Search Results (89)

Dybowski’s frog (Rana dybowskii) supports a multi-billion-dollar aquaculture sector in northern China and plays a critical ecological role in forest ecosystems. Despite its immense economic value, germplasm degradation and the mystery surrounding its homomorphic sex-determination system present major bottlenecks for the industry. Here, we integrated PacBio HiFi long-read sequencing, Illumina short-read sequencing, and High-Throughput Chromosome Conformation Capture (Hi-C) technologies to assemble the first chromosome-level reference genome of R. dybowskii. The final assembled genome size is 3.77 Gb, with a contig N50 of 16.27 Mb and a scaffold N50 of 41.54 Mb. A total of 97.82% of the sequences were successfully anchored onto 12 definitive pseudochromosomes corresponding to haploid chromosome number. Repetitive elements account for 65.61% of the genome, characterized by an unusual dominance of DNA transposons (37.19%) over retrotransposons, suggesting a genomic landscape shaped by extreme cold adaptation. Combining multi-tissue transcriptomic evidence, we structurally predicted 26,862 protein-coding genes, and the predicted gene set showed a BUSCO completeness of 96.1%. Functional annotation successfully categorized 96.55% of the total genes. This genomic resource successfully fills a crucial phylogenetic gap in the Rana genus, driving high-efficiency molecular breeding and sustainable conservation of this economic amphibian. Full article

Given the ongoing global decline in biodiversity, species reintroduction has become an important strategy for the conservation of endangered wildlife. Père David’s deer (Elaphurus davidianus), a historically extinct-in-the-wild species successfully reintroduced in China, represents a useful model for evaluating ecological responses following reintroduction into different habitats. Increasing evidence suggests that fecal microbiota can serve as a non-invasive indicator of host-associated microbial communities and their variation under different conditions. In this study, we investigated the fecal microbiota of a reintroduced population in the Daqingshan National Nature Reserve (Inner Mongolia). A total of 90 fresh fecal samples were collected between December 2021 and October 2023 across different seasonal periods. High-throughput 16S rRNA gene sequencing was used to characterize microbial community structure, and comparative analyses were conducted alongside published datasets from populations in Beijing and Shishou. The results revealed significant seasonal variation in microbial community composition and diversity, with distinct clustering of rainy, dry, and transitional (October) samples. Several taxa exhibited differential enrichment between seasons, suggesting temporal shifts in microbial community structure. A comparative analysis with other populations (Beijing and Shishou) revealed differences in microbial composition at broad taxonomic levels, suggesting potential variations related to regional environmental conditions, diet, and management practices. Overall, the observed patterns are consistent with seasonal variation in plant resource availability and highlight the potential influence of geographic context on microbial community structure. This study provides baseline data on the fecal microbiota of Père David’s deer in a semi-arid steppe environment and the potential indication of host suitability from the perspective of the microbiome. Full article

This study explored the differences in slaughter performance, blood biochemical indices, and ruminal and colonic microbiota between 6-month-old male and female Small-tailed Han sheep, a typical meat-wool dual-purpose breed in China. Twenty weaned lambs (10 males and 10 females) with uniform body condition were reared under unified feeding management until 6 months of age, followed by slaughter sampling and microbial sequencing detection. Results showed that male lambs had significantly higher pre-slaughter live weight, carcass weight and serum ALP content than females (p < 0.05), with lower BUN and β-BHBA levels (p < 0.05). High-throughput sequencing of the 16S rDNA gene in rumen fluid and colon contents revealed that microbial alpha diversity in the rumen was extremely significantly higher than that in the colon (p < 0.01), and their microbial community structures were distinctly separated (p = 0.001). Sex had no significant effect on overall microbial diversity, but altered specific flora and functional pathways: male rumen had higher Actinobacteriota abundance, while female colon had enriched galactose metabolism and male colon had enhanced folate-mediated one-carbon pool pathway. These findings clarify the tissue specificity of gastrointestinal microbiota and sex-related phenotypic differences, providing a theoretical basis for sex-specific feeding of Small-tailed Han sheep. Full article

To explore the application potential of insect-derived functional microorganisms in short-cycle leafy vegetable production, we evaluated the effects of Serratia marcescens BRC-CXG2, isolated from larvae of Monochamus alternatus, on romaine lettuce in a pot experiment. Plant growth traits, biomass accumulation, nutritional quality, endogenous hormones, and rhizosphere microbial communities were systematically evaluated. The results demonstrated that inoculation significantly promoted seedling development. Plant height and root length increased by 48.7% and 29.1%, respectively, while shoot and root dry weights were 1.78- and 1.85-fold higher than those of the control. Vitamin C and total sugar contents increased by 76.4% and 98%, respectively. The levels of gibberellins (GA₃)-, indole-3-acetic acid (IAA)-, and abscisic acid (ABA)-immunoreactive equivalents increased by 1.5-, 1.29-, and 1.75-fold. High-throughput 16S rDNA gene and ITS amplicon sequencing further revealed that inoculation reshaped the composition of bacterial and fungal communities in the rhizosphere. Collectively, these findings demonstrate that insect-derived S. marcescens exhibits significant growth-promoting potential in short-cycle leafy vegetable systems, with effects associated with hormone regulation, enhanced total sugar accumulation, and shifts in rhizosphere microbial community structure. Full article

Previously, the role of decreased biodiversity of gut microbiota in polycystic ovary syndrome (PCOS) was demonstrated, but the objective criteria for assessing the representation of microorganisms associated with hyperandrogenemia (HA) were limited. A total of 175 premenopausal women (26 women with PCOS and HA and 149 women without HA, including 19 healthy controls) were recruited during the Eastern Siberia PCOS Epidemiology and Phenotype (ESPEP) Study (2016–2019). Methods included a questionnaire survey, clinical examination, pelvic U/S, blood and feces sampling. Gut microbiome was analyzed by high-throughput sequencing of the V1–V3 of the variable regions of the 16S rRNA gene (Illumina MiSeq, San Diego, CA, USA). Amplicon libraries of 16S rDNA were processed using the QIIME2 bioinformatics pipeline. All data were analyzed using R 3.6.3. The gut microbiocenosis in women with HA was characterized by a higher representation of Lactobacillus and a lower prevalence of the Clostridia class. For Faecalibacterium, Christensenellaceae_R-7_group, and [Eubacterium] eligens group the cut-off values of their relative presence, associated with HA, were estimated as: ≤0.043%, ≤0.039%, and ≤0.02%, respectively. Conclusions: Women with PCOS-associated HA demonstrate a lower prevalence, predominantly, of Clostridia class gut microorganisms, compared with those without any forms of HA. The study presents the quantitative criteria for assessing the representation of gut microorganisms, negatively associated with hyperandrogenic phenotypes of PCOS. The threshold values proposed may be useful to justify the administration of probiotics in PCOS patients with HA. Full article

Soil degradation remains a major challenge in sub-Saharan Africa, particularly within smallholder farming systems characterized by low-input agriculture and unsustainable land use practices. Sustainable agriculture production requires a good understanding of soil characteristics across diverse farming contexts. This study assessed soil health and microbial diversity across three contrasting systems: long-term fallow (aggregated farm A), high-input (aggregated farm B), and conventional smallholder (non-aggregated farm C) farms experiencing declining productivity. Soil samples collected from the three contrasting systems were analyzed for physicochemical properties and microbial communities using high-throughput DNA sequencing. Microbial communities were characterized by using amplicon sequencing targeting bacterial 16S rRNA and fungal ITS gene regions, allowing taxonomic profiling and inference of microbial diversity patterns. The two aggregated farms predominantly had clay soils, with pH values ranging from 6.78 to 7.39 and organic carbon content from 1.17% to 1.64%. In contrast, conventional farms had loamy to clayey soils with a pH value of 5.88 and an organic carbon content of 1.25%. Both types of aggregated farms showed moderate to high concentrations of total nitrogen (0.12–0.13%), phosphorus (38.79–151.36 mg/kg), and potassium (548.84–943.52 mg/kg), along with elevated levels of calcium and magnesium, though fertilizer application was inconsistent across the sites. Microbial diversity analysis revealed significant differences among the systems. The dominant bacterial phyla were Pseudomonadota (48.5%), Acidobacteriota (34.2%) and Actinomycetota (19.6%), while the primary fungi included Ascomycota, Basidiomycota and Mortierellomycota. Functional profiling using COG and KEGG databases showed distinct variations in microbial potentials, with a high diversity of Actinobacteria, Acidobacteria and Proteobacteria. Functional profiles inferred from amplicon-based predictions represent potential metabolic capabilities and should be interpreted cautiously as indicative rather than direct functional gene quantification. Correlation analyses between soil and microbial communities provided essential baseline data to support the development of sustainable farming practices and land restoration strategies aimed at improving soil fertility and agricultural productivity in these degraded landscapes. Full article

The Qinghai–Xizang Plateau, known as the “Asian Water Tower”, hosts numerous lakes that are highly sensitive to climate change. Ciliates, key microbial eukaryotes in aquatic ecosystems, play crucial roles in biogeochemical cycling and food web dynamics. However, their community assembly mechanisms in such extreme habitats remain poorly understood. In July 2020, we investigated the ciliate community in Basomtso Lake. A total of 15 sampling sites were established along the horizontal gradient, and 11 vertical depth samples were collected at a central site (B15), resulting in 75 water samples for eDNA analysis. Using 18S rRNA gene high-throughput sequencing, we identified 610 ciliate amplicon sequence variants (ASVs), with the class Spirotrichea being the dominant taxonomic group. Distance–decay relationships indicated a significantly stronger community turnover rate along the vertical gradient compared to the horizontal gradient. Analyses using the neutral community model and null model revealed that community assembly was primarily stochastic. However, increasing vertical environmental heterogeneity enhanced the role of deterministic, niche-based selection. Random forest modeling identified resistivity (RES) and water temperature (WT) as the key predictors for horizontal and vertical community variation, respectively. Furthermore, Threshold Indicator Taxa Analysis (TITAN) detected specific taxa exhibiting pronounced sensitivity to gradients in RES and WT. Our findings demonstrate that horizontal community structure is governed primarily by dispersal limitation, whereas vertical zonation is shaped by environmental filtering driven primarily by RES and WT gradients under extreme plateau conditions. This study provides new insights into the mechanisms sustaining microbial diversity and ecosystem resilience in climatically vulnerable high-altitude lakes. Full article

Antibiotic resistance genes (ARGs) and microbial communities in pig and cow dung from rural China were systematically profiled using high-throughput quantitative PCR arrays and 16S rDNA amplicon sequencing to assess their environmental dissemination and public health risks. The abundance and diversity of ARGs were markedly higher in pig dung than in cow dung. A total of 56 ARGs were enriched in pig dung, including β-lactamase genes (blaCMY, blaCTX-M) and macrolide resistance genes (ermB, ermF), along with several genes related to aminoglycoside and macrolide–lincosamide–streptogramin B resistance. In contrast, only eight ARGs were enriched in cow dung. Microbial community analysis revealed that cow dung was dominated by UCG-005, UCG-010, Methanocorpusculum, and Fibrobacter, taxa typically associated with ruminant digestion. In pig dung, Ignatzschineria, Lactobacillus, Pseudomonas, Streptococcus, Treponema, and conditional pathogens such as Escherichia coli and Leptospira were significantly enriched, indicating higher pathogen-related risks. Functional prediction identified 26 KEGG level-2 and 136 level-3 pathways, showing stronger xenobiotic degradation and amino acid metabolism in pig dung, whereas cow dung was enriched in energy metabolism and chemotaxis pathways. Moreover, the higher abundance of mobile genetic elements (e.g., intI1 and IS613) in pig dung suggests a greater potential for horizontal ARG transfer. Integrating ARG, microbial, and pathogen data reveals that pig dung acts as a composite source of “ARG–pathogen” contamination with enhanced transmission potential. These findings provide localized, data-driven evidence for developing safer livestock waste management practices, such as composting and biogas utilization, and contribute to antibiotic resistance mitigation strategies in rural China. Full article

Osorno volcano (41.1° S, 72° W) is located in the Andean Southern Volcanic Zone. The volcano lies within a national park as part of the protected areas system. This setting provides an opportunity to compare soil microbial communities between sectors with (H) and without (NI) anthropogenic activities within a volcanic territory. To do so, we selected one of the most visited volcanoes in Chilean Patagonia to examine composition, diversity (taxonomic and phylogenetic), and co-presence and mutual exclusion interaction networks between members of volcanic soil bacterial communities. Soil DNA was extracted, and the 16S rRNA gene was analyzed by high-throughput DNA sequencing, followed by taxonomic identification. The most prevalent phylum across all sites (H and NI) was Pseudomonadota, followed by Acidobacteriota, Actinobacteriota, and Chloroflexota. Based on taxonomic and phylogenetic indices, we found that the diversity of bacteria was significantly less in the humanized area than in the non-intervened areas. Beta diversity analysis also revealed a clear separation between humanized and non-intervened soils. Additionally, a decrease in network connectivity was observed at NI sites. Our results provide clear evidence that anthropogenic factors, such as tourism, vehicle parking, and combustion processes, are key drivers shaping bacterial community structure in volcanic soils, with potential consequences for ecosystem health and the capacity to provide ecosystem services. Full article

As one of the key vectors for the transmission of Dengue fever, Aedes albopictus is highly ecologically adaptable. The development of environmentally compatible biological defence and control technologies has therefore become an urgent need for vector biological control worldwide. This study constructed and used double-stranded RNA (dsRNA) expression vectors targeting the cyp314a1 and cyp315a1 genes of Ae. albopictus to transform Chlamydomonas reinhardtii and Chlorella vulgaris, achieving RNA interference (RNAi)-mediated gene silencing. The efficacy of the RNAi recombinant algal strain biocide against Ae. albopictus was evaluated by administering it to Ae. albopictus larvae. The results showed that the oral administration of the cyp314a1 and cyp315a1 RNAi recombinant C. reinhardtii/C. vulgaris strains was lethal to Ae. albopictus larvae and severely affected their pupation and emergence. The recombinant algal strains triggered a burst of ROS (Reactive Oxygen Species) in the mosquitoes’ bodies, resulting in significant increases in the activities of the superoxide dismutase (SOD), peroxiredoxin (POD) and catalase (CAT), as well as significant upregulation of the mRNA levels of the CME pathway genes in larvae. In the simulated field experiment, the number of Ae. albopictus was reduced from 1000 to 0 in 16 weeks by the RNAi recombinant Chlorella, which effectively controlled the population of mosquitoes. Meanwhile, the levels of nitrogen (N), phosphorus (P), nitrate, nitrite, ammonia and COD (Chemical Oxygen Demand) in the test water decreased significantly. High-throughput sequencing analyses of 18S rDNA and 16S rDNA showed that, with the release of RNAi recombinant Chlorella into the test water, the biotic community restructuring dominated by resource competition caused by algal bloom, as well as the proliferation of anaerobic bacteria and the decline of aerobic bacteria triggered by anaerobic conditions, are the main trends in the changes in the test water. This study is an important addition to the use of RNAi recombinant microalgae as a biocide. Full article

CRISPR (clustered regularly interspaced short palindromic repeats)-Cas (CRISPR-associated protein) nucleases enable precise genome editing, but off-target cleavage remains a critical challenge. Here, we report the development of MAD7_HF, a high-fidelity variant of the MAD7 nuclease engineered through a bacterial screening system leveraging the DNA gyrase-targeting toxic gene ccdB. This system couples survival to efficient on-target cleavage and minimal off-target activity, mimicking the transient action required for high-precision editing. Through iterative selection and sequencing validation, we identified MAD7_HF, harboring three substitutions (R187C, S350T, K1019N) that enhanced discrimination between on- and off-target sites. In Escherichia coli assays, MAD7_HF exhibited a >20-fold reduction in off-target cleavage across multiple mismatch contexts while maintaining on-target efficiency comparable to wild-type MAD7. Structural modeling revealed that these mutations stabilize the guide RNA-DNA hybrid at on-target sites and weaken interactions with mismatched sequences. This work establishes a high-throughput bacterial screening strategy that allows the identification of Cas12a variants with improved specificity at a given target site, providing a useful framework for future efforts to develop precision genome-editing tools. Full article

Apricots are affected by many abiotic and biotic factors that could negatively impact their vitality and yield, leading to branch and tree dieback. Knowledge of the microbiome composition is key to choosing the optimal measurement strategy. The effect of the two different growing systems, i.e., organic (ORG) and integrated pest management (IPM), on the apricot fungal microbiome was studied. The inner bark was used to isolate DNA, and the present fungi were analyzed using a metagenomics high-throughput sequencing (HTS) profiling approach of the data obtained based on the Illumina sequencing of the ITS1-ITS2 amplicons of the 18S rRNA gene. Of the 20 analyzed samples, Ascomycota was the dominant phylum, and Dothiomycetes was the most abundant. Basidiomycota was the less frequent, with Tremellomycetes being the predominant within this phylum. PCA analysis showed the complete separation of the samples obtained from the orchards grown under the ORG and IPM systems. Cladosporia, Alternaria, Aureobasidium, and Visniacozyma were detected in all samples, but they dominated the IPM samples. Filobasiadiales were recognized as an indicator species for ORG management, while Caliciales, Lecanorales, Lichinales, Mycosphaerellales, Myriangiales, Phacidiales, Teloschistales, and Thelebolales were identified as indicator species for IPM management. Based on the order and genus levels, a significantly higher fungal microbiome richness was detected in the ORG samples. This could be connected to the environmentally beneficial growing system applied in the orchard, but it is impossible to assess the risk of trunk disease development or premature apricot tree decline. Full article

Global agricultural intensification has exacerbated soil compaction and nitrogen (N) inefficiency, thereby threatening sustainable crop production. Sub-soiling, a tillage technique that fractures subsurface layers while preserving surface structure, offers potential solutions by modifying soil physical properties and enhancing microbial-mediated N cycling. This study investigated the effects of subsoiling depth (0, 20, and 40 cm) on soil microbial communities and N transformations in a semi-arid maize system in China. The results demonstrated that subsoiling to a depth of 40 cm (D2) significantly enhanced the retention of nitrate-N and ammonium-N, which correlated with improved soil porosity and microbial activity. High-throughput 16S rDNA sequencing revealed subsoiling depth-driven reorganization of microbial communities, with D2 increasing the abundance of Proteobacteria (+11%) and ammonia-oxidizing archaea (Nitrososphaeraceae, +19.9%) while suppressing denitrifiers (nosZ gene: −41.4%). Co-occurrence networks indicated greater complexity in microbial interactions under subsoiling, driven by altered aeration and carbon redistribution. Functional gene analysis highlighted a shift from denitrification to nitrification-mineralization coupling, with D2 boosting maize yield by 9.8%. These findings elucidate how subsoiling depth modulates microbiome assembly to enhance N retention, providing a mechanistic basis for optimizing tillage practices in semi-arid agroecosystems. Full article

The plant microbiome plays a crucial role in the health of the tea plant, while Bacillus thuringiensis (Bt) is widely utilized as a biological pesticide in tea gardens, promoting sustainable agricultural practices. However, the effects of Bt spraying on tea quality and the structure and function of the phyllosphere microbiome remain unclear. This study evaluated the effects of Bt spraying on tea quality, microbiome composition, diversity, and potential functions using tea leaf quality measurements and high-throughput sequencing of the 16S/ITS rDNA genes. Results showed that spraying Bt1 significantly increased the contents of free amino acids (by 15.27%), flavonoids (by 18.00%), soluble sugars (by 62.55%), and key compounds such as epicatechin gallate (by 10.50%), gallocatechin gallate (by 122.52%), and epigallocatechin gallate (by 61.29%), leading to improved leaf quality. Co-occurrence network analysis indicated that the community structure of both epiphytic and endophytic microbes became more complex after Bt treatment. The abundance of beneficial bacteria, such as Novosphingobium, Methylobacterium, and Sphingomonas, increased significantly, while pathogenic fungi like Aspergillus and Phyllosticta decreased. Functional prediction indicated enhanced amino acid metabolism, secondary metabolism, and carbohydrate metabolism, particularly the biosynthesis of flavonoids, which supports disease resistance and boosts secondary metabolite levels. Furthermore, Bt application reduced pathogenic fungi, enhancing the tea plant’s resistance to diseases. Overall, foliar spraying of Bt can positively alter the phyllosphere microbiome by enriching beneficial bacteria and improving metabolic functions, ultimately enhancing tea plant resistance and quality, and providing a scientific basis for sustainable pest management in tea cultivation. Full article

Phytoplankton are essential indicators of aquatic ecosystem health. Traditional phytoplankton detection methods using microscopy struggle to identify species with small particle sizes or unclear morphological characteristics. In contrast, molecular methods have high accuracy but struggle to simultaneously detect prokaryotic and eukaryotic organisms due to primer specificity. As algal blooms can be caused by both prokaryotes and eukaryotes, methods that can detect both are required. This study used both microscopic detection and high-throughput sequencing methods to analyze phytoplankton in seagoing waters in eastern coastal China. Two high-throughput sequencing primers targeting 16S rDNA for prokaryotes and 18S rDNA for eukaryotes were used, and the results were compared with those of microscopic analysis. Microscopy identified 230 phytoplankton species across 73 genera, mainly belonging to Bacillariophyta, Chlorophyta, Euglenophyta, Cyanophyta, Dinophyta, and Chrysophyta. Twenty-four species across 16 sampling stations exceeded 1 million cells/L. High-throughput sequencing yielded 8642 prokaryotic and 7375 eukaryotic operational taxonomic units, with 432 identified as phytoplankton. Chlorophyta and Bacillariophyta had the highest species richness, accounting for 34% and 17%, respectively. High-throughput sequencing detected more species than microscopic detection but relied on gene reference databases and provided only the relative abundance of species based on operational taxonomic unit counts. Full article