Search Results (110)

Cellulose, the most abundant organic polymer in soil, is degraded by the action of microbial communities. Cellulolytic taxa are widespread in soils, enhancing the biodegradation of cellulose by the synergistic action of different cellulase enzymes. β-glucosidases are the last enzymes responsible for the degradation of cellulose by producing glucose from the conversion of the disaccharide cellobiose. Different soils from the states of Delaware, Maryland, New Jersey, and New York were analyzed by direct DNA extraction, PCR analysis, and next generation sequencing of amplicon sequences coding for β-glucosidase genes. To determine the community structure and diversity of microorganisms carrying β-glucosidase genes, amplicon sequence variant analysis was performed. Results showed that the majority of β-glucosidase genes did not match any known phylum or genera with an average of 84% of sequences identified as unclassified. The forest soil sample from New York showed the highest value with 95.62%. When identification was possible, the bacterial phyla Pseudomonadota, Actinomycetota, and Chloroflexota were found to be dominant microorganisms with β-glucosidase genes in soils. The Delaware soil showed the highest diversity with phyla and genera showing the presence of β-glucosidase gene sequences in bacteria, fungi, and plants. However, the Chloroflexota genus Kallotanue was detected in 3 out of the 4 soil locations. When phylogenetic analysis of unclassified β-glucosidase genes was completed, most sequences aligned with the Chloroflexota genus Kallotenue and the Pseudomonadota species Sphingomonas paucimobilis. Since most sequences did not match known phyla, there is tremendous potential to discover new enzymes for possible biotechnological and pharmaceutical applications. Full article

The transforming growth factor beta (TGF-$\mathsf{\beta }$) gene family is widely distributed across the animal kingdom, playing a crucial role in various cellular processes and maintaining overall health and homeostasis. The present study identified 34 TGF-$\mathsf{\beta }$ family genes based on the genome sequence in Tupaia belangeri, which were classified into the TGF-$\mathsf{\beta }$, bone morphogenetic protein (BMP), growth differentiation factor (GDF), glial cell-derived neurotrophic factor (GDNF), and Activin/Inhibin subfamilies. A phylogenetic analysis revealed the evolutionary relationships among members of the TGF-$\mathsf{\beta }$ family in T. belangeri and their homologous genes in Homo sapiens, Mus musculus, and Pan troglodytes, indicating a high degree of conservation throughout evolution. A chromosomal distribution and collinearity analysis demonstrated the localization of these genes within the genome of T. belangeri and their collinearity with genes from other species. A gene structure and motif analysis further illustrated the conservation and diversity among TGF-$\mathsf{\beta }$ family members. A protein interaction network analysis highlighted the central roles of TGFB1, TGFB3, BMP7, and BMP2 in signal transduction. A functional enrichment analysis underscored the significance of the TGF-$\mathsf{\beta }$ signaling pathway in the biological processes of T. belangeri, particularly in cell proliferation, differentiation, and apoptosis. We assessed the impact of cold acclimation treatment on the expression of TGF-$\mathsf{\beta }$ family proteins in the adipose tissue (white adipose tissue [WAT] and brown adipose tissue [BAT]) of T. belangeri using ELISA technology, finding that protein expression levels in the experimental group were significantly higher than those of in the control group. These results suggested that cold acclimation may enhance the adaptability of T. belangeri to cold environments by modulating the expression of TGF-$\mathsf{\beta }$ family genes. This study offers new insights into the role of the TGF-$\mathsf{\beta }$ family in the cold acclimation adaptation of T. belangeri, providing a scientific foundation for future genetic improvements and strategies for cold acclimation. Full article

Backgoround: The genus Pseudomonas encompasses metabolically versatile bacteria widely distributed in diverse environments, including clinical settings. Among these, Pseudomonas kurunegalensis is a recently described environmental species with limited clinical characterization. Objective and Methods: In this study, we report the genomic and phenotypic characterization of a P. kurunegalensis isolate, Pam1317368, recovered from a catheterized urine sample of a post-renal transplant patient without symptoms of urinary tract infection. Initial identification by MALDI-TOF MS misclassified the isolate as Pseudomonas monteilii. Whole-genome sequencing and average nucleotide identity (ANI) analysis (≥95%) confirmed its identity as P. kurunegalensis. The methodology included genomic DNA extraction, Illumina sequencing, genome assembly, ANI calculation, antimicrobial susceptibility testing, resistance gene identification and phylogenetic analysis. Results: Antimicrobial susceptibility testing revealed multidrug resistance, including carbapenem resistance mediated by the metallo-β-lactamase gene VIM-2. Additional resistance determinants included genes conferring resistance to fluoroquinolones and aminoglycosides. Phylogenetic analysis placed the isolate within the P. kurunegalensis clade, closely related to environmental strains. Conclusions: Although the clinical significance of this finding remains unclear, the presence of clinically relevant resistance genes in an environmental Pseudomonas species isolated from a human sample highlights the value of genomic surveillance and accurate species-level identification in clinical microbiology. Full article

Terpenoids are the most structurally diverse class of natural products (NPs). Despite their abundance, the functional diversity of bacterial terpene synthases (TPSs), particularly from Streptomyces species, remains largely unexplored. In this study, fourteen Streptomyces strains were subjected to genome sequencing and bioinformatic analysis to systematically mine class I TPSs. A total of forty-eight TPSs were identified and categorized through phylogenetic analysis, and five representative TPSs distantly related to known TPSs were selected for functional investigation. Biochemical assays revealed that TAC28_6116 is a sesquiterpene synthase producing thujopsan-2β-ol (1) and thujopsene (2), marking the first report of thujopsan-2β-ol production from a bacterial source. TAC49_7078 is a diterpene synthase responsible for the formation of ent-phomacta-1(15),3,7-triene (3). Notably, TAC43_2999 was identified as a novel sesterterpene synthase that produced compound 5 in vitro, while the generation of a previously undescribed compound 6, sestermalaysiene, was exclusively detected during in vivo fermentation using the engineered Escherichia coli chassis optimized for terpenoid biosynthesis. Structural elucidation of sestermalaysiene was supported by nuclear magnetic resonance (NMR) analysis and quantum chemical calculations. Its formation might proceed via a rare [4 + 2] cycloaddition mechanism. Overall, this work expands our knowledge of the catalytic diversity of bacterial TPSs and offers promising biocatalysts for terpenoid engineering and discovery. Full article

Bovine anaplasmosis, caused by Anaplasma marginale, is a major tick-borne disease in tropical and subtropical regions of the world, leading to significant production losses. Prolonged convalescence periods are common and surviving animals often become subclinical carriers. This study aimed to detect and characterise A. marginale in bovines in smallholder dairy farms across diverse climatic zones of Pakistan using molecular methods. In total, 321 blood DNA samples from apparently healthy cattle (n = 174) and buffaloes (n = 147) from six districts in Pakistan were tested for A. marginale using a nested PCR assay, targeting part of the major surface protein B gene (msp1β) as a genetic marker, followed by agarose gel electrophoresis and selective sequencing of amplicons from test-positive samples. Of the 321 DNA samples tested, 135 (42.1%) were test-positive for A. marginale. Prevalence was significantly higher in cattle (64.4%; 112/174) than in buffaloes (15.6%; 23/147), and female bovines (43.5%; 108/248) were more frequently infected than males (37%; 27/73). Phylogenetic analysis of the msp1β sequence data (n = 42) revealed that A. marginale from Pakistan clustered with those from Brazil, Thailand, South Africa, and the USA. This study represents the first comprehensive investigation of A. marginale from bovines from diverse agroecological zones of Pakistan and will further stimulate population genetic studies of A. marginale and investigations into the economic impact of subclinical infections in bovines in smallholder farming systems. Full article

Arabinogalactan proteins (AGPs) constitute a diverse class of hydroxyproline-rich glycoproteins implicated in various aspects of plant growth and development. However, their functional characterization in cotton (Gossypium spp.) remains limited. As a globally significant economic crop, cotton serves as the primary source of natural fiber, making it essential to understand the genetic mechanisms underlying its growth and development. This study aims to perform a comprehensive genome-wide identification and characterization of the AGP gene family in Gossypium spp., with a particular focus on elucidating their structural features, evolutionary relationships, and functional roles. A genome-wide analysis was conducted to identify AGP genes in Gossypium spp., followed by classification into distinct subfamilies based on sequence characteristics. Protein motif composition, gene structure, and phylogenetic relationships were examined to infer potential functional diversification. Subcellular localization of a key candidate gene, GhAGP50, was determined using fluorescent protein tagging, while gene expression patterns were assessed through β-glucuronidase (GUS) reporter assays. Additionally, hormonal regulation of GhAGP50 was investigated via treatments with methyl jasmonate (MeJA), abscisic acid (ABA), indole-3-acetic acid (IAA), and gibberellin (GA). A total of 220 AGP genes were identified in Gossypium spp., comprising 19 classical AGPs, 28 lysine-rich AGPs, 55 AG peptides, and 118 fasciclin-like AGPs (FLAs). Structural and functional analyses revealed significant variation in gene organization and conserved motifs across subfamilies. Functional characterization of GhAGP50, an ortholog of AGP18 in Arabidopsis thaliana, demonstrated its role in promoting epidermal hair formation in leaves and stalks. Subcellular localization studies indicated that GhAGP50 is targeted to the nucleus and plasma membrane. GUS staining assays revealed broad expression across multiple tissues, including leaves, inflorescences, roots, and stems. Furthermore, hormonal treatment experiments showed that GhAGP50 expression is modulated by MeJA, ABA, IAA, and GA, suggesting its involvement in hormone-mediated developmental processes. This study presents a comprehensive genome-wide analysis of the AGP gene family in cotton, providing new insights into their structural diversity and functional significance. The identification and characterization of GhAGP50 highlight its potential role in epidermal hair formation and hormonal regulation, contributing to a deeper understanding of AGP functions in cotton development. These findings offer a valuable genetic resource for future research aimed at improving cotton growth and fiber quality through targeted genetic manipulation. Full article

The phyllosphere microbiome of aquatic macrophytes constitutes an integral component of freshwater ecosystems, serving crucial functions in global biogeochemical cycling and anthropogenic pollutant remediation. In this study, we examined the assembly mechanisms of epiphytic bacterial communities across four phylogenetically diverse macrophyte species (Scirpus validus, Hippuris vulgaris, Nymphoides peltatum, and Myriophyllum spicatum) inhabiting Ningwu Mayinghai Lake (38.87° N, 112.20° E), a vulnerable subalpine freshwater system in Shanxi Province, China. Through 16S rRNA amplicon sequencing, we demonstrate marked phyllospheric microbiome divergence, as follows: Gammaproteobacteria dominated S. validus, H. vulgaris and N. peltatum, while Alphaproteobacteria dominated in M. spicatum. The nitrate, nitrite, and pH value of water bodies and the chlorophyll, leaf nitrogen, and carbon contents of plant leaves are the main driving forces affecting the changes in the β-diversity of epiphytic bacterial communities of four plant species. The partitioning of assembly processes revealed that deterministic dominance governed S. validus and M. spicatum, where niche-based selection contributed 67.5% and 100% to community assembly, respectively. Conversely, stochastic processes explained 100% of the variability in H. vulgaris and N. peltatum microbiomes, predominantly mediated by dispersal limitation and ecological drift. This investigation advances the understanding of microbial community structural dynamics and diversity stabilization strategies in aquatic macrophyte-associated microbiomes, while establishing conceptual frameworks between plant–microbe symbiosis and the ecological homeostasis mechanisms within vulnerable subalpine freshwater ecosystems. The empirical references derived from these findings offer novel perspectives for developing conservation strategies aimed at sustaining biodiversity equilibrium in high-altitude lake habitats, particularly in the climatically sensitive regions of north-central China. Full article

This study analyzed eleven isolates of colistin-resistant Pseudomonas aeruginosa, originating from Portugal and Taiwan, which are associated with various pathologies. The results revealed significant genetic diversity among the isolates, with each exhibiting a distinct genetic profile. A prevalence of sequence type ST235 was observed, characterizing it as a high-risk clone, and serotyping indicated a predominance of type O11, associated with chronic respiratory infections in cystic fibrosis (CF) patients. The phylogenetic analysis demonstrated genetic diversity among the isolates, with distinct clades and complex evolutionary relationships. Additionally, transposable elements such as Tn3 and IS6 were identified in all isolates, highlighting their importance in the mobility of antibiotic resistance genes. An analysis of antimicrobial resistance profiles revealed pan-drug resistance in all isolates, with a high prevalence of genes conferring resistance to β-lactams and aminoglycosides. Furthermore, additional analyses revealed mutations in regulatory networks and specific loci previously implicated in colistin resistance, such as pmrA, cprS, phoO, and others, suggesting a possible contribution to the observed resistant phenotype. This study has a strong impact because it not only reveals the genetic diversity and resistance mechanisms in P. aeruginosa but also identifies mutations in regulatory genes associated with colistin resistance. Full article

Precipitation variability profoundly influences soil microbial diversity, community assembly processes, and co-occurrence networks. However, the responses of soil microbial structure to relative precipitation changes in alpine regions remain uncertain. To address this, we conducted a two-year field precipitation manipulation experiment in alpine steppe and alpine desert steppe ecosystems at the source of the Yarlung Zangbo River on the Tibetan Plateau. The experiment simulated 25%, 50%, and 75% increases and decreases in precipitation to examine how soil microbial communities respond to altered precipitation regimes. Our results reveal that microbial responses varied with precipitation magnitude, grassland type, and microbial kingdom. In the alpine steppe, bacterial α-diversity exhibited a negative asymmetric response to altered precipitation at both species and phylogenetic levels. Both bacterial and fungal species α-diversity tended to respond more strongly to changes in precipitation at high gradients in the alpine steppe than in the alpine desert steppe. Microbial co-occurrence networks in the alpine steppe were generally more responsive to altered precipitation than those in the alpine desert steppe. Furthermore, fungal α-diversity at both species and phylogenetic levels, as well as β-diversity, responded more strongly to altered precipitation than bacterial communities. These findings suggest that precipitation-driven shifts in microbial community composition and network structure vary across alpine grassland ecosystems, with fungal communities exhibiting greater sensitivity than bacterial communities. As warming intensifies precipitation variability, these microbial shifts may have cascading effects on soil biogeochemical processes and ecosystem stability, underscoring the necessity for ecosystem-specific conservation frameworks and adaptive management strategies tailored to alpine grasslands. Full article

Petota includes more than 100 species (wild and cultivated), presenting a rich variety of corolla colors and associated traits. This variability provides important opportunities for investigating the differentiation of orthologous genes’ functions and their evolutionary pathways. However, the genetic underpinnings of this diversity in corolla colors are still to be further explored. In our previous study, a locus responsible for corolla color in potato was mapped to a 740 kb region on chromosome 10, which contains the AN2 gene previously identified as a regulation gene for corolla color. In the present study, this locus was further refined to a 380 kb interval through recombinant analysis. Targeted analysis of anthocyanidins and carotenoids revealed that purple corollas exhibit significantly higher levels of petunidin and delphinidin, while showing significantly lower levels of lutein and β-carotene compared to yellow corollas. Transcriptome and qRT-PCR analysis indicated that StMYB180, rather than AN2, is the candidate gene responsible for regulating coloration, specifically on the abaxial side of the corolla in potato. Expression analysis revealed that StMYB180 is exclusively highly expressed in corolla and leaf tissues, with purple coloration on the abaxial side of both corollas and leaves. Phylogenetic analysis further suggests that corolla color-regulatory genes may be closely tied to the origin and evolutionary trajectory of potato species. This study provides valuable insights into the regulation of tissue-specific expression of anthocyanin biosynthesis in potato and lays the groundwork for understanding the evolution of orthologous genes in the Petota section. Full article

The semi-humid evergreen broadleaved forest (SEBF) is the zonal vegetation type of western subtropical regions in China. Under human and natural disturbance, the area of SEBFs is severely shrinking, with remaining fragments scattered across mountains of the Central Yunnan Plateau. To explore the mechanisms of community assembly and species maintenance in the severely fragmented SEBFs, we selected three sites—Jinguangsi Provincial Nature Reserve, Huafoshan Scenic Area, and Qiongzhusi Forest Park—across the range of this vegetation type, and sampled a total of 42 plots of forest dominated by Castanopsis orthacantha Franch., the most widely distributed community type of SEBFs. We compared the species richness and composition of the communities of different age classes, employed the net relatedness index to characterize the phylogenetic structure of communities, and used Mantel tests and partial Mantel tests to quantify the impacts of spatial distance, age class, and habitat factors (including climate, topography, and soil) on species turnover across different spatial scales (i.e., intra- and inter-site) for trees, shrubs, and herbs, respectively. The results indicated the following: (1) In the young stage, the C. orthacantha communities exhibited a species richness statistically lower than those in middle-aged and mature communities. Notably, the difference in species richness among age classes was merely significant for shrub and herb species. Moreover, the phylogenetic structure changed towards over-dispersion with increasing community age. (2) The age class of the community played a pivotal role in determining taxonomic β diversity in the tree layer, while climate and soil factors significantly influenced β diversity in the shrub and herb layers of the communities. (3) Environmental filtering emerged as the predominant force shaping community assembly at the intra-site scale, whereas spatial distance was the primary determinant at the inter-site scale. Meanwhile, dispersal limitation versus biological interaction seemed to dominate the community dynamics of the C. orthacantha communities in the early versus middle and old ages, respectively. Our results highlight the variability in community assembly processes across different spatial and temporal scales, providing insights into the priority of the conservation and restoration of severely degraded zonal SEBFs. Expanding research to broader scales and other SEBF types, as well as considering the impacts of climate change and human activities, would provide further insights into understanding the mechanisms of community assembly and effective conservation strategies. Full article

β-ketoacyl-CoA synthase (KCS) enzymes play a pivotal role in plants by catalyzing the first step of very long-chain fatty acid (VLCFA) biosynthesis. This process is crucial for plant development and stress responses. However, the understanding of KCS genes in maize remains limited. In this study, we present a comprehensive analysis of ZmKCS genes, identifying 29 KCS genes that are unevenly distributed across nine maize chromosomes through bioinformatics approaches. These ZmKCS proteins varied in length and molecular weight, suggesting functional diversity. Phylogenetic analysis categorized 182 KCS proteins from seven species into six subgroups, with maize showing a closer evolutionary relationship to other monocots. Collinearity analysis revealed 102 gene pairs between maize and three other monocots, whereas only five gene pairs were identified between maize and three dicots, underscoring the evolutionary divergence of KCS genes between monocotyledonous and dicotyledonous plants. Structural analysis revealed that 20 out of 29 ZmKCS genes are intronless. Subcellular localization prediction and experimental validation suggest that most ZmKCS proteins are likely localized at the plasma membrane, with some also present in mitochondria and chloroplasts. Analysis of the cis-acting elements within the ZmKCS promoters suggested their potential involvement in abiotic stress responses. Notably, expression analysis under abiotic stresses highlighted ZmKCS17 as a potential key gene in the stress response of maize, which presented an over 10-fold decrease in expression under salt and drought stresses within 48 h. This study provides a fundamental understanding of ZmKCS genes, paving the way for further functional characterization and their potential application in maize breeding for enhanced stress tolerance. Full article

As a globally significant economic crop, the seed size of soybean (Glycine max [L.] Merr.) is jointly regulated by internal genetic factors and external environmental signals. This study discovered that the GLN family proteins in soybean are similar to the KIX-PPD-MYC transcriptional repressor complex in Arabidopsis, potentially influencing seed size by regulating the expression of the downstream gene GIF1. Additionally, β-1,3-glucanase (βGlu) plays a crucial role in antifungal activity, cell composition, flower development, pollen development, abiotic resistance, seed germination, and maturation in soybean. Through a detailed analysis of the structure, chromosomal localization, phylogenetic relationships, and expression situations in different tissues at different stages of the soybean GLN gene family members, this research certifies a theoretical foundation for subsequent research on the biological functions of GLN genes in soybean. This research incorporated a comprehensive genomic identification and expression analysis of the GLN gene family in soybean. The results indicate that the 109 soybean GLN genes are unevenly distributed across soybean chromosomes and exhibit diverse expression patterns in different tissues, suggesting they may have distinct functions in soybean morphogenesis. GO enrichment analysis shows that the GLN gene family may participate in a variety of biological activities, cellular components, and molecular biological processes, particularly in catalytic activity, cellular components, and metabolic processes. These findings provide important information for comprehending the role of the GLN gene family in soybean and offer potential targets for molecular breeding of soybean. Full article

β-glucosidases (BGLUs) are abundant enzymes in plants that play pivotal roles in cell wall modification, hormone signal transduction, secondary metabolism, defense against herbivores, and volatile compound release. Bletilla striata, a perennial herb revered for its therapeutic properties, lacks a comprehensive analysis of its BGLU gene family despite the critical role these genes play in plant secondary metabolism. This study aims to perform a genome-wide analysis of the BGLU gene family in B. striata (BsBGLU) to elucidate their functions and regulatory mechanisms in secondary metabolite biosynthesis. We conducted a genome-wide screening to identify BsBGLU, followed by phylogenetic analysis to classify these genes into groups. Sequence characteristics were analyzed to predict functional roles. Simple sequence repeat (SSR) markers were examined to assess conservation and polymorphism among different landraces. Expression profiles of BsBGLUs were evaluated under sodium acetate and salicylic acid elicitor treatments and across different tissues. The accumulation of phylogenetic metabolites in different treatments and tissues was also analyzed by HPLC and LCMS detection to explore the correlation between gene expression and metabolite accumulation. A total of 23 BsBGLU genes were identified and classified into eight distinct groups. Sequence analysis suggested diverse functions related to hormone responses, secondary metabolism, and stress resistance. BsBGLUs with SSR sequences were conserved yet showed polymorphism among different B. striata landraces. Under elicitor treatments, expression profiling revealed that BsBGLUs significantly modulate the synthesis of secondary metabolites such as dactylorhin A and militarine. Tissue-specific expression analysis indicated that BsBGLU15 and BsBGLU28 were highly expressed in tubers compared to other tissues, suggesting their central role and a potential negative regulatory effect in metabolite accumulation. The elicitor NaAc can regulate metabolite synthesis by modulating the expression of BsBGLUs. The BsBGLU gene family in B. striata is integral to the modulation of secondary metabolite biosynthesis and accumulation and can respond to elicitors to promote the synthesis of militarine. These findings provide a theoretical foundation for the further exploration of BsBGLU gene functions and their regulatory mechanisms, advancing the production of medicinally active compounds in B. striata. Full article

Background/Objectives: Carbapenem resistance poses a significant health threat. This study reports the first detection and characterization of a novel variant of New Delhi metallo-β-lactamase (bla_NDM-60) in Escherichia coli from the United Arab Emirates (UAE), including its genetic context and relationship to global strains. Methods: NDM-60-producing E. coli was isolated from a rectal swab during routine screening. Characterization involved whole-genome sequencing, antimicrobial susceptibility testing, and comparative genomic analysis with 66 known NDM variants. Core genome analysis was performed against 42 global E. coli strains, including the single other reported NDM-60-positive isolate. Results: The strain demonstrated extensive drug resistance, including resistance to novel β-lactam/β-lactamase inhibitor combinations, notably taniborbactam. NDM-60 differs from the closely related NDM-5 by a single amino acid substitution (Asp202Asn) and two amino acid substitutions (Val88Leu and Met154Leu) compared to NDM-1. NDM-60 is located on a nonconjugative IncX3 plasmid. The strain belongs to sequence type 940 (ST940). Phylogenetic analysis revealed high diversity among the global ST940 strains, which carry a plethora of resistance genes and originated from humans, animals, and the environment from diverse geographic locations. Conclusions: NDM-60 emergence in the UAE represents a significant evolution in carbapenemase diversity. Its presence on a nonconjugative plasmid may limit spread; however, its extensive resistance profile is concerning. Further studies are needed to determine the prevalence, dissemination, and clinical impact of NDM-60. NDM evolution underscores the ongoing challenge in managing antimicrobial resistance and the critical importance of vigilant molecular surveillance. It also highlights the pressing demand to discover new antibiotics to fight resistant bacteria. Full article