology as a scientific basis to study the thinking of health issues in the community environment. In addition, the results of the questionnaire survey are used to perform analysis and discussion in order to investigate the regular characteristics of the various research objects, as well as their preferences and psychological needs for color. This is done with the goal of providing empirical support for the improvement of the community environment and the health of the people living in it. In the end, the results of the questionnaire survey are compiled with four different design concepts. These design principles include functionality, naturalness, beauty, and safety. And the design intention and optimization strategy from the three directions the overall building, planting, and paving in the community healthy environment are then presented. This is done in order to create a colorful and comfortable healthy environment for the community life of people and to support the development of people's physical and mental health. [ABSTRACT FROM AUTHOR]

The Arctic is a water-rich region, with freshwater systems covering 16 % of the northern permafrost landscape. The thawing of this permafrost creates new freshwater ecosystems, while at the same time modifying the existing lakes, streams, and rivers that are impacted by thaw. Here, we describe the current state of knowledge regarding how permafrost thaw affects lentic and lotic systems, exploring the effects of both thermokarst (thawing and collapse of ice-rich permafrost) and deepening of the active layer (the surface soil layer that thaws and refreezes each year). Within thermokarst, we further differentiate between the effects of thermokarst in lowland areas, vs. that on hillslopes. For almost all of the processes that we explore, the effects of thaw vary regionally, and between lake and stream systems. Much of this regional variation is caused by differences in ground ice content, topography, soil type, and permafrost coverage. Together, these modifying variables determine the degree to which permafrost thaw manifests as thermokarst, whether thermokarst leads to slumping or the formation of thermokarst lakes, and the manner in which constituent delivery to freshwater systems is altered by thaw. Differences in thaw-enabled constituent delivery can be considerable, with these modifying variables determining, for example, the balance between delivery of particulate vs. dissolved constituents, and inorganic vs. organic materials. Changes in the composition of thaw-impacted waters, coupled with changes in lake morphology, can strongly affect the physical and optical properties of thermokarst lakes. The ecology of thaw-impacted systems is also likely to change, with thaw-impacted lakes and streams having unique microbiological communities, and showing differences in respiration, primary production, and food web structure that are largely driven by differences in sediment, dissolved organic matter and nutrient delivery. The degree to which thaw enables the delivery of dissolved vs. particulate organic matter, coupled with the composition of that organic matter and the morphology and stratification characteristics of recipient systems will play an important role in determining the balance between the release of organic matter as greenhouse gases (CO2 and CH4), its burial in sediments, and its loss downstream. The magnitude of thaw impacts on northern aquatic ecosystems is increasing, as is the prevalence of thaw-impacted lakes and streams. There is therefore an urgent need to address the key gaps in understanding in order to predict the full effects of permafrost thaw on aquatic ecosystems throughout the Arctic, and their consequential feedbacks to climate. [ABSTRACT FROM AUTHOR]

Permafrost thaw ponds and lakes are widespread across the northern landscape and may play a central role in global biogeochemical cycles, yet knowledge about their microbial ecology is limited. We sampled a set of thaw ponds and lakes as well as shallow rock-basin lakes that are located in distinct valleys along a North-South permafrost degradation gradient. We applied high-throughput sequencing of the 16S rRNA gene to determine co-occurrence patterns among bacterial taxa, and then analyzed these results relative to environmental variables to identify factors controlling bacterial community structure. Network analysis was applied to identify possible ecological linkages among the bacterial taxa and with abiotic and biotic variables. The results showed an overall high level of shared taxa among bacterial communities within each valley, however the bacterial co-occurrence patterns were non-random, with evidence of habitat preferences. There were taxonomic differences in bacterial assemblages among the different valleys that were statistically related to dissolved organic carbon concentration, conductivity and phytoplankton biomass. Co-occurrence networks revealed complex interdependencies within the bacterioplankton communities and showed contrasting linkages to environmental conditions among the main bacterial phyla. The thaw pond networks were composed of a limited number of highly connected taxa. This "small world network" property would render the communities more robust to environmental change but vulnerable to the loss of microbial keystone species. [ABSTRACT FROM AUTHOR]

Nitrogen (N) and phosphorus (P) additions to forest ecosystems are known to influence various above-ground properties, such as plant productivity and composition, and below-ground properties, such as soil nutrient cycling. However, our understanding of how soil microbial communities and their functions respond to nutrient additions in subtropical plantations is still not complete. In this study, we added N and P to Chinese fir plantations in subtropical China to examine how nutrient additions influenced soil microbial community composition and enzyme activities. The results showed that most soil microbial properties were responsive to N and/or P additions, but responses often varied depending on the nutrient added and the quantity added. For instance, there were more than 30% greater increases in the activities of β-Glucosidase (βG) and N-acetyl-β-D-glucosaminidase (NAG) in the treatments that received nutrient additions compared to the control plot, whereas acid phosphatase (aP) activity was always higher (57 and 71 %, respectively) in the P treatment. N and P additions greatly enhanced the PLFA abundanceespecially in the N2P treatment, the bacterial PLFAs (bacPLFAs), fungal PLFAs (funPLFAs) and actinomycic PLFAs (actPLFAs) were about 2.5, 3 and 4 times higher, respectively, than in the CK. Soil enzyme activities were noticeably higher in November than in July, mainly due to seasonal differences in soil moisture content (SMC). (5G or NAG activities were significantly and positively correlated with microbial PLFAs. There were also significant relationships between gram-positive (G+) bacteria and all three soil enzymes. These findings indicate that G+ bacteria is the most important microbial community in C, N, and P transformations in Chinese fir plantations, and that (βG and NAG would be useful tools for assessing the biogeochemical transformation and metabolic activity of soil microbes. We recommend combined additions of N and P fertilizer to promote soil fertility and microbial activity in this kind of plantation. [ABSTRACT FROM AUTHOR]

Fourteen Ganoderma lucidum strains from different geographic regions were identified using ITS region sequencing. Based on the sequences obtained, the genomic relationship between the analyzed strains was determined. All G. lucidum strains were also genetically characterized using the AFLP technique. G. lucidum strains included in the analysis displayed an AFLP profile similarity level in the range from 9.6 to 33.9%. Biolog FF MicroPlates were applied to obtain data on utilization of 95 carbon sources and mitochondrial activity. The analysis allowed comparison of functional diversity of the fungal strains. The substrate utilization profiles for the isolates tested revealed a broad variability within the analyzed G. lucidum species and proved to be a good profiling technology for studying the diversity in fungi. Significant differences have been demonstrated in substrate richness values. Interestingly, the analysis of growth and biomass production also differentiated the strains based on the growth rate on the agar and sawdust substrate. In general, the mycelial growth on the sawdust substrate was more balanced and the fastest fungal growth was observed for GRE3 and FCL192. [ABSTRACT FROM AUTHOR]

Genome resequencing is now routine in other taxa, but large genome size and lackof reference assemblies have limited the ability to apply resequencing to molluscs. Endnote 1 Aword count of the collected papers in the Theo Murphy issue also shows that "mollusc" is the most popular name for a member of the phylum: 690 uses for "mollusc" in 13 papers versus 66 uses in 10 for "mollusk". Royalsocietypublishing.org/journal/rstb Introduction Cite this article: Davison A, Neiman M. 2021 Pearls of wisdom - a Theo Murphy issue on molluscan genomics. Thus, work by Calcino et al. [11] and others [12] using recently published complete genomes from representatives of eight wild-caught mollusc species to investigate the prevalence of hemizygous regions has implications for understanding genome dynamics across the other animal phyla. [Extracted from the article]

Poor and unreliable knowledge of the status of freshwater fisheries limits their inclusion in governance processes, thereby impeding effective management measures. This threatens the livelihoods of people, particularly in developing countries. Improved knowledge is required to draw the attention of policymakers and stimulate effective management measures to accelerate the sustainability of the freshwater fisheries. In line with this requirement, this paper provides the state of knowledge of the aquatic ecosystem and fisheries of the Lake Edward system, East Africa, focusing on lakes Edward, George and the Kazinga channel. The state of knowledge was accomplished by reviewing existing data and information on aspects of primary productivity and water quality, invertebrates, fish fauna, fish life history and ecology, and fisheries. The waterbodies have been monitored since the 1930s, albeit sporadically, providing data on all the above aspects but with substantial temporal gaps. Adequate and updated data and information exist on the water quality status of the water bodies, extant aquatic taxa (including fishes) and fish catches but with uncertainties in the latter. Data and information gaps exist on the abundance of biotic communities, fish life history, quantitative trophic ecology and fisheries management reference points. The aggregated data and information can directly support decisions for fisheries management. We recommend regular monitoring to fill the data and information gaps, more comprehensive stock assessments and the development of aquatic ecosystem models. [ABSTRACT FROM AUTHOR]

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With this paper we invite the reader to join us to a field trip to Guinea-Bissau through our eyes as primatologists and to explore the entanglements between humans and non-human primates. The first time we went to the field was in 2003. After staying with an NGO for a while, we set up a field station in a protected area that was home to chimpanzees (Madina Field Station). However, soon we realized that «protected areas», «high-quality forest», or «suitable habitat for chimpanzees» would not make any difference for research - and, most importantly, for this ape's conservation - without taking into consideration the locals' attitudes. Humanized landscapes most probably will become the rule in the future, so finding a way for a peaceful coexistence is urgent. [ABSTRACT FROM AUTHOR]

The issue of biological invasions in aquatic ecosystems is becoming increasingly severe in the contemporary world. Due to the lack of monitoring and management systems for aquatic invasive species, the difficulty in identifying aquatic invasive species, and the limited effectiveness of conventional control methods in aquatic environments, biological control in water bodies is comparatively more challenging than other types of interventions. In recent years, environmental DNA (eDNA) survey methods have rapidly developed in various fields, such as biological monitoring, community ecology, paleoenvironmental research, conservation biology, and invasion ecology, due to their unique advantages of being rapid, sensitive, efficient, and non-invasive. Because of these characteristics, this innovative molecular approach has gained wider acceptance and is being increasingly utilized for the detection of biological diversity in aquatic environments. Furthermore, it has emerged as a novel technology to address the pressing and significant issue of aquatic invasive species in the vast freshwater and marine resources of the East Asian region. This paper summarizes a variety of literature sources to summarize the major aquatic invasive species in East Asian countries and the current application status of eDNA technology in their survey processes. Using China as a case study, it expounds on the prospective incorporation of the 4E strategy with eDNA technology for the surveillance of biological invasions. Furthermore, it explores the potential prospects of eDNA technology in species diversity management and policy formulation, offering theoretical guidance for establishing aquatic invasive species monitoring systems. From a technological standpoint, the integration of eDNA technology with the 4E strategy holds significant potential for application, thereby offering a promising reference for the formulation of policies related to the management of aquatic biological invasions and biodiversity. [ABSTRACT FROM AUTHOR]

In this paper, a new stochastic four-species predator-prey model with disease in the first prey is proposed and studied. First, we present the stochastic model with some biological assumptions and establish the existence of globally positive solutions. Moreover, a condition for species to be permanent and extinction is provided. The above properties can help to save the dangered population in the ecosystem. Through Lyapunov functions, we discuss the asymptotic stability of a positive equilibrium solution for our model. Furthermore, it is also shown that the system has a stationary distribution and indicating the existence of a stable biotic community. Finally, our results of the proposed model have revealed the effect of random fluctuations on the four species ecosystem when adding the alternative food sources for the predator population. To illustrate our theoretical findings, some numerical simulations are presented. [ABSTRACT FROM AUTHOR]

Since their emergence in the 1980s, environmental virtue ethics (EVEs) have aimed to provide an alternative to deontological and consequentialist approaches for guiding ecological actions in the context of the global environmental crisis. The deterioration of the ecological situation and the challenges in addressing collective action problems caused by global changes have heightened interest in these ethics. They offer a framework for meaningful individual actions independently of the commitment of other actors. However, by shifting the focus onto individuals, EVEs appear to grapple with the tension between anthropocentrism and respect for nature, as well as between self-flourishing and concern for other living beings. This article argues that this difficulty is rooted in the neglect within EVEs of the communitarian aspect of ancient virtue ethics. Drawing from Baird Callicott's ecocentric approach and Val Plumwood's works, this paper explores the possibility of conceiving ecological communities as collective frameworks in which both public and private virtues are defined and practiced. [ABSTRACT FROM AUTHOR]

The aim of this paper is to compare the taxonomic composition and species diversity of the macrozoobenthos in Maritsa River (Bulgaria) and Han River (South Korea). Samples were collected at 15 selected sites in each river, including some of their main tributaries in 2020 and 2021. The number of the taxa recorded in Maritsa River was more than twice as great as in Han River: 192 taxa belonging to 19 systematic groups compared to 88 taxa belonging to 18 groups respectively. The order Ephemeroptera had the highest species richness: 31 taxa in the Bulgarian rivers and 26 taxa in the South Korean ones. The macrozoobenthic communities responded and adapted to the various conditions and impacts in the water environment with changes in the species composition and structure. The analysis of the similarity in the taxonomic composition showed low resemblance between all study sites but displayed distinct separations between the rivers and the two years. In general, the species structure of the macrozoobenthic communities in the studied rivers in Bulgaria was better than that in Han River. In both years, high species diversity was recorded at the reference sites in the rivers, characterized by conditions closely resembling natural environments. The species richness and the evenness of macrozoobenthos were very low at sites downstream subjected to considerable anthropogenic pressure. Some of the communities in Han River were almost destroyed completely. [ABSTRACT FROM AUTHOR]

For example (examples I use here are from my actual experiences with students), an undergraduate biology major who joins my lab as a second-year student might have a great background in general biology and may even have excellent grades in math classes. ASLO: Your paper shows that green algae can acquire new genes through incorporation of large... B MM b : Horizontal gene transfer (HGT) in algae and other protists is a well-established phenomenon, specifically HGT from other cellular sources like bacteria. Each year, ASLO honors aquatic scientists of various career stages for their exceptional work in advancing the fields of limnology and oceanography. Some of my most productive and enjoyable projects have resulted from graduate and undergraduate students, or Post Docs and students, working together. [Extracted from the article]

(1) Background: This paper discusses the impact of agricultural activities on stream health, particularly in relation to dairy cow fecal pollution. The study explores the fecal microbiome of cattle and the potential ecological implications of aging fecal pollution on waterways. (2) Methods: The study examines changes in the bacterial community available for mobilization from in-situ decomposing cowpats and the effects of simulated rainfall. The microbiome of individual cowpats was monitored over 5.5 months. We used 16S rRNA metagenomics and machine learning software, FEAST (Fast Expectation-mAximization for microbial Source Tracking), for bacterial and fecal source assignments. (3) Results: The phyla Bacillota and Bacteroidota are dominant in the fecal microbiota of fresh cow feces but shift to Pseudomonodota, Actinomycetota, and environmental Bacteroidota in aged cowpats. Potential impacts of these bacterial community shifts on inputs to local agricultural streams are discussed in relation to water quality monitoring and aging sources of fecal contamination. We identified taxon orders that are potential indicators of fresh cattle sources (Oscillospirales and Bacteroidales) and aged sources (Peptostreptococcales-Tissierellales) in water bodies. (4) The paper highlights that bacterial metagenomic profiling can inform our understanding of the ecology of microbial communities in aquatic environments and the potential impacts of agricultural activities on ecosystem health. [ABSTRACT FROM AUTHOR]

Biological evolution is generally regarded as a stochastic or probabilistic process, per the ideas of Darwin in the nineteenth century. Even if this is true at the meso-scale, it still may, however, be impacted by overarching constraints that we have not yet identified. In this paper, we revisit the subject of mammal faunal regions with a mind to explore a potential kind of macroevolutionary influence. We first identify an optimum seven-region mammal faunal classification system based on spatial and phylogenetic data from a comprehensive 2013 review, and then examine the possibility that this classification provides supporting evidence for a Spinoza-influenced philosophical/theoretical model of the "natural system" concept developed by one of the authors in the 1980s. The hierarchical pattern of regional affinities revealed does do this. [ABSTRACT FROM AUTHOR]

The article introduces that Conservation Biology is presenting the Rising Star Award for the best student-led paper published in the journal in 2015 to recognize an outstanding student researcher and communicator. The winner of the inaugural Rising Star Award is Franziska Humair for her paper "E-Commerce Trade in Invasive Plants."

The article discusses the interaction between climate change and anthropogenic pressures in the eutrophication process. Eutrophication, which is the excessive supply of nutrients to estuarine and coastal regions, poses a significant threat to ecosystems worldwide. The article explores the complex link between climate change and eutrophication, highlighting the potential exacerbation of eutrophication and its negative impacts due to climate-driven factors such as temperature changes, wind patterns, and sea level rise. The research topic also covers various themes related to eutrophication assessment, biogeochemical consequences, anthropogenic pressures, climate variability, ecosystem comparisons, and the effects of eutrophication on ecosystem services. The volume includes six papers contributed by scientists from different countries, providing insights into the effects of different factors on marine ecosystems. [Extracted from the article]

This article is an editorial for a thematic issue on Polar and Alpine Microbiology in the journal FEMS Microbiology Ecology. The issue focuses on the microbial ecology of cold habitats and the importance of understanding the biodiversity and functional roles of microorganisms in these environments. The issue includes 30 peer-reviewed papers, most of which were presented at the 9th International Conference on Polar and Alpine Microbiology (PAM22). The papers cover a range of topics, including microbial communities, adaptation, carbon and nitrogen turnover, and plant-microbe interactions, with a particular emphasis on Arctic, mountain, and Antarctic regions. The issue is dedicated to the late researcher S. Craig Cary, who made significant contributions to the study of microbial life in extreme environments. [Extracted from the article]

The paper illustrates how the recovery and valorisation of protected natural areas can constitute, for the local communities of small inland areas in Italy, a flywheel of sustainable development with beneficial effects for the entire 'country system'. Through a SWOT analysis and having selected the indicators for the chosen territory, which is the Roccamonfina Volcanic Area and Garigliano Mouth Regional Natural Park in the Campania Region, the characteristics of the area were highlighted as well as all the municipalities that contribute to defining the park area. The methodology adopted was chosen to identify a sample area whose peculiarities are applied and scalable to other contexts with similar conditions. The paper aims to contribute to the debate on the valorisation of protected areas in Southern Italy to promote the enhancement of production potential in sectors such as enhancing ecological quality, agricultural supply chains and projects linked to tourism sustainability. Promoting the role of agriculture, through the valorisation of quality agricultural supply chains and projects linked to tourism sustainability, can contribute to the economic development of Italy's inland areas. The authors believe that the sustainable development of southern Italy's protected areas can take place in territories with a characteristic identity based on environmental quality, territorial cohesion and the recovery of food habits. In the absence of adequate solutions, the protected natural areas and the communities that inhabit them risk deterioration, with the consequent loss of identities—cultural, historical, territorial—that must instead be preserved, handed down and enhanced. [ABSTRACT FROM AUTHOR]

Examination of climatic and oceanographic changes through the Holocene (11.75 ka–present) allows for an improved understanding and contextualization of modern climate change. Climate records of the Holocene can be utilized as a "baseline" from which to compare modern climate and can also provide insights into how environments experience and recover from change. However, individual studies on Holocene climate in the literature tend to focus on a distinct geographic location, a specific proxy record, or a certain aspect of climate (e.g., upwelling or precipitation), resulting in localized, record-specific trends rather than a comprehensive view of climate variability through the Holocene. Here we synthesize the major oceanographic and terrestrial changes that have occurred in the Western United States (bounded by 30 to 52 ∘ N and 115 to 130 ∘ W) through the most recent 11.75 kyr and explore the impacts of these changes on marine and terrestrial ecosystems. We present a novel spatiotemporal analysis of Holocene marine and terrestrial temperature, hydroclimate, and fire activity across the Early, Middle, and Late Holocene using a coded analysis of over 40 published studies. Following coded analysis of temperature, hydroclimate, and fire activity in the paper, we include a broader literature review of environmental change through the Holocene, including an examination of the impacts of multi-millennial climate trends on ecological communities. We find that the Early Holocene is characterized by warming relative to pre-Holocene conditions, including warm sea surface conditions, a warm and dry Pacific Northwest, a warm and wet Southwest, and overall spatial and temporal stability. In the Middle Holocene, these patterns reverse; this interval is characterized by cool sea surface temperatures, a cool and wet Pacific Northwest and warm and dry Southwest. The Late Holocene is the most variable interval, both spatially and temporally, and a novel spatial trend appears in terrestrial climate with warmer coastal areas and cooler inland areas. Human communities interacted with the environment throughout the entire Holocene, as evidenced in archeological and paleoenvironmental records, yet the recent Era of Colonization (1850–present) represents an unprecedented environmental interval in many records. Broadly, our analysis shows linkages between terrestrial and oceanographic conditions, distinct environmental phases through time, and emphasizes the importance of local factors in controlling climate through the dynamic Holocene. [ABSTRACT FROM AUTHOR]

Marsh Fern (Thelypteris palustris) is a hygrophytic plant uncommon to the flora of Bulgaria. It is also a vulnerable species, with small and isolated localities in several parts of the country. This paper provides new data on syntaxonomy of the communities in which this fern participates, as well as on a new important locality near Pleven town, Danubian Plain. The paper also attempts to summarize the published and more recent information on the distribution of this species in Bulgaria. [ABSTRACT FROM AUTHOR]

One of the effective tools to study the variation between communities is the use of pairwise dissimilarity indices. Besides species as variables, the involvement of trait information provides valuable insight into the functioning of ecosystems. In recent years, a variety of indices have been proposed to quantify functional dissimilarity between communities. These indices follow different approaches to account for between‐species similarities in calculating community dissimilarity, yet they all have been proposed as straightforward tools. In this paper, we review the trait‐based dissimilarity indices available in the literature and identify the most important conceptual and technical properties that differentiate among them, and that must be considered before their application. We identify two primary aspects that need to be considered before choosing a functional dissimilarity index. The first one is the way communities are represented in the trait space. The three main types of representations are the typical values, the discrete sets using the combination of species × sites and species × traits matrices, and the hypervolumes. The second decision is the concept of dissimilarity to follow, including two options: distances and disagreements. We use the above scheme to discuss the available functional dissimilarity indices and evaluate their relations to each other, their capabilities, and accessibility. [ABSTRACT FROM AUTHOR]

Complex mixtures of substances are in the atmosphere and they can cause diseases in humans and biological communities after acute or chronic exposition. This paper focuses on the physical measurement of particulate matter, a proxy for air pollution, and a biological method for mutation assessment due to plants' exposure to air pollution. The objective of this research was to characterize the air pollution seasonality in municipalities in southern Brazil, and also to understand the relation between air pollution and the biological response of the Tradescantia sp. clone 4430. The optical sensor SDS011 was used for measurements of particulate matter (PM) and the Trad-SHM bioassay was chosen to quantify the mutagenic alterations that occurred in stamen hairs during the study period, with PM data being measured every 5 seconds and the flowers being harvested approximately every two weeks for laboratory analysis. The Pearson test was applied to verify the correlation between PM and mutations in stamen hair as a result of which it was observed that there is a positive correlation between these data, with the highest value found being r = 0.61. Also, the period with the highest occurrence of pink cells was between autumn and spring, the same period in which an unusual increase in PM concentrations was also observed, a period that corresponds to a less favorable dispersion of pollutants in the atmosphere. The use of Tradescantia sp. clone 4430 showed sensitivity to the environments in which it was exposed. Biomonitoring is an important tool for understanding the effects of pollutants on the ecosystem. [ABSTRACT FROM AUTHOR]

Anthropogenic forcing caused the biodiversity loss and stability decline of communities. There is still controversy over whether the decline in biodiversity will lead to a decrease in community stability. The stability of biological communities is related to both biodiversity and structure, and this paper aims to reveal the human impacts on diatom communities' biodiversity and structure. We studied the richness, β‐diversity and network distance of diatom communities in Qinghai‐Xizang, Yunnan‐Sichuan and Lower Yangtze River Basin, China through empirical dataset and simulation method. The results showed that the diatoms richness in the Qinghai‐Xizang and the Yunnan‐Sichuan region was lower and the network distance was higher than that of the Lower Yangtze River Basin. β‐diversity in the Lower Yangtze River Basin was the lowest and the diatom network distance responds negatively to human population densities in China. The simulation showed that the network distance kept constant during random species loss, and declined while specialist species were lost or replaced by generalist species. The results suggested diatom communities' homogeneity and stability decline were associated with human activities. Human impacts may cause biodiversity loss targeted to specialist species or no biodiversity loss while generalist species replace those specialist species. This study showed that how diversity changes determined ecological stability depends on the type of species changes. [ABSTRACT FROM AUTHOR]

This paper summarizes the open community conventions developed by the Ecological Forecasting Initiative (EFI) for the common formatting and archiving of ecological forecasts and the metadata associated with these forecasts. Such open standards are intended to promote interoperability and facilitate forecast communication, distribution, validation, and synthesis. For output files, we first describe the convention conceptually in terms of global attributes, forecast dimensions, forecasted variables, and ancillary indicator variables. We then illustrate the application of this convention to the two file formats that are currently preferred by the EFI, netCDF (network common data form), and comma‐separated values (CSV), but note that the convention is extensible to future formats. For metadata, EFI's convention identifies a subset of conventional metadata variables that are required (e.g., temporal resolution and output variables) but focuses on developing a framework for storing information about forecast uncertainty propagation, data assimilation, and model complexity, which aims to facilitate cross‐forecast synthesis. The initial application of this convention expands upon the Ecological Metadata Language (EML), a commonly used metadata standard in ecology. To facilitate community adoption, we also provide a Github repository containing a metadata validator tool and several vignettes in R and Python on how to both write and read in the EFI standard. Lastly, we provide guidance on forecast archiving, making an important distinction between short‐term dissemination and long‐term forecast archiving, while also touching on the archiving of code and workflows. Overall, the EFI convention is a living document that can continue to evolve over time through an open community process. [ABSTRACT FROM AUTHOR]