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Microbiology Spectrum Jun 2024The coccidian parasite is the causative agent for foodborne outbreaks of cyclosporiasis disease and multiple annual fresh produce recalls. The aim of this study was to...
UNLABELLED
The coccidian parasite is the causative agent for foodborne outbreaks of cyclosporiasis disease and multiple annual fresh produce recalls. The aim of this study was to identify potential cross-reacting species for the 18S rRNA and MIT1C gene target real-time quantitative polymerase chain reaction (qPCR) assays. The environmental samples evaluated were irrigation pond water, produce wash water, and wastewater treatment sludge from a previous study with qPCR detections of by the 18S rRNA gene target qPCR. From these samples, longer regions of the 18S rRNA gene and the mitochondrial cytochrome c oxidase subunit III gene () were sequenced. Of 65 irrigation pond water samples with positive test results using the 18S rRNA gene qPCR assay, none had MIT1C qPCR assay detections or sequences that clustered with based on sequencing of the and 18S rRNA gene. Sequences from these samples clustered around coccidia sequences found in bird, fish, reptile, and amphibian hosts. Of 26 sludge samples showing detections by either qPCR assay, 14 (54%) could be confirmed as containing by sequencing of and 18S rRNA gene regions. In three of the remaining sludge samples, sequenced reads clustered with coccidia from rodents. This study demonstrated that caution should be taken when interpreting qPCR detection data in environmental samples and sequencing steps will likely be needed for confirmation.
IMPORTANCE
Fresh produce is a leading transmission source in cyclosporiasis outbreaks. It is therefore essential to understand the role that produce-growing environments play in the spread of this disease. To accomplish this, sensitive and specific tests for environmental and irrigation waters must be developed. Potential cross-reactions of real-time quantitative polymerase chain reaction (qPCR) assays have been identified, hindering the ability to accurately identify this parasite in the environment. Amplicon sequencing of the cox3 and 18S rRNA genes revealed that all irrigation pond water and two sludge samples that initially detected by qPCR were most likely cross-reactions with related coccidian organisms shed from birds, fish, reptiles, amphibians, and rodents. These results support that a single testing method for environmental samples is likely not adequate for sensitive and specific detection of .
PubMed: 38916361
DOI: 10.1128/spectrum.00906-24 -
PeerJ 2024The Jambato Harlequin toad (), a formerly abundant species in the Andes of Ecuador, faced a dramatic population decline in the 1980s, with its last recorded sighting in...
The Jambato Harlequin toad (), a formerly abundant species in the Andes of Ecuador, faced a dramatic population decline in the 1980s, with its last recorded sighting in 1988. The species was considered Extinct by the IUCN until 2016, when a fortuitous discovery of one Jambato by a local boy reignited hope. In this study, we present findings from an investigation conducted in the Angamarca parish, focusing on distribution, abundance, habitat preferences, ecology, disease susceptibility, and dietary habits of the species. In one year we identified 71 individuals at different stages of development in various habitats, with a significant presence in agricultural mosaic areas and locations near water sources used for crop irrigation, demonstrating the persistence of the species in a complex landscape, with considerable human intervention. The dietary analysis based on fecal samples indicated a diverse prey selection, primarily comprising arthropods such as Acari, Coleoptera, and ants. Amphibian declines have been associated with diseases and climate change; notably, our study confirmed the presence of the pathogen (), but, surprisingly, none of the infected Jambatos displayed visible signs of illness. When analyzing climatic patterns, we found that there are climatic differences between historical localities and Angamarca; the temporal analysis also exposes a generalized warming trend. Finally, in collaboration with the local community, we developed a series of management recommendations for terrestrial and aquatic environments occupied by the Jambato.
Topics: Animals; Ecuador; Bufonidae; Ecosystem; Batrachochytrium; Conservation of Natural Resources
PubMed: 38915382
DOI: 10.7717/peerj.17344 -
Scientific Reports Jun 2024Reintroduction efforts are increasingly used to mitigate biodiversity losses, but are frequently challenged by inadequate planning and uncertainty. High quality...
Reintroduction efforts are increasingly used to mitigate biodiversity losses, but are frequently challenged by inadequate planning and uncertainty. High quality information about population status and threats can be used to prioritize reintroduction and restoration efforts and can transform ad hoc approaches into opportunities for improving conservation outcomes at a landscape scale. We conducted comprehensive environmental DNA (eDNA) and visual encounter surveys to determine the distribution of native and non-native aquatic species in two high-priority watersheds to address key uncertainties-such as the distribution of threats and the status of existing populations-inherent in restoration planning. We then used these occurrence data to develop a menu of potential conservation actions and a decision framework to benefit an endangered vertebrate (foothill yellow-legged frog, Rana boylii) in dynamic stream systems. Our framework combines the strengths of multiple methods, allowing managers and conservation scientists to incorporate conservation science and site-specific knowledge into the planning process to increase the likelihood of achieving conservation goals.
Topics: Animals; Conservation of Natural Resources; Rivers; DNA, Environmental; Biodiversity; Endangered Species; Ecosystem; Ranidae
PubMed: 38906892
DOI: 10.1038/s41598-024-64612-5 -
PloS One 2024Predicting and explaining species occurrence using environmental characteristics is essential for nature conservation and management. Species distribution models...
BACKGROUND
Predicting and explaining species occurrence using environmental characteristics is essential for nature conservation and management. Species distribution models consider species occurrence as the dependent variable and environmental conditions as the independent variables. Suitable conditions are estimated based on a sample of species observations, where one assumes that the underlying environmental conditions are known. This is not always the case, as environmental variables at broad spatial scales are regularly extrapolated from point-referenced data. However, treating the predicted environmental conditions as accurate surveys of independent variables at a specific point does not take into account their uncertainty.
METHODS
We present a joint hierarchical Bayesian model where models for the environmental variables, rather than a set of predicted values, are input to the species distribution model. All models are fitted together based only on point-referenced observations, which results in a correct propagation of uncertainty. We use 50 plant species representative of the Dutch flora in natural areas with 8 soil condition predictors taken during field visits in the Netherlands as a case study. We compare the proposed model to the standard approach by studying the difference in associations, predicted maps, and cross-validated accuracy.
FINDINGS
We find that there are differences between the two approaches in the estimated association between soil conditions and species occurrence (correlation 0.64-0.84), but the predicted maps are quite similar (correlation 0.82-1.00). The differences are more pronounced in the rarer species. The cross-validated accuracy is substantially better for 5 species out of the 50, and the species can also help to predict the soil characteristics. The estimated associations tend to have a smaller magnitude with more certainty.
CONCLUSION
These findings suggests that the standard model is often sufficient for prediction, but effort should be taken to develop models which take the uncertainty in the independent variables into account for interpretation.
Topics: Bayes Theorem; Soil; Plants; Ecosystem; Netherlands; Models, Biological; Conservation of Natural Resources; Environment
PubMed: 38905294
DOI: 10.1371/journal.pone.0304942 -
ELife Jun 2024Comprehensive biodiversity data is crucial for ecosystem protection. The mobile app, launched in Japan, efficiently gathers species observations from the public using...
Comprehensive biodiversity data is crucial for ecosystem protection. The mobile app, launched in Japan, efficiently gathers species observations from the public using species identification algorithms and gamification elements. The app has amassed >6 million observations since 2019. Nonetheless, community-sourced data may exhibit spatial and taxonomic biases. Species distribution models (SDMs) estimate species distribution while accommodating such bias. Here, we investigated the quality of data and its impact on SDM performance. Species identification accuracy exceeds 95% for birds, reptiles, mammals, and amphibians, but seed plants, molluscs, and fishes scored below 90%. Our SDMs for 132 terrestrial plants and animals across Japan revealed that incorporating data into traditional survey data improved accuracy. For endangered species, traditional survey data required >2000 records for accurate models (Boyce index ≥ 0.9), while blending the two data sources reduced this to around 300. The uniform coverage of urban-natural gradients by data, compared to traditional data biased towards natural areas, may explain this improvement. Combining multiple data sources better estimates species distributions, aiding in protected area designation and ecosystem service assessment. Establishing a platform for accumulating community-sourced distribution data will contribute to conserving and monitoring natural ecosystems.
Topics: Biodiversity; Animals; Smartphone; Japan; Conservation of Natural Resources; Mobile Applications; Ecosystem; Plants
PubMed: 38899444
DOI: 10.7554/eLife.93694 -
Parasitology Research Jun 2024Introduced species have a major impact on freshwater ecosystems, particularly on islands. Numerous fish species have been introduced in Corsica (Mediterranean island,...
Introduced species have a major impact on freshwater ecosystems, particularly on islands. Numerous fish species have been introduced in Corsica (Mediterranean island, southern France) as part of planned programs or clandestinely. The introduction of non-native freshwater fish species can have a range of impacts on the recipient ecosystem, including through the co-introduction of its pathogens. A sample of introduced perch Perca fluviatilis Linnaeus, 1758 from the artificial reservoir of Padula was examined following a report of parasites by an angler. The analyses revealed the occurrence of Eustrongylides sp. (Nematoda) and Clinostomum complanatum (Digenea), two zoonotic parasites in P. fluviatilis. Both parasites are reported for the first time in France. Eustrongylides sp. and C. complanatum may have been introduced with their fish intermediate hosts or through their final bird hosts. The occurrence of the two parasites raises concerns from both a veterinary and human health perspective as they can use a wide range of amphibians as intermediate hosts and can be acquired in humans through the consumption of raw or undercooked fish.
Topics: Animals; France; Fish Diseases; Perches; Introduced Species; Trematoda; Zoonoses; Trematode Infections; Islands; Humans
PubMed: 38898308
DOI: 10.1007/s00436-024-08264-4 -
Communications Biology Jun 2024DNA methylation maintenance is essential for cell fate inheritance. In differentiated cells, this involves orchestrated actions of DNMT1 and UHRF1. In mice, the...
DNA methylation maintenance is essential for cell fate inheritance. In differentiated cells, this involves orchestrated actions of DNMT1 and UHRF1. In mice, the high-affinity binding of DPPA3 to the UHRF1 PHD finger regulates UHRF1 chromatin dissociation and cytosolic localization, which is required for oocyte maturation and early embryo development. However, the human DPPA3 ortholog functions during these stages remain unclear. Here, we report the structural basis for human DPPA3 binding to the UHRF1 PHD finger. The conserved human DPPA3 VRT motif binds to the acidic surface of UHRF1 PHD finger, whereas mouse DPPA3 binding additionally utilizes two unique α-helices. The binding affinity of human DPPA3 for the UHRF1 PHD finger was weaker than that of mouse DPPA3. Consequently, human DPPA3, unlike mouse DPPA3, failed to inhibit UHRF1 chromatin binding and DNA remethylation in Xenopus egg extracts effectively. Our data provide novel insights into the distinct function and structure of human DPPA3.
Topics: Animals; Ubiquitin-Protein Ligases; Humans; CCAAT-Enhancer-Binding Proteins; Mice; Protein Binding; PHD Zinc Fingers; DNA Methylation; Chromatin; Amino Acid Sequence; Xenopus laevis
PubMed: 38898124
DOI: 10.1038/s42003-024-06434-9 -
Anais Da Academia Brasileira de Ciencias 2024The following work presents the first study applying the passive acoustic monitoring of anurans at lotic environments for a long time. This study aims to test the...
The following work presents the first study applying the passive acoustic monitoring of anurans at lotic environments for a long time. This study aims to test the efficiency of the passive acoustic monitoring method and active monitoring in detecting anurans in lotic environments of Itinguçu State Park. Specifically, we tested whether species richness differs when comparing active and passive monitoring surveys. Therefore, this study aims to test the efficiency of the passive acoustic monitoring method and active monitoring in detecting anurans in lotic environments of the Itinguçu State Park. The passive acoustic monitoring period was 72 uninterrupted hours at each collection point with intervals of 45 days. Finally, species richness was calculated, and the efficiency of the methods was compared in different scenarios. Our results demonstrated that the park has species that vocalize day and night, but most at night, there is overlapping acoustic niche; waterfall environments harm the quality of recordings; and in lotic environments the active monitoring method was more efficient than the passive acoustic monitoring in all sampling scales. Although the passive acoustic monitoring was not as efficient in a low temporal scale, it tends to increase in efficiency with longer sampling duration.
Topics: Animals; Peru; Acoustics; Anura; Parks, Recreational; Environmental Monitoring; Vocalization, Animal; Biodiversity
PubMed: 38896695
DOI: 10.1590/0001-3765202420231057 -
Molecules (Basel, Switzerland) May 2024With the global population on the rise, an escalating interest exists in environmentally sustainable and friendly protein sources. Insects have emerged as multifaceted...
With the global population on the rise, an escalating interest exists in environmentally sustainable and friendly protein sources. Insects have emerged as multifaceted resources, viewed not only as potential food items, but also as sources of traditional medicines and proteins. This study utilized response surface methodology (RSM) to ascertain the optimal extraction conditions for proteins from used in toad feeding, denoted as MDPs-T. The yield of MDPs-T was elevated to 18.3% ± 0.2% under these optimized conditions. Subsequently, the particle size, ζ-potentials, and structures of MDPs-T were analyzed and compared with the proteins derived from fed on a normal diet (MDPs-ND). This comparative analysis utilized a range of advanced techniques, involving UV spectroscopy, Fourier transform infrared spectroscopy (FT-IR), X-ray diffraction (XRD), high-performance gel permeation chromatography (HPGPC), and scanning electron microscopy (SEM). The outcomes have revealed a marginal disparity in the physical and chemical properties between MDPs-T and MDPs-ND. Derosination led to a reduction in the particle size of the MDPs by 10.98% to 62.81%. MDPs-T exhibited a higher proportion of low-molecular-weight components relative to MDPs-ND. Additionally, in a comparative analysis of amino acids, MDPs-T displayed a greater abundance of essential and total amino acids relative to MDPs-ND. Consequently, MDPs-T holds potential as a valuable food supplement for human consumption or as a nutrient-rich feed supplement for animals.
Topics: Animals; Houseflies; Insect Proteins; Larva; Spectroscopy, Fourier Transform Infrared; Bufonidae; X-Ray Diffraction; Particle Size; Animal Feed
PubMed: 38893470
DOI: 10.3390/molecules29112595 -
International Journal of Molecular... May 2024Extreme weather poses huge challenges for animals that must adapt to wide variations in environmental temperature and, in many cases, it can lead to the local...
Extreme weather poses huge challenges for animals that must adapt to wide variations in environmental temperature and, in many cases, it can lead to the local extirpation of populations or even the extinction of an entire species. Previous studies have found that one element of amphibian adaptation to environmental stress involves changes in mitochondrial gene expression at low temperatures. However, to date, comparative studies of gene expression in organisms living at extreme temperatures have focused mainly on nuclear genes. This study sequenced the complete mitochondrial genomes of five Asian hylid frog species: , , , and . It compared the phylogenetic relationships within the Hylidae family and explored the association between mitochondrial gene expression and evolutionary adaptations to cold stress. The present results showed that in , transcript levels of 12 out of 13 mitochondria genes were significantly reduced under cold exposure ( < 0.05); hence, we put forward the conjecture that . adapts by entering a hibernation state at low temperature. In , the transcripts of 10 genes (, , , , , , , , and ) were significantly reduced in response to cold exposure, and five mitochondrial genes in (, , , and ) also showed significantly reduced expression and transcript levels under cold conditions. By contrast, transcript levels of and in . were significantly increased at low temperatures, possibly related to the narrow distribution of this species primarily at low latitudes. Indeed, has little ability to adapt to low temperature (4 °C), or maybe to enter into hibernation, and it shows metabolic disorder in the cold. The present study demonstrates that the regulatory trend of mitochondrial gene expression in amphibians is correlated with their ability to adapt to variable climates in extreme environments. These results can predict which species are more likely to undergo extirpation or extinction with climate change and, thereby, provide new ideas for the study of species extinction in highly variable winter climates.
Topics: Animals; Genome, Mitochondrial; Anura; Phylogeny; Cold-Shock Response; Cold Temperature; Adaptation, Physiological; Gene Expression Regulation
PubMed: 38892163
DOI: 10.3390/ijms25115967