Search Results (1,137)

The gut microbiota plays an essential role in the host’s metabolism. Its composition and structure depend on biological and environmental factors. This work was designed to identify the composition and structure of the wild and captive red grouper (Epinephelus morio) microbiota and make predictions regarding its metabolic functions. Our hypothesis stated that wild and captive individuals would share the most abundant taxonomic groups, forming a core microbiota, and individuals in captivity might have exclusive taxonomic groups. Metagenomic DNA was extracted from the intestinal contents of wild and captive individuals. The 16S rRNA gene was amplified and sequenced using Illumina pair-end technology. QIIME2 pipeline was used for sequence analysis and alpha and beta diversity assessment. PICRUSt was used to infer metabolic functions. Twenty-nine phyla were identified; the most abundant were Pseudomonadota, Bacillota, Fusobacteriota, and Actinomycetota. The dominant genera were Photobacterium, Vibrio, Cetobacterium, and Escherichia-Shigella. The metabolic prediction analysis suggested that the Epinephelus morio gut microbiota is related to food digestion, the immune system, antioxidant enzymes, antibiotic resistance, and vitamin B12 transport. We concluded that the microbiota of E. morio established in captivity is sensitive to environmental changes such as water pollution, which can cause a decrease in diversity. Full article

China’s southwestern karst landscapes support remarkable cavefish diversity, especially within Sinocyclocheilus, the world’s largest cavefish genus. Using integrative taxonomic methods, we describe Sinocyclocheilus wanlanensis sp. nov., found in a subterranean river in Guizhou Province. This species lacks horn-like cranial structures; its eyes are either reduced to a dark spot or absent. It possesses a pronounced nuchal hump and a forward-protruding, duckbill-shaped head. Morphometric analysis of 28 individuals from six species shows clear separation from related taxa. Nano-CT imaging reveals distinct vertebral and cranial features. Phylogenetic analyses of mitochondrial cytb and ND4 genes place S. wanlanensis within S. angularis group as sister to S. bicornutus, with p-distances of 1.7% (cytb) and 0.7% (ND4), consistent with sister-species patterns within the genus. Sinocyclocheilus wanlanensis is differentiated from S. bicornutus by its eyeless or degenerate-eye condition and lack of bifurcated horns. It differs from S. zhenfengensis, its morphologically closest species, in having degenerate or absent eyes, shorter maxillary barbels, and pelvic fins that reach the anus. The combination of morphological and molecular evidence supports its recognition as a distinct species. Accurate documentation of such endemic and narrowly distributed taxa is important for conservation and for understanding speciation in cave habitats. Full article

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

Soil bacteria drive biogeochemical cycles and influence disease suppression, playing pivotal roles in sustainable agriculture. Using Illumina MiSeq sequencing, we assessed how six ridge-furrow film mulching patterns affect soil bacterial diversity in a continuous potato system. The Shannon index showed significantly higher diversity in fully mulched treatments (T2–T3) versus controls (CK), suggesting mulching enhances microbial community richness. This result suggests that complete mulching combined with ridge planting (T2) may significantly enhance bacterial proliferation in soil. The bacterial communities were predominantly composed of Acidobacteria, Pseudomonadota, Bacteroidota, Chloroflexota, and Planctomycetota. Among these, Acidobacteria showed the highest abundance, with ridge planting patterns favoring greater Acidobacteria richness compared to furrow planting. In contrast, Pseudomonadota exhibited higher abundance under half-mulching conditions than under complete mulching. At class level, Acidobacteria and Proteobacteria emerged as the most abundant groups, with Proteobacteria constituting 22.6–35.7% of total microbial populations. Notably, Proteobacteria demonstrated particular dominance under the complete mulching with ridge planting pattern (T2). At the genus level, Subgroup_6_norank represented the most dominant taxon among the 439 identified bacterial genera, accounting for 14.0–20.2% of communities across all treatments, with half-mulching ridge planting (T4) showing the highest relative abundance. Our findings demonstrate that different ridge-furrow film mulching patterns significantly influence soil microbial diversity. While traditional non-mulched (CK) and mulched flat plots (T1) exhibited similar impacts on bacterial community structure, other treatments displayed distinct taxonomic profiles. Complete mulching patterns, particularly ridge planting (T2), appear most conducive to microbial development, suggesting their potential to enhance soil biogeochemical cycling in continuous cropping systems. These results provide valuable insights for optimizing mulching practices to improve soil health in agricultural ecosystems. Full article

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

Artificial reservoirs in arid regions provide unique ecological environments for studying the spatial and functional dynamics of plankton communities under the combined stressors of climate change and anthropogenic activities. This study conducted a systematic investigation of the phytoplankton community structure and its environmental drivers in 17 artificial reservoirs in the Ili region of Xinjiang in August and October 2024. The Ili region is located in the temperate continental arid zone of northwestern China. A total of 209 phytoplankton species were identified, with Bacillariophyta, Chlorophyta, and Cyanobacteria comprising over 92% of the community, indicating an oligarchic dominance pattern. The decoupling between numerical dominance (diatoms) and biomass dominance (cyanobacteria) revealed functional differentiation and ecological complementarity among major taxa. Through multivariate analyses, including Mantel tests, principal component analysis (PCA), and redundancy analysis (RDA), we found that phytoplankton community structures at different ecological levels responded distinctly to environmental gradients. Oxidation-reduction potential (ORP), dissolved oxygen (DO), and mineralization parameters (EC, TDS) were key drivers of morphological operational taxonomic unit (MOTU). In contrast, dominant species (SP) were more responsive to salinity and pH. A seasonal analysis demonstrated significant shifts in correlation structures between summer and autumn, reflecting the regulatory influence of the climate on redox conditions and nutrient solubility. Machine learning using the random forest model effectively identified core taxa (e.g., MOTU1 and SP1) with strong discriminatory power, confirming their potential as bioindicators for water quality assessments and the early warning of ecological shifts. These core taxa exhibited wide spatial distribution and stable dominance, while localized dominant species showed high sensitivity to site-specific environmental conditions. Our findings underscore the need to integrate taxonomic resolution with functional and spatial analyses to reveal ecological response mechanisms in arid-zone reservoirs. This study provides a scientific foundation for environmental monitoring, water resource management, and resilience assessments in climate-sensitive freshwater ecosystems. Full article

Background/Objectives: Bacteriophages infecting the genus Streptococcus play a crucial role in microbial ecology and have potential applications in biotechnology and medicine. Despite their importance, significant gaps remain in our understanding of their lysis modules. This study aims to address these deficiencies by analyzing the genomic diversity and lysis module organization in Streptococcus phages. Methods: A search was conducted in the NCBI RefSeq database to identify phage genomes infecting Streptococcus. A representative panel was selected based on taxonomic diversity. Lysis modules were annotated and visualized, functional domains in endolysins were identified, and holins were characterized. Results: A total of 205 phage genomes were retrieved from the NCBI RefSeq database, of which 185 complete genomes were analyzed. A subset of 34 phages was selected for in-depth analysis, ensuring the representation of taxonomic diversity. The lysis modules were annotated and visualized, revealing five distinct organizations. Among the 256 identified endolysins, 25 distinct architectural organizations were observed, with amidase activity being the most prevalent. Holins were classified into 9 of the 74 families listed in the Transporter Classification Database, exhibiting one to three transmembrane domains. Conclusions: This study provides insights into the structural diversity of lysis modules in Streptococcus phages, paving the way for future research and potential biotechnological applications. Full article

Background/Objectives: Cardiovascular diseases remain the leading cause of global mortality, with the gut microbiome emerging as a critical factor. This study aimed to characterize gut microbiome composition and metabolic pathways in individuals with low cardiovascular risk (LCR) compared to healthy controls to reveal insights into early disease shifts. Methods: We performed shotgun metagenomic sequencing on fecal samples from 25 LCR individuals and 25 matched healthy controls. Participants underwent a comprehensive cardiovascular evaluation. Taxonomic classification used MetaPhlAn 4, and functional profiling employed HUMAnN 3. Results: Despite similar alpha diversity, significant differences in bacterial community structure were observed between groups (PERMANOVA, p < 0.05). The LCR group showed enrichment of Faecalibacterium prausnitzii (p = 0.035), negatively correlating with atherogenic markers, including ApoB (r = −0.3, p = 0.025). Conversely, Fusicatenibacter saccharivorans positively correlated with ApoB (r = 0.4, p = 0.006). Metabolic pathway analysis revealed upregulation of nucleotide biosynthesis, glycolysis, and sugar degradation pathways in the LCR group, suggesting altered metabolic activity. Conclusions: We identified distinct gut microbiome signatures in LCR individuals that may represent early alterations associated with cardiovascular disease development. The opposing correlations between F. prausnitzii and F. saccharivorans with lipid parameters highlight their potential roles in cardiometabolic health. These findings suggest gut microbiome signatures may serve as indicators of early metabolic dysregulation preceding clinically significant cardiovascular disease. Full article

Aeromonas spp. are opportunistic pathogens that are widely distributed in water sources, with several species being associated with fish and human diseases. We have previously identified an Aeromonas AB005 isolate from diseased Acipencer baerii. This isolate was identified as A. hydrophila based on the 16S rRNA and gyrB gene sequences. However, this novel strain does not produce indole and tested negative for ornithine decarboxylase and d-xylose fermentation—differences that set it apart from typical A. hydrophila strains. In the present study, this strain was subjected to whole-genome sequencing and compared with the genomes of the type strain (Aeromonas hydrophila ATCC 7966^T) and other Aeromonas spp. Comprehensive genome analysis suggests that AB005 represents a distinct species within the genus. The draft genome of the AB005 strain comprises 4,780,815 base pairs with a GC content of 61.2% and contains 6104 predicted protein-coding sequences along with numerous genes implicated in antibiotic resistance. The core/pan-genome analysis reveals extensive genetic diversity, indicative of a dynamic genomic structure. These findings collectively underscore the taxonomic distinction of the AB005 strain as a novel species and highlight its potential pathogenic implications in aquaculture and public health settings. Full article

Aquatic fungi serve as core ecological engines in freshwater ecosystems, driving organic matter decomposition and energy flow to sustain environmental balance. Wetlands, with their distinct hydrological dynamics and nutrient-rich matrices, serve as critical habitats for these microorganisms. As an internationally designated Ramsar Site, Yunnan Dashanbao Black-Necked Crane National Nature Reserve in China not only sustains endangered black-necked cranes but also harbors a cryptic reservoir of aquatic fungi within its peat marshes and alpine lakes. This study employed high-throughput sequencing to characterize fungal diversity and community structure across 12 understudied wetland sites in the reserve, while analyzing key environmental parameters (dissolved oxygen, pH, total nitrogen, and total phosphorus). A total of 5829 fungal operational taxonomic units (OTUs) spanning 649 genera and 15 phyla were identified, with Tausonia (4.17%) and Cladosporium (1.89%) as dominant genera. Environmental correlations revealed 19 genera significantly linked to abiotic factors. FUNGuild functional profiling highlighted saprotrophs (organic decomposers) and pathogens as predominant trophic guilds. Saprotrophs exhibited strong associations with pH, total nitrogen, and phosphorus, whereas pathogens correlated primarily with pH. These findings unveil the hidden diversity and ecological roles of aquatic fungi in alpine wetlands, emphasizing their sensitivity to environmental gradients. By establishing baseline data on fungal community dynamics, this work advances the understanding of wetland microbial ecology and informs conservation strategies for Ramsar sites. Full article

Protists represent a major component of eukaryotic diversity within the soil microbiome, playing critical roles in mediating carbon and nitrogen cycling and influencing nutrient availability and soil health. Their diversity is shaped by multiple factors, including temperature, pH, organic matter content, and land use. In this study, we investigated the protist diversity in rhizosphere soils from both wild and cultivated date palm varieties. Our results identified nitrate, nitrite, calcium, and carbon content as key soil factors significantly correlated with protist diversity. Only 9.2% (42) of operational taxonomic units (OTUs) were shared across all soil samples, suggesting that these taxa possess traits enabling adaptation to extreme environmental conditions. The dominant protist families belonged to Rhizaria, Alveolata, Amoebozoa, and Archaeplastida, primarily comprising bacterial consumers, alongside taxa from Stramenopiles, Opisthokonta, Hacrobia, and Excavata. At the class level, Filosa-Sarcomonadea, Colpodea, Variosea, Tubulinea, and Chlorophyceae were the most abundant. Filosa-Sarcomonadea and Colpodea were positively correlated with bacterial and fungal genera, suggesting their role as consumers, while Variosea showed a negative correlation with bacteria, reflecting predator-prey dynamics. Notably, the protist community composition in wild date palm rhizosphere soils was distinct from that in cultivated soils, with Opisthokonta being particularly abundant, likely reflecting adaptation to drought conditions. Overall, this study highlights the significant differences in protist diversity and community structure between wild and cultivated date palm ecosystems. Full article

This study presents a bibliographic review of the genus Menegazzia in Chile, the first in over two decades, updating new records, the taxonomic placement of the genus, and the synonymization of species. Up to twenty species have been cited in the country, considering that M. albida, M. hollermayeri, and M. norstictca are synonyms of the valid species M. wilsonii, M. dispora, and M sanguinascens. A fully revised dichotomous key and color photographs are included to facilitate accurate identification, especially given the genus’s morphological convergence and sparse reproductive structures. For the first time, the divergence times of Menegazzia lineages are discussed in relation to major Southern Hemisphere geologic events, suggesting a dispersal-driven distribution with a crown age of approximately 21.2 Ma. This review consolidates fragmented data, integrates recent molecular findings, and emphasizes the genus’s value as an ecological and biogeographic indicator in Chilean temperate forests. Full article

Background: Ligusticum L. plants exhibit significant morphological variation in leaves, flowers, bracteoles and mericarps, thus the classifications of members for the genus have always been controversial. Among them, the taxonomic problem of Ligusticum multivittatum Franch. is the most prominent, which has not been sufficiently resolved so far. Methods: to clarify the taxonomic position of Ligusticum multivittatum, we performed phylogenetic analyses based on plastome data and ITS sequences. Meanwhile, we conducted comprehensively comparative plastome analyses between Ligusticum multivittatum and fifteen Ligusticopsis species. Results: Both analyses robustly supported that Ligusticum multivittatum nested in genus Ligusticopsis Leute and formed a clade with fifteen Ligusticopsis species, belonged to the Selineae tribe, which was distant from the type species of Ligusticum (Ligusticum scoticum), located in the Acronema clade.The comparative results showed that sixteen plastomes were highly similar and conservative in genome structure, size, gene content and arrangement, codon bias, SSRs and SC/IR. These findings imply that Ligusticum multivittatum is a member of Ligusticopsis, which was further verified by their shared morphological characters: stem base clothed in fibrous remnant sheaths, white petals, pinnate bracteoles, dorsally compressed mericarps with slightly prominent dorsal ribs, winged lateral ribs and numerous vittae in the commissure and in each furrow. Therefore, combining with the evidences of phylogenetic analyses, plastome comparison and morphological features, we affirmed that Ligusticum multivittatum indeed belonged to Ligusticopsis and transformed it into Ligusticopsis conducted by Pimenov was reasonable. Conclusions: Our study not only confirms the classification of Ligusticum multivittatum by integrating evidences, but also provides a reference for resolving taxonomy of contentious taxa. Full article

Fire is a key ecological driver in tropical savannas, yet its effects on plant biodiversity remain understudied in Amazonian savannas. This study investigates how fire recurrence influences taxonomic and functional diversity in savanna ecosystems in northeastern Amazonia. We conducted vegetation surveys across five phytophysiognomies in Amapá State, Brazil, and compiled trait data for 226 plant species. Generalized Additive Mixed Models (GAMMs) were used to evaluate the relationships between fire frequency and diversity metrics across five landscape scales. The results showed that taxonomic diversity—particularly Shannon diversity—exhibited a unimodal response to fire recurrence, with peak diversity occurring at intermediate fire frequencies. Abundance increased with fire frequency, indicating potential dominance by fire-tolerant species. Functional diversity responded more subtly: functional richness and dispersion showed weak, non-linear associations with fire, while functional evenness remained stable. These findings suggest that recurrent fire can reduce taxonomic diversity without strongly altering functional structure, possibly due to functional redundancy among species. The use of multiscale models revealed that biodiversity–fire relationships vary with spatial context. In conclusion, this study highlights the moderate resilience of Amazonian savannas to fire recurrence and emphasizes the need to incorporate these ecosystems into fire management plans in climate change scenarios. Full article

The green octopus, Octopus hubbsorum, is a merobenthic species that inhabits warm-temperate waters in the eastern Pacific. However, its similarity to some morphological characteristics of and its slight genetic divergence from Octopus mimus has led to the proposal that both species are conspecific. The objective of this study was the morphological and molecular identification of eggs and paralarvae of the green octopus, O. hubbsorum, to provide information contributing to clarifying its taxonomy and relationship with O. mimus. The results obtained show that although O. hubbsorum has similarities with O. mimus in terms of egg size, chromatophore pattern, number of suckers, and presence of Kölliker’s organs, the O. hubbsorum paralarvae observed in this study are smaller (1.6 mm) and have a thin layer of loose skin, not described for O. mimus. Likewise, the morphology of the beak, radula, and suckers of O. hubbsorum is described for the first time and there are no studies of these structures for O. mimus. The phylogenetic analysis (mitochondrial cytochrome C oxidase subunit I and III genes) showed that both species form a monophyletic clade but belong to separate subclades. In conclusion, although the slight genetic divergence between these two species suggests conspecificity, their disjoint geographic distribution (O. hubbsorum is found in warm-temperate waters and O. mimus in cold-temperate waters) suggests the hypothesis of being two separate species with a close phylogenetic relationship. However, further research (morphological and population analyses) is required to solve taxonomic uncertainty. Full article