Search Results (1,829)

Protecting threatened elasmobranch species despite limited data on their distribution and abundance is a critical challenge, particularly in the context of increasing human impacts on marine ecosystems. In the northeastern Atlantic, species such as the leafscale gulper shark, Portuguese dogfish, spurdog, and spotted ray are facing pressures from overfishing, bycatch, habitat degradation, and climate change. The OSPAR Commission has listed these species as threatened and/or declining and aims to protect them by reliably identifying suitable habitats and integrating these areas into Marine Protected Areas (MPAs). In this study, we present a spatial modelling framework using regression-based approaches to identify suitable habitats for these four species. Results show that suitable habitats of the spotted ray (25.8%) and spurdog (18.8%) are relatively well represented within existing MPAs, while those of the deep-water sharks are underrepresented (6.0% for leafscale gulper shark, and 6.8% for Portuguese dogfish). Our findings highlight the need for additional MPAs in deep-sea continental slope areas, particularly west and northwest of Scotland and Ireland. Such expansions would support OSPAR’s goal to protect 30% of its maritime area by 2030 and could benefit broader deep-sea biodiversity, including other vulnerable demersal species and benthic communities. Full article

The genus Panax contains traditional herbs that have been widely used in traditional medicine. The active constituents, collectively known as ginsenosides, are well characterized in the most representative species, P. notoginseng. However, the major bioactive chemical constituents of P. stipuleanatus together with P. vietnamensis are relatively less studied. In this study, an untargeted metabolomic analysis was performed in P. notoginseng, P. stipuleanatus, and P. vietnamensis using root and leaf organs. Further metabolomic differences in P. stipuleanatus were compared with those of the two most prevalent species. The analysis results revealed tissue-specific qualitative and quantitative metabolic differences in each species. Several differentially accumulated metabolites were enriched in the biosynthesis of secondary metabolites, including the biosynthesis of ginsenosides I. The ginsenosides Rb1, Rf, Rg1, Rh1, Rh8, and notoginsenosides E, M, and N had a higher abundance level in the roots of both P. notoginseng and P. vietnamensis. In P. stipuleanatus, the accumulation of potentially important ginsenosides is mainly found in the leaf. In particular, the dammarane-type ginsenosides Rb3, Rb1, Mx, and F2 as well as the notoginsenosides A, Fe, Fa, Fd, L, and N were identified to have a higher accumulation in the leaf. The strong positive correlation network of different ginsenosides probably enhanced secondary metabolism in each species. The comparative analysis revealed a significant differential accumulation of metabolites in the leaves of both species. The various compounds of dammarane-type ginsenoside, such as Rb1, Rg1, Rg6, Rh8, Rh10, Rh14, and majoroside F2, had a significantly higher concentration level in the leaves of P. stipuleanatus. In addition, several notoginsenoside compounds such as A, R1, Fe, Fd, and Ft1 showed a higher abundance in the leaf. These results show that the abundance level of major ginsenosides is significant in P. stipuleanatus and provides an important platform to improve the ginsenoside quality of Panax species. Full article

This study evaluated the effectiveness of eDNA metabarcoding in assessing fish communities in two urban lakes (First Lake and Second Lake) in Zagreb, Croatia, following IAS removal. Water samples were collected in April and June 2024 and analyzed using MiFish primers targeting the 12S rRNA gene. The results indicated that the cleanup efforts were largely successful, as several IAS previously recorded in these lakes were not detected (Ameiurus melas, Lepomis gibbosus, and Hypophthalmichthys spp.). However, some others persisted in low relative abundances, such as grass carp (Ctenopharyngodon idella), topmouth gudgeon (Pseudorasbora parva), and prussian/crucian carp (Carassius sp.). Species composition differed between lakes, with common carp (Cyprinus carpio) dominating Maksimir First Lake, while chub (Squalius cephalus) was prevalent in Maksimir Second Lake. Unexpected eDNA signals from salmonid and exotic species suggest potential input from upstream sources, human activity, or the nearby Zoo Garden. These findings underscore the utility of eDNA metabarcoding in biodiversity monitoring and highlight the need for continuous surveillance and adaptive management strategies to ensure long-term IAS control. Full article

A total of 32 fish species were detected in Xinglin Bay using a combination of environmental DNA metabarcoding (eDNA) and traditional morphological survey methods (TSM), covering eight orders, fifteen families, and twenty-six genera. The dominant order was Perciformes, accounting for 43.75% of the total species. Among the identified species, there were ten non-native fish species. Compared with the TSM, the eDNA detected 13 additional fish species, including two additional non-native fish species—Gambusia affinis (Baird and Girard, 1853) and Micropterus salmoides (Lacepède, 1802). In addition, the relative abundance of fish from both methods revealed that tilapia was overwhelmingly dominant, accounting for 80.75% and 75.68%, respectively. Furthermore, the AS-ISK assessment revealed that all non-native fish species were classified as medium or high-risk, with five identified as high-risk species, four of which belong to tilapia. These findings demonstrated that tilapia are the dominant and high-risk invasive species in Xinglin Bay and should be prioritized for management. Population reduction through targeted harvesting of tilapia is recommended as the primary control strategy. Additionally, the study highlights the effectiveness of eDNA in monitoring fish community structure in brackish ecosystems. Full article

Tropical forests continue to experience high levels of habitat loss and degradation, with wildfires becoming a frequent component of human-modified landscapes. Here we investigate the response of palm species to the conversion of old-growth forests to successional mosaics, including forest patches burned during wildfires. Palms (≥50 cm height) were recorded once in 2023–2024, across four habitat classes: terra firme old-growth stands, regenerating forest stands associated with slash-and-burn agriculture, old-growth stands burned once and twice, and active cassava fields, in the Tapajós-Arapiuns Extractive Reserve, in the eastern Brazilian Amazon. The flammability of palm leaf litter and forest litter were also examined to assess the potential connections between palm proliferation and wildfires. A total of 10 palm species were recorded in this social forest (including slash-and-burn agriculture and resulting successional mosaics), with positive, negative, and neutral responses to land use. Species richness did not differ among forest habitats, but absolute palm abundance was greatest in disturbed habitats. Only Attalea spectabilis Mart. (curuá) exhibited increased relative abundance across disturbed habitats, including active cassava field. Attalea spectabilis accounted for almost 43% of all stems in the old-growth forest, 89% in regenerating forests, 90% in burned forests, and 79% in crop fields. Disturbed habitats supported a five-to-ten-fold increment in curuá leaves as a measure of habitat flammability. Although curuá litter exhibited lower flame temperature and height, its lower carbon and higher volatile content is expected to be more sensitive to fire ignition and promote the spread of wildfires. The conversion of old-growth forests into social forests promotes the establishment of palm-dominated forests, increasing the potential for a forest transition further fueled by wildfires, with effects on forest resilience and social reproduction still to be understood. Full article

Microbiome analysis has revolutionized our understanding of various biological processes, spanning human health and epidemiology (including antimicrobial resistance and horizontal gene transfer), as well as environmental and agricultural studies. At the heart of microbiome analysis lies the characterization of microbial communities through the quantification of microbial taxa and their dynamics. In the study of bacterial abundances, it is becoming more relevant to consider their relationship, to embed these data in the framework of network theory, allowing characterization of features like node relevance, pathways, and community structure. In this study, we address the primary biases encountered in reconstructing networks through correlation measures, particularly in light of the compositional nature of the data, within-sample diversity, and the presence of a high number of unobserved species. These factors can lead to inaccurate correlation estimates. To tackle these challenges, we employ simulated data to demonstrate how many of these issues can be mitigated by applying typical transformations designed for compositional data. These transformations enable the use of straightforward measures like Pearson’s correlation to correctly identify positive and negative relationships among relative abundances, especially in high-dimensional data, without having any need for further corrections. However, some challenges persist, such as addressing data sparsity, as neglecting this aspect can result in an underestimation of negative correlations. Full article

Goats are considered to be the ideal climate-resilient animal species in the tropics. Fewer studies are documented assessing the heat stress response of caprine ruminal microbiota, which can also be a crucial indicator of the resilience and/or adaptability of animals. This study was conducted to comparatively assess the heat stress responses of two indigenous goat breeds, Nandidurga and Bidri, based on changes associated with the rumen fermentation pattern and distribution pattern of rumen microbiota. A total of 24 adult animals were randomly allocated into four groups of six animals each, NC (n = 6; Nandidurga control), NHS (n = 6; Nandidurga heat stress), BC (n = 6; Bidri control) and BHS (n = 6; Bidri heat stress). The animals were reared in climate chambers for a duration of 45 days wherein the NC and BC animals were maintained under thermoneutral temperature while the NHS and BHS animals were subjected to simulated heat stress. Heat stress was observed to significantly reduce the rumen ammonia, extracellular CMCase, intracellular carboxy methyl cellulase (CMCase) and total CMCase both in Nandidurga and Bidri goats. In addition to this, a significant reduction in acetate, propionate and total volatile fatty acids (VFAs) was observed in Nandidurga goats. The V3–V4 16s rRNA sequencing further revealed a significant alteration in the rumen microbiota in heat-stressed Nandidurga and Bidri goats. While both the breeds exhibited nearly similar responses in the rumen microbial abundance levels due to heat stress, breed-specific differences were also observed. Furthermore, the LEFSe analysis revealed a significant alteration in the abundances of microbes at the genus level, which were observed to be relatively greater in Bidri goats than Nandidurga goats. Furthermore, these alterations were predicted to impair the functional pathways, especially pathways associated with metabolism. This study therefore provided an insight into the rumen microbial dynamics in heat-stressed goats. Though both the breeds exhibited excellent resilience to the subjected heat stress, there were relatively less ruminal alterations in Nandidurga goats than in Bidri goats. Full article

In chili cultivation, obstacles to continuous cropping significantly compromise crop yield and soil health, whereas crop rotation can enhance the microbial environment of the soil and reduce disease incidence. However, its effects on the diversity of rhizosphere soil microbial communities are not clear. In this study, we analyzed the composition and characteristics of rhizosphere soil microbial communities under chili continuous cropping (CC) and chili–cotton crop rotation (CR) using high-throughput sequencing technology. CR treatment reduced the alpha diversity indices (including Chao1, Observed_species, and Shannon index) of bacterial communities and had less of an effect on fungal community diversity. Principal component analysis (PCA) revealed distinct compositional differences in bacterial and fungal communities between the treatments. Compared with CC, CR treatment has altered the structure of the soil microbial community. In terms of bacterial communities, the relative abundance of Firmicutes increased from 12.89% to 17.97%, while the Proteobacteria increased by 6.8%. At the genus level, CR treatment significantly enriched beneficial genera such as RB41 (8.19%), Lactobacillus (4.56%), and Bacillus (1.50%) (p < 0.05). In contrast, the relative abundances of Alternaria and Fusarium in the fungal community decreased by 6.62% and 5.34%, respectively (p < 0.05). Venn diagrams and linear discriminant effect size analysis (LEfSe) further indicated that CR facilitated the enrichment of beneficial bacteria, such as Bacillus, whereas CC favored enrichment of pathogens, such as Firmicutes. Fusarium solani MG6 and F. oxysporum LG2 are the primary chili root-rot pathogens. Optimal growth occurs at 25 °C, pH 6: after 5 days, MG6 colonies reach 6.42 ± 0.04 cm, and LG2 5.33 ± 0.02 cm, peaking in sporulation (p < 0.05). In addition, there are significant differences in the utilization spectra of carbon and nitrogen sources between the two strains of fungi, suggesting their different ecological adaptability. Integrated analyses revealed that CR enhanced soil health and reduced the root rot incidence by optimizing the structure of soil microbial communities, increasing the proportion of beneficial bacteria, and suppressing pathogens, providing a scientific basis for microbial-based soil management strategies in chili cultivation. Full article

The scarab species Protaetia brevitarsis, an edible insect, has been used in traditional medicine, as animal feed, and for converting agricultural organic wastes into biofertilizer. The intestinal tract, which contains a diverse array of microbiota, including viruses, plays a critical role in animal health and homeostasis. We previously conducted a comparative analysis of the gut microbiota of third-instar larvae of P. brevitarsis obtained from five different farms and found significant differences in the composition of the gut bacterial microbiota between farms. To better understand the gut microbiota, the composition of DNA viruses in the hindgut contents of P. brevitarsis larvae obtained from five farms was investigated using metagenomic sequencing in this study. The β-diversity was significantly different between metagenomic data obtained from the five farms (PERMANOVA, pseudo-F = 46.95, p = 0.002). Family-based taxonomic analysis indicated that the relative abundance of viruses in the gut overall metagenome varied significantly between farms, with viral reads comprising approximately 41.2%, 15.0%, 4.3%, 4.0%, and 1.6% of metagenomic sequences from the farms Tohamsan gumbengi farm (TO), Secomnalagum gumbengi (IS), Gumbengi brothers (BR), Kyungpook farm (KB), and Jhbio (JH), respectively. More than 98% of the DNA viruses in the hindgut were bacteriophages, mainly belonging to the Siphoviridae family. At the species level, Phage Min1, infecting the genus Microbacterium, was detected in all farms, and it was the most abundant bacteriophage in intestinal microbiota, with a prevalence of 0.9% to 29.09%. The detected eukaryotic DNA viruses accounted for 0.01% to 0.06% of the intestinal microbiota and showed little or no relationship with insect viruses. Therefore, they most likely originated from contaminated feed or soil. These results suggest that the condition of substrates used as feed is more important than genetic factors in shaping the intestinal viral microbiota of P. brevitarsis larvae. These results can be used as reference data for understanding the hindgut microbiota of P. brevitarsis larvae and, more generally, the gut virome of insects. Full article

Conspicuous declines in native grassland habitats have triggered sharp reductions in grassland birds, dragonflies, butterflies, and native plant populations and diversity. We compared these biotic groups among three crop type treatments: corn, alfalfa, and a perennial native grass, Virginia wild rye, (Elymus virginicus L.) or VWR. This crop type had 2-3X higher bird, dragonfly, butterfly and plant species richness, diversity, and faunal abundance relative to alfalfa and corn types. VWR crop fields also support more obligate grassland bird species and higher populations of dragonfly and butterfly species associated with grasslands and wet meadows. In contrast, the corn and alfalfa types support few or no obligatory grassland birds and mostly non-native insects such as the white cabbage looper (Artogeia rapae L.), the common yellow sulfur butterfly (Colias philodice Godart.), and the mobile and migratory common green darner dragonfly (Anax junius Drury.). In sum, the VWR perennial native grass crop type offers a special opportunity to improve the diversity and abundance of grassland bird species, beneficial insect species, and many native plant species within agricultural landscapes. Full article

In a greenhouse experiment, we examined the behavior of biochar in arable soil to demonstrate that these supplements can boost soil carbon storage, as well as to track changes in microbial biomass and identify the microbial communities that use these biochars. In order to ascertain if biochar can consistently alter soil microbial activities, we studied the impact of biochar combination treatments on 16S rRNA gene diversity. In soil treated with biochar, there was a rise in the relative abundance of taxa belonging to the phyla Actinobacteria and Gemmatimonadetes, despite the overall diversity decreasing with biochar addition. According to all of these observations, pyrogenic carbon has a major effect on the composition of the soil microbial community and enriches keystone taxa within the parent soil microbial community. Certain species experienced increases throughout the biochar-amended incubation period, despite the total diversity declining following biochar amendments. The phyla Actinobacteria and Gemmatimonadetes increased in the relative abundance of bacteria in soil treated with biochar, according to DNA sequencing of these species. In summary, these findings show that biochar significantly impacts the constitution and composition of the soil microbial community and enriches important taxa within the parent soil microbial community. Full article

Currently, due to the complexity of obtaining samples, specific features of laboratory processing and analysis of the results, there is a lack of data on the microbial signature of the small intestine in healthy and diseased states of the upper gastrointestinal tract. Objective: To investigate the characteristics of the small intestinal microbiome in acute pancreatitis of varying severity and to identify correlations with clinical factors. Methods: This study included 30 patients with acute pancreatitis of varying severity treated between 1 January 2019 and 31 December 2021. The composition of the microbiota was analyzed by metagenomic sequencing of the 16S rRNA gene from jejunal samples. Results: The mortality rate in the study group was 23.3%. The small intestinal microbiome was dominated by Streptococcus (median relative abundance 19.2%, interquartile range 6.4–35.1%), Veillonella (3.4%; 0.6–7%), Granulicatella (2.7%; 0.6–5%), Fusobacterium (2.2%; 0.3–5.9%), Prevotella (1.5%; 0.3–8%), Haemophilus (0.9%; 0.2–10%), Gemella (0.8%; 0.2–4.3%), and Lactobacillus (0.2%; 0.1–0.9%). More severe disease was associated with decreased abundance of Neisseria mucosa, Parvimonas micra, and Megasphaera micronuciformis. In contrast, the relative abundance of the genera Streptococcus (species S. rubneri/parasanguinis/australis), Actinomyces, and several genera within the family Enterobacteriaceae was higher in these patients. Conclusions: The state of the microbiota has important prognostic value and correlates with the duration from the onset of the pain syndrome to the time of receiving qualified care in the hospital. Full article

Plastic debris is a pervasive and persistent threat to marine ecosystems. Microplastics (plastics < 5 mm) are increasing in a variety of marine habitats, including open water systems, shorelines, and benthic sediments. It remains unclear how microplastics distribute and accumulate in marine systems and the extent to which this pollutant is accessible to marine taxa. We examined subtidal benthic sediments and beach sediments in critical nearshore habitats for forage fish species—Pacific sand lance (Ammodytes personatus), Pacific herring (Clupea pallasi), and surf smelt (Hypomesus pretiosus)—to quantify microplastic concentrations in the spawning and deep-water habitats of these fish and better understand how microplastics accumulate and distribute in nearshore systems. In the San Juan Islands, we examined an offshore subtidal bedform in a high-flow channel and beach sites of protected and exposed shorelines. We also examined 12 beach sites proximate to urban areas in Puget Sound. Microplastics were found in all samples and at all sample sites. Microfibers were the most abundant, and flakes were present proximate to major shipyards and marinas. Microplastics were significantly elevated in Puget Sound compared to the San Juan Archipelago. Protected beaches had elevated concentrations relative to exposed beaches and subtidal sediments. Microplastics were in higher concentrations in sand and fine-grain sediments, poorly sorted sediments, and artificial sediments. Microplastics were also elevated at sites confirmed as spawning habitats for forage fish. The model results indicate that both current speed and proximate urban populations influence nearshore microplastic concentrations. Our research provides new insights into how microplastics are distributed, deposited, and retained in marine sediments and shorelines, as well as insight into potential exposure in benthic, demersal, and shoreline habitats. Further analyses are required to examine the relative influence of urban populations and shipping lanes and the effects of physical processes such as wave exposure, tidal currents, and shoreline geometry. Full article

To investigate the characteristics of rhizosphere soil microbial communities associated with Schisandra sphenanthera across different altitudinal gradients and to reveal the driving factors of microbial community dynamics, this study collected rhizosphere soil samples at four elevations: 900 m (HB1), 1100 m (HB2), 1300 m (HB3), and 1500 m (HB4). High-throughput sequencing and molecular ecological network analysis were employed to analyze the microbial community composition and species interactions. A null model was applied to elucidate community assembly mechanisms. The results demonstrated that bacterial communities were dominated by Proteobacteria, Acidobacteriota, Actinobacteriota, and Chloroflexi. The relative abundance of Proteobacteria increased with elevation, while that of Acidobacteriota and Actinobacteriota declined. Fungal communities were primarily composed of Ascomycota and Basidiomycota, with both showing elevated relative abundances at higher altitudes. Diversity indices revealed that HB2 exhibited the highest bacterial Chao, Ace, and Shannon indices but the lowest Simpson index. For fungi, HB3 displayed the highest Chao and Ace indices, whereas HB4 showed the highest Shannon index and the lowest Simpson index. Ecological network analysis indicated stronger bacterial competition at lower elevations and enhanced cooperation at higher elevations, contrasting with fungal communities that exhibited increased competition at higher altitudes. Altitude and soil nutrients were negatively correlated with soil carbon content, while plant nutrients and fungal diversity positively correlated with soil carbon. Null model analysis suggested that deterministic processes dominated bacterial community assembly, whereas stochastic processes governed fungal assembly. These findings highlight significant altitudinal shifts in the microbial community structure and assembly mechanisms in S. sphenanthera rhizosphere soils, driven by the synergistic effects of soil nutrients, plant growth, and fungal diversity. This study provides critical insights into microbial ecology and carbon cycling in alpine ecosystems, offering a scientific basis for ecosystem management and conservation. Full article

Rheum cordatum Losinsk is a plant species distributed in Kazakhstan but remains relatively understudied despite its promising biological potential. The present study aimed to explore leaf extracts of R. cordatum by utilizing advanced green extraction technologies including supercritical CO₂ (ScCO₂), subcritical ethanol (Sc) and ultrasound-assisted extraction (UAE) to characterize their phytochemical composition and evaluate their antioxidant and antimicrobial activities. A total of 53 phytochemical compounds were identified, with gallic acid (30.71 µg/mg UAE-EtOH-4h), rutin (21.93 µg/mg ScCO₂-150) and hesperidin (14.98 µg/mg ScCO₂-150) being notably abundant. Among the tested extracts, ScCO₂ extraction at 150 bar (ScCO₂-150) demonstrated the highest antioxidant activity, exhibiting IC₅₀ values of 0.0132 mg/mL (DPPH) and 0.0462 mg/mL (ABTS), coupled with the highest total phenolic content (140 mg GAE/g). Moreover, the ScCO₂-150 extract showed pronounced antimicrobial efficacy, particularly against Bacillus subtilis Pseudomonas aeruginosa and Staphylococcus aureus, with minimum inhibitory concentrations (MIC) ranging from 125 to 250 µg/mL. These findings highlight the considerable potential of R. cordatum leaves as a valuable, abundant and sustainable source of natural antioxidants and antimicrobial agents, with supercritical CO₂ extraction presenting substantial advantages in selectively obtaining bioactive phytochemicals. Full article