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Search Results (511)

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Keywords = taxonomical variability

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12 pages, 659 KiB  
Article
Classification of Apples (Malus × domestica borkh.) According to Geographical Origin, Variety and Production Method Using Liquid Chromatography Mass Spectrometry and Random Forest
by Jule Hansen, Iris Fransson, Robbin Schrieck, Christof Kunert and Stephan Seifert
Foods 2025, 14(15), 2655; https://doi.org/10.3390/foods14152655 - 29 Jul 2025
Viewed by 166
Abstract
Apples are one of the most popular fruits in Germany, valued for their regional availability and health benefits. When deciding which apple to buy, several characteristics are important to consumers, including the taxonomic variety, organic cultivation and regional production. To verify that these [...] Read more.
Apples are one of the most popular fruits in Germany, valued for their regional availability and health benefits. When deciding which apple to buy, several characteristics are important to consumers, including the taxonomic variety, organic cultivation and regional production. To verify that these characteristics are correctly declared, powerful analytical methods are required. In this study, ultra-high performance liquid chromatography quadrupole time-of-flight mass spectrometry (UHPLC-Q-ToF-MS) is applied in combination with random forest to 193 apple samples for the analysis of various authentication issues. Accuracies of 93.3, 85.5, 85.6 and 90% were achieved for distinguishing between German and non-German, North and South German, organic and conventional apples and for six different taxonomic varieties. Since the classification models largely use different parts of the data, which is shown by variable selection, this method is very well suited to answer different authentication issues with one analytical approach. Full article
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19 pages, 4407 KiB  
Article
Mitochondrial Genome of Scutiger ningshanensis (Anura, Megophryidae, Scutiger): Insights into the Characteristics of the Mitogenome and the Phylogenetic Relationships of Megophryidae Species
by Siqi Shan, Simin Chen, Chengmin Li, Lingyu Peng, Dongmei Zhao, Yaqing Liao, Peng Liu and Lichun Jiang
Genes 2025, 16(8), 879; https://doi.org/10.3390/genes16080879 - 26 Jul 2025
Viewed by 251
Abstract
Background/Objectives: Scutiger ningshanensis (Fang, 1985) is an endemic Chinese amphibian species within the genus Scutiger (Megophryidae). Despite its ecological significance, its mitochondrial genome architecture and evolutionary relationships remain poorly understood. Given the high structural variability in Megophryidae mitogenomes and unresolved phylogenetic patterns [...] Read more.
Background/Objectives: Scutiger ningshanensis (Fang, 1985) is an endemic Chinese amphibian species within the genus Scutiger (Megophryidae). Despite its ecological significance, its mitochondrial genome architecture and evolutionary relationships remain poorly understood. Given the high structural variability in Megophryidae mitogenomes and unresolved phylogenetic patterns in Scutiger, this study aims to (1) characterize the complete mitogenome of S. ningshanensis, (2) analyze its molecular evolution, and (3) clarify its phylogenetic position and divergence history within Megophryidae. Methods: The complete mitochondrial genome was sequenced and annotated, followed by analyses of nucleotide composition, codon usage bias, and selection pressures (Ka/Ks ratios). Secondary structures of rRNAs and tRNAs were predicted, and phylogenetic relationships were reconstructed using maximum likelihood and Bayesian methods. Divergence times were estimated using molecular clock analysis. Results: The mitogenome of S. ningshanensis is 17,282 bp long, encoding 13 protein-coding genes (PCGs), 22 tRNAs, 2 rRNAs, and a control region, with a notable AT bias (61.05%) with nucleotide compositions of T (32.51%), C (24.64%), G (14.3%), and A (28.54%). All tRNAs exhibited cloverleaf structures except trnS1, which lacked a DHU stem. Phylogenetic analysis confirmed the monophyly of Scutiger, forming a sister clade to Oreolalax and Leptobrachium, and that S. ningshanensis and S. liubanensis are sister species with a close evolutionary relationship. Positive selection was detected in Atp8 (Ka/Ks > 1), suggesting adaptation to plateau environments, while other PCGs underwent purifying selection (Ka/Ks < 1). Divergence time estimation placed the origin of Megophryidae at~47.97 MYA (Eocene), with S. ningshanensis diverging~32.67 MYA (Oligocene). Conclusions: This study provides the first comprehensive mitogenomic characterization of S. ningshanensis, revealing its evolutionary adaptations and phylogenetic placement. The findings enhance our understanding of Megophryidae’s diversification and offer a genomic foundation for future taxonomic and conservation studies. Full article
(This article belongs to the Section Cytogenomics)
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23 pages, 15846 KiB  
Article
Habitats, Plant Diversity, Morphology, Anatomy, and Molecular Phylogeny of Xylosalsola chiwensis (Popov) Akhani & Roalson
by Anastassiya Islamgulova, Bektemir Osmonali, Mikhail Skaptsov, Anastassiya Koltunova, Valeriya Permitina and Azhar Imanalinova
Plants 2025, 14(15), 2279; https://doi.org/10.3390/plants14152279 - 24 Jul 2025
Viewed by 303
Abstract
Xylosalsola chiwensis (Popov) Akhani & Roalson is listed in the Red Data Book of Kazakhstan as a rare species with a limited distribution, occurring in small populations in Kazakhstan, Uzbekistan, and Turkmenistan. The aim of this study is to deepen the understanding of [...] Read more.
Xylosalsola chiwensis (Popov) Akhani & Roalson is listed in the Red Data Book of Kazakhstan as a rare species with a limited distribution, occurring in small populations in Kazakhstan, Uzbekistan, and Turkmenistan. The aim of this study is to deepen the understanding of the ecological conditions of its habitats, the floristic composition of its associated plant communities, the species’ morphological and anatomical characteristics, and its molecular phylogeny, as well as to identify the main threats to its survival. The ecological conditions of the X. chiwensis habitats include coastal sandy plains and the slopes of chinks and denudation plains with gray–brown desert soils and bozyngens on the Mangyshlak Peninsula and the Ustyurt Plateau at altitudes ranging from −3 to 270 m above sea level. The species is capable of surviving in arid conditions (less than 100 mm of annual precipitation) and under extreme temperatures (air temperatures exceeding 45 °C and soil surface temperatures above 65 °C). In X. chiwensis communities, we recorded 53 species of vascular plants. Anthropogenic factors associated with livestock grazing, industrial disturbances, and off-road vehicle traffic along an unregulated network of dirt roads have been identified as contributing to population decline and the potential extinction of the species under conditions of unsustainable land use. The morphometric traits of X. chiwensis could be used for taxonomic analysis and for identifying diagnostic morphological characteristics to distinguish between species of Xylosalsola. The most taxonomically valuable characteristics include the fruit diameter (with wings) and the cone-shaped structure length, as they differ consistently between species and exhibit relatively low variability. Anatomical adaptations to arid conditions were observed, including a well-developed hypodermis, which is indicative of a water-conserving strategy. The moderate photosynthetic activity, reflected by a thinner palisade mesophyll layer, may be associated with reduced photosynthetic intensity, which is compensated for through structural mechanisms for water conservation. The flow cytometry analysis revealed a genome size of 2.483 ± 0.191 pg (2n/4x = 18), and the phylogenetic analysis confirmed the placement of X. chiwensis within the tribe Salsoleae of the subfamily Salsoloideae, supporting its taxonomic distinctness. To support the conservation of this rare species, measures are proposed to expand the area of the Ustyurt Nature Reserve through the establishment of cluster sites. Full article
(This article belongs to the Section Plant Ecology)
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30 pages, 2062 KiB  
Article
Building a DNA Reference for Madagascar’s Marine Fishes: Expanding the COI Barcode Library and Establishing the First 12S Dataset for eDNA Monitoring
by Jean Jubrice Anissa Volanandiana, Dominique Ponton, Eliot Ruiz, Andriamahazosoa Elisé Marcel Fiadanamiarinjato, Fabien Rieuvilleneuve, Daniel Raberinary, Adeline Collet, Faustinato Behivoke, Henitsoa Jaonalison, Sandra Ranaivomanana, Marc Leopold, Roddy Michel Randriatsara, Jovial Mbony, Jamal Mahafina, Aaron Hartmann, Gildas Todinanahary and Jean-Dominique Durand
Diversity 2025, 17(7), 495; https://doi.org/10.3390/d17070495 - 18 Jul 2025
Viewed by 422
Abstract
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, [...] Read more.
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
(This article belongs to the Special Issue 2025 Feature Papers by Diversity’s Editorial Board Members)
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23 pages, 11464 KiB  
Article
Characterization of Water Quality and the Relationship Between WQI and Benthic Macroinvertebrate Communities as Ecological Indicators in the Ghris Watershed, Southeast Morocco
by Ali El Mansour, Saida Ait Boughrous, Ismail Mansouri, Abdellali Abdaoui, Wafae Squalli, Asmae Nouayti, Mohamed Abdellaoui, El Mahdi Beyouda, Christophe Piscart and Ali Ait Boughrous
Water 2025, 17(14), 2055; https://doi.org/10.3390/w17142055 - 9 Jul 2025
Viewed by 431
Abstract
The Ghris watershed in southern Morocco is a significant ecological and agricultural area. However, due to the current impacts of climate change, farming activities, and pollution, data on its quality and biological importance need to be updated. Therefore, this study aimed to evaluate [...] Read more.
The Ghris watershed in southern Morocco is a significant ecological and agricultural area. However, due to the current impacts of climate change, farming activities, and pollution, data on its quality and biological importance need to be updated. Therefore, this study aimed to evaluate the physico-chemical and biological quality of surface water in the Ghris River. The Water Quality Index (WQI) and the Iberian Biological Monitoring Working Group (IBMWP) index were used to assess water quality along four sampling sites in 2024. The collected data were analyzed with descriptive and multivariate statistics. In total, 424 benthic macroinvertebrates belonging to seven orders were identified in the surface waters of the Ghris basin. These microfauna were significantly variable among the studied sites (p < 0.05). Station S4 is significantly rich in species, including seven orders and nine families of macroinvertebrates, followed by Station S2, with seven orders and eight families. Stations S3 and S1 showed less species diversity, with three orders and one family, respectively. The Insecta comprised 95.9% of the abundance, while the Crustacea constituted just 4.1%. The physico-chemical parameters significantly surpassed (p < 0.05) the specified norms of surface water in Morocco. This indicates a decline in the water quality of the studied sites. The findings of the principal component analysis (PCA) demonstrate that the top two axes explain 87% of the cumulative variation in the data. Stations 2 and 3 are closely associated with high concentrations of pollutants, notably Cl, SO42−, NO3, and K+ ions. Dissolved oxygen (DO) showed a slight correlation with S2 and S3, while S4 was characterized by high COD and PO4 concentrations, low levels of mineral components (except Cl), and average temperature conditions. Bioindication scores for macroinvertebrate groups ranging from 1 to 10 enabled the assessment of pollution’s influence on aquatic biodiversity. The IBMWP biotic index indicated discrepancies in water quality across the sites. This study gives the first insight and updated data on the biological and chemical quality of surface water in the Ghris River and the entire aquatic ecosystem in southeast Morocco. These data are proposed as a reference for North African and Southern European rivers. However, more investigations are needed to evaluate the impacts of farming, mining, and urbanization on the surface and ground waters in the study zone. Similarly, it is vital to carry out additional research in arid and semi-arid zones since there is a paucity of understanding regarding taxonomic and functional diversity, as well as the physico-chemical factors impacting water quality. Full article
(This article belongs to the Section Biodiversity and Functionality of Aquatic Ecosystems)
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19 pages, 1439 KiB  
Article
Applied Metagenomic Profiling of Domestic Cat Feces from Cali, Colombia: An Exploratory Approach
by Monica Pimienta, Hernan Florez-Rios, Angie Patiño-Montoya, Anyelo Florez, Lizeth Mejia, Raul Sedano and Andres Castillo
Appl. Microbiol. 2025, 5(3), 67; https://doi.org/10.3390/applmicrobiol5030067 - 8 Jul 2025
Viewed by 376
Abstract
This exploratory study presents the first metagenomic assessment of the gut microbiome in domestic cats from Cali, Colombia. Fecal samples were collected from 10 healthy, sterilized domestic cats, aged 8 months to over 2 years, with variation in sex (7 females, 3 males), [...] Read more.
This exploratory study presents the first metagenomic assessment of the gut microbiome in domestic cats from Cali, Colombia. Fecal samples were collected from 10 healthy, sterilized domestic cats, aged 8 months to over 2 years, with variation in sex (7 females, 3 males), diet (processed or raw), and outdoor access (5 with, 5 without). Using 16S rRNA gene metabarcoding and pooled shotgun metagenomic sequencing, the study characterized the taxonomic composition and functional potential of the feline gut microbiome. Dominant phyla included Bacillota and Bacteroidota, with substantial inter-individual variation. Peptoclostridium was the most consistently abundant genus, while Megamonas and Megasphaera showed higher variability. Shotgun analysis detected antibiotic resistance genes (ErmG, ErmQ) and virulence factors (pfoA, plc, colA, nanJ, nagI) in Clostridium perfringens, highlighting potential zoonotic risk. The composition of the gut microbiota was influenced primarily by diet and outdoor access, while age and gender had more moderate effects. The study concludes that lifestyle and environmental factors play a key role in shaping the gut microbiome of domestic cats. We recommend further longitudinal and larger-scale studies to better understand the dynamics of feline microbiota and their implications for animal and public health within a One Health framework. Full article
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12 pages, 1858 KiB  
Article
Botanical Studies Based on Textual Evidence in Eastern Asia and Its Implications for the Ancient Climate
by Haiming Liu, Huijia Song, Fei Duan and Liang Shen
Atmosphere 2025, 16(7), 824; https://doi.org/10.3390/atmos16070824 - 7 Jul 2025
Viewed by 206
Abstract
Understanding morphological descriptions of plants documented by ancient peoples over 1000 years ago and identifying the species they described are critical for reconstructing the natural geographic distribution of plant taxa, tracking taxonomic variations, and inferring historical climate dynamics. Analyzing shifts in plant communities [...] Read more.
Understanding morphological descriptions of plants documented by ancient peoples over 1000 years ago and identifying the species they described are critical for reconstructing the natural geographic distribution of plant taxa, tracking taxonomic variations, and inferring historical climate dynamics. Analyzing shifts in plant communities and climatic conditions during this period is essential to unravel the interplay among floristic composition, climate fluctuations, and anthropogenic impacts. However, research in this field remains limited, with greater emphasis placed on plant taxa from hundreds of millions of years ago. Investigations into flora and climate during the last two millennia are sparse, and pre-millennial climatic conditions remain poorly characterized. In this study, a historical text written 1475 years ago was analyzed to compile plant names and morphological features, followed by taxonomic identification. The research identified three gymnosperm species (one in Pinaceae, two in Cupressaceae), 1 Tamaricaceae species (dicotyledon), and 19 dicotyledon species. However, three plant groups could only be identified at the genus level. Using textual analysis and woody plant coexistence methods, the climate of 1475 years ago in western Henan Province, located in the middle-lower Yellow River basin in East Asia, was reconstructed. Results indicate that the mean temperature of the coldest month (MTCM) was approximately 1.3 °C higher than modern values. In comparison, the mean temperature of the warmest month (MTWM) and mean annual temperature (MAT) were lower than present-day levels. This suggests slightly cooler overall conditions with milder seasonal extremes in ancient Luoyang—a finding supported by contemporaneous studies. Furthermore, annual precipitation (AP), precipitation of the warmest quarter (PWQ), and precipitation of the coldest quarter (PCQ) in the Luoyang region 1475 years ago exceeded modern measurements, despite the area’s monsoonal climate. This suggests significantly higher atmospheric moisture content in ancient air masses compared to today. This study provides floristic and climatic baseline data for advancing our understanding of global climate variability at millennial scales. Full article
(This article belongs to the Section Climatology)
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19 pages, 4822 KiB  
Article
Hybrid Deep Learning Framework for High-Accuracy Classification of Morphologically Similar Puffball Species Using CNN and Transformer Architectures
by Eda Kumru, Güney Ugurlu, Mustafa Sevindik, Fatih Ekinci, Mehmet Serdar Güzel, Koray Acici and Ilgaz Akata
Biology 2025, 14(7), 816; https://doi.org/10.3390/biology14070816 - 5 Jul 2025
Viewed by 413
Abstract
Puffballs, a group of macrofungi belonging to the Basidiomycota, pose taxonomic challenges due to their convergent morphological features, including spherical basidiocarps and similar peridial structures, which often hinder accurate species-level identification. This study proposes a deep learning-based classification framework for eight ecologically [...] Read more.
Puffballs, a group of macrofungi belonging to the Basidiomycota, pose taxonomic challenges due to their convergent morphological features, including spherical basidiocarps and similar peridial structures, which often hinder accurate species-level identification. This study proposes a deep learning-based classification framework for eight ecologically and taxonomically important puffball species: Apioperdon pyriforme, Bovista plumbea, Bovistella utriformis, Lycoperdon echinatum, L. excipuliforme, L. molle, L. perlatum, and Mycenastrum corium. A balanced dataset of 1600 images (200 per species) was used, divided into 70% training, 15% validation, and 15% testing. To enhance generalizability, images were augmented to simulate natural variability in orientation, lighting, and background. In this study, five different deep learning models (ConvNeXt-Base, Swin Transformer, ViT, MaxViT, EfficientNet-B3) were comparatively evaluated on a balanced dataset of eight puffball species. Among these, the ConvNeXt-Base model achieved the highest performance, with 95.41% accuracy, and proved especially effective in distinguishing morphologically similar species such as Mycenastrum corium and Lycoperdon excipuliforme. The findings demonstrate that deep learning models can serve as powerful tools for the accurate classification of visually similar fungal species. This technological approach shows promise for developing automated mushroom identification systems that support citizen science, amateur naturalists, and conservation professionals. Full article
(This article belongs to the Special Issue Artificial Intelligence Research for Complex Biological Systems)
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9 pages, 734 KiB  
Proceeding Paper
Comparative Evaluation of 16S rRNA and Housekeeping Gene-Specific Primer Pairs for Rhizobia and Agrobacteria Metagenomics
by Romain Kouakou Fossou and Adolphe Zézé
Biol. Life Sci. Forum 2025, 46(1), 1; https://doi.org/10.3390/blsf2025046001 - 2 Jul 2025
Viewed by 291
Abstract
Of many housekeeping genes, gyrB and rpoB are used as alternative markers to 16S rDNA to analyze Rhizobia and Agrobacteria communities. However, the extent to which the targeted genes and their corresponding primers could be suitable in metagenomic studies within communities belonging to [...] Read more.
Of many housekeeping genes, gyrB and rpoB are used as alternative markers to 16S rDNA to analyze Rhizobia and Agrobacteria communities. However, the extent to which the targeted genes and their corresponding primers could be suitable in metagenomic studies within communities belonging to the two taxa remains elusive. This work evaluates in silico the taxonomic resolution of partial regions of two housekeeping and 16S rRNA genes in differentiating between Rhizobia and Agrobacteria. The study confirmed V5–V7 as the best 16S rDNA variable region for differentiating all the genera at a 100% threshold. However, rpoB and gyrB markers outcompeted the 16S rDNA in terms of taxonomic resolution regardless of the threshold, possibly replacing the use of 16S rDNA V-regions in metagenomics studies of Rhizobia and Agrobacteria. Full article
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37 pages, 2700 KiB  
Review
A Review of Botany, Phytochemistry, and Biological Activities of Fragaria vesca and Fragaria viridis Widespread in Kazakhstan
by Gayane A. Atazhanova, Gulnissa K. Kurmantayeva, Yana K. Levaya, Margarita Yu Ishmuratova and Marlen K. Smagulov
Plants 2025, 14(13), 2027; https://doi.org/10.3390/plants14132027 - 2 Jul 2025
Viewed by 463
Abstract
According to current taxonomic consensus, the genus Fragaria L. (family Rosaceae) comprises nine recognized species: Fragaria × ananassa (Duchartre ex Weston) Duchesne ex Rozier, Fragaria bucharica Losinsk., Fragaria viridis subsp. campestris (Steven) Pael., Fragaria chiloensis (L.) Mill., Fragaria moschata Duchesne ex Weston, Fragaria [...] Read more.
According to current taxonomic consensus, the genus Fragaria L. (family Rosaceae) comprises nine recognized species: Fragaria × ananassa (Duchartre ex Weston) Duchesne ex Rozier, Fragaria bucharica Losinsk., Fragaria viridis subsp. campestris (Steven) Pael., Fragaria chiloensis (L.) Mill., Fragaria moschata Duchesne ex Weston, Fragaria orientalis Losinsk., Fragaria vesca L., Fragaria virginiana Mill., and Fragaria viridis Duchartre. Within the flora of Kazakhstan, two species are of particular significance: F. vesca L. and F. viridis Weston. The genus Fragaria L. is notable for its high content of diverse classes of biologically active compounds, which exhibit a broad spectrum of pharmacological and physiological activities. This review focuses on two Fragaria species native to the flora of Kazakhstan: F. vesca L. and F. viridis Weston. It summarizes recent advances in their botanical characterization, phytochemical profiling, extraction methodologies, and biological activities. Available evidence indicates that the phytochemical composition of extracts obtained from these species is modulated by a range of environmental and biological factors. These include habitat conditions, climate variability, chemotypic diversity, and the specific extraction protocols applied. Particular emphasis is placed on modern extraction techniques and the identification of low-molecular-weight metabolites. These include anthocyanins, volatile organic compounds, flavonoids, and phenolic acids, which contribute significantly to the observed biological effects. The review findings support the relevance of continued research into the potential application of these species as sources for the development of novel therapeutic and prophylactic agents. In addition, they highlight their promise for use in the formulation of biologically active compounds intended for food supplements and cosmetic products. Full article
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25 pages, 6926 KiB  
Article
Spatial Distribution of Cadmium in Avocado-Cultivated Soils of Peru: Influence of Parent Material, Exchangeable Cations, and Trace Elements
by Richard Solórzano, Rigel Llerena, Sharon Mejía, Juancarlos Cruz and Kenyi Quispe
Agriculture 2025, 15(13), 1413; https://doi.org/10.3390/agriculture15131413 - 30 Jun 2025
Viewed by 1057
Abstract
Potentially toxic elements such as cadmium (Cd) in agricultural soils represent a global concern due to their toxicity and potential accumulation in the food chain. However, our understanding of cadmium’s complex sources and the mechanisms controlling its spatial distribution across diverse edaphic and [...] Read more.
Potentially toxic elements such as cadmium (Cd) in agricultural soils represent a global concern due to their toxicity and potential accumulation in the food chain. However, our understanding of cadmium’s complex sources and the mechanisms controlling its spatial distribution across diverse edaphic and geological contexts remains limited, particularly in underexplored agricultural regions. Our study aimed to assess the total accumulated Cd content in soils under avocado cultivation and its association with edaphic, geochemical, and geomorphological variables. To this end, we considered the total concentrations of other metals and explored their associations to gain a better understanding of Cd’s spatial distribution. We analyzed 26 physicochemical properties, the total concentrations of 22 elements (including heavy and trace metals such as As, Ba, Cr, Cu, Hg, Ni, Pb, Sb, Se, Sr, Tl, V, and Zn and major elements such as Al, Ca, Fe, K, Mg, and Na), and six geospatial variables in 410 soil samples collected from various avocado-growing regions in Peru in order to identity potential associations that could help explain the spatial patterns of Cd. For data analysis, we applied (1) univariate statistics (skewness, kurtosis); (2) multivariate methods such as Spearman correlations and principal component analysis (PCA); (3) spatial modeling using the Geodetector tool; and (4) non-parametric testing (Kruskal–Wallis test with Dunn’s post hoc test). Our results indicated (1) the presence of hotspots with Cd concentrations exceeding 3 mg·kg−1, displaying a leptokurtic distribution (skewness = 7.3); (2) dominant accumulation mechanisms involving co-adsorption and cation competition (Na+, Ca2+), as well as geogenic co-accumulation with Zn and Pb; and (3) significantly higher Cd concentrations in Leptosols derived from Cretaceous intermediate igneous rocks (diorites/tonalites), averaging 1.33 mg kg−1 compared to 0.20 mg·kg−1 in alluvial soils (p < 0.0001). The factors with the greatest explanatory power (q > 15%, Geodetector) were the Zn content, parent material, geological age, and soil taxonomic classification. These findings provide edaphogenetic insights that can inform soil cadmium (Cd) management strategies, including recommendations to avoid establishing new plantations in areas with a high risk of Cd accumulation. Such approaches can enhance the efficiency of mitigation programs and reduce the risks to export markets. Full article
(This article belongs to the Section Agricultural Soils)
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11 pages, 258 KiB  
Article
Gram-Negative Microbiota Derived from Trout Fished in Slovakian Water Sources and Their Relationship to Postbiotics
by Andrea Lauková, Anna Kandričáková, Jana Ščerbová, Monika Pogány Simonová and Rudolf Žitňan
Pathogens 2025, 14(7), 644; https://doi.org/10.3390/pathogens14070644 - 28 Jun 2025
Viewed by 427
Abstract
Regarding the trout microbiota, most information is focused on lactic acid bacteria, which can show beneficial properties. However, in trout farming, mostly pathogenic Gram-positive species were reported, such as Staphylococcus aureus, Listeria monocytogenes, and/or Clostridium spp. In this study, free-living trout [...] Read more.
Regarding the trout microbiota, most information is focused on lactic acid bacteria, which can show beneficial properties. However, in trout farming, mostly pathogenic Gram-positive species were reported, such as Staphylococcus aureus, Listeria monocytogenes, and/or Clostridium spp. In this study, free-living trout were analyzed for Gram-negative microbiota that can cause loss as disease-stimulating agents. Bacteriocin postbiotics should be one of the approaches used to eliminate these agents. In total, 21 strains of different species isolated from the intestinal tract of 50 trout in Slovakia (Salmo trutta and Salmo gairdnerii) were taxonomically allotted into 13 species and 9 genera. This method showed variability in microbiota identified using MALDI-TOF mass spectrometry with the following species: Acinetobacter calcoaceticus, Citrobacter gillenii, Citrobacter freundii, Escherichia coli, Hafnia alvei, Kluyvera cryocrescens, K. intermedia, Leclercia adecarboxylata, Raoultella ornithinolytica, Pseudomonas fragi, Ps. putida, Ps. lundensis, Ps. teatrolens, and Serratia fonticola. Most strains were susceptible to the antibiotics used, reaching inhibitory zones up to 29 mm. On the other hand, 3 out of 21 strains (14%) were susceptible to nine enterocins- postbiotics (Hafnia alvei Hal281, Pseudomonas putida Pp391, and Ps. fragi Pf 284), with inhibitory activity in the range of 100–6400 AU/mL. Full article
(This article belongs to the Section Bacterial Pathogens)
17 pages, 2072 KiB  
Article
Macrostructure of Malus Leaves and Its Taxonomic Significance
by Yuerong Fan, Huimin Li, Jingze Ma, Ting Zhou, Junjun Fan and Wangxiang Zhang
Plants 2025, 14(13), 1918; https://doi.org/10.3390/plants14131918 - 22 Jun 2025
Viewed by 509
Abstract
Leaves are the most ubiquitous plant organs, whose macrostructures exhibit close correlations with environmental factors while simultaneously reflecting inherent genetic and evolutionary patterns. These characteristics render them highly significant for plant taxonomy, ecology, and related disciplines. Therefore, this study presents the first comprehensive [...] Read more.
Leaves are the most ubiquitous plant organs, whose macrostructures exhibit close correlations with environmental factors while simultaneously reflecting inherent genetic and evolutionary patterns. These characteristics render them highly significant for plant taxonomy, ecology, and related disciplines. Therefore, this study presents the first comprehensive evaluation of Malus leaf macrostructures for infraspecific classification. By establishing a trait-screening system, we conducted a numerical taxonomic analysis of leaf phenotypic variation across 73 Malus germplasm (34 species and 39 cultivars). Through ancestor-inclined distribution characteristic analysis, we investigated phylogenetic relationships at both the genus level and infraspecific ranks within Malus. A total of 21 leaf phenotypic traits were selected from 50 candidate traits based on the following criteria: high diversity, abundance, and evenness (D ≥ 0.50, H ≥ 0.80, and E ≥ 0.60); significant intraspecific uniformity and interspecific distinctness (CV¯ ≤ 10% and CV ≥ 15%). Notably, the selected traits with low intraspecific variability (CV¯ ≤ 10%) exhibit environmental robustness, likely reflecting low phenotypic plasticity of these specific traits under varying conditions. This stability enhances their taxonomic utility. It was found that the highest ancestor-inclined distribution probability reached 90% for 10 traceable cultivars, demonstrating reliable breeding lines. Based on morphological evidence, there was a highly significant correlation between the evolutionary orders of (Sect. Docyniopsis → Sect. Sorbomalus → Sect. Malus) and group/sub-groups (B1 → B2 → A). This study demonstrates that phenotypic variation in leaf macrostructures can effectively explore the affinities among Malus germplasm, exhibiting taxonomic significance at the infraspecific level, thereby providing references for variety selection. However, hybrid offspring may exhibit mixed parental characteristics, leading to blurred species boundaries. And convergent evolution may create false homologies, potentially misleading morphology-based taxonomic inferences. The inferred taxonomic relationships present certain limitations that warrant further investigation. Full article
(This article belongs to the Section Plant Development and Morphogenesis)
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15 pages, 2623 KiB  
Article
Preliminary Insights into the Gut Microbiota of Captive Tigers in Republic of Korea: Influence of Geographic and Individual Variation
by Beoul Kim, Saebom Lee, You-Jeong Lee, Yong-Myung Kang, Man Hee Rhee, Dongmi Kwak, Yong-Gu Yeo, Ju Won Kang, Taehwan Kim and Min-Goo Seo
Microorganisms 2025, 13(6), 1427; https://doi.org/10.3390/microorganisms13061427 - 19 Jun 2025
Viewed by 385
Abstract
The gut microbiome plays a crucial role in the health and physiology of tigers (Panthera tigris), influencing digestion, immune function, and overall well-being. While numerous studies have characterized the gut microbiota of domestic carnivores and some wild felids, comparative analyses across [...] Read more.
The gut microbiome plays a crucial role in the health and physiology of tigers (Panthera tigris), influencing digestion, immune function, and overall well-being. While numerous studies have characterized the gut microbiota of domestic carnivores and some wild felids, comparative analyses across different tiger subspecies under varying environmental contexts remain limited. In this exploratory study, we investigated the gut microbiome diversity and composition of 15 captive tigers, including both Siberian (P. tigris altaica) and Bengal (P. tigris tigris) subspecies, housed in two different regions in Korea. Using 16S rRNA gene sequencing of fecal samples, we analyzed microbial diversity across multiple taxonomic levels. Preliminary analyses revealed significant differences in microbial composition between geographic locations, whereas sex-based differences appeared minimal. Alpha and beta diversity metrics demonstrated substantial inter-individual variability, likely influenced by regional and environmental factors. Given the small sample size and the confounding between subspecies and housing location, the findings should be regarded as preliminary and not generalized beyond this specific cohort. Nevertheless, these insights highlight the potential utility of gut microbiome profiling for health monitoring and management in captive-tiger populations. Future research incorporating larger, more diverse cohorts will be essential to validate these trends and clarify the roles of diet, health status, and enrichment in shaping the gut microbiota. Full article
(This article belongs to the Section Gut Microbiota)
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16 pages, 1678 KiB  
Article
The Diversity and Composition of Insect Communities in Urban Forest Fragments near Panama City
by Jeancarlos Abrego and Enrique Medianero
Biology 2025, 14(6), 721; https://doi.org/10.3390/biology14060721 - 18 Jun 2025
Viewed by 376
Abstract
Fragments of urban forests can host a remarkable diversity of insects, even in environments that have been greatly transformed. This study evaluates the diversity, abundance, and composition of insects that belong to seven families in four urban forest fragments near Panama City, i.e., [...] Read more.
Fragments of urban forests can host a remarkable diversity of insects, even in environments that have been greatly transformed. This study evaluates the diversity, abundance, and composition of insects that belong to seven families in four urban forest fragments near Panama City, i.e., Ciudad del Saber (CDS), Parque Natural Metropolitano (PNM), Corozal (COR), and Albrook (ALB). A total of 2038 individuals were collected via Malaise traps and categorized into 403 morphospecies, 75 genera, and 43 subfamilies. The highest richness of morphospecies was observed in CDS (223), whereas PNM exhibited the highest abundance of individuals (862). The alpha diversity indices (Shannon-Wiener > 4.3; Margalef > 21; Pielou ≈ 1.0; and Simpson’s inverse > 0.95) reflected communities that were characterized by high levels of diversity and equity. The level of similarity observed among the fragments was moderate (Diserud–Odegaard index = 0.543), thus indicating differences among the sites evaluated as part of this research in terms of their taxonomic composition. These results provide evidence concerning the variability of entomological communities in tropical urban landscapes and the role of forest fragments as possible reservoirs of biodiversity. Full article
(This article belongs to the Section Conservation Biology and Biodiversity)
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