Search Results (1,074)

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

Temperature fluctuations caused by climate change and global warming pose a threat to fish. The burbot (lota lota) population is particularly sensitive to increased water temperature, but the systematic impacts of high-temperature exposure on their liver and intestinal health remain unclear. In January of 2025, we collected wild adult burbot individuals from the Ussuri River (water temperature: about 2 °C), China. The burbot were exposed to 2 °C, 7 °C, 12 °C, 17 °C, and 22 °C environments for 96 h; then, the liver and intestinal contents were subsequently collected for histopathology observation, immunohistochemistry, biochemical index assessment, and transcriptome/16S rDNA sequencing analysis. There was obvious liver damage including hepatocyte necrosis, fat vacuoles, and cellular peripheral nuclei. Superoxide dismutase (SOD), catalase (CAT), and glutathione peroxidase (GSH-Px) activities were elevated and subsequently decreased. Additionally, the malondialdehyde (MDA) level significantly increased with increasing temperature. These results indicate that 7 °C (heat stress temperature), 12 °C (tipping point for normal physiological metabolism status), 17 °C (tipping point for individual deaths), and 22 °C (thermal limit) are critical temperatures in terms of the physiological response of burbot during their breeding period. In the hepatic transcriptome profiling, 6538 differentially expressed genes (DEGs) were identified, while KEGG enrichment analysis showed that high-temperature stress could affect normal liver function by regulating energy metabolism, immune, and apoptosis-related pathways. Microbiomics also revealed that acute heat stress could change the intestinal microbe community structure. Additionally, correlation analysis suggested potential regulatory relationships between intestinal microbe taxa and immune/apoptosis-related DEGs in the liver. This study revealed the potential impact of environmental water temperature changes in cold habitats in winter on the physiological adaptability of burbot during the breeding period and provides new insights for the ecological protection of burbot in the context of global climate change and habitat warming. Full article

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

Soil salinity adversely affects crop growth and development, leading to reduced soil fertility and agricultural productivity. The indigenous salt-tolerant plant growth-promoting rhizobacteria (PGPR), as a sustainable microbial resource, do not only promote growth and alleviate salt stress, but also improve the soil microecology of crops. The strain H5 isolated from saline-alkali soil in Bachu of Xinjiang was studied through whole-genome analysis, functional annotation, and plant growth-promoting, salt-tolerant trait gene analysis. Phylogenetic tree analysis and 16S rDNA sequencing confirmed its classification within the genus Halomonas. Functional annotation revealed that the H5 genome harbored multiple functional gene clusters associated with plant growth promotion and salt tolerance, which were critically involved in key biological processes such as bacterial survival, nutrient acquisition, environmental adaptation, and plant growth promotion. The pot experiment under moderate salt stress demonstrated that seed inoculation with Halomonas sp. H5 not only significantly improved the agronomic traits of tomato seedlings, but also increased plant antioxidant enzyme activities under salt stress. Additionally, soil analysis revealed H5 treatment significantly decreased the total salt (9.33%) and electrical conductivity (8.09%), while significantly improving organic matter content (11.19%) and total nitrogen content (10.81%), respectively (p < 0.05). Inoculation of strain H5 induced taxonomic and functional shifts in the rhizosphere microbial community, increasing the relative abundance of microorganisms associated with plant growth-promoting and carbon and nitrogen cycles, and reduced the relative abundance of the genera Alternaria (15.14%) and Fusarium (9.76%), which are closely related to tomato diseases (p < 0.05). Overall, this strain exhibits significant potential in alleviating abiotic stress, enhancing growth, improving disease resistance, and optimizing soil microecological conditions in tomato plants. These results provide a valuable microbial resource for saline soil remediation and utilization. Full article

This study analyzed the heavy metal tolerance and chromium reduction and the potential of plant growth to promote Rhizobium sp. OS-1. By genetic makeup, the Rhizobium strain is nitrogen-fixing and phosphate-solubilizing in metal-contaminated agricultural soil. Among the Rhizobium group, bacterial strain OS-1 showed a significant tolerance to heavy metals, particularly chromium (900 µg/mL), zinc (700 µg/mL), and copper. In the initial investigation, the bacteria strains were morphologically short-rod, Gram-negative, appeared as light pink colonies on media plates, and were biochemically positive for catalase reaction and the ability to ferment glucose, sucrose, and mannitol. Further, bacterial genomic DNA was isolated and amplified with the 16SrRNA gene and sequencing; the obtained 16S rRNA sequence achieved accession no. HE663761.1 from the NCBI GenBank, and it was confirmed that the strain belongs to the Rhizobium genus by phylogenetic analysis. The strain’s performance was best for high hexavalent chromium [Cr(VI)] reduction at 7–8 pH and a temperature of 30 °C, resulting in a total decrease in 96 h. Additionally, the adsorption isotherm Freundlich and Langmuir models fit best for this study, revealing a large biosorption capacity, with Cr(VI) having the highest affinity. Further bacterial chromium reduction was confirmed by an enzymatic test of nitro reductase and chromate reductase activity in bacterial extract. Further, from the metal biosorption study, an Artificial Neural Network (ANN) model was built to assess the metal reduction capability, considering the variables of pH, temperature, incubation duration, and initial metal concentration. The model attained an excellent expected accuracy (R² > 0.90). With these features, this bacterial strain is excellent for bioremediation and use for industrial purposes and agricultural sustainability in metal-contaminated agricultural fields. Full article

This study describes the first complete genomic sequence of an NDM-19 and QnrS11-producing multidrug-resistant (MDR) Escherichia coli isolate collected from a fecal swab from a poultry farm in 2019 in Egypt. The bla_NDM-19 was identified by PCR screening and DNA sequencing. The isolate was then subjected to antimicrobial susceptibility testing, conjugation and transformation experiments, and complete genome sequencing. The chromosome of strain M2-13-1 measures 4,738,278 bp and encodes 4557 predicted genes, with an average G + C content of 50.8%. M2-13-1 is classified under ST167, serotype O101:H5, phylogroup A, and shows an MDR phenotype, having minimum inhibitory concentrations (MICs) of 64 mg/L for both meropenem and doripenem. The genes bla_NDM-19 and qnrS11 are present on 49,816 bp IncX3 and 113,285 bp IncFII: IncFIB plasmids, respectively. M2-13-1 harbors genes that impart resistance to sulfonamides (sul1), trimethoprim (dfrA14), β-lactams (bla_TEM-1B), aminoglycosides (aph(6)-Id, aph(3′)-Ia, aph(3″)-Ib, aac(3)-IV, and aph(4)-Ia), tetracycline (tet(A)), and chloramphenicol (floR). It was susceptible to aztreonam, colistin, fosfomycin, and tigecycline. The genetic context surrounding bla_NDM-19 includes ISAba125-IS5-bla_NDM-19-ble_MBL-trpF-hp1-hp2-IS26. Hierarchical clustering of the core genome MLST (HierCC) indicated M2-13-1 clusters with global ST167 E. coli lineages, showing HC levels of 100 (HC100) core genome allelic differences. Plasmids of the IncX3 group and the insertion sequence (ISAba125) are critical vehicles for the dissemination of bla_NDM and its related variants. To our knowledge, this is the first genomic report of a bla_NDM-19/IncX3-carrying E. coli isolate of animal origin globally. Full article

Metarhizium (M.) granulomatis and M. viride have previously been described as pathogens causing hyalohyphomycosis in various species of captive chameleons and bearded dragons (Pogona vitticeps). Previous studies yielded different genotypes of M. granulomatis and M. viride based on sequencing of the internal transcribed spacer 1-5.8S rDNA (ITS-1-5.8S) and a fragment of the large subunit of the 28S rDNA (LSU). The aim of this study was to clarify the relationships between these genotypes and obtain a more accurate phylogenetic classification by sequencing two different loci of the RNA polymerase II second largest subunit (NRPB2), referred to as RPB1 and RPB2, and the translation elongation factor 1 alpha (EF1α). A total of 23 frozen isolates from 21 lizards, including the first isolates of M. granulomatis and M. viride from Parson’s chameleons (Calumma parsonii), were available for phylogenetic analysis. A total of 13 isolates belonged to the M. granulomatis complex and 10 isolates belonged to the M. viride complex. Following the amplification and sequencing of the protein-coding genes, the resulting nucleotide sequences were analyzed, trimmed and assembled. These were further analyzed with regard to differences in single-nucleotide polymorphisms (SNPs) and amino acid structure. In consideration of the results of the present analyses, a phylogenetic reclassification is recommended. Three different genotypes of M. granulomatis can be distinguished, which can be phylogenetically addressed as subspecies. Six subspecies can be distinguished regarding M. viride. Full article

Neisseria gonorrhoeae, the causative agent of gonorrhea, represents a major public health concern due to its increasing antimicrobial resistance. While often asymptomatic—particularly in extragenital infections—untreated cases can lead to severe complications and further transmission. Despite global efforts to monitor antimicrobial resistance, data on the molecular determinants underlying decreased susceptibility in N. gonorrhoeae remain scarce in Peru. This study aimed to detect mutations in the penA and 23S rRNA genes, which confer decreased susceptibility to cephalosporins and azithromycin resistance. We extracted DNA from 124 N. gonorrhoeae-positive clinical rectal specimens collected in Aptima Combo 2 transport tubes from MSM patients. These DNA samples were then screened using the Mismatch Amplification Mutation Assay-based real-time PCR (MAMA-qPCR) to identify mutations in the 23S rRNA and penA genes. Each sample underwent separate reactions to detect A2059G and C2611T mutations in the 23S rRNA gene, and 86 of these samples were further tested in individual qPCR assays for the penA D345 deletion (D345del) or G545S mutations. Sanger sequencing was performed on all DNA samples positive for 23S rRNA mutations by MAMA-qPCR assay, and on 27 DNA samples that yielded sufficient penA amplicons for additional sequencing. Using the MAMA-qPCR assay for the 23S rRNA gene, 64 of 124 samples amplified in the A2059G reaction: 2 (3.1%) carried the mutation, and 62 were classified as wild type. In the C2611T reaction, 42 of 124 samples amplified, and none of them carried the mutation. Using the MAMA-qPCR assay for the penA gene, we only analyzed 86 samples, as the remaining 38 samples had insufficient DNA yield. A total of 44 of the 86 samples amplified in the D345del reaction: 5 (11.4%) carried the D345del, and 39 were classified as wild type. In the G545S reaction, 4 (6.4%) carried the mutation, and 58 were classified as wild type. Finally, sequencing of the penA gene in the 27 samples revealed mutations related to decreased susceptibility to cephalosporins. This study identified genetic mutations conferring resistance to azithromycin and decreased susceptibility to cephalosporins, providing an overview of the circulating mutations conferring resistance in N. gonorrhoeae strains in Peru. Full article

Sustainable agriculture requires replacing agrochemicals with environmentally friendly products. One alternative is bacterial inoculants with plant-growth-promoting (PGP) activity. Bacterial consortia offer advantages over single-strain inoculants, as they possess more PGP traits and allow the exploitation of bacterial synergies. Synthetic bacterial communities (SynComs) can be used as inoculants that are thoroughly characterized and assessed for efficiency and safety. Here, we describe the construction of a SynCom composed of seven bacterial strains isolated from the rhizosphere of tomato plants and other orchard vegetables. The strains were identified by 16S rDNA sequencing as Pseudomonas spp. (two isolates), Rhizobium sp., Ensifer sp., Microbacterium sp., Agromyces sp., and Chryseobacterium sp. The metagenome of the combined strains was sequenced, allowing the identification of PGP traits and the assembly of their individual genomes. These traits included nutrient mobilization, phytostimulation, and biocontrol. When inoculated into tomato plants in an agricultural soil, the SynCom caused minor effects in soil and rhizosphere bacterial communities. However, it had a high impact on the gene expression pattern of tomato plants. These effects were more significant at the systemic than at the local level, indicating a priming effect in the plant, as signaling through jasmonic acid and ethylene appeared to be altered. Full article

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

Soybean (Glycine max) is a protein-rich legume crop that plays an important role in achieving food security. The aim of this study was to isolate soybean-nodulating rhizobia from Côte d’Ivoire soils and evaluate their potential as efficient strains in order to develop local bioinoculants. For this objective, 38 composite soil samples were collected from Côte d’Ivoire’s five major climatic zones. These soils were used as substrate to trap the nodulating rhizobia using the promiscuous soybean variety R2-231. A total of 110 bacterial strains were isolated and subsequently identified. The analysis of ITS (rDNA16S-23S), glnII and recA sequences revealed a relatively low genetic diversity of these native rhizobia. Moreover, the ITS phylogeny showed that these were scattered into two Bradyrhizobium clades dominated by the B. elkanii supergroup, with ca. 75% of all isolates. Concatenated glnII-recA sequence phylogeny confirmed that the isolates belong in the majority to ‘B. brasilense’, together with B. vignae and some putative genospecies of Bradyrhizobium that needs further elucidation. The core gene phylogeny was found to be incongruent with nodC and nifH phylogenies, probably due to lateral gene transfer influence on the symbiotic genes. The diversity and composition of the Bradyrhizobium species varied significantly among different sampling sites, and the key explanatory variables identified were carbon (C), magnesium (Mg), nitrogen (N), pH, and annual precipitation. Based on both shoot biomass and leaf relative chlorophyll content, three isolates consistently showed a higher symbiotic effectiveness than the exotic inoculant strain Bradyrhizobium IRAT-FA3, demonstrating their potential to serve as indigenous elite strains as bioinoculants. Full article

In this paper, cultivable actinobacteria were isolated, cultured, and identified from the heavily algal-bloomed waters of Taihu Lake using 16S rRNA gene sequencing. Among the isolates, a single strain exhibiting vigorous cyanocidal activity against Microcystis aeruginosa FACHB-905 was selected for further investigation. The cyanocidal efficacy and underlying mechanisms of this strain, designated TH05, were assessed through using chlorophyll content, cyanobacterial inhibition rate, and cyanobacterial cell morphology measurements. In addition, oxidative stress responses, expression of key functional genes in FACHB-905, and variations in microcystin concentrations were comprehensively evaluated. Cyanobacterial blooms caused by Microcystis aeruginosa pose serious ecological and public health threats due to the release of microcystins (MCs). In this study, we evaluated the cyanocidal activity and mechanism of a novel actinomycete strain, Streptomyces sp. TH05. Optimization experiments revealed that a light–dark cycle of 12 h/12 h, temperature of 25 °C, and pH 7 significantly enhanced cyanocidal efficacy. Under these conditions, TH05 achieved an 84.31% inhibition rate after seven days of co-cultivation with M. aeruginosa. Scanning electron microscopy revealed two distinct cyanocidal modes: direct physical attachment of TH05 mycelia to cyanobacterial cells, causing cell wall disruption, and indirect membrane damage via extracellular bioactive compounds. Biochemical analyses showed increased levels of malondialdehyde (MDA), superoxide dismutase (SOD), and catalase (CAT) during the first five days, peaking at 2.47-, 2.12-, and 1.91-fold higher than control levels, respectively, indicating elevated oxidative stress. Gene expression analysis using elf-p as a reference showed that TH05 modulated key genes associated with photosynthesis (PsaB, PstD1, PstD2, RbcL), DNA repair and stress response (RecA, FtsH), and microcystin biosynthesis (McyA, McyD). All genes were upregulated except for RbcL, which was downregulated. In parallel, microcystin content peaked at 32.25 ng/L on day 1 and decreased to 16.16 ng/L by day 9, which was significantly lower than that of the control group on day 9 (29.03 ng/L). These findings suggest that strain TH05 exhibits potent and multifaceted cyanocidal activity, underscoring its potential for application in the biological control of cyanobacterial blooms. Full article

The involvement of oral bacteria in the pathogenesis of distant organs, such as the heart, lungs, brain, liver, and intestine, has been shown. We analyzed the distribution of bacterial species in the resected aortic valve by 16S rRNA metagenomic analysis and directly compared their gene sequences with those in the oral cavity. Thirty-two patients with aortic stenosis or aortic regurgitation who underwent aortic valve replacement were enrolled in this study. Antibody titer against periodontal pathogenic bacteria in the patient’s serum was analyzed. The genetic background and distribution of bacterial species on subgingival plaque, the dorsal surface of the tongue, and the resected aortic valve were analyzed. Patients with aortic valve disease were shown to have more severe periodontal disease by the detection of antibodies against Socransky’s red-complex bacteria of periodontitis. Bacterial DNA was detected in the aortic valves of 12 out of 32 patients. The genomic sequences of the V3-V4 region of the 16S rRNA in some bacteria isolated from the aortic valves of six patients who underwent metagenomic analysis were identical to those found in the oral cavity. The findings indicate that bacteria detected in the aortic valve may be introduced through oral dysbiosis, a condition characterized by an imbalance in the oral microbiota that increases the risk of periodontal disease and dental caries. Oral dysbiosis and the resulting potential bacteremia are associated with the pathogenesis of aortic valve diseases. Full article

The long-term monocropping of red kidney beans in agricultural fields can lead to the occurrence of soil-borne diseases. Alterations in the composition of the soil microbial community are a primary cause of soil-borne diseases and a key factor in continuous cropping obstacles. Research exploring how different cultivation modes can modify the diversity and composition of the rhizosphere microbial community in red kidney beans, and thus mitigate the effects of continuous cropping obstacles, is ongoing. This study employed three cultivation modes: the continuous monocropping of red kidney beans, continuous monocropping of soybeans, and red kidney bean–soybean intercropping. To elucidate the composition and diversity of rhizosphere microbial communities, we conducted amplicon sequencing targeting the V3-V4 hypervariable regions of the bacterial 16S rRNA gene and the ITS1 region of fungal ribosomal DNA across distinct growth stages. The obtained sequencing data provide a robust basis for estimating soil microbial diversity. We observed that, under the intercropping mode, the composition of both bacteria and fungi more closely resembled that of soybean monocropping. The monocropping of red kidney beans increased the richness of rhizosphere bacteria and fungi and promoted the accumulation of pathogenic microorganisms. In contrast, intercropping cultivation and soybean monocropping favored the accumulation of beneficial bacteria such as Bacillus and Streptomyce, reduced pathogenic fungi including Alternaria and Mortierell, and exhibited less microbial variation across different growth stages. Compared to the monocropping of red kidney beans, these systems demonstrated more stable microbial structure and composition. The findings of this study will inform sustainable agricultural practices and soil management strategies. Full article

Horizontal gene transfer (HGT), the non-Mendelian transfer of genetic material between organisms, is relatively frequent in prokaryotes, whereas its extent among eukaryotes remains unclear. Here, we raise the hypothesis of a possible cross-phylum HGT event involving 5S ribosomal DNA (rDNA). A specific type of 5S rDNA sequence from the anuran Xenopus laevis was highly similar to a 5S rDNA sequence of the genome of its flatworm parasite Protopolystoma xenopodis. A maximum likelihood analysis revealed phylogenetic incongruence between the gene tree and the species trees, as the 5S rDNA sequence from Pr. xenopodis was grouped along with the sequences from the anurans. Sequence divergence analyses of the gene region and non-transcribed spacer also agree with an HGT event from Xenopus to Pr. xenopodis. Additionally, we examined whether contamination of the Pr. xenopodis genome assembly with frog DNA could explain our findings but found no evidence to support this hypothesis. These findings highlight the possible contribution of HGT to the high diversity observed in the 5S rDNA family. Full article