Search Results (90)

From a One Health perspective, the Ría de Vigo (NW Spain) represents a complex socio-ecological system where urban, industrial, and aquaculture activities converge, creating vulnerabilities due to the interconnection between human, animal, and environmental health. This study evaluates the utility of a multi-marker environmental DNA (eDNA) metabarcoding approach as an early warning tool to detect potentially harmful eukaryotic pathogens near wastewater discharge points in three distinct municipalities of the Ría de Vigo. Water and sediment samples were analyzed using the V4 and V9 regions of the 18S rRNA gene and the ITS-2 region for fungi. Bioinformatics analysis was performed with DADA2 and taxonomic assignments were based on SILVA and UNITE databases. Eukaryotic diversity varied by site and marker, with the highest richness found in inner estuary sediments. The V9 region provided broader taxonomic coverage, while V4 produced higher read abundances. Putative pathogens, including human, zoonotic, and aquaculture-related taxa, were more prevalent in inner estuarine zones. Pathogens such as Rhodotorula mucilaginosa, Acanthamoeba sp., Cryptosporidium sp., and harmful algae (HA) were detected. The findings emphasize the importance of a multi-marker strategy, sediment inclusion, and landscape-scale variables to improve early pathogen detection, contributing to effective eDNA-based surveillance systems for coastal health management. Full article

Multiple invasive plants (IPS) can coexist in the same community. The intensity of interspecific interactions among multiple plants may progressively alter with the differences in the species number of IPS (S_i) under different invasion scenarios. However, the correlation between plant taxonomic diversity, S_i, the invasion intensity of IPS, the community invasibility and the intensity of interspecific interactions among multiple plants under different invasion scenarios remains unclear. This study aims to estimate the differences in the intensity of interspecific interactions among multiple plants, the taxonomic diversity of plants, the invasion intensity of IPS and the invasibility of the plant community under different invasion scenarios along a gradient of S_i. This study used a comparative field survey method in four cities in Jiangsu (including Lianyungang, Yancheng, Nantong and Zhenjiang), China. The species number of plants and plant richness decreased under the mono-invasion achieved by one IP compared to the uninvaded communities. Plant taxonomic diversity was negatively associated with the invasion intensity of IPS and the community invasibility. Plant taxonomic diversity was positively associated with S_i. The intensity of interspecific interactions among multiple plants decreased across all invasion scenarios. The intensity of interspecific interactions among multiple plants showed a significant positive association with the ratio of the max and min relative coverage of all plants, but a significant negative association with plant evenness. Therefore, the ratio of the max and min relative coverage of all plants and plant evenness may be the main factor regulating the intensity of interspecific interactions among multiple plants under different invasion scenarios, rather than S_i. Full article

Retrogressive succession alters soil conditions and microbial community dynamics in cold-region wetlands, yet its ecological implications remain understudied. This study explored the structure and function of soil microbial communities across three successional stages: swamp (SP), swamped meadow (SM), and meadow (MW). High-throughput 16S rRNA gene sequencing identified 2852 operational taxonomic units (OTUs), with 1682 shared among all stages (58.85%). Alpha diversity indices, including Shannon, Chao, ACE, and Sobs, were significantly higher in MW, with the Shannon index increasing by approximately 32% compared to SP, indicating enhanced richness and evenness. In contrast, Simpson and Coverage indices were highest in SP. Proteobacteria, Actinobacteriota, and Acidobacteriota were dominant phyla, showing distinct distributions across stages. Beta diversity analysis (PCoA and NMDS) revealed clear separation of microbial communities. Soil organic carbon (SOC), pH, soil water content (SWC), cation exchange capacity (CEC), and bulk density (BD) significantly influenced microbial composition and distribution. Functional prediction using FAPROTAX and BugBase indicated a shift from anaerobic metabolism, nitrogen fixation, and cellulolysis in the SP to aerobic chemoheterotrophy and stress tolerance in MW. These results demonstrate that microbial communities adapt to changing soil environments during retrogressive succession, highlighting their role in ecosystem function and resilience in cold-region wetlands. Full article

The superfamily Tellinoidea is one of the most diverse groups of marine bivalves, with significant ecological and economic value. To date, the availability of complete mitochondrial genome data within Tellinoidea remains limited, and the taxonomic coverage is still insufficient to resolve its internal controversies. The current study aims to further explore the phylogenetic relationships within Tellinoidea through denser sampling. We have newly sequenced the mitochondrial genomes of 13 species, among which seven genera are being published for the first time. Combined with the published mitogenomes and transcriptomic data, we constructed the most comprehensive Tellinoidea phylogeny to date through maximum likelihood and Bayesian Inference analyses. Our findings support the monophyly of the superfamily Tellinoidea, with Semelidae nesting as a monophyletic group within Tellinidae. We also support the paraphyly of Tellinidae based on the mitochondrial genome data for the first time, identifying that the two subfamilies (Macominae and Tellininae) are polyphyletic. Gene rearrangement analysis reveals a relatively high degree of variation in Semelidae. By expanding the mitochondrial genome dataset, this study provides new insights into the phylogeny of Tellinoidea and underscores the need for further sampling of species to reassess the phylogenetic relationships of Tellinidae and the entire Tellinoidea. Full article

Coral reef and their ecological services of food production and shoreline protection are threatened by unsustainable use. To better understand their status, multiple approaches to estimating fisheries sustainability were compared, namely fisheries-independent stock biomass and recovery rates, fisheries-dependent landed catches, balanced harvest and gear use metrics, and fish length measurements. A community biomass recovery was established over a 45-year no-fishing stock recovery time series from seven fisheries reserves and compared to catch- and length-based estimates of sustainability. The logistic production rates (r = 0.09 ± 0.06 95% confidence interval (CI)) and maximum equilibrium total biomass (~150 ± 30 tons/km²) indicated a broad range of potential maximum sustainable yields, with a likely range of 1.1 to 3.9 (95% CI; mean = 3.8) tons/km²/year. In contrast, the mean annual linear biomass growth rates in reserves were lower but less variable than logistic surplus production estimates, ranging from 2.1 to 3.5 (mean = 2.8 tons/km²/year). Realized catches at landing sites were lower still, ranging from 1.43 to 1.52 (mean = 1.48 ± 0.2 tons/km²/y). Differences between production estimates and capture were largely attributable to changes in taxonomic composition and an imbalance in the estimated proportionality of production potential versus actual capture rates. Lost potential capture was likely due to differences in the vulnerability of taxa to fishing and a lack of compensatory increased production among fishing-resistant taxa. Large proportional losses of catch were measured among snappers, unicorn fish, sweetlips, goatfish, and soldierfish, while smaller proportional gains in the catch samples were found among resident herbivorous rabbitfish, parrotfish, and groupers. Many of these declining taxa have vulnerable schooling life histories that are likely to require special habitat and reserve characteristics. Evaluations of sustainability from length measurements found 17 or 7% of total and 12% of caught species had sample sizes minimally sufficient for evaluation (>30 individuals from 413 catches, 2284 captured individuals composed of 144 species) of length and spawning metrics of sustainability. Seven of these species met length-based and three met spawning potential ratio thresholds for sustainability. Consequently, length-based evaluations had poor species coverage and therefore we were unable to evaluate the sustainability of the larger fish community. Recommendations for future research include a better understanding of the consequences of variability in spillover and proportionality of production potential for sustainability. Management recommendations are to focus management on the recovery of species abundant in unfished locations but not contributing to fisheries yield. Full article

This study investigates the effects on hard-bottom macro-zoobenthic communities of converting a mariculture plant into an Integrated Multi-Trophic Aquaculture (IMTA) system. This study was conducted from 2018 to 2021 in the semi-enclosed Mar Grande basin of Taranto (northern Ionian Sea), on a facility located 600 m off the coastline, with a production capacity of 100 tons per year of seabass (Dicentrarchus labrax) and seabream (Sparus aurata). The results from seasonal sampling performed in a treatment site, where bioremediators (filter-feeding invertebrates such as sponges, polychaetes, mussels, and macroalgae) were deployed, and a control site without bioremediators were compared. Before the IMTA installation, the hard substrates under the cages were sparsely inhabited, with significant sediment coverage. By 2021, the treatment site exhibited revitalized and more diverse macro-zoobenthic communities, with species richness increasing from 83 taxa in 2018 to 104 taxa, including notable growth in sponges, annelids, mollusks, and bryozoans. In contrast, the control site showed no substantial changes in biodiversity over the same period. Biodiversity indices, including Shannon and Margalef indices, improved significantly at the treatment site, particularly during summer months, highlighting a more resilient and balanced benthic environment. Taxonomic distinctness (delta+) and multivariate analyses (PERMANOVA, PCO) confirmed significant spatial and temporal shifts in community structure at the treatment site, driven by IMTA implementation. SIMPER analysis identified key taxa contributing to these changes, which played a pivotal role in structuring the community. The emergence of filter feeders, predators, and omnivores at the treatment site suggests enhanced nutrient cycling and trophic complexity, while the decline in opportunistic species further supports improved environmental conditions. These findings demonstrate the potential of IMTA to promote recovery and sustainable mariculture practices, also offering a comprehensive understanding of its positive effects on hard-bottom benthic community dynamics. Full article

Cultural ecosystem services provide intangible benefits such as recreation and aesthetic enjoyment but are difficult to quantify compared to provisioning or regulating ecosystem services. Recent technologies offer alternative indicators, such as social media data, to identify popular locations and their features. This study demonstrates how large volumes of citizen science and social media data can be analyzed to reveal patterns of human interactions with nature through unconventional, scalable methods. By applying spatial statistical methods, data from the citizen science platform iNaturalist are analyzed and compared with ground-truth visitation data. To minimize data bias, records are grouped by taxonomic information and applied to the metropolitan area of Seoul, South Korea (2005–2022). The taxonomic information included in the iNaturalist data were investigated using a standard global biodiversity database. The results show citizen science data effectively quantify public preferences for scenic locations, offering a novel approach to mapping cultural ecosystem services when traditional data are unavailable. This method highlights the potential of large-scale citizen-generated data for conservation, urban planning, and policy development. However, challenges like bias in user-generated content, uneven ecosystem coverage, and the over- or under-representation of locations remain. Addressing these issues and integrating additional metadata—such as time of visit, demographics, and seasonal trends—could provide deeper insights into human–nature interactions. Overall, the proposed method opens up new possibilities for using non-traditional data sources to assess and map ecosystem services, providing valuable information for conservation efforts, urban planning, and environmental policy development. Full article

The liverwort flora in Zov Tigra National Park in southern Sikhote-Alin (Primorye Territory, south of the Russian Far East), which has one of the richest regional floras, was studied to assess its taxonomic diversity, and analyzed using a new approach to determine altitudinal distribution patterns. This new approach is based on probabilistic models of the altitudinal distribution of individual taxa proposed for identifying altitudinal groups of species. This method can be used to analyze patterns of the distribution of species of various taxonomic groups in cases where a sufficiently representative dataset is available and may be especially relevant in regions where altitudinal zonation is not obvious or changes in the altitudinal fractions of the dominant vegetation are too continuous. The proposed method revealed three altitudinal groups that were more clearly differentiated than groups of taxa based on altitudinal vegetation belts. Based on the obtained results, the most important bioclimatic indices correlated with the altitudinal distribution of liverworts were identified: annual mean temperature (BIO1), annual precipitation (BIO12), isothermality (BIO3), and factors associated with the temperature and amount of precipitation during the warmest period of the year, including the maximum temperature of the warmest month (BIO5), the mean temperature of the wettest quarter (BIO8), the mean temperature of the warmest quarter (BIO10), precipitation during the wettest month (BIO13), precipitation during the wettest quarter (BIO16), and precipitation during the warmest quarter (BIO18). This study reports 130 species, 1 variety, and 1 subspecies. Pseudolophozia debiliformis and Scapania praetervisa are newly recorded for Sikhote-Alin and the Primorye Territory. Diplophyllum albicans and Cephaloziella rubella are newly reported for the Primorye Territory. The national park liverwort flora can be classified as boreal–temperate circumpolar–East Asian. Given the high taxonomic diversity and coverage of all altitudinal zones represented in the region, the liverwort flora in Zov Tigra National Park can serve as a model for all liverwort floras in southern Sikhote-Alin. Full article

Background/Objectives: This study explores the genome sequencing data from the infection of Pseudomonas fluorescens UFV 041 by the bacteriophage Pijolavirus UFJF_PfSW6, aiming to identify and characterize prophages induced in the host bacterium during the infection. Methods: Scaffolds from sequencing data were analyzed, and reads were mapped to identify potential prophages using phage-to-host coverage metrics. The putative prophage scaffold was annotated, taxonomically classified, and its integration in the host bacterium was verified by PCR amplification of two target genes. We also tested whether mitomycin treatment could induce the prophage to enter the lytic cycle. Results: The prophage UFJF_PfPro was identified with a high phage-to-host coverage ratio. Its genome is 32,700 bp in length, containing 42 genes, 3 terminators, and 11 promoters, with 98.84% completeness. PCR confirmed its integration into P. fluorescens UFV 041, but mitomycin treatment did not induce the lytic cycle. The UFJF_PfPro genome shares 38.60% similarity with the closest lytic phages in the Phitrevirus genus, below genus and species assignment thresholds. A viral proteomic tree clustered UFJF_PfPro with Phitrevirus in a clade representing the Peduoviridae family. Conclusions: The UFJF_PfPro is a prophage integrated into the P. fluorescens UFV 041 genome, but we were unable to induce it to enter the lytic cycle using mitomycin treatment. The genome of UFJF_PfPro encodes all structural proteins typical of the Caudoviricetes class and shares low genomic similarity with species of the genus Phitrevirus, suggesting that UFJF_PfPro represents a new genus and species within the Peduoviridae family. Full article

Coastal areas support seagrass meadows, which offer crucial ecosystem services, including erosion control and carbon sequestration. However, these areas are increasingly impacted by human activities, leading to habitat fragmentation and seagrass decline. In situ surveys, traditionally performed to monitor these ecosystems, face limitations on temporal and spatial coverage, particularly in intertidal zones, prompting the addition of satellite data within monitoring programs. Yet, satellite remote sensing can be limited by too coarse spatial and/or spectral resolutions, making it difficult to discriminate seagrass from other macrophytes in highly heterogeneous meadows. Drone (unmanned aerial vehicle—UAV) images at a very high spatial resolution offer a promising solution to address challenges related to spatial heterogeneity and the intrapixel mixture. This study focuses on using drone acquisitions with a ten spectral band sensor similar to that onboard Sentinel-2 for mapping intertidal macrophytes at low tide (i.e., during a period of emersion) and effectively discriminating between seagrass and green macroalgae. Nine drone flights were conducted at two different altitudes (12 m and 120 m) across heterogeneous intertidal European habitats in France and Portugal, providing multispectral reflectance observation at very high spatial resolution (8 mm and 80 mm, respectively). Taking advantage of their extremely high spatial resolution, the low altitude flights were used to train a Neural Network classifier to discriminate five taxonomic classes of intertidal vegetation: Magnoliopsida (Seagrass), Chlorophyceae (Green macroalgae), Phaeophyceae (Brown algae), Rhodophyceae (Red macroalgae), and benthic Bacillariophyceae (Benthic diatoms), and validated using concomitant field measurements. Classification of drone imagery resulted in an overall accuracy of 94% across all sites and images, covering a total area of 467,000 m². The model exhibited an accuracy of 96.4% in identifying seagrass. In particular, seagrass and green algae can be discriminated. The very high spatial resolution of the drone data made it possible to assess the influence of spatial resolution on the classification outputs, showing a limited loss in seagrass detection up to about 10 m. Altogether, our findings suggest that the MultiSpectral Instrument (MSI) onboard Sentinel-2 offers a relevant trade-off between its spatial and spectral resolution, thus offering promising perspectives for satellite remote sensing of intertidal biodiversity over larger scales. Full article

Aquatic biodiversity includes a variety of unique species, their habitats, and their interactions with each other. Albania has a large hydrographic network including rivers, lakes, wetlands and coastal marine areas, contributing to a high level of aquatic biodiversity. Currently, evaluating aquatic biodiversity relies on morphological species identification methods, but DNA-based taxonomic identification could improve the monitoring and assessment of aquatic ecosystems. This study aims to evaluate the coverage of COI DNA barcodes in the reference libraries for the known aquatic animal species present in the coastal lagoons of Albania. In this study, the six most studied coastal lagoons of Albania were selected. Species data were gathered from the scientific literature and publicly available sites and studies. The collected species lists were taxonomically standardised using global public taxonomic databases like WORMS. The standardised lists were used to analyse the barcode gap of COI based on two public DNA barcode libraries: Barcode of Life Data Systems (BOLD) and NCBI GenBank. The results show that the COI DNA barcode gap in the coastal lagoons of Albania ranges from 7% (Lagoon of Patok) to 33% (Karavasta Lagoon). Fishes and Amphibia represent the groups with the lowest barcode gap (8% each), while Annelida shows the highest (47%). In conclusion, the COI gene marker for DNA-based biodiversity assessments is reliable for the coastal lagoons of Albania. Full article

The dry forests of southern Ecuador are characterized by a great floristic variety and high endemism rates in different taxonomic groups; however, these forests are disappearing at an alarming rate due to anthropogenic disturbances. Epiphytic cryptogams (bryophytes and lichens) are important in seasonally dry tropical forests (SDTFs) and, due to their physiology (poikilohydric species), are sensitive to the changes associated with specific human disturbances. We examined the response of epiphytic cryptogams to habitat disturbance in SDTFs (natural and semi-natural forests) by registering the frequency and coverage of epiphytic cryptogams on 182 trees. We recorded a total of 53 epiphytic cryptogams (47 lichens and 6 bryophytes). A greater number of species was found in the natural forest, with 51 species, than the semi-natural forests (DFs), which had 45 species. We found that total richness tended to decrease with increased intensity of disturbance. The impoverishment was particularly related to the reduction in tree density and diversity (e.g., selective logging) in semi-natural compared to natural forests. However, the epiphytic composition showed little relationship with forests disturbance. We conclude that anthropic disturbance, particularly selective logging, are the main factors affecting the diversity of epiphytic cryptogams in the SDTFs from southern Ecuador. Full article

Anguimorpha, within the order Squamata, represents a group with distinct morphological and behavioral characteristics in different ecological niches among lizards. Within Anguimorpha, there is a group characterized by limb loss, occupying lower ecological niches, concentrated within the subfamily Anguinae. Lizards with limbs and those without exhibit distinct locomotor abilities when adapting to their habitats, which in turn necessitate varying degrees of energy expenditure. Mitochondria, known as the metabolic powerhouses of cells, play a crucial role in providing approximately 95% of an organism’s energy. Functionally, mitogenomes (mitochondrial genomes) can serve as a valuable tool for investigating potential adaptive evolutionary selection behind limb loss in reptiles. Due to the variation of mitogenome structures among each species, as well as its simple genetic structure, maternal inheritance, and high evolutionary rate, the mitogenome is increasingly utilized to reconstruct phylogenetic relationships of squamate animals. In this study, we sequenced the mitogenomes of two species within Anguimorpha as well as the mitogenomes of two species in Gekkota and four species in Scincoidea. We compared these data with the mitogenome content and evolutionary history of related species. Within Anguimorpha, between the mitogenomes of limbless and limbed lizards, a branch-site model analysis supported the presence of 10 positively selected sites: Cytb protein (at sites 183 and 187), ND2 protein (at sites 90, 155, and 198), ND3 protein (at site 21), ND5 protein (at sites 12 and 267), and ND6 protein (at sites 72 and 119). These findings suggested that positive selection of mitogenome in limbless lizards may be associated with the energy requirements for their locomotion. Additionally, we acquired data from 205 mitogenomes from the NCBI database. Bayesian inference (BI) and Maximum Likelihood (ML) trees were constructed using the 13 mitochondrial protein-coding genes (PCGs) and two rRNAs (12S rRNA and 16S rRNA) from 213 mitogenomes. Our phylogenetic tree and the divergence time estimates for Squamata based on mitogenome data are consistent with results from previous studies. Gekkota was placed at the root of Squamata in both BI and ML trees. However, within the Toxicofera clade, due to long-branch attraction, Anguimorpha and (Pleurodonta + (Serpentes + Acrodonta)) were closely related groupings, which might indicate errors and also demonstrate that mitogenome-based phylogenetic trees may not effectively resolve long-branch attraction issues. Additionally, we reviewed the origin and diversification of Squamata throughout the Mesozoic era, suggesting that Squamata originated in the Late Triassic (206.05 Mya), with the diversification of various superfamilies occurring during the Cretaceous period. Future improvements in constructing squamate phylogenetic relationships using mitogenomes will rely on identifying snake and acrodont species with slower evolutionary rates, ensuring comprehensive taxonomic coverage of squamate diversity, and increasing the number of genes analyzed. Full article

Herbaria constitute a form of documentation, store and secure comparative material, as well as constitute an extra original gene bank. They are an invaluable database among others for the biological, ethnobotanical and agricultural sciences. The digitization of herbarium collections significantly facilitates access to archival materials; however, searching them is still time-consuming. Therefore, our work aims to analyze the herbarium collection of 8801 sheets for specimens representing the economically important family Amaranthaceae (Chenopodiaceae-Amaranthaceae clade) deposited the oldest herbarium in Poland, the herbarium of the Jagiellonian University (KRA). These specimens have been collected from almost all the continents in dozens of countries for over 200 years. The analyses conducted, including the taxonomic coverage, geographical characteristics and origin, temporal coverage and utility importance of representative species, present the discussed resources in a more accessible way and may become a more attractive form for scientists potentially interested in more advanced research work. Full article

Raw milk and dairy products can serve as potential vectors for transmissible bacterial, viral and protozoal diseases, alongside harboring antimicrobial-resistance genes. This study monitors the changes in the antimicrobial-resistance gene pool in raw milk and cheese, from farm to consumer, utilizing next-generation sequencing. Five parallel sampling runs were conducted to assess the resistance gene pool, as well as phage or plasmid carriage and potential mobility. In terms of taxonomic composition, in raw milk the Firmicutes phylum made up 41%, while the Proteobacteria phylum accounted for 58%. In fresh cheese, this ratio shifted to 93% Firmicutes and 7% Proteobacteria. In matured cheese, the composition was 79% Firmicutes and 21% Proteobacteria. In total, 112 antimicrobial-resistance genes were identified. While a notable reduction in the resistance gene pool was observed in the freshly made raw cheese compared to the raw milk samples, a significant growth in the resistance gene pool occurred after one month of maturation, surpassing the initial gene frequency. Notably, the presence of extended-spectrum beta-lactamase (ESBL) genes, such as OXA-662 (100% coverage, 99.3% identity) and OXA-309 (97.1% coverage, 96.2% identity), raised concerns; these genes have a major public health relevance. In total, nineteen such genes belonging to nine gene families (ACT, CMY, EC, ORN, OXA, OXY, PLA, RAHN, TER) have been identified. The largest number of resistance genes were identified against fluoroquinolone drugs, which determined efflux pumps predominantly. Our findings underscore the importance of monitoring gene pool variations throughout the product pathway and the potential for horizontal gene transfer in raw products. We advocate the adoption of a new approach to food safety investigations, incorporating next-generation sequencing techniques. Full article