Variation In Abundance Research Articles

Global Trends of Antibiotic Resistance Genes in Staphylococcus aureus: A Comprehensive Genomic Analysis.

Staphylococcus aureus (S. aureus) is a pathogen capable of causing severe diseases and exhibiting resistance to multiple antibiotics. However, there is a significant lack of comprehensive research on the global prevalence of its antibiotic resistance genes (ARGs). This study provided a comprehensive analysis of ARGs in S. aureus, using 113,842 S. aureus genome sequences from the National Center for Biotechnology Information database. The results revealed that a significant majority (84%) of these genomes harbored at least one ARG, with a total of 389,464 ARG sequences identified across 19 major types and 103 subtypes. These ARGs exhibited varied abundances and diversities, linked primarily to clinical cases worldwide. ARGs for fluoroquinolones, multidrug resistance, bacitracin, tetracyclines, beta-lactams, and aminoglycosides were notably abundant, ranging from 3.16 × 10-5 to 1.49 copies of ARG per million bp. Variations in the abundance and diversity of ARGs were observed between countries, with middle- and low-income countries showing higher gene abundance but lower diversity compared with high-income countries. Temporal analysis over 30 years showed a fluctuating decline in ARG abundance alongside an increase in diversity, suggesting evolving resistance mechanisms. The study also explored the role of mobile genetic elements in ARG dissemination, finding a substantial proportion of ARG subtypes associated with plasmids and insertion sequence elements, indicating their potential for spread across borders. The global distribution of mobile ARGs was further analyzed, revealing the extensive reach of certain ARGs across countries. This research provides valuable insights into the prevalence and dissemination of antibiotic resistance in S. aureus on a global scale, aiding in the development of effective monitoring and control strategies to combat ARGs in S. aureus and other pathogens.

Exploring action-law of microplastic abundance variation in river waters at coastal regions of China based on machine learning prediction

Surface waters, particularly the river systems, constitute a vital freshwater resource for human beings and aquatic life on Earth. In economically developed and densely populated coastal regions, river water is facing severe microplastic pollution, posing a threat to public health and ecological safety. Reliable prediction of microplastic abundance (MPA) can significantly reduce the costs associated with microplastic field sampling and analysis. This study employed spatial correlation, geographical detector, principal component analysis and five mainstream machine learning models to analyze 79 datasets of MPAs in seven coastal areas of China and performed correlation, regression and attribution analyses based on 19 terrestrial influencing factors that potentially affect the MPA life cycle processes (generation, aging, and migration). The results showed that the Neural Network (NN) and the Gaussian Process Regression (GPR) models achieved the best prediction performance, with the predicted R2 close to 1. Principal component analysis and Shapley additive explanations concluded that meteorological factors, in particular the annual geotemperature, surface solar radiation, and annual relative humidity, had a key influence on the aging of microplastics. The second key factor in improving the MPA prediction ability was the dynamic description of microplastic migration, which was primarily governed by hydrological factors such as annual precipitation and average terrain slope. Unexpectedly, the effects of land use and level of urbanization were relatively small in describing the generation of microplastics. Only the percentage of built areas was strongly correlated with the MPA levels. Note that the MPA prediction and its contribution factors may vary across different basins. Nevertheless, the findings of this study are applicable to predicting and analyzing the distribution of microplastics in other coastal rivers, and for indicating the main contributing factors, ultimately serving as a basis for guiding microplastic pollution control strategies in different river basins.

Testing the sources of the peculiar abundances in globular clusters

This work aims to analyze some of the polluters proposed in the self-enrichment scenarios put forward to explain the multiple populations in globular clusters (GCs), extending previous studies. Three scenarios with different polluter stars were tested: asymptotic giant branch stars (AGBs), high-mass interacting binaries (IBs), and fast rotating massive stars (FRMSs). With abundance data available from the Apache Point Observatory Galactic Evolution Experiment (APOGEE) survey and ΔY estimates from precise Hubble Space Telescope (HST) photometry, twenty-six clusters were studied, increasing the number of clusters in previous studies by more than a factor of three. We also included the study of the abundances of N, C, Mg, and Al, extending previous studies that mainly focused on the abundances of He, O, and Na. In addition, we constructed an empirical model to test whether one could explain the chemical signatures of the “enriched” population of GC stars with a fixed source and dilution process based on empirical data. In agreement with work by other authors, we found that the proposed polluters can generally predict the qualitative abundance patterns in GC stars and in some cases quantitatively predict some elements, but in most cases when we compare the model yields with the observations, we find that they cannot explain the entire set of observed abundance patterns. The empirical model succeeds in reproducing the abundances of Al for a given ΔY (and vice versa), showing that there is a direct relationship between Al and He, with one increasing proportionally to the other. However, the empirical model fails to reproduce the observed abundances of Na and N, in agreement with the results of previous works. The observed decoupling between the maximum abundances of CNO-cycle elements such as N and Na with those of Al and He provides new information and constraints for future models and could take us a step closer to understanding the origin of the peculiar abundance variations of GC stars.

Data gap or biodiversity gap? Evaluating apparent spatial biases in community science observations of Odonata in the east-central United States

Odonates (dragonflies and damselflies) have become popular study organisms for insect-based climate studies, due to the taxon’s strong sensitivity to environmental conditions, and an enthusiastic following by community scientists due to their charismatic appearance and size. Where formal records of this taxon can be limited, public efforts have provided nearly 1,500,000 open-sourced odonate records through online databases, making real-time spatio-temporal monitoring more feasible. While these databases can be extensive, concerns regarding these public endeavors have arisen from a variety of sources: records may be biased by human factors (ex: density, technological access) which may cause erroneous interpretations. Indeed, records of odonates in the east-central US documented in the popular database iNaturalist bear striking patterns corresponding to political boundaries and other human activities. We conducted a ‘ground-truthing’ study using a structured sampling method to examine these patterns in an area where community science reports indicated variable abundance, richness, and diversity which appeared to be linked to observation biases. Our observations were largely consistent with patterns recorded by community scientists, suggesting these databases were indeed capturing representative biological trends and raising further questions about environmental drivers in the observed data gaps.

Microplastic Pollution in Riparian Soils of the Rapidly Growing City of Thimphu, Bhutan

Plastic has become a vitally important material for humans; however, the large amount of plastic waste generated annually pollutes the environment. Plastic decomposition generates microplastics (MPs), which have emerged as a concerning global environmental pollutant because of their potential to be more harmful to the environment than their larger counterparts. This study examined the occurrence and abundance of MPs in riparian soils (RS) of a rapidly growing city in Thimphu, Bhutan. Additionally, the study investigated the relationships between the abundance of MP and several variables, such as the physicochemical properties of the soil, land use, the distance to impervious cover (IC), the plot IC%, surface plastic, textile waste, and the distance to upstream drainage outlets within the riparian zone (RZ). A density separation technique was used to extract MPs. The results showed that RS in urban sites had higher concentrations of MPs (93.3%) than in other land use (7.7%, p = 0.04). Blue MPs (46.2%) were the most common plastic colour. In urban RS, MPs ranged from 0 to 500 particles/kg. MP concentration showed a positive correlation with available phosphorus (p = 0.01) and the distance to the upstream drainage outlets (p = 0.01). Our findings highlight the nature and pathways of MP pollution in rapidly growing cities, where economic growth often overshadows environmental management. We also identify opportunities for these cities to mitigate MP pollution by reclaiming surface plastic and textile waste, stepping up recycling initiatives, and disposing of plastic-ridden waste in low-impact landfills.

Divergent temporal responses of native macroinvertebrate communities to biological invasions.

Biological invasions pose a major threat to biodiversity, ecosystem functioning, and human well-being. Non-native species can have severe ecological impacts that are transformative, affecting ecosystems across both short-term and long-term timescales. However, few studies have determined the temporal dynamics of impact between these scales, impeding future predictions as invasion rates continue to rise. Our study uses a meta-analytical approach to dissect the changing taxonomic and functional impacts of biological invasions on native macroinvertebrate populations and communities in freshwater ecosystems across Europe, using a recently collated European long-term time series spanning several decades. Our findings reveal a complex temporal pattern: while initial stages of invasions (i.e. five years after the first record of non-native species) often exhibited benign impacts on macroinvertebrate abundance, richness, or functional diversity, the long-term (i.e. the period following the early invasion) effects became predominantly negative. This pattern was consistent between taxonomic and functional metrics for impacts at both the population and species level, with taxonomic metrics initially positively affected by invasions and functional metrics being more stable before also declining. These results suggest that even initially benign or positively perceived impacts could be eventually superseded by negative consequences. Therefore, understanding the magnitude of invasion effects increasingly requires long-term studies spanning several years or decades to offer insights into effective conservation strategies prioritising immediate and future biodiversity protection efforts. These findings also highlight the importance of integrating multiple taxonomic, functional and temporal components to inform adaptive management approaches to mitigate the negative effects of current and future biological invasions.

Complete mitochondrial genome assembly of Juglans regia unveiled its molecular characteristics, genome evolution, and phylogenetic implications

BackgroundThe Persian walnut (Juglans regia), an economically vital species within the Juglandaceae family, has seen its mitochondrial genome sequenced and assembled in the current study using advanced Illumina and Nanopore sequencing technology.ResultsThe 1,007,576 bp mitogenome of J. regia consisted of three circular chromosomes with a 44.52% GC content encoding 39 PCGs, 47 tRNA, and five rRNA genes. Extensive repetitive sequences, including 320 SSRs, 512 interspersed, and 83 tandem repeats, were identified, contributing to genomic complexity. The protein-coding sequences (PCGs) favored A/T-ending codons, and the codon usage bias was primarily shaped by selective pressure. Intracellular gene transfer occurred among the mitogenome, chloroplast, and nuclear genomes. Comparative genomic analysis unveiled abundant structure and sequence variation among J. regia and related species. The results of selective pressure analysis indicated that most PCGs underwent purifying selection, whereas the atp4 and ccmB genes had experienced positive selection between many species pairs. In addition, the phylogenetic examination, grounded in mitochondrial genome data, precisely delineated the evolutionary and taxonomic relationships of J. regia and its relatives. We identified a total of 539 RNA editing sites, among which 288 were corroborated by transcriptome sequencing data. Furthermore, expression profiling under temperature stress highlighted the complex regulation pattern of 28 differently expressed PCGs, wherein NADH dehydrogenase and ATP synthase genes might be critical in the mitochondria response to cold stress.ConclusionsOur results provided valuable molecular resources for understanding the genetic characteristics of J. regia and offered novel perspectives for population genetics and evolutionary studies in Juglans and related woody species.

Use of long-term underwater camera surveillance to assess the effects of the largest Amazonian hydroelectric dam on fish communities

The increase in the construction of mega dams in tropical basins is considered a threat to freshwater fish diversity. Although difficult to detect in conventional monitoring programs, rheophilic species and those reliant on shallow habitats comprise a large proportion of fish diversity in tropical basins and are among the most sensitive species to hydropower impacts. We used Baited Remote Underwater Video (BRUV), an innovative, non-invasive sampling technique, to record the impacts caused by Belo Monte, the third largest hydropower project in the world, on fishes inhabiting fast waters in the Xingu River. BRUV were set in a river stretch of ~ 240 km for 7 years, 2 before and 5 after the Belo Monte operation. We explored the spatial and temporal variation in fish diversity (α, β, and γ) and abundance (MaxN) using generalized additive models. We also investigated the variation of environmental variables and tested how much information we gained by including them in the diversity and abundance models. Belo Monte altered the flow regime, water characteristics, and fishery yield in the Xingu, resulting in changes in the fish community structure. Temporally, we observed sharp declines in α diversity and abundance, far exceeding those from a previous study conducted with more conventional sampling methods (i.e., catch-based) in the region. γ-diversity was also significantly reduced, but we observed a non-expected increase in β diversity over time. The latter may be associated with a reduction in river connectivity and an increase in environmental heterogeneity among river sectors. Unexpected signs of recovery in diversity metrics were observed in the last years of monitoring, which may be associated with the maintenance of flow levels higher than those previously planned. These results showed that BRUV can be a useful and sensitive tool to monitor the impacts of dams and other enterprises on fish fauna from clear-water rivers. Moreover, this study enhances our comprehension of the temporal variations in freshwater fish diversity metrics and discusses the prevalent assumption that a linear continuum in fish-structure damage associated with dam impoundments may exhibit temporal non-linearity.

Microbial ocean-atmosphere transfer: the influence of sewage discharge into coastal waters on bioaerosols from an urban beach in the subtropical Atlantic

All over the world, the oceans are the final destination of sewage transported by river estuaries, rainwater and other coastal discharges. The risks to human health related to direct contact with water and consumption of contaminated fish are well known, but little is known about the potential for atmospheric exposure to pollutants and pathogens from contaminated seawater. The release of microbial particles from the sea into the atmosphere occurs mainly by the eruption of rising bubbles through the sea surface microlayer (SML) or by sea spray. We investigated the heterotrophic bacteria density and relative abundance in SML and bioaerosols originated on the seafront of Fortaleza (Atlantic coastal zone, northeastern Brazil) influenced by wastewater disposal. There was a difference in the density of total heterotrophic bacteria (THB) according to the matrix analyzed during two seasons: the bacterial count was highest in the SML during the rainy season while the highest number of bacteria in bioaerosols samples was recorded during the dry season. Twenty-nine bacterial taxonomic groups were identified with variable abundance for both environments. These were the same in both matrices, with environmental variables influencing their abundance and composition. The contribution of the marine and continental environments in shaping the microbiota of the SML and coastal bioaerosols was clear, with the constant and representative presence of Enterobacteria standing out. The aerosolization of bacteria resulting from the discharge of untreated sewage is an important issue related to coastal environmental health and ecological safety.

Desertification indirectly affects soil fauna by reducing complexity of soil habitats and diversity of energy sources

Soil fauna is closely linked to ecological functions such as biogeochemical cycling, soil structure, ecosystem sustainability and trophic interactions. However, little consideration has been given to how desertification influences the abundance and diversity of soil fauna in arid areas. In this study, soil fauna was sampled in four desert habitats (gravel, sand, salt and mud desert) in northwest China. At the same time, the plant traits, geographic location and soil properties were investigated. We also measured contribution of environmental factors explained faunal community diversity and abundance, and by what pathways desertification controls soil fauna. The results showed that total abundance and diversity of soil fauna in the mud desert were significantly (P < 0.05) higher than salt, sand and gravel deserts. Soil fauna diversity, composition and community were more sensitive to desertification-induced changes in soil properties than to changes in plant traits and geographic locations (changes in soil properties explained 68.9 % and 73.7 % of the variation in diversity and abundance of soil fauna community, respectively). Among them, the available phosphorus, volumetric water content had a significant positive effect on community diversity and abundance, while pH had a significant negative effect (P < 0.01). The results of piecewise structural equation modeling imply that desertification may have mainly indirect impacts on soil fauna community, and that direct effects are almost zero. In summary, regardless of the type of desertification, it will affect the material cycle, energy flow and information transfer of ecosystems by destroying the soil habitats and vegetation conditions, and will affect the structure and diversity of soil fauna from the bottom up.

Spatial modelling and estimation of mammals' mortalities by Pantanal 2020 megafires

Abstract Extreme wildfire events, such as the Pantanal 2020 megafires, are expected to become more common. Assessing the impacts of such extreme events on wildlife is imperative for conservation planning. Direct observation of carcasses can provide valuable information on how these impacts relate to spatial heterogeneity. Here, we use double‐observer carcass surveys to assess the numbers and spatial patterns of direct mortalities of medium‐ to large‐sized mammals resulting from the Pantanal 2020 megafires in a large reserve (1080 km2) in the northern Pantanal wetland. Accounting for imperfect detection, we model the spatial variation in mortality occurrence and abundance, testing the effects of habitat‐related variables and wildfire severity using multi‐species N‐mixture models. We found that 26 out of 27 species of medium and large‐sized mammals died from the fires with a mean estimate of around 49 thousand individuals. The most affected species included capuchin monkeys, agoutis, peccaries, tapirs, brocket deer, tamanduas, coatis and capybaras. Direct mortality of mammals by wildfires was affected by landscape factors related to species habitats, species traits (probably related to escape or refuge strategies), and the intensity of the wildfires. Mortalities presented a general positive relationship with non‐flooded forests (a fire‐sensitive habitat in Pantanal) and with the severity of wildfires. Artificial water bodies, a common landscape structure in Pantanal, had 7.5 times more deaths than other areas. Synthesis and applications: With the approach used, we were able to: (i) identify mortality hotspots associated with landscape features; (ii) simultaneously identify the most affected species and assess the average relationships for all the assemblage of medium‐ and large‐sized mammals. We discuss conservation and management actions in two contexts: species prioritization for rescuing and monitoring; and territory prioritization for fire prevention and fighting.

Striped Field Mouse Invading Human-Modified Environments of Lithuania during Last Five Decades

The striped field mouse (Apodemus agrarius) is expanding in several European countries, but the details of this process are not always documented due to a lack of long-term studies. We conducted an analysis of changes in relative abundances and proportions of A. agrarius in small mammal communities in nine different habitat groups in Lithuania during 1975–2023. We found an increase in the abundance and proportion of A. agrarius, increasing synanthropization of the species, and tolerance to anthropogenization of habitats. Temporal variations in the relative abundance and proportion of species were observed, with lower values in February–July and higher values in September–January. The main finding is a remarkable increase in species presence in the country after the 1990s, with a peak observed in the 2010s–2020s, confirmed by eight local studies. During these decades, it was the third most abundant species, representing 19.8–20.0% of the individuals caught. It is also important to note that A. agrarius has recently been most abundant in commensal habitats (0.029 ± 0.006 individuals/trap day), with the highest species proportion in agricultural areas (24.8 ± 1.8%). There are many indications that the expansion of A. agrarius in Lithuania is becoming invasive.

Variations in the germinal center response revealed by genetically diverse mouse strains.

The humoral response is complex and involves multiple cellular populations and signaling pathways. Bacterial and viral infections, as well as immunization regimens, can trigger this type of response, promoting the formation of microanatomical cellular structures called germinal centers (GCs). GCs formed in secondary lymphoid organs support the differentiation of high-affinity plasma cells and memory B cells. There is growing evidence that the quality of the humoral response is influenced by genetic variants. Using 12 genetically divergent mouse strains, we assessed the impact of genetics on GC cellular traits. At steady state, in the spleen, lymph nodes and Peyer's patches, we quantified GC B cells, plasma cells and follicular helper Tcells. These traits were also quantified in the spleen of mice following immunization with a foreign antigen, namely, sheep red blood cells, in addition to the number and size of GCs. We observed both strain- and organ-specific variations in cell type abundance, as well as for GC number and size. Moreover, we find that some of these traits are highly heritable. Importantly, the results of this study inform on the impact of genetic diversity in shaping the GC response and identify the traits that are the most impacted by genetic background.

Ecological and faunistic features of fleas in the Transcaucasian mounthill natural plague foci in Azerbaijan

Among all vectors of natural focal infections, fleas are the most active. In this respect, entomological and epizootological monitoring has always been of great importance. This article, based on the material collected from the Transcaucasian foothill natural plague focus, presents the results of a study of flea species diversity, the landscape and geographical area of their distribution. The goal of this work was to determine the diversity of flea species, their distribution and abundance based on the results of epizootological studies conducted in areas with different landscapes in the Transcaucasian foothill natural plague focus of Azerbaijan. The material for the study was obtained during epizootological studies and observations conducted in the spring and autumn seasons of 2020–2023. in the Transcaucasian foothill natural plague focus of Azerbaijan (Bozchol, Mil-Mugan, Eastern and Western Jeyranchel, Gobustan, Absheron, semi-deserts of Kilazi, Sitalchay). Collection, packaging, transportation, and marketing of the material were carried out on the basis of relevant biosafety rules and delivered for further study to the Special Dangerous İnfections Control Center. In total, 61,087 nest tracks were examined, and 7,939 fleas were collected and delivered. The material was processed and identified in the laboratory in accordance with the current regulatory and methodological document on the safety of working with pathogenic biological agents (PBA) of pathogenicity groups I–IV. As a result of sample identification, the species composition of fleas was determined and grouped by geographical areas and landscapes. Research was also carried out (using the PCR method) for the presence of the plague causative agent - Yersinia pestis. According to the results of the study, it was found that, regardless of the biocenotic and climatic characteristics of individual sectors of the Transcaucasian foothill natural plague focus of Azerbaijan, there may be enough carriers of infectious diseases and their growth increases over the years. The frequency of occurrence of the prevailing genera of fleas - Xenopsylla and Nosopsyllus- depends on the natural and climatic conditions of the focus being studied. The analysis for the presence of the plague causative agent among all fleas caught and studied did not give positive results. For the timely detection of epizootics among wild rodents and bloodsuckers, it is important to conduct regular epizootic surveys in enzootic areas for plague.

Microplastic-contamination in the flesh and gastrointestinal tract of nile tilapia (Oreochromis niloticus) reared in floating net cages at lake Ranu Grati, Pasuruan, East Java, Indonesia

In recent years, microplastics (MPs) have emerged as a prominent environmental problem in waters and environments, including lake waters. Microplastics in freshwater, such as those in floating net cages (FNC), can be consumed by Nile tilapia (Oreochromis niloticus), one of the commercially available cultivated fish in Indonesia. This study aims to determine the prevalence of microplastics and compare their characteristics in the surface water, flesh, and gastrointestinal tract (GIT) of Nile Tilapia (O. niloticus) at Lake Ranu Grati, Pasuruan, East Java, Indonesia. Visual characteristics of MPs were observed using a stereo microscope, and polymers were analysed by ATR-FTIR (Attenuated Total Reflection-Fourier Transform Infrared Spectroscopy). The abundance of MPs from water sample locations in Lake Ranu Grati reached 1116 MPs particles. In the water samples, the inner and outer sides of the FNC are dominated by the MPs with a size range of 251–500 µm and 1001-2000 µm in the milieu of Ranu Grati Lake. The most common MPs' types and colours are fibre and black, dominated by Polyethylene (PE). In 25 O. niloticus samples, 576 particles of MPs were found in the flesh and 724 particles in the gastrointestinal tract (GIT). This study found no significant variation in microplastic abundance between flesh and GIT samples (p>0.05; Mann-Whitney U test). Microplastics in Nile Tilapia flesh samples were dominated by blue fibres with a size range of 101–250 µm, and the polymer found was PA (polyamide). Meanwhile, in the GIT samples, microplastics were dominated by black fibre, with a size range of 251–500 µm, and the polymer found was PA (polyamide).

Supragingival Plaque Microbiomes in a Diverse South Florida Population.

Trillions of microbes comprise the human oral cavity, collectively acting as another bodily organ. Although research is several decades into the field, there is no consensus on how oral microbiomes differ in underrepresented groups such as Hispanic, Black, and Asian populations living in the United States. Here, using 16S ribosomal RNA sequencing, we examine the bacterial ecology of supragingival plaque from four quadrants of the mouth along with a tongue swab from 26 healthy volunteers from South Florida (131 total sequences after filtering). As an area known to be a unique amalgamation of diverse cultures from across the globe, South Florida allows us to address the question of how supragingival plaque microbes differ across ethnic groups, thus potentially impacting treatment regiments related to oral issues. We assess overall phylogenetic abundance, alpha and beta diversity, and linear discriminate analysis of participants based on sex, ethnicity, sampling location in the mouth, and gingival health. Within this cohort, we find the presence of common phyla such as Firmicutes and common genera such as Streptococcus. Additionally, we find significant differences across sampling locations, sex, and gingival health. This research stresses the need for the continued incorporation of diverse populations within human oral microbiome studies.

Ichnological indicators of physico-chemical stresses in wave- to tide-dominated Miocene shallow marine environments (Argentine Patagonia)

An integrated analysis of ichnological and sedimentological features in ancient successions provides a robust dataset of high-resolution interpretations of environmental parameters, encompassing both depositional and ecological aspects. By characterising discrete and recurring bioturbation patterns in the Puerto Madryn Formation (Late Miocene, Argentine Patagonia), we arrive at key knowledge about predominant environmental stresses within transgressive phase shallow marine and estuarine systems, shedding light on their palaeoenvironmental implications. Given the inherent complexities of coastal settings, including the challenges posed by omission/erosion surfaces, it becomes imperative to consider the intricate interplay of multiple depositional processes and environmental factors.Through a detailed integration of sedimentological and ichnological approaches, we discern the establishment of a wave-dominated system overlain by a tide-dominated estuarine system.The wave-dominated marine system involves tabular bodies extending laterally over tens of kilometres, with upward fining and coarsening successions from the mid- to lower-shoreface to offshore-shelf environments. The influence of waves and tides on these systems is discussed in the absence of physical sedimentary structures and the need to find elements that bring us closer to elucidating whether waves or tidal processes influence shoreface to offshore systems. The ichnological assemblages allow for the characterisation of Cruziana ichnofacies with proximal (Taenidium and Thalassinoides), archetypal (Asterosoma, Chondrites, Cylindrichnus, Ophiomorpha, ?Rhizocorallium, Rosselia, Scolicia, Sinusichnus, Siphonichnus, Teichichnus, and Thalassinoides), and distal expressions (Chondrites, Helicodromites, Phycodes, Thalassinoides, and ?Zoophycos) in the lower shoreface to lower offshore and transitional settings with the shelf. However, the transition from these deposits to Chondrites-dominated beds associated with lower offshore to shelf environments—determined by changes in oxygenation, nutrients, and energy conditions—impedes assignment of all the successions to a particular ichnofacies.The tide-dominated estuarine system features wide, channel-shaped bodies filled with sandy to heterolithic facies, interpreted as intertidal and subtidal deposits. To differentiate between estuary mouths and other settings, the analysis involved characterisation of transgressive and regressive surfaces, ichnological assemblages, and facies distribution, determining net sediment movement—whether landwards or seawards—and its influence on system classification. The ichnological assemblages could be assigned to the Skolithos (Arenicolites, Gyrolithes, Maiakarichnus, Ophiomorpha, Schaubcylindrichnus, Skolithos, and Thalassinoides) and Cruziana ichnofacies (Ophiomorpha, Rosselia, Scolicia, and Siphonichnus). Variations in diversity and abundance often help to determine certain stressful conditions, although the transition to more open areas is discussed, addressing how it could modify the typical models linked with a direct relationship between abundance/diversity and physico-chemical stress.

Trait-based study predicts glycerol/diol dehydratases as a key function of the gut microbiota of hindgut-fermenting carnivores

BackgroundMicrobial pdu and cob-cbi-hem gene clusters encode the key enzyme glycerol/diol dehydratase (PduCDE), which mediates the transformation of dietary nutrients glycerol and 1,2-propanediol (1,2-PD) to a variety of metabolites, and enzymes for cobalamin synthesis, a co-factor and shared good of microbial communities. It was the aim of this study to relate pdu as a multipurpose functional trait to environmental conditions and microbial community composition. We collected fecal samples from wild animal species living in captivity with different gut physiology and diet (n = 55, in total 104 samples), determined occurrence and diversity of pdu and cob-cbi-hem using a novel approach combining metagenomics with quantification of metabolic and genetic biomarkers, and conducted in vitro fermentations to test for trait-based activity.ResultsFecal levels of the glycerol transformation product 1,3-propanediol (1,3-PD) were higher in hindgut than foregut fermenters. Gene-based analyses indicated that pduC harboring taxa are common feature of captive wild animal fecal microbiota that occur more frequently and at higher abundance in hindgut fermenters. Phylogenetic analysis of genomes reconstructed from metagenomic sequences identified captive wild animal fecal microbiota as taxonomically rich with a total of 4150 species and > 1800 novel species but pointed at only 56 species that at least partially harbored pdu and cbi-cob-hem. While taxonomic diversity was highest in fecal samples of foregut-fermenting herbivores, higher pduC abundance and higher diversity of pdu/cbi-cob-hem related to higher potential for glycerol and 1,2-PD utilization of the less diverse microbiota of hindgut-fermenting carnivores in vitro.ConclusionOur approach combining metabolite and gene biomarker analysis with metagenomics and phenotypic characterization identified Pdu as a common function of fecal microbiota of captive wild animals shared by few taxa and stratified the potential of fecal microbiota for glycerol/1,2-PD utilization and cobalamin synthesis depending on diet and physiology of the host. This trait-based study suggests that the ability to utilize glycerol/1,2-PD is a key function of hindgut-fermenting carnivores, which does not relate to overall community diversity but links to the potential for cobalamin formation.5QUW1NVLR3PN1Ur7W1hKTuVideo

Disentangling the influence of reservoir abundance and pathogen shedding on zoonotic spillover of the Leptospira agent in urban informal settlements.

Rats are major reservoirs for pathogenic Leptospira, the bacteria causing leptospirosis, particularly in urban informal settlements. However, the impact of variation in rat abundance and pathogen shedding rates on spillover transmission to humans remains unclear. This study aimed to investigate how spatial variation in reservoir abundance and pathogen pressure affect Leptospira spillover transmission to humans in a Brazilian urban informal settlement. A longitudinal eco-epidemiological study was conducted from 2013 to 2014 to characterize the spatial distribution of rat abundance and Leptospira shedding rates in rats and determine the association with human infection risk in a cohort of 2,206 community residents. Tracking plates and live-trapping were used to measure rat abundance and quantify rat shedding status and load. In parallel, four sequential biannual serosurveys were used to identify human Leptospira infections. To evaluate the role of shedding on human risk, we built three statistical models for: (1) the relative abundance of rats, (2) the shedding rate by individual rats, and (3) human Leptospira infection, in which "total shedding", obtained by multiplying the predictions from those two models, was used as a risk factor. We found that Leptospira shedding was associated with older and sexually mature rats and varied spatially and temporally-higher at valley bottoms and with seasonal rainfall (December to March). The point estimate for "total shedding" by rat populations was positive, i.e., Leptospira infection risk increased with total shedding, but the association was not significant [odds ratio (OR) = 1.1; 95% confidence interval (CI): 0.9, 1.4]. This positive trend was mainly driven by rat abundance, rather than individual rat shedding (OR = 1.8; 95% CI: 0.6, 5.4 vs. OR = 1.0; 95% CI: 0.7, 1.4]. Infection risk was higher in areas with more vegetative land cover (OR = 2.4; 95% CI: 1.2, 4.8), and when floodwater entered the house (OR = 2.4; 95% CI: 1.6, 3.4). Our findings indicate that environmental and hydrological factors play a more significant role in Leptospira spillover than rat associated factors. Furthermore, we developed a novel approach combining several models to elucidate complex links between animal reservoir abundance, pathogen shedding and environmental factors on zoonotic spillover in humans that can be extended to other environmentally transmitted diseases.

Identification and Evaluation of Diploid and Tetraploid Passiflora edulis Sims.

Passiflora edulis Sims (2n = 18) is a perennial plant with high utilization values, but its spontaneous polyploidy in nature has yet to be seen. Thus, this study aims to enhance our understanding of polyploidy P. edulis and provide rudimentary knowledge for breeding new cultivars. In this study, colchicine-induced tetraploid P. edulis (2n = 36) was used as experimental material (T1, T2, and T3) to explore the variances between it and its diploid counterpart in morphology, physiology, and biochemical characteristics, and a comparison of their performance under cold stress was conducted. We measured and collected data on phenotype parameters, chlorophyll contents, chlorophyll fluorescence, photosynthesis, osmotic substances, and antioxidant enzymes. The results showed that tetraploid P. edulis exhibited a shorter phenotype, more giant leaves, darker leaf color, and longer and fewer roots. Moreover, the physiological and biochemical analysis indicated that the tetraploid P. edulis had better photosynthesis systems and higher chlorophyll fluorescence parameters than the diploid P. edulis. Additionally, the tetraploid P. edulis had higher activity of antioxidant enzymes (SOD, POD, CAT) and lower MDA content to maintain better resistance in low temperatures. Overall, we conclude that there were apparent differences in the morphological, physiological, and biochemical traits of the tetraploid and diploid P. edulis. The tetraploid plants showed better photosynthesis systems, higher osmotic substance content, and antioxidant enzyme activity than the diploid, even under cold stress. Our results suggest that tetraploids with more abundant phenotype variation and better physiological and biochemical traits may be used as a new genetic germplasm resource for producing new P. edulis cultivars.