Search Results (50)

Madagascar harbors a rich marine biodiversity, yet detailed knowledge of its fish species remains limited. Of the 1689 species listed in 2018, only 22% had accessible cytochrome oxidase I (COI) sequences in public databases. In response to growing pressure on fishery resources, this study aims to strengthen biodiversity monitoring tools. Its objectives were to enrich the COI database for Malagasy marine fishes, create the first 12S reference library, and evaluate the taxonomic resolution of different 12S metabarcodes for eDNA analysis, namely MiFish, Teleo1, AcMDB, Ac12S, and 12SF1/R1. An integrated approach combining morphological, molecular, and phylogenetic analyses was applied for specimen identification of fish captured using various types of fishing gear in Toliara and Ranobe Bays from 2018 to 2023. The Malagasy COI database now includes 2146 sequences grouped into 502 Barcode Index Numbers (BINs) from 82 families, with 14 BINs newly added to BOLD (The Barcode of Life Data Systems), and 133 cryptic species. The 12S library comprises 524 sequences representing 446 species from 78 families. Together, the genetic datasets cover 514 species from 84 families, with the most diverse being Labridae, Apogonidae, Gobiidae, Pomacentridae, and Carangidae. However, the two markers show variable taxonomic resolution: 67 species belonging to 35 families were represented solely in the COI dataset, while 10 species from nine families were identified exclusively in the 12S dataset. For 319 species with complete 12S gene sequences associated with COI BINs (Barcode Index Numbers), 12S primer sets were used to evaluate the taxonomic resolution of five 12S metabarcodes. The MiFish marker proved to be the most effective, with an optimal similarity threshold of 98.5%. This study represents a major step forward in documenting and monitoring Madagascar’s marine biodiversity and provides a valuable genetic reference for future environmental DNA (eDNA) applications. Full article

Background: The passion fruit (Passiflora edulis Sims) is a diploid plant (2n = 2x = 18) and is a perennial scrambling vine in Southern China. However, the occurrence and spread of stem rot in passion fruit severely impact its yield and quality. Methods: In this study, we re-sequenced a BC₁F₁ population consisting of 158 individuals using whole-genome resequencing. We constructed a high-density genetic linkage map and identified the quantitative trait locus (QTL), and analyzed candidate genes associated with stem rot resistance in passion fruit. Results: Based on the passion fruit reference genome (MER), a high-density genetic linkage map was constructed with 1,180,406 single nucleotide polymorphisms (SNPs). The map contains nine linkage groups, covering a total genetic distance of 1559.03 cM, with an average genetic distance of 311.81 cM. The average genetic distance between 4206 bins was 0.404 cM, and the average gap length was 10.565 cM. The collinearity correlation coefficient between the genetic map and the passion fruit genome was 0.9994. Fusarium solani was used to infect the BC₁F₁ population, and the resistance to stem rot showed a continuous distribution. A QTL, qPSR5, was mapped to the 113,377,860 bp–114,811,870 bp genomic region on chromosome 5. We performed RNA sequencing (RNA-seq) and real-time quantitative polymerase chain reaction (RT-qPCR) to analyze the expression levels of predicted genes in the candidate region and identified ZX.05G0020740 and ZX.05G0020810 as ideal candidate genes for stem rot resistance in passion fruit. Conclusions: The findings in this study not only lay the foundation for cloning the qPSR5 responsible for stem rot resistance but also provide genetic resources for the genetic improvement of passion fruit. Full article

Prince Mohammed bin Salman Royal Reserve (PMBSRR or the Reserve) is located in the northwest of Saudi Arabia and covers an area of 24,500 km² of both marine and terrestrial ecosystems. Bat surveys have been undertaken between 2022 and 2024 across PMBSRR as part of the Reserve’s groundbreaking conservation efforts and this is the first published checklist of the bat species present within the Reserve. Survey methods included bat capture, roost inspection, and acoustic recordings. Tissue and faecal samples were taken during the surveys and compared to a global database to confirm the species present. The survey results confirmed the presence of 18 species belonging to 14 genera of eight families. This research has greatly expanded our knowledge on the diversity of bats within the Kingdom, increasing the reported bat species in the Tabuk region by seven species, with the addition of Rhyneptesicus nasutus, Rhinolophus hipposideros, Nycteris thebaica, Tadarida aegyptiaca, Rhinopoma microphyllum, Taphozous nudiventris, and Taphozous perforatus and increasing the number of species within Saudi Arabia by one species, with the addition of Vansonia rueppellii. Full article

We used WRF-Chem to simulate ash transport from eruptions of Chile’s Calbuco volcano on 22–23 April 2015. Massive ash and SO₂ ejections reached the upper troposphere, and particulates transported over South America were observed over Argentina, Uruguay, and Brazil via satellite and surface data. Numerical simulations with the coupled Weather Research and Forecasting–Chemistry (WRF-Chem) model from 22 to 27 April covered eruptions and particle propagation. Chemical and aerosol parameters utilized the GOCART (Goddard Chemistry Aerosol Radiation and Transport) model, while the meteorological conditions came from NCEP-FNL reanalysis. In WRF-Chem, we implemented a more efficient methodology to determine the Eruption Source Parameters (ESP). This permitted each simulation to consider a sequence of eruptions and a time varying ESP, such as the eruption height and mass and the SO₂ eruption rate. We used two simulations (GCTS1 and GCTS2) differing in the ash mass fraction in the finest bins (0–15.6 µm) by 2.4% and 16.5%, respectively, to assess model efficiency in representing plume intensity and propagation. Analysis of the active synoptic components revealed their impact on particle transport and the Andes’ role as a natural barrier. We evaluated and compared the simulated Aerosol Optical Depth (AOD) with VIIRS Deep Blue Level 3 data and SO₂ data from Ozone Mapper and Profiler Suite (OMPS) Limb Profiler (LP), both of which are sensors onboard the Suomi National Polar Partnership (NPP) spacecraft. The model successfully reproduced ash and SO₂ transport, effectively representing influencing synoptic systems. Both simulations showed similar propagation patterns, with GCTS1 yielding better results when compared with AOD retrievals. These results indicate the necessity of specifying lower mass fraction in the finest bins. Comparison with VIIRS Brightness Temperature Difference data confirmed the model’s efficiency in representing particle transport. Overestimation of SO₂ may stem from emission inputs. This study demonstrates the feasibility of our implementation of the WRF-Chem model to reproduce ash and SO₂ patterns after a multi-eruption event. This enables further studies into aerosol–radiation and aerosol–cloud interactions and atmospheric behavior following volcanic eruptions. Full article

Soil erosion within agricultural landscapes has significant environmental and economic impacts and is strongly driven by reduced residue cover in agricultural fields. Large-area soil erosion models such as the Daily Erosion Project are important tools for understanding the patterns of soil erosion, but they rely on the accurate estimation of crop residue cover over large regions to infer the tillage practices, an erosion model input. Remote sensing analyses are becoming accepted as a reliable way to estimate crop residue cover, but most use localized training datasets that may not scale well outside small study areas. An alternative source of training data may be commonly conducted tillage surveys that capture information via rapid “windshield” surveys. In this study, we utilized the Google Earth Engine to assess the utility of three crop residue survey types (windshield tillage surveys, windshield binned residue surveys, and photo analysis surveys) and one synthetic survey (retroactively binned photo analysis data) as sources of training data for crop residue cover regressions. We found that neither windshield-based survey method was able to produce reliable regressions but that they can produce reasonable distinctions between low-residue and high-residue fields. On the other hand, both photo analysis and retroactively binned photo analysis survey data were able to produce reliable regressions with r² values of 0.57 and 0.56, respectively. Overall, this study demonstrates that photo analysis surveys are the most reliable dataset to use when creating crop residue cover models, but we also acknowledge that these surveys are expensive to conduct and suggest some ways these surveys could be made more efficient in the future. Full article

The Tabuk region is located in the northern part of Saudi Arabia, and it has an area of 117,000 km² between longitudes 26° N and 29° N and latitudes 34° E and 38° E. King Salman Bin Abdulaziz Royal Natural Reserve (KSRNR) is the largest natural reserve in Saudi Arabia and covers about 130,700 km². It represents a new tourist attraction area in the Tabuk region. Human activities around the lake may lead to changes in water quality, with subsequent changes in microenvironment components, including microbial diversity. The current study was designed to assess possible changes in bacterial communities of the water sediment at some natural lakes and artificial waterpoints of KSRNR. Water samples were collected from ten different locations within KSRNR: W1, W2, W3 (at the border of the royal reserve); W4, W5, W6, W7 (at the middle); and W8, W9, and W10 (artificial waterpoints). The total DNA of the samples was extracted and subjected to 16S rRNA sequencing and metagenomic analysis; also, the environmental parameters (temperature and humidity) were recorded for all locations. Metagenomic sequencing yielded a total of 24,696 operational taxonomic units (OTUs), which were subsequently annotated to 193 phyla, 215 classes, 445 orders, 947 families, and 3960 genera. At the phylum level, Pseudomonadota dominated the microbial communities across all samples. At the class level, Gammaproteobacteria, Clostridia, Alphaproteobacteria, Bacilli, and Betaproteobacteria were the most prevalent. The dominant families included Enterobacteriaceae, Pseudomonadaceae, Clostridiaceae, Comamonadaceae, and Moraxellaceae. At the genus level, Pseudomonas, Clostridium, Acinetobacter, Paenibacillus, and Acidovorax exhibited the highest relative abundances. The most abundant species were Hungatella xylanolytica, Pseudescherichia vulneris, Pseudorhizobium tarimense, Paenibacillus sp. Yn15, and Enterobacter sp. Sa187. The observed species richness revealed substantial heterogeneity across samples using species richness estimators, Chao1 and ACE, indicating particularly high diversity in samples W3, W5, and W6. Current study results help in recognizing the structure of bacterial communities at the Tubaiq area in relation to their surroundings for planning for environmental protection and future restoration of affected ecosystems. The findings highlight the dominance of various bacterial phyla, classes, families, and genera, with remarkable species richness in some areas. These results underscore the influence of human activities on microbial diversity, as well as the significance of monitoring and conserving the reserve’s natural ecosystems. Full article

This study investigates soil loss in the Wadi Bin Abdullah watershed using the Revised Universal Soil Loss Equation (RUSLE) combined with advanced tools, such as remote sensing and the Geographic Information System (GIS). By leveraging the ALOS PALSAR Digital Elevation Model (DEM), Climate Hazards Group InfraRed Precipitation with Station data (CHIRPS) rainfall data, and the Digital Soil Map of the World (DSMW), the research accurately evaluates soil loss loads. The methodology identifies significant variations in soil loss rates across the entire watershed, with values ranging from 1 to 1189 tons per hectare per year. The classification of soil loss into four stages—very low (0–15 t/ha/yr), low (15–45 t/ha/yr), moderate (45–75 t/ha/yr), and high (>75 t/ha/yr)—provides a nuanced perspective on soil loss dynamics. Notably, 20% of the basin exhibited a soil loss rate of 36 tons per hectare per year. These high rates of soil erosion are attributed to certain factors, such as steep slopes, sparse vegetation cover, and intense rainfall events. These results align with regional and global studies and highlight the impact of topography, land use, and soil properties on soil loss. Moreover, the research emphasizes the importance of integrating empirical soil loss models with modern technological approaches to identify soil loss-prone locations and precisely quantify soil loss rates. These findings provide valuable insights for developing environmental management strategies aimed at mitigating the impacts of soil loss, promoting sustainable land use practices, and supporting resource conservation efforts in arid and semi-arid regions. Full article

Agricultural cargo vehicles are responsible for applying severe soil pressures. However, the ground straw cover can attenuate the loads applied by wheels to the soil surface. This research evaluated the effect of three tires, p1—Radial Very Flex, p2—Radial Improved Flex, and a p3—Bias Ply tire, on three amounts of straw on the soil surface (0, 15, and 30 Mg ha⁻¹). We adopted a completely randomized design (CRD) with a rigid surface for three replications for the total contact area and punctual area claws. The soil bin test verified the deformable surface, tread marks, and soil penetration resistance (SPR). The tire’s claw design determines its punctual contact area, and the construction model determines the total contact area. The contact area in the soil bin increased linearly due to a increase in straw covering, reducing sinkage; p2 to 30 Mg ha⁻¹ straw shows the most significant contact area, p1 and p3 showed no difference. A straw increase from 0 to 30 Mg ha⁻¹ increased the contact areas by 25.5, 38.0, and 20.0% for p1, p2, and p3, respectively. Compared to the rigid surface, the p1 and p3 contact areas in the soil bin increased 6.2, 6.8, and 7.8 times in bare soil, 15, and 30 Mg ha⁻¹; for p2, this increase was up to 4.2, 4.5, and 5.9 times on the same surfaces. Keeping the straw on the soil improves its physical quality by reducing the SPR, so the straw has a buffer function in the wheel–soil relationship. Full article

Mesocotyl elongation of rice seedlings is a key trait for deep sowing tolerance and well seedling establishment in dry direct sowing rice (DDSR) production. Subsets of the Rice Diversity Panel 1 (RDP1, 294 accessions) and Hanyou 73 (HY73) recombinant inbred line (RIL) population (312 lines) were screened for mesocotyl length (ML) via dark germination. Six RDP1 accessions (Phudugey, Kasalath, CA902B21, Surjamkuhi, Djimoron, and Goria) had an ML longer than 10 cm, with the other 19 accessions being over 4 cm. A GWAS in RDP1 detected 118 associated SNPs on all 12 chromosomes using a threshold of FDR-adjusted p < 0.05, including 11 SNPs on chromosomes 1, 4, 5, 7, 10, and 12 declared by −log₁₀(P) > 5.868 as the Bonferroni-corrected threshold. Using phenotypic data of three successive trials and a high-density bin map from resequencing genotypic data, four to six QTLs were detected on chromosomes 1, 2, 5, 6, and 10, including three loci repeatedly mapped for ML from two or three replicated trials. Candidate genes were predicted from the chromosomal regions covered by the associated LD blocks and the confidence intervals (CIs) of QTLs and partially validated by the dynamic RNA-seq data in the mesocotyl along different periods of light exposure. Potential strategies of donor parent selection for seedling establishment in DDSR breeding were discussed. Full article

Pixel clustering is a technique of content-adaptive data embedding in the area of high-performance reversible data hiding (RDH). Using pixel clustering, the pixels in a cover image can be classified into different groups based on a single factor, which is usually the local complexity. Since finer pixel clustering seems to improve the embedding performance, in this manuscript, we propose using two factors for two-dimensional pixel clustering to develop high-performance RDH. Firstly, in addition to the local complexity, a novel factor was designed as the second factor for pixel clustering. Specifically, the proposed factor was defined using the rotation-invariant code derived from pixel relationships in the four-neighborhood. Then, pixels were allocated to the two-dimensional clusters based on the two clustering factors, and cluster-based pixel prediction was realized. As a result, two-dimensional prediction-error histograms (2D-PEHs) were constructed, and performance optimization was based on the selection of expansion bins from the 2D-PEHs. Next, an algorithm for fast expansion-bin selection was introduced to reduce the time complexity. Lastly, data embedding was realized using the technique of prediction-error expansion according to the optimally selected expansion bins. Extensive experiments show that the embedding performance was significantly enhanced, particularly in terms of improved image quality and reduced time complexity, and embedding capacity also moderately improved. Full article

Reversible data hiding (RDH) techniques recover the original cover image after data extraction. Thus, they have gained popularity in e-healthcare, law forensics, and military applications. However, histogram shifting using a reversible data embedding technique suffers from low embedding capacity and high variability. This work proposes a technique in which the distribution obtained from the cover image determines the pixels that attain a peak or zero distribution. Afterward, adjacent histogram bins of the peak point are shifted, and data embedding is performed using the least significant bit (LSB) technique in the peak pixels. Furthermore, the robustness and embedding capacity are improved using the proposed dynamic block-wise reversible embedding strategy. Besides, the secret data are encrypted before embedding to further strengthen security. The experimental evaluation suggests that the proposed work attains superior stego images with a peak signal-to-noise ratio (PSNR) of more than 58 dB for 0.9 bits per pixel (BPP). Additionally, the results of the two-sample t-test and the Kolmogorov–Smirnov test reveal that the proposed work is resistant to attacks. Full article

Free-living terrestrial mites (Acari) have persisted through numerous glacial cycles in Antarctica. Very little is known, however, of their genetic diversity and distribution, particularly within the Ross Sea region. To redress this gap, we sampled mites throughout the Ross Sea region, East Antarctica, including Victoria Land and the Queen Maud Mountains (QMM), covering a latitudinal range of 72–85 °S, as well as Lauft Island near Mt. Siple (73 °S) in West Antarctica and Macquarie Island (54^oS) in the sub-Antarctic. We assessed genetic diversity using mitochondrial cytochrome c oxidase subunit I gene sequences (COI-5P DNA barcode region), and also morphologically identified voucher specimens. We obtained 130 sequences representing four genera: Nanorchestes (n = 30 sequences), Stereotydeus (n = 46), Coccorhagidia (n = 18) and Eupodes (n = 36). Tree-based analyses (maximum likelihood) revealed 13 genetic clusters, representing as many as 23 putative species indicated by barcode index numbers (BINs) from the Barcode of Life Datasystems (BOLD) database. We found evidence for geographically-isolated cryptic species, e.g., within Stereotydeus belli and S. punctatus, as well as unique genetic groups occurring in sympatry (e.g., Nanorchestes spp. in QMM). Collectively, these data confirm high genetic divergence as a consequence of geographic isolation over evolutionary timescales. From a conservation perspective, additional targeted sampling of understudied areas in the Ross Sea region should be prioritised, as further diversity is likely to be found in these short-range endemic mites. Full article

This work presents the first outcomes resulting from a DNA barcode reference library of lepidopteran species from Malta. The library presented here was constructed from the specimens collected between 2015 and 2019 and covers the genetic barcodes of 146 species (ca. 25% of lepidopterous Maltese fauna), including four newly recorded Lepidoptera species from the Maltese islands: Apatema baixerasi, Bostra dipectinialis, Oiketicoides lutea, and Phereoeca praecox. The DNA reference barcode library constructed during this study was analyzed in conjunction with publicly available DNA barcodes and used to assess the ability of the local DNA barcodes to discriminate species. Results showed that each species occupies a different BOLD BIN; therefore, DNA barcoding was able to discriminate between the studied species. Our data led to the formation of 12 new BOLD BINs—that is, OTUs that were identified during this work—while nearly 46% of the barcodes generated during this study were never recorded on conspecifics, further indicating the uniqueness of genetic diversity on these central Mediterranean islands. The outcomes of this study highlight the integrative taxonomic approach, where molecular taxonomy plays an important role for biodiversity investigation in its entirety. Full article

Heat smut is a fungal soil-borne disease caused by Sporisorium reilianum, and affects the development of male and female tassels. Our previous research found that the tassel symptoms in maize infected with Sporisorium reilianum significantly differed in inbred lines with Sipingtou blood, and exhibited stable heredity over time at multiple locations. In this study, cytological analysis demonstrated that the cellular organization structures of three typical inbred lines (Huangzao4, Jing7, and Chang7-2) showed significant discrepancies at the VT stage. QTLs that control the different symptoms of maize tassels infected with Sporisorium reilianum were located in two F₂ populations, which were constructed using three typical inbred lines. The BSA (bulked segregation analysis) method was used to construct mixed gene pools based on typical tassel symptoms. The QTLs of different symptoms of maize tassels infected with Sporisorium reilianum were detected with 869 SSR markers covering the whole maize genome. The mixed gene pools were screened with polymorphic markers between the parents. Additional SSR markers were added near the above marker to detect genotypes in partially single plants in F₂ populations. The QTL controlling tassel symptoms in the Huangzao4 and Jing7 lines was located on the bin 1.06 region, between the markers of umc1590 and bnlg1598, and explained 21.12% of the phenotypic variation with an additive effect of 0.6524. The QTL controlling the tassel symptoms of the Jing7 and Chang7-2 lines was located on the bin 2.07 region, between the markers of umc1042 and bnlg1335, and explained 11.26% phenotypic variation with an additive effect of 0.4355. Two candidate genes (ZmABP2 and Zm00001D006403) were identified by a conjoint analysis of label-free quantification proteome sequencings. Full article

Urban areas worldwide are in the race to become smarter, and the Kingdom of Saudi Arabia (KSA) is no exception. Many of these have envisaged a chance to establish devoted municipal access networks to assist all kinds of city administration and preserve services needing data connectivity. Organizations unanimously concentrate on sustainability issues with key features of general trends, particularly the combination of the 3Rs (reduce waste, reuse and recycle resources). This paper demonstrates how the incorporation of the Internet of Things (IoT) with data access networks, geographic information systems and combinatorial optimization can contribute to enhancing cities’ administration systems. A waste-gathering approach based on supplying smart bins is introduced by using an IoT prototype embedded with sensors, which can read and convey bin volume data over the Internet. However, from another perspective, the population and residents’ attitudes directly affect the control of the waste management system. The conventional waste collection system does not cover all areas in the city. It works based on a planned scheme that is implemented by the authorized organization focused on specific popular and formal areas. The conventional system cannot observe a real-time update of the bin status to recognize whether the waste level condition is ‘full,’ ‘not full,’ or ‘empty.’ This paper uses IoT in the container and trucks that secure the overflow and separation of waste. Waste source locations and population density influence the volume of waste generation, especially waste food, as it has the highest amount of waste generation. The open public area and the small space location problems are solved by proposing different truck sizes based on the waste type. Each container is used for one type of waste, such as food, plastic and others, and uses the optimization algorithm to calculate and find the optimal route toward the full waste container. In this work, the situations in KSA are evaluated, and relevant aspects are explored. Issues relating to the sustainability of organic waste management are conceptually analyzed. A genetic-based optimization algorithm for waste collection transportation enhances the performance of waste-gathering truck management. The selected routes based on the volume status and free spaces of the smart bins are the most effective through those obtainable towards the urgent smart bin targets. The proposed system outperforms other systems by reducing the number of locations and smart bins that have to be visited by 46% for all waste types, whereas the conventional and existing systems have to visit all locations every day, resulting in high cost and consumption time. Full article