Search Results (87)

The diversity of cyanobacteria from the semi-arid region of Rajasthan, India, remains vastly unexplored and warrants systematic investigation. We isolated two cyanobacterial strains (SN2022/33 & AT2016/25) of non-heterocytous, filamentous cyanobacterium from samples of sandy soil biological crusts and investigated them using a polyphasic approach. Based on 16S rRNA gene sequence identity, both strains formed a distinct lineage, with 16S sequence identity (p-distance) < 95% to the closest sister genera Trichocoleus, Venetifunis, Trichothermofontia, and Pinocchia. Analyses of 16S-23S Internal Transcribed Spacer (ITS) secondary structures (D1-D1′, BoxB, and V3 helixes) yielded substantial differences from phylogenetically associated taxa. Morphologically, both strains corresponded to members of the family Trichocoleusaceae (Leptolyngbyales), with tapered filaments and conical-pointed end cells. Most significantly, this taxon exhibited a form of true branching, with prolific unilateral or bilateral extrusions, something that had previously been the exclusive purview of members of the Nostocaceae. The combined evidence from conventional and molecular studies supports the recognition of the isolates as a novel taxon hereby described as Edaphifilum ginni gen. et sp. nov., in accordance with the International Code of Nomenclature (ICN) for Algae, Fungi, and Plants. Full article

The effects of environmental factors on zooplankton within the marginal ice zone (MIZ) of the Barents Sea remain poorly understood. To address this knowledge gap, we investigated mesozooplankton communities across the central, northern, and northeastern regions in April 2016. Abundance and biomass ranged from 90 to 997 individuals m⁻³ and from 1.1 to 48.6 mg dry mass m⁻³ (0.3 to 13.6 g dry mass m⁻²), respectively. Oithona similis was the most abundant taxon, while calanoid copepods, including Calanus spp., Metridia longa, and Pseudocalanus spp., dominated total biomass. The spatial distribution of mesozooplankton communities was closely linked to the physical properties of water masses. Cluster analysis identified two distinct assemblages associated with Polar Front Water and Arctic Water. Redundancy analysis and generalized linear models identified temperature, mean salinity, mean chlorophyll a concentration, and sea ice concentration as significant predictors of abundance and biomass. The dominance of older life stages within major copepod taxa indicated a winter status for the mesozooplankton community. Regional and temporal comparisons of mesozooplankton biomass with prior May–June data from central and northwestern areas highlighted higher productivity in the northern and northeastern MIZ. This increase is potentially related to the warming trends observed in the Arctic since the 2000s. Our research provides novel insights into Arctic marine zooplankton assemblages and serves as a valuable baseline for future ecological monitoring and modeling of the Barents Sea ecosystem in the context of global climate change. Full article

Background/Objectives: A comprehensive analysis of the mitochondrial genomes of Japetella diaphana and Amphitretus pelagicus was conducted to investigate their genomic composition, gene size, sequence characteristics, and phylogenetic positioning within the Amphitretidae family. Methods: A rigorous phylogenetic analysis was performed utilizing a dataset comprising 13 protein-coding genes, two ribosomal RNAs, and 22 transfer RNAs derived from 26 cephalopod mitochondrial genomes, representing 25 species across seven families, Vampyroteuthidae, Tremoctopodidae, Octopodidae, Enteroctopodidae, Bolitaenidae, Argonautidae, and Amphitretidae, along with outgroup Nautilus macromphalus. Results: Notably, both focal species demonstrated a pronounced adenine–thymine bias in their mitochondrial genomes, with A. pelagicus exhibiting gene rearrangements and two extensive non-coding regions. The analysis, employing both the maximum likelihood and Bayesian inference methodologies, revealed a monophyletic relationship between Bolitaenidae and Vitreledonellidae, as well as a sister taxon relationship between Amphitretidae and Tremoctopodidae. The majority of species were classified into the Amphitretidae and Bolitaenidae clades, with numerous species exhibiting close phylogenetic relationships. Conclusions: This study provides novel insights into the evolutionary relationships within Octopodiformes, underscoring the significance of mitochondrial genome data in resolving phylogenetic relationships among cephalopods. The findings contribute to our understanding of the evolutionary history of octopi and pose implications for their classification and conservation. Furthermore, the results underscore the necessity for continued research into the evolutionary relationships among cephalopod taxa. Full article

A supplemental description of Lamproglena barbicola Fryer, 1961 is provided based on specimens collected from the gills of Labeobarbus altianalis (Boulenger, 1900) from the Nyando River, Lake Victoria Basin, Kenya, using an integrated approach of scanning electron microscopy (SEM) and molecular analysis (18S, 28S rDNA, and cox1 gene regions). Morphologically, the specimens conform to L. barbicola and closely resemble Lamproglena hoi Dippenaar, Luus-Powell & Roux, 2001; however, SEM revealed a previously undescribed feature on the uniramous antennule in L. barbicola, namely indistinctly three-segmented, tapering from a broad base to the apex, basal segment much longer than distal, comprising 14 setae of varying sizes, ventral laterally, absence of distinctive anterior fringe of setae on the antennule, as well as several characters that differentiate L. barbicola from L. hoi, including 5 setae at the basal endopod of leg one, five cuticular protuberances in the oral region, 19 setae on the basal antennular segment, and 10 setae on the distal segment, with 1 seta on each ramus. The phylogenetic analysis confirms L. barbicola as a sister taxon of L. hoi, supporting their close relationship. The genetic divergence presented as the uncorrected genetic p-distances between L. barbicola and L. hoi are 23.1% and 0.45% for cox1 and 28S rDNA regions, respectively, with observed nucleotide differences of 145 and 3 bp between the sequences, respectively. There was no interspecific variability detected in the 18S rDNA sequences. This study provides novel molecular sequences and the first high-resolution SEM images, which reveal additional taxonomic features for L. barbicola, establishing a robust reference for future identification. Full article

This opinion article proposes that arthropods, with their tremendous biodiversity and evolutionary resilience, can offer abundant opportunities for integrative, transdisciplinary, solution-focused research. To support this proposal, we first (1) introduce arthropods and showcase their deep evolutionary history and tremendous diversity. Next, we (2) briefly discuss the role of arthropods in the history of human innovation and highlight some of the challenges they have helped us overcome. We provide select examples of the importance and innovation of arthropods in food, medicine, agriculture, materials, and technology. We then discuss (3) arthropods and grand challenges, articulating how they are both part of the problem and key to the solution. (4) We discuss multiple models for creating transdisciplinary research teams—1. challenge-focused, 2. taxon-focused, and 3. innovatively open-ended with respect to challenge and taxon—and the scales at which they can be created—local/regional/global. Finally, (5) we suggest that arthropods can provide a centering focal point for transdisciplinary research; an inspirational magnet that can pull together distinct scholars to coalesce and collaborate around a common nature-based theme. Our strategic next steps include exploring open-ended arthropod-focused research teams, as they would be well-positioned to tackle multiple solution-based collaborations, and such collaborations are likely to lead to novel discoveries and nature-inspired innovations. Full article

The gut microbiota of insects plays a fundamental role in modulating host physiology, including nutrition, development, and adaptability to environmental challenges. The rice water weevil, Lissorhoptrus oryzophilus Kuschel (Coleoptera: Curculionidae), is a major invasive pest of rice worldwide, yet the composition and functional profile of its gut microbial community remain poorly characterized. Here, we employed metagenome sequencing on the Illumina NovaSeq X Plus platform to explore the gut microbial diversity and predicted functions in adults of L. oryzophilus. Our results revealed a rich microbial community, comprising 26 phyla, 42 classes, 72 orders, 111 families, and 191 genera. The bacterial microbiota was overwhelmingly dominated by the phylum Proteobacteria (85.13% of total abundance). At the genus level, Pantoea (48.86%) was the most predominant taxon, followed by Wolbachia (14.57%) and Rickettsia (11.81%). KEGG analysis suggested that the gut microbiota is primarily associated with metabolic pathways such as membrane transport, carbohydrate and amino acid metabolism, cofactor and vitamin metabolism, energy metabolism, and signal transduction. eggNOG annotation further highlighted significant gene representation in amino acid and carbohydrate transport and metabolism, while CAZy annotation revealed glycosyl transferases (GTs) and glycoside hydrolases (GHs) as the dominant carbohydrate-active enzymes. This study provides the first comprehensive insight into the gut microbiome of L. oryzophilus adults, highlighting its potential role in the ecological success of this invasive pest. Our findings lay groundwork for future research aimed at developing novel microbial-based strategies for the sustainable management of L. oryzophilus. Full article

Understanding the mechanisms that assemble diverse forest communities is a central goal in ecology. Phylogenetic analyses based on DNA barcodes have advanced this field, but their use of sequences evolving at constant rates may not capture adaptations to specific environmental drivers. Light is a critical factor shaping forest structure, particularly in the vertical dimension. This study introduces a novel phylogenetic approach using the blue-light receptor gene, cryptochrome (Cry), which is directly involved in plant light perception and adaptation. We reconstructed a Cry-based phylogeny for 96 tree species in a 20 ha subtropical forest dynamics plot and analyzed community structure using the net relatedness index (NRI) and nearest taxon index (NTI) across horizontal habitats, successional stages, and vertical canopy layers. Compared to traditional DNA barcoding, the Cry phylogeny revealed distinct patterns, showing consistent phylogenetic structure across different habitats—a finding indicative of convergent evolution in light-sensing systems. Furthermore, the Cry-based analysis demonstrated a stronger and more consistent signal in the forest’s vertical structure, with significant phylogenetic clustering in upper canopy layers, directly linking light adaptation to community stratification. Over time, both NRI and NTI values increased, suggesting succession leads to greater phylogenetic overdispersion and highlighting an increased role for environmental filtering among closely related taxa. Our results validate Cry as a powerful functional gene marker for phylogenetics, providing unique insights into how light environment filters species and shapes the vertical assembly of forest communities. Full article

The AGC kinases constitute a large and ancient gene superfamily with origins that coincided with the appearance of multicellularity. Three AGC kinase families—protein kinase A (PKA), protein kinase G (PKG), and protein kinase C (PKC)—mediate the actions of neuropeptide hormones, biogenic amines, and other ligands on various physiological processes in metazoans. Metazoans express two PKG types. Jawed vertebrates express three PKA catalytic (C) subunits, four regulatory (R) subunits, and twelve PKCs, organized into conventional, novel delta-like, novel epsilon-like, atypical, and protein kinase N (PKN) subfamilies. By contrast, invertebrate PKA and PKC sequences are not well characterized. Consequently, limited database resources can result in misidentification or mischaracterization of proteins and can lead to misinterpretation of experimental data. A broad phylogenetic and sequence analysis of CrusTome transcriptome and GenBank databases was used to characterize 640 PKA-C sequences, 1122 PKA-R sequences, and 1844 PKC sequences distributed among the Annelida, Arthropoda, Chordata, Cnidaria, Nematoda, Mollusca, Echinodermata, Porifera, Platyhelminthes, and Tardigrada. Phylogenetic analysis and multiple sequence alignments revealed conservation of certain PKA-C, PKA-R and PKC isoforms across metazoans, as well as diversification of additional taxon-specific isoforms. Decapods expressed four PKA-C isoforms, designated PKA-C₁, -C_D1, -C_GLY1, and -C_GLY2; five PKA-R isoforms, designated PKA-RI₁, -RI_D1, -RII_GLY, and -RII_D1; and five PKC isoforms, designated PKN_D1-3, conventional cPKC_D1, novel nPKC_D1δ and nPKC_D1ε, and atypical aPKC_D1. PKA-C_GLY1, -C_GLY2, and -RII_GLY had glycine-rich N-terminal sequences that were unique to crustaceans. These data suggest lineage-specific diversification that retained the core catalytic function of each kinase, while regions outside of the kinase domain may provide specialized regulatory mechanisms and/or spatiotemporal subcellular localization in invertebrate tissues. Full article

This study reports the discovery of four novel Pinnularia species—P. latocentra sp. nov., P. rhombocentra sp. nov., P. seouloflexuosa sp. nov., and P. paristriata sp. nov.—from urban freshwater streams in South Korea. Species delimitation was achieved using a polyphasic approach that integrated light and scanning electron microscopy, ecological profiling, and molecular evidence from SSU rRNA and rbcL sequences. Each taxon was confirmed as morphologically and genetically distinct from its closest congeners. Our findings broaden the recognized diversity of Pinnularia in East Asia and demonstrate that urban streams, often regarded as degraded habitats, can harbor hidden diatom diversity and ecological complexity. By clarifying diagnostic traits, validating type material in a recognized repository, and aligning molecular and morphological evidence, this study contributes to a more robust taxonomy of Pinnularia. These results also highlight the importance of polyphasic taxonomy and the strategic inclusion of urban habitats in diatomological surveys and biodiversity assessments. Full article

Mucor species are fast-growing filamentous fungi, widespread in natural ecosystems. As opportunistic pathogens, some species can cause mucormycoses in humans and animals, while others hold significant economic value in food fermentation and bioengineering. In this study, four novel species were identified from soil samples collected in Xizang Autonomous Region and Yunnan Province, China, and their establishment as new species was supported by morphological characteristics and molecular data (ITS-LSU-RPB1), with phylogenetic analyses conducted using the Maximum Likelihood (ML) and Bayesian Inference (BI) methods. M. globosporus sp. nov. is characterized by producing globose chlamydospores. M. multimorphus sp. nov. is distinguished by swelling in the sporangiophores. M. polymorphus sp. nov. is differentiated by polymorphic chlamydospores. And M. xizangensis sp. nov. reflects its geographical origin in the Xizang Autonomous Region. Comprehensive descriptions of each novel taxon are presented herein. This study constitutes the ninth segment in an ongoing series elucidating early-diverging fungal diversity in China, expanding the understanding of the phylogeny of Mucor fungi and extending the worldwide number of known Mucor species to 137. Full article

Staphylococcus aureus is a leading cause of skin and soft tissue infections (SSTIs), yet the bacterial genomic adaptations underlying the transition from nasal colonization to invasive infection remain incompletely defined. We sequenced and analyzed 157 S. aureus isolates (126 from SSTIs and 31 from asymptomatic nasal colonization) from a primary care network in South Texas. Using genome-wide association studies, non-synonymous single-nucleotide variant (NSNV) profiling, and machine learning, we identified strain-specific adaptations in metabolic and regulatory pathways. SSTI isolates exhibited significant enrichment of nitrogen assimilation, purine biosynthesis, menaquinone production, and anaerobic respiration genes. Elevated copy number and colocalization of phage-linked metabolic genes—including nirB, narH, and nifR3—suggest a pathoadaptive genomic island supporting infection-specific energy generation. The enrichment of α/β-hydrolase domain-encoding genes was associated with clinical severity. To quantify severity, we developed the Purulent Ulcer Skin (PUS) score, which integrates wound size, drainage, and erythema. The α/β-hydrolase and lipoprotein genes were significantly associated with higher PUS scores (higher SSTI severity) and phage-encoded virulence gene products were linked to larger wound size. Machine learning prioritized purL and other metabolic loci as key infection classifiers. NSNVs and unitig-level changes co-localized within nutrient transport, stress resistance, and cytolytic genes, supporting a model of multi-layered genomic selection. Metagenomic assemblies of nasal microbiota were enriched for Staphylococcus, Enterococcus, and Micrococcus species, core metabolic pathways, and taxon-specific virulence determinants. This underscores the roles of metabolic and virulent co-networks within nasal commensals and their adaptive capacity for pathogenic transition. These findings provide a potential genomic blueprint of S. aureus pathoadaptation during SSTI and are a step towards the development of novel therapeutic targets. Full article

We report a case of catheter-associated bloodstream infection caused by a putative novel species in the genus Erwinia, identified using whole-genome sequencing (WGS). A female adolescent receiving long-term home parenteral nutrition via a central venous catheter (CVC) presented with a fever. Gram-negative rods were isolated from two CVC-derived blood culture sets, while peripheral cultures remained negative. Conventional identification methods, including VITEK 2, Phoenix M50, MALDI-TOF MS, and 16S rRNA and rpoB gene sequencing, failed to achieve species-level identification. WGS was performed on the isolate using Illumina MiSeq. Genomic analysis revealed a genome size of 5.39 Mb with 56.8% GC content and high assembly completeness. The highest average nucleotide identity (ANI) was 90.3% with Pantoea coffeiphila, and ≤85% with known Erwinia species, suggesting that it represents a distinct taxon. Phylogenetic analyses placed the isolate within the Erwinia clade but separate from any known species. Antimicrobial susceptibility testing showed broad susceptibility. This case highlights the utility of WGS for the identification of rare or novel organisms not captured by conventional methods and expands the clinical spectrum of Erwinia species. While the criteria for species delineation were met, the phenotypic characterization remains insufficient to formally propose a new species. Full article

Tree diseases affecting Camellia japonica have emerged as a significant threat to the health and longevity of this ornamental tree, particularly in countries where this tree species is widely distributed and cultivated. Among these, Pestalotiopsis spp. have been frequently reported and are considered one of the most impactful fungal pathogens, causing leaf blight or leaf spot, in multiple countries. Understanding the etiology and distribution of these diseases is essential for effective management and conservation of C. japonica populations. The traditional methods based on pathogen isolation and pure culture cultivation for diagnosis of tree diseases are labor intensive and time-consuming. In addition, the frequent coexistence of the major pathogens with other endophytes within a single C. japonica tree, coupled with inconsistent symptom expression and the occurrence of pathogens in asymptomatic hosts, further complicates disease diagnosis. These challenges highlight the urgent need to develop more rapid, accurate, and efficient diagnostic or monitoring tools to improve disease monitoring and management on trees, including C. japonica. To address these challenges, we applied a metagenomic approach to screen fungal communities within C. japonica trees. This method enabled comprehensive detection and characterization of fungal taxa present in symptomatic and asymptomatic tissues. By analyzing the correlation between fungal dominance and symptom expression, we identified key pathogenic taxa associated with disease manifestation. To validate the metagenomic approach, we employed a combined strategy integrating metagenomic screening and traditional fungal isolation to monitor foliar diseases in C. japonica. The correlation between dominant taxa and symptom expression was confirmed. Simultaneously, traditional isolation enabled the identification of a novel species, Pestalotiopsis, as the causal agent of leaf spot disease on C. japonica. In addition to confirming previously known pathogens, our study led to the discovery and preliminary characterization of a novel fungal taxon with pathogenic potential. Our findings provide critical insights into the fungal community of C. japonica and lay the groundwork for developing improved, rapid diagnostic tools for effective disease monitoring and management of tree diseases. Full article

Dioscorea is a genus comprising over 600 species, many of which possess edible tubers that are commonly referred to as yams. While Dioscorea is a significant crop across the globe, it holds a unique cultural significance to the people of Tonga in western Polynesia. Presently, Dioscorea is known for its essential role in festivals and ceremonies, as well as for its nutritional contributions to Tongan diets. To understand and to assess the significance of Dioscorea in the distant past, however, archeologists rely on plant residues (e.g., starch granules) preserved on ancient tools. This study provides the necessary first step in archeological starch analysis by examining the granule morphometrics of two culturally significant Dioscorea species, D. alata and D. bulbifera from Tonga. Tubers from three individuals of each species were collected on the island of Vava’u and processed for starch granule extraction and analysis. Morphometric characteristics, including two novel that describe shape (eccentricity ratio and hilum angle), were measured on approximately 300 granules per species. When statistically compared, these novel characteristics allow D. alata and D. bulbifera to be readily distinguished from one another, and therefore increase confidence in assigning archeological granules to a specific taxon. Full article

The strain A-9^T, isolated from Oncorhynchus mykiss (rainbow trout) in a Turkish aquaculture facility, was characterized through integrated phenotypic, phylogenetic, and genomic analyses. Whole-genome sequencing revealed a 5.21 Mb circular chromosome (GC content: 58.16%) and three plasmids encoding proteins for mobilization and toxin–antitoxin systems. Multilocus phylogenetic analysis (MLPA) using seven housekeeping genes supported the distinct lineage of A-9^T. Digital DNA–DNA hybridization (77.6–78.6%) and average nucleotide identity values (96.59–97.58%) confirmed taxonomic divergence from all currently recognized A. salmonicida subspecies. Comparative proteomic and pangenomic analyses identified 328 strain-specific genes, including virulence factors, secretion system components (Type II and Type VI), and efflux-related proteins. Although genes encoding Type III secretion systems and biofilm formation were absent, A-9^T harbored a broad virulence gene repertoire and resistance determinants, including OXA-956, cphA5, and FOX-20, supporting a multidrug-resistant phenotype. Based on its genomic, phenotypic, and functional distinctiveness, we propose the novel taxon Aeromonas salmonicida subsp. oncorhynchi subsp. nov. (type strain A-9^T = LMG 33538^T = DSM 117494^T), expanding the taxonomic landscape of the A. salmonicida complex and offering insights into fish-associated bacterial evolution. Full article