A greedy algorithm for aligning DNA sequences

Streptomycetes as a promising source of antimicrobial compounds: A GC-MS-based dereplication study

The extensive microbial resistance to existing antimicrobial medicines presents a significant issue in treating diverse microbial infections, whereas actinomycetes remain a viable source of antimicrobial natural products. We planned to employ gas chromatography-mass spectrometry (GC-MS)-based dereplication analysis to investigate the chemical profile of a bioactive actinomycete. Our actinomycete MFS-I31 demonstrated broad antimicrobial potential against the bacterial pathogens Staphylococcus aureus (ATCC 43300), Listeria monocytogenes (ATCC 7644), Escherichia coli (ATCC 25922), and Salmonella enterica (ATCC 14028), as well as the yeast-like fungus Candida albicans (ATCC 60193). The 16S rRNA gene sequencing of the MFS-I31 isolate exhibited a powerful resemblance to Streptomyces species. The characterization of the major antibacterial compounds in its cell-free supernatant (CFS) revealed good stability at different temperatures ranging from 4 °C to 93 °C, whereas the activity was diminished upon precipitation using ammonium sulphate indicating the proteinaceous nature of the major antimicrobial compounds. Notably, the proton nuclear magnetic resonance (1H NMR) revealed peaks in both aromatic and aliphatic areas, demonstrating the variety of the principal secondary metabolites in the crude extract of Streptomyces sp. MFS-I31. Moreover, the GC-MS-based dereplication research of our actinomycete revealed the richness of its chemical profile with different classes of compounds, including volatile molecules with antimicrobial properties. Finally, the contact bioautography demonstrated the good chance of isolating antimicrobial natural products from Streptomyces sp. MFS-I31 if it would be subjected to chemical isolation work. To summarize, soil Streptomycetes remain a valuable source of many antimicrobial natural compounds, particularly when implementing chemical profiling and dereplication studies.

Discovery of tobacco necrosis virus A in a diseased Colombian Cannabis sativa plant

Plant viral infections pose a significant threat to global crop productivity. Despite their profound impact on agriculture, plant viruses have been relatively understudied, primarily due to technological limitations associated with classical molecular methods. However, the advent of RNA Next-Generation Sequencing (NGS) RNA-seq analysis has revolutionized virus characterization in environmental settings, overcoming previous limitations and providing a powerful tool for studying plant viruses. In an RNA-seq experiment conducted on a diseased Colombian Cannabis sativa hemp plant, we identified a linear positive-sense single-stranded RNA genome belonging to Tobacco Necrosis Virus A (TNV-A), a common cause of necrotic lesions in plants such as tobacco and tulipa. The affected Cannabis sativa hemp plant exhibited severe symptoms, including alterations in pigmentation, leaf morphology such as chlorosis, necrotic tissue formation, and surface wear on the leaves. The complete genome sequence of the Cannabis sativa TNV-A was 3656 nucleotides long, containing five putative ORFs, and was classified in the family Tombusviridae, genus Alphanecrovirus, and belonging to the Necro-like clade based on RdRp protein phylogenetic analysis. Our analysis revealed a well-conserved RdRp protein among the Alphanecroviruses, with 89 % of the amino acid residues in the peptide being entirely conserved. In contrast, the coat protein exhibited significantly higher variability, with only 49.3 % of the residues being 100 % conserved. Regarding the viral genome expression of Cannabis sativa TNV-A, we observed that the virus was highly abundant in the leaves of the diseased plant, ranking among the topmost abundant transcripts, occupying the percentile position of 3 %. Overall, our study generated the first reference genome of TNV-A virus in the tropical region and reported the first case of this virus infecting a Cannabis sativa plant.

Draft genome sequences of related Paeniglutamicibacter sp. isolates from two disparate cave systems

We present the genome assemblies of two similar Paeniglutamicibacter strains, ORCA_105 and MACA_103, isolated from Mammoth and Oregon Cave systems, respectively. These closely related, but distinct genomes will provide a resource for those studying genomic adaptation to caves.

Complete genome sequence of Novosphingobium sp. strain BL-52-GroH shows unusual dual chromosome architecture

Novosphingobium sp. BL-52-GroH was isolated from soil at the University of Mississippi campus. This strain's nanopore-sequenced genome showed two circular megabase-length chromosomes and two plasmids. Annotation showed housekeeping genes on both chromosomes, marking this Novosphingobium strain as another example in the genus with dual chromosome architecture.

Local Genomic Epidemiology of Acinetobacter baumannii Circulating in Hospital and Non-hospital Environments in Kano, Northwest Nigeria

Acinetobacter baumannii is a pathogenic bacterium of public health significance, capable of rapidly spreading within and between environments. The local epidemiology and transmission pattern of A. baumannii strains circulating in hospitals and non-hospital environments is rarely studied, and hence this is investigated in Kano, Nigeria. A cross-sectional study design was used to collect 172 samples from clinical, hospital, and non-hospital samples. Acinetobacter baumannii isolates were identified and confirmed using microbiological and molecular techniques. Variants of blaOXA-51 were determined through amplicon sequencing, while whole genome sequencing was performed on 22 isolates to determine their allelic variants/sequence types (ST), resistance/virulence genes, insertion sequences, plasmids, single-nucleotide polymorphism (SNPs) and investigate phylogenetic relationships between the isolates. Twenty-seven A. baumannii were isolated from door handle and toilet floors of student hostels (14), soil and sullage samples (3 each), bed, chair, and drawer of hospital environments (9), and 1 from the urine of a patient. All these isolates belong to only 2 variants of blaOXA51-like genes, 16 (48.8%) are blaOXA-66 and 11 (33.3%) are blaOXA-180. About 70% of the isolates were susceptible to many antibiotics, and 8 resistance genes encoding aminoglycoside, tetracycline, and sulphonamide resistance were acquired by only strains harbouring blaOXA-66, and between 37 and 39 virulence genes were harboured by all the variants. Intrinsic blaADC-25 encoding resistance to β-lactams was found in all A. baumannii strains. The 2 variants had Pasteur scheme MLST allelic profiles ST2 and 267, which are not commonly reported in Nigeria. Few isolates from hospital and non-hospital sources form a cluster with SNPs number distances within the two clusters in the range of 85-100, suggesting a close relationship. The 2 variants circulate in both environments, suggesting transmission in both directions. Detection of ST267 (blaOXA-180 variant) in a clinical sample indicates an environment-to-human transmission.

Anti-phenolic glycolipid antibodies in Mycobacterium bovis infected cattle

Mycobacterium bovis, the causative agent of bovine tuberculosis (bTB), causes significant financial losses in the agricultural industry. Additionally, M. bovis transmission from animals to humans can result in zoonotic TB, especially in low- and middle-income countries (LMICs), highlighting the need to enhance One Health surveillance to mitigate this threat. Antibodies directed against a major mycobacterial cell wall component of M. leprae, phenolic glycolipid-I (PGL-I), have shown excellent performance in identifying M. leprae infection in humans and animals. In this study, we therefore investigated whether antibodies against M. bovis PGL similarly represent a useful biomarker for M. bovis infection in cattle. Comparing sera from naturally M. bovis-infected and the single intradermal comparative cervical tuberculin test (SICCT)-negative cattle, we assessed the potential of M. bovis PGL antibodies to identify this mycobacterial infection. Our results show that serum levels of anti-M. bovis PGL IgG and -IgM in M. bovis-infected cattle were significantly higher than in the SICCT-negative cattle. The sensitivity for anti-M. bovis PGL IgM in infected animals was, however, moderate (44.9 %) and the false-positive rate was 6.3 % in SICCT-negative cattle. Notably, vaccination with BCG- or heat-killed M. bovis did not affect serum levels of anti-M. bovis PGL IgM in cattle. Moreover, none of the 57 anti-M. bovis PGL-seropositive cattle tested positive in the anti-M. leprae PGL-I assay. This study shows for the first time that anti M. bovis PGL antibodies can be detected in infected cattle: anti-M. bovis PGL IgM is a highly specific, but moderately sensitive biomarker for M. bovis infection in cattle, showing potential for differentiate infected from vaccinated animals (DIVA). It could be a valuable component in a multi-biomarker approach for diagnosing bTB.

Characterization of Fusarium oxysporum f. sp. lini based on ITS and SSR Markers and identification of resistance of Indian Linseed (Linum usitatissimum L.) to Fusarium oxysporum f. sp. lini

Different isolates of Fusarium oxysporum f. sp. lini (Fol) collected from seven linseedgrowing states in India were analyzed for their cultural characteristics, pathogenicity, and genetic diversity using ITS and SSR markers. The isolates exhibited varying colony colors (white, pink, purple) and textures (fluffy, appressed), with white being the most common. Pathogenicity tests on 52 linseed cultivars using a virulent isolate (Fol-4) revealed wilt incidence ranging from 2 to 87%, with RLC-92, RLC-148, RLC-133, Selection EC99001, and Binwa showing resistance. Further screening of 23 cultivars against six Fol isolates identified RLC-92, JLS-95, and RLC-148 as resistant across all tested isolates. ITS analysis generated a 650 bp amplicon, confirming 99-100% sequence identity with F. oxysporum (GenBank Accession Nos. ON714898 to ON714911). Genetic diversity analysis using cluster analysis, Jaccard's similarity coefficient, PCA, and SSR heatmap revealed two primary clusters with significant variability, with isolate Fol-13 emerging as a distinct outlier. These findings enhance the understanding of genetic variation in F. oxysporum f. sp. lini, aiding in disease resistance breeding and linseed wilt management strategies.

Ecology and Pathogenicity for Honey Bee Brood of Recently Described Paenibacillus melissococcoides and Comparison With Paenibacillus dendritiformis, Paenibacillus thiaminolyticus

Honey bee colonies contain thousands of individuals living in close proximity in a thermally homeostatic nest, creating ideal conditions for the thriving of numerous pathogens. Among the bacterial pathogens, Paenibacillus larvae infects larvae via the nutritive jelly that adult workers feed them, causing the highly contagious American foulbrood disease. Further Paenibacillus species were anecdotally found in association with honey bees, including when affected by another disease, European foulbrood (EFB). However, their pathogenicity remains largely unknown. Our results indicate that Paenibacillus dendritiformis, Paenibacillus thiaminolyticus and newly described Paenibacillus melissococcoides are pathogenic towards honey bee brood and that their virulence correlates with their sporulation ability, which confers them resistance to the bactericidal properties of the nutritive jelly. Our survey occasionally but increasingly detected P. melissococcoides in confirmed and idiopathic cases of EFB but never in healthy colonies, suggesting that this bacterium is an emerging pathogen of honey bee brood. Overall, our results suggest that virulence traits allowing a pathogenic or opportunistically pathogenic habit towards honey bee brood are frequent in Paenibacillus spp., but that their degree of adaptation to this host varies. Our study clarifies the ecology of this ubiquitous genus, especially when infecting honey bees.

Phylogenetic Diversity and Geographic Distribution of Atlantic Salmon Calicivirus in Major Salmon Farming Regions

Salovirus is a genus within the family Caliciviridae, which contains a single member species, Salovirus nordlandense, also known as Atlantic salmon calicivirus (ASCV). While previous work has shown that ASCV can replicate in fish cell lines and establish systemic infection in vivo, its exact role in disease remains unclear and very little is known about its geographic distribution and evolution among Atlantic salmon. To expand the phylogenetic range of ASCV and better understand its potential role in disease, we screened publicly available transcriptomes for ASCV-like sequences. Notably, we detected ASCV in sequencing projects of Atlantic salmon (Salmo salar) (n = 40) and wild common whitefish (Coregonus lavaretus) (n = 1), across Chile, Scotland and Norway. Our phylogenetic analysis identified two viral species, which we provisionally name Salovirus nordlandense 1 and 2, each containing distinct genotypes. Both viral species were found in all three countries, with no clear geographic pattern, indicating that saloviruses have spread through the Atlantic salmon trade. It was notable that 88% of these transcriptomes were generated for the study of other pathogens, including infectious salmon anaemia virus, piscine myocarditis virus and Piscirickettsia salmonis, suggesting that saloviruses might be frequently associated with co-infections. Overall, this study indicates that viruses, like ASCV, can silently spread through aquacultural practices, potentially contributing to a variety of fish diseases.

Are Ophiolitic Substrates Drivers for Reticulate Evolution in Armeria (Plumbaginaceae)?

Ultramafic substrates can play a role in fostering ecological adaptation and microevolutionary dynamics. The Armeria denticulata complex includes two flowering plant species (A. denticulata and A. saviana): the former is a strict serpentinophyte endemic to Tuscany and western Liguria, while the latter grows on limestone/jasper in a small area of southern Tuscany. Intriguingly, northern Apennine populations of A. arenaria subsp. praecox, a subspecies otherwise endemic to the western Alps, grow on ophiolites. Finally, the central-southern Italian endemic A. gracilis is instead linked to limestone. We aimed at understanding whether substrate specificity and/or hybridization promoted speciation in the A. denticulata complex, despite similar ecological conditions failing to cause speciation in the nearby A. arenaria. We used Genome skimming and Illumina sequencing to assemble plastomes (152 kb) and data from the nuclear genome (ribosomal DNA subunits and 36 single-copy markers; 27 kb in total) used to infer phylogenies and evaluate different reticulate evolution scenarios by calculating gene tree probabilities under the Coalescent model. The phylogenomic analyses were complemented by morphometric data using a matrix of 134 individuals × 27 characters. Morphometric data were analyzed both by fitting a Gaussian Mixture Model to compute population-wise Jensen-Shannon Distances and a Neighbor-Net network, and by inferring a standard linear discriminant analysis. Both morphometric and phylogenomic results suggest A. saviana is a species of homoploid hybrid origin, involving A. denticulata s.str. (ovule donor) and A. gracilis (pollen donor). A single population of A. denticulata from inner Tuscany (Monte Ferrato) could have originated from an introgression/hybridization event between A. denticulata s.str. (pollen donor) and A. arenaria subsp. praecox (ovule donor). Accordingly, our results suggest that substrate specificity and hybridization/introgression prompted microevolutionary processes in the Armeria denticulata complex.

Genome-wide investigation of cytokinin oxidase/dehydrogenase (CKX) family genes in Brassica juncea with an emphasis on yield-influencing CKX

Rapeseed mustard (Brassica juncea) is an important edible oilseed crop whose yield is impacted not only by the biotic and abiotic stresses but the low productivity of the cultivars also has a great impact over it. In the past, cytokinin oxidase/dehydrogenase (CKX) family gene manipulation has increased yield and stress tolerance and has been cloned and characterized in different plant species. Cytokinin oxidase/dehydrogenase (CKX) is an important enzyme regulating cytokinin homeostasis and regulating the yield and tolerance traits in plants. This study demonstrated a comprehensive investigation of the CKX gene family in B. juncea cv. Varuna. As a result, a total of 24 CKX genes were identified across the 36 chromosomes (AABB) and classified into seven distinct subgroups. These seven subgroups were annotated based on their homology with their counterparts present in Arabidopsis thaliana. Expression pattern analysis by RT-qPCR in the high-and low-yielding B. juncea cultivars showed that all 24 CKX expressed differentially in various tissues; most were expressed in leaves, stems and developing siliques. The two functional domains, FAD-binding and Cytokinin-binding domains required for CKX activity, were conserved across the CKX family genes. Our findings systematically revealed the evolutionary dynamics of the BjCKX family genes. They led the foundation for subsequent validation of the CKX for their functional role in yield enhancement in B. juncea.

Escherichia coli causing bloodstream infections in Mexican paediatric patients: molecular typing, antimicrobial resistance, virulence factors, and clinical features

BACKGROUND

Escherichia coli is one of the main pathogens causing bloodstream infections (BSIs) in paediatric patients. It is classified into pathogenic (B2, D and F) and commensal (A, B1 and C) phylogroups, with virulence mainly attributed to adhesins, toxins and iron acquisition systems. In recent years, the global spread of high-risk clones such as ST131 and ST405, often associated with extended-spectrum beta-lactamases (ESBLs), has contributed to increased resistance and limited treatment options. The BSI mortality rate in children varies from 14 to 21.6%. This study aimed to describe resistant mechanisms; virulence factors and clonal distribution of E. coli isolates that cause BSIs in children in Mexico and clinical features.

METHODS

Thirty-eight ceftriaxone (CRO)-resistant E. coli isolates were included. Beta-lactamase and virulence genes were detected by PCR. Molecular typing included phylogroup determination, sequence types (ST), and pulsed-field gel electrophoresis (PFGE). Clinical information was acquired.

RESULTS

CTX-M was the most frequently identified beta-lactamase (82%) and aac(6')-Ib-cr was present in 45%. Phylogroup distribution was A (21.1%), C (7.9%), D (28.9%), B2 (23.7%), and F (18.4%). The most common virulence factor was fimH (71%), while papC, sat and irp2 were significantly more frequently in the pathogenic phylogroups (P = 0.029, 0.011 and 0.006, respectively). PFGE identified 5 clusters, 20 non-related isolates and 4 non-typeable. Predominant clonal complexes (CC) were CC405 (23.7%) and CC131 (21.1%), with 82% of isolates belonging to high-risk clones. Survival rates differed significantly with moderate high-grade fever (P = 0.022). All patients who died had complications, compared to 34.8% of survivors (P < 0.0001). Mortality was higher in adolescents (53.3%), patients with leukaemia or lymphoma (40%), those with hospital-acquired infections (86.8%), those with an abdominal or pulmonary focus (33.3% each). No significant differences were found in of haematological parameters.

CONCLUSIONS

Both commensal and pathogenic E. coli strains cause BSIs in paediatric patients with underlying diseases. Resistance to 3GCs and 4GCs is mainly mediated by CTX-M, hence treatment with carbapenems was used. Infection-related deaths were more frequent in patients infected by pathogenic phylogroups, where papC, sat, and irp2 were more prevalent. High-risk clones were widely distributed among isolates.

Recent duplications and rare structural variations revealed by comparative sequence analysis of low molecular weight glutenin subunits (LMW-GS) genes re-identified using LMWgsFinder in 26 genomes of the grass family

KEY MESSAGE

LMWgs Finder developed by this study was used to re-identify the LMW-GS genes in a total of 26 genomes across the grass family and several important and novel findings were obtained. LMW-GS are one of the primary components of wheat (Triticum aestivum L.) seed storage proteins, which have an important impact on wheat end-use quality traits. Identifying LMW-GS genes accurately within wheat genomes has consistently presented a significant challenge. LMWgsFinder developed by this study was used to re-identify the LMW-GS genes in a total of 26 genomes of the grass family. Apart from six species, a total of 291 LMW-GS genes were identified. Except for the two versions of the TaCS (Triticum aestivum Chinese Spring) genome, only 38.13% (98/257) of the LMW-GS genes identified by LMWgsFinder were annotated in the coding sequence annotation files (provided by the sequencing research groups) of the remaining 18 genomes. EnSpm-like transposon activity mediated recent duplication or triplication of the same LMW-GS gene has been observed in 8 wheat species for the first time, indicating that the replication of LMW-GS genes has been ongoing alongside the evolution of wheat. Several cases of rare structural variations associated with the loss or acquisition of LMW-GS gene function have been discovered and experimentally verified. Twenty-one new LMW-GS genes were discovered in 15 species of Triticeae. The results of this study provide the first empirical support at the DNA level, with confirmed chromosomal localization information, for the widely accepted notion that LMW-GS genes undergo gene duplication during wheat evolution. Additionally, this study offers gene sequence resources and a wealth of valuable information for further research on LMW-GS gene function, molecular-assisted selection, gene aggregation breeding, and molecular design breeding.

AMHY and sex determination in egg-laying mammals

BACKGROUND

Egg-laying mammals (monotremes) evolved multiple sex chromosomes independently of therian mammals and lack the sex-determining gene SRY. The Y-localized anti-Müllerian hormone gene (AMHY) is the candidate sex-determination gene in monotremes. Here, we describe the evolution of monotreme AMHX and AMHY gametologues and for the first time, investigate their expression during gonad sexual differentiation in a monotreme.

RESULTS

Monotreme AMHX and AMHY have significant sequence divergence at the promoter, gene, and protein level, likely following an original allele inversion in the early stages of monotreme sex chromosome differentiation but retaining the conserved features of TGF-β molecules. We show that the expression of sexual differentiation genes in the echidna fetal gonad, including DMRT1 and SOX9, is significantly different from that of therian mammals. Importantly, AMHY is expressed exclusively in the male gonad during sexual differentiation consistent with a role as the primary sex-determination gene whereas AMHX is expressed in both sexes. Experimental ectopic expression of platypus AMHX or AMHY in the chicken embryo did not masculinize the female urogenital system, as does chicken AMH, a possible result of mammalian-specific changes to AMH proteins preventing function in the chicken.

CONCLUSIONS

Our results provide insight into the early steps of monotreme sex chromosome evolution and sex determination with developmental expression data strongly supporting AMHY as the primary male sex-determination gene of platypus and echidna.

Patiño A, Curiel-Quesada E, Martínez-Gonzáles CR, Villanueva-Silva R, Raymundo T, Pérez-Valdespino A. Quorum Sensing and Mobility Inhibition of Pathogenic Bacteria by Fulvifomes mexicanus sp. nov

The development of antimicrobial resistance drives the search for molecules capable of inhibiting bacterial virulence. Fungi of the Basidiomycota phylum constitute an important source of compounds with antimicrobial activity. The present paper describes a new species named Fulvifomes mexicanus sp. nov. based on morphological and phylogenetic analyses. The methanolic extract of basidiome of this fungus inhibited the motility of Pseudomonas aeruginosa ATCC 9027 and the production of violacein by Chromobacterium violaceum CV026. The metabolomic study of the extract by liquid chromatography-high-resolution electrospray ionization mass spectrometry (LC-HRESIMS) and molecular networking analyses revealed the presence of a complex composition of metabolites including hispidin derivatives, terpenoids, phenols, furanones, alkylglycerols, pyrones, and γ-butyrolactones, among others. Overall, this work represents the first chemical and biological study of a new species of Fulvifomes mexicanus as a source of antipathogenic metabolites for the development of novel antimicrobial agents.

A Novel flaB Gene-Based Profiling Approach for the Rapid and Accurate Detection of Borreliella and Borrelia Species in Ticks

The increasing incidence of tick-borne diseases in Europe necessitates the development of accurate and high-throughput molecular tools for detecting pathogens in tick populations. In this study, we present a novel flaB gene-based profiling method for the detection and identification of Borrelia and Borreliella species in Ixodes ricinus ticks, combining newly designed primers with next-generation sequencing (NGS). The method was evaluated alongside conventional nested PCR targeting the flaB gene, as well as microbial profiling based on the V4 region of the rrs gene, using tick DNA extracted from 1088 specimens pooled into 94 samples. Our results demonstrate that the flaB gene-based profiling approach was the highest-performing out of the three methods, detecting Borreliaceae DNA in 83 DNA pools, compared to 58 and 56 pools using nested PCR and V4 rrs profiling, respectively. A total of 23 distinct flaB sequence variants were identified, corresponding to five Borreliaceae species: Borreliella afzelii, Bl. garinii, Bl. valaisiana, Bl. burgdorferi, and Borrelia miyamotoi. Additionally, the method enabled putative strain-level discrimination within species. Our results highlight the value of flaB gene-based profiling as a robust tool for ecological and epidemiological studies of Borreliaceae diversity in ticks.

Unravelling the consortium of the cercarial dermatitis in lake from a basin of Argentinian Central Andes: histological and phylogenetic insights of Chilina snail and their fluke partner

In the context of a research program dealing with the symbiotic associations between aquatic snails and trematodes, we studied a host-parasite consortium in Lake El Nihuil (Mendoza, Argentina), a water body from Atuel river basin (Central Andes) in which recent outbreaks of cercarial dermatitis ('swimmer's itch') occurred. According to the morphological traits and molecular phylogenetic analyses (mitochondrial COI and 16S rRNA genes), the gastropod host was assigned to the endemic genus Chilina. The snails hosted and released a schistosomatid brevifurcate apharingeate cercaria, whose phylogenetic position was inferred using 28S rRNA subunit gene and 18S-ITS1-5.8S rRNA ribosomal region. The parasite was placed in a clade together with sequences from 'Furcocercariae Lineage II', avian schistosomes closely related to the recently named genus Nasusbilharzia, whose final host, the endemic black-necked swan, occurs in Lake El Nihuil. The infected specimens of Chilina sp. showed abundant parasite larvae placed between haemocoelic spaces and connective tissues, modifying the histological architecture of the digestive gland-gonad complex. Parasites produced a decrease in the number of glandular acini and atrophy of the reproductive tissue. This work suggests a displacement of the swimmer's itch outbreaks towards lower latitudes, highlighting the need for the implementation of multidisciplinary studies to monitor these emerging diseases in association with specific symbiotic consortiums.

Comparison of Anti-Biofilm Potential of Rhamnolipid Biosurfactant, Chemical Agents, and Coliphage Against E. coli Biofilm

Biosurfactants are amphipathic microbial products that are released extracellularly or remain attached to the cell surface. The strong biofilm anti-adhesive and anti-biofilm properties of biosurfactants make them suitable candidates for application aimed at destroying troublesome bacterial biofilm. To investigate the anti-adhesion and biofilm disruptive properties of natural rhamnolipid biosurfactant, targeted isolation of a hydrocarbonoclastic bacteria from hydrocarbon-contaminated soil of Dakor, Gujarat, India, led to the isolation of bacteria producing biosurfactant, identified as Pseudomonas aeruginosa. DKR. The orcinol test preliminarily indicated that the biosurfactant was indeed rhamnolipid. The Fourier transform infrared spectroscopy and nuclear magnetic resonance further confirmed the biosurfactant as rhamnolipid. Pseudomonas aeruginosa DKR produced 25 mg/ml rhamnolipid that reduced the surface tension to 22.4 mN/m and possessed CMC (critical micellar concentration) of 130 mg/L. Sub-inhibitory dilution (0.25 mg/ml) of purified rhamnolipid DKR demonstrated superior antiadhesive and antibiofilm properties against biofilm-forming E. coli strains isolated from drinking water coolers in comparison to subinhibitory concentrations of common chemical surfactants, chelating agents, and weak acids used. Coliphage AM isolated on selected E. coli strains as hosts also demonstrated an appreciable biofilm anti-adhesive and anti-biofilm effect at 106 Pfu/ml. This study emphasizes the utility of rhamnolipid biosurfactant DKR and Coliphage AM in lieu of chemicals as natural and eco-friendly agents in applications to eradicate biofilm from drinking water cooling containers, etc.

Molecular Surveillance for Potential Zoonotic Pathogens in Troglophilus Bats: Detection and Molecular Characterization of Bat Coronaviruses in Southern Italy

The recent COVID-19 pandemic has renewed interest in bats, as they are natural hosts for numerous viruses, some of which have crossed species boundaries. Despite continued efforts in the past, the ecology of bat-related viruses in a significant part of national territories, such as Italy, remains largely unexplored. Herein, we describe the detection and molecular characterization of bat coronaviruses, identified during a viral survey on selected potential zoonotic pathogens (lyssavirus and coronaviruses) carried out in Sicily, southern Italy. A total number of 330 samples were collected from 149 bats in a period (November 2020-April 2023) overlapping the COVID-19 pandemic. All samples tested negative for lyssavirus and SARS-CoV-2, while 12 bats (8.05%) tested positive to a pan-coronavirus assay. Both alphacoronaviruses and betacoronaviruses were identified in samples from three species (Miniopterus schreibersii, Rhinolophus ferrumequinum, and Rhinolophus hipposideros). Strain sequences were related to coronaviruses detected in the last decade in northern Italy as well as in other countries bordering the Mediterranean basin, suggesting a widespread diffusion of these strains. This study supports the need for further monitoring efforts and early detection of circulating coronavirus genotypes, particularly for those which have been repeatedly emerging as zoonotic spillovers.

Duplex PCR assay to determine sex and mating status of Ixodes scapularis (Acari: Ixodidae), vector of the Lyme disease pathogen

Ticks are a major health threat to humans and other animals, through direct damage, toxicoses, and transmission of pathogens. An estimated half a million people are treated annually in the United States for Lyme disease, a disease caused by the bite of a black-legged tick (Ixodes scapularis Say, 1821) infected with the bacterial pathogen Borrelia burgdorferi. This tick species also transmits another 6 human-disease causing pathogens, for which vaccines are currently unavailable. While I. scapularis are sexually dimorphic at the adult life stage, DNA sequence differences between male and female I. scapularis that could be used as a sex-specific marker have not yet been established. Here we identify sex-specific DNA sequences for I. scapularis (male heterogametic system with XY), using whole-genome resequencing and restriction site-associated DNA sequencing. Then we identify a male-specific marker that we use as the foundation of a molecular sex identification method (duplex PCR) to differentiate the sex of an I. scapularis tick. In addition, we provide evidence that this molecular sexing method can establish the mating status of adult females that have been mated and inseminated with male-determining sperm. Our molecular tool allows the characterization of mating and sex-specific biology for I. scapularis, a major pathogen vector, which is crucial for a better understanding of their biology and controlling tick populations.

Genetic Sequencing of a Bacterial Pneumonia Vaccine Produced in 1916

Background/Objectives: Bacterial vaccines were first developed and used in the late 1800s to prevent chicken cholera and anthrax. Bacterial pneumonia vaccines were widely used during the 1918 influenza pandemic, despite the influenza A/H1N1 virus not yet being identified. Studies showed that bacterial pathogens, including Haemophilus influenzae, Streptococcus pneumoniae, and Streptococcus pyogenes, contributed significantly to fatal secondary bacterial pneumonias during the pandemic. In this study, we aimed to characterize the microbial composition of two ampules of a mixed bacterial influenza vaccine produced in 1916, which were labeled as containing killed Bacillus influenzae, Pneumococci, and Streptococcus pyogenes. Methods: DNA was extracted from two 1916-era vaccine ampules, and due to low DNA yields, whole genome amplification (WGA) was performed prior to construction of Illumina sequencing libraries. Deep sequencing was conducted, followed by bioinformatic analysis to identify bacterial DNA content. Consensus genomes were assembled for predominant species, and further analyzed for serotype, phylogeny, and antibiotic resistance genes. Results: The amount of recoverable DNA from these century-old vaccine ampules was limited. The sequencing results revealed minimal detectable S. pneumoniae DNA. The first ampule contained predominantly H. influenzae DNA, while the second vial primarily contained Enterococcus faecium DNA, in addition to S. pyogenes DNA. Consensus genomes for H. influenzae, S. pyogenes, and E. faecium were assembled and analyzed for serotype, phylogeny, and antibiotic resistance genes. Conclusions: This study presents the first genomic analysis of century-old bacterial pneumonia vaccine ampules from the 1918 influenza pandemic era. The findings provide a unique historical perspective on early vaccine formulations and highlight the limitations of early vaccine production.

eDNA metabarcoding of marine invertebrate communities at RO desalination plant outfalls in Cyprus

Seawater desalination has become an essential part of the drinking water supply of many arid countries in the world - including Cyprus and the wider Mediterranean - Middle Eastern region. In this study, the microinvertebrate fauna near the outfall sites of 2 seawater desalination plants, Dhekelia and Larnaca, in Cyprus was assessed by microscopy-based classical taxonomy and eDNA metabarcoding. The results show impact of desalination brine discharge on marine benthic communities. The community structure and the impact of abiotic factors was more prominent in the sediments than the water, and the alpha diversity results from metabarcoding were consistent with the results from microscopy but differed taxonomically.

Draft genomic sequences of a rare environmental pathogen, Comamonas kerstersii, from immunocompromised patients with acute gastroenteritis

Comamonas kerstersii is a ubiquitous, aerobic, motile gram-negative bacteria considered commensal but has played a significant role as a potential pathogen causing clinical infections. Here, we report the genomic sequences of five C. kerstersii isolated from immunocompromised patients with acute gastroenteritis.

A Complex of Lance Flies (Diptera: Lonchaeidae) Infesting Figs in Veracruz, Mexico, with the Description of a New Species

The black fig fly, Silba adipata, and a complex of Neosilba species have emerged as major fig pests in Veracruz, Mexico. To assess infestation patterns and species composition, we sampled figs during one production cycle (March-October 2024) in two plantations. A total of 1647 S. adipata (821 females, 826 males) and 1250 Neosilba spp. (628 females, 622 males) emerged from samples. One species, Neosilba recurva, is described as new based on the characteristics of the male genitalia and COI sequencing. Neosilba spp. outnumbered S. adipata in the preharvest period, after which S. adipata became dominant. S. adipata emerged ~14 days earlier than Neosilba spp. Infestation by S. adipata caused uniform fig reddening, while Neosilba spp. produced patchy redness near larval exit holes. Approximately 65% of figs were lost to lonchaeid infestation preharvest. Based on male genitalia, we identified Neosilba batesi and N. recurva sp. nov. (that together comprised 64% of samples), as well as Neosilba sp.1 (26%) and N. glaberrima (10%), but COI sequences revealed greater diversity. Neosilba batesi formed a clade that did not match a Floridan sequence. Neosilba glaberrima clustered near N. pendula from Brazil, but another sequence diverged, suggesting the presence of an additional, undescribed species, Neosilba sp.2? Neosilba recurva and Neosilba sp.1, together with the newly described N. flavitarsis from Veracruz, formed distinct genetic branches, supporting their specific status.

Detection of Trypanosoma cruzi DNA in Blood of the Lizard Microlophus atacamensis: Understanding the T. cruzi Cycle in a Coastal Island of the Atacama Desert

Trypanosoma cruzi, the protozoan causative of Chagas disease, is primarily transmitted through blood-sucking insects and infects mammalian and some reptilian hosts. In Chile, insects of the Mepraia genus are key vectors of T. cruzi in its wild transmission cycle. High prevalence and mixed infection of T. cruzi lineages have been reported in a Mepraia population on Santa María Island in the Atacama Desert. However, no small mammals have been reported. The island's vertebrate community is dominated by the lizard Microlophus atacamensis and marine and scavenger birds. This study aimed to research blood samples of M. atacamensis for the presence of T. cruzi DNA (kDNA and satDNA) using conventional PCR (cPCR) and quantitative real-time PCR (qPCR) and estimate parasitemia. Our findings reveal that 39.4% of 33 individuals were positive with both cPCR and qPCR, while when assessing infection with either technique, it rises up to 81.8%. These findings confirm that M. atacamensis is a host of T. cruzi, suggesting its potential role as a key reservoir in the island's transmission cycle. This study provides new insights into the life cycle of T. cruzi in the coastal Atacama Desert, highlighting the importance of reptiles in the epidemiology of this parasite.

Microbacterium chionoecetis sp. nov. and Agrococcus chionoecetis sp. nov.: Novel Gut Bacteria from Red Snow Crab

Two yellow-coloured, Gram-stain-positive, oxidase-negative, aerobic, non-motile, and rod-shaped strains, labelled as ProA8T and ProA11T, were isolated from digestive tract of red snow crab (Chionoecetes japonicus). Strain ProA8T grow at temperature range of 15-35°C, while strain ProA11T grow at temperature range of 15-40°C. Phylogenetic and 16S rRNA gene sequence analysis revealed that strains ProA8T and ProA11T belonged to the genera Microbacterium and Agrococcus, respectively. Strain ProA8T was closely affiliated with Microbacterium yannicii JCM 18959T (98.8%) and strain ProA11T was most closely related to Agrococcus baldri IAM 15147T (98.9%). The genome sizes of ProA8T and ProA11T were 4,373,776 bp and 2,665,899 bp, with DNA G+C contents of 70.5% and 70.1%, respectively. The genomic relatedness values of ProA8T and ProA11T with their respective reference strains were <32.0% (for digital DNA-DNA hybridization) and <87.0% (for average nucleotide identity). Biosynthetic gene analysis showed the presence of genes for resorcinol production in ProA8T and ectoine biosynthesis in ProA11T, indicating ecological and biotechnological significance. Virulence analyses determined that strains ProA8T and ProA11T were non-pathogenic to humans, highlighting their safe application in biotechnological field. The major cellular fatty acids reported in ProA8T and ProA11T were anteiso-C15:0, iso-C16:0, and anteiso-C17:0. Overall, the polyphasic taxonomic data suggest that both strains ProA8T and ProA11T represent two novel species within the genera Microbacterium and Agrococcus, respectively. Accordingly, we propose the names Microbacterium chionoecetis sp. nov., with the type strain ProA8T (= KCTC 49861T = JCM 37392T) and Agrococcus chionoecetis sp. nov., with the type strain ProA11T (= KCTC 49958T = JCM 37393T).

The Combination of Start-Codon-Targeted (SCoT) and Falling Stone (FaSt) Transposon-Specific Primers Provides an Efficient Marker Strategy for Prunus Species

A novel primer (FaSt-R) targeting the Prunus-specific Falling Stone (FaSt) non-autonomous transposon was combined with start-codon-targeted (SCoT) primers to assess genetic diversity in 12 cultivars from six Prunus species and 28 cultivars of European plum. Compared to SCoT-only analyses, the SCoT-FaSt combination produced fewer total bands but a higher percentage of polymorphic bands, while maintaining comparable values for polymorphism information content, resolving power, gene diversity, and Shannon's index. SCoT-FaSt markers generated bands across a broader size range, which made gel patterns less dense, enabling the more accurate detection of differentially amplified fragments. Neighbor-joining and principal component analyses confirmed that SCoT-FaSt markers provided sufficient phylogenetic resolution at both interspecific and intraspecific levels. The sequencing of 32 SCoT-FaSt amplicons revealed FaSt elements in 26 fragments, with SCoT primers preferentially annealing to GC-rich exonic and intergenic regions. Seventeen protein-coding and one RNA-coding gene were partially identified, with FaSt elements localized in UTRs and introns of genes with key physiological functions. Comparative analysis indicated a biased distribution of FaSt elements between the Cerasus and Prunus subgenera. In silico findings suggest that FaSt elements are more fragmented in cherry species, potentially contributing to subgeneric divergence. Overall, the SCoT-FaSt marker system is effective for evaluating Prunus genetic diversity, reconstructing phylogenetic relationships, and elucidating the genomic impact of an active Mutator-like transposon.

Duckweed genomes and epigenomes underlie triploid hybridization and clonal reproduction

The Lemnaceae (duckweeds) are the world's smallest but fastest-growing flowering plants. Prolific clonal propagation facilitates continuous micro-cropping for plant-based protein and starch production and holds tremendous promise for sequestration of atmospheric CO2. Here, we present chromosomal assemblies, annotations, and phylogenomic analysis of Lemna genomes that uncover candidate genes responsible for the unique metabolic and developmental traits of the family, such as anatomical reduction, adaxial stomata, lack of stomatal closure, and carbon sequestration via crystalline calcium oxalate. Lemnaceae have selectively lost genes required for RNA interference, including Argonaute genes required for reproductive isolation (the triploid block) and haploid gamete formation. Triploid hybrids arise commonly among Lemna, and we have found mutations in highly conserved meiotic crossover genes that could support polyploid meiosis. Further, mapping centromeres by chromatin immunoprecipitation suggests their epigenetic origin despite divergence of underlying tandem repeats and centromeric retrotransposons. Syntenic comparisons with Wolffia and Spirodela reveal that diversification of these genera coincided with the "Azolla event" in the mid-Eocene, during which aquatic macrophytes reduced high atmospheric CO2 levels to those of the current ice age. Facile regeneration of transgenic fronds from tissue culture, aided by reduced epigenetic silencing, makes Lemna a powerful biotechnological platform, as exemplified by recent engineering of high-oil Lemna that outperforms oil-seed crops.

Unraveling the Antagonistic Potential of Trichoderma for Combating Sclerotinia Rot of Mustard

Identification of a sustainable alternative for the restricted range of current antifungal agents is one of decisive objective in modern agriculture. Consequently, extensive global research are been ongoing for unraveling the eco-friendly and effective bio agents that will be capable of controlling pathogens. This study explores the efficacy of Trichoderma isolates in combating Sclerotinia rot in mustard, primarily caused by Sclerotinia sclerotiorum. In this study, 12 Trichoderma isolates (designated as PBTMSR) were isolated using baiting technique from mustard rhizospheric soil as potential biocontrol agents and their cultural, morphological, molecular characteristics were studied along with in vitro and in field antagonistic potential assessment for selecting most promising isolates for the management of this disease. Cultural, biochemical characterization of all the isolates confirmed that the all the isolates belonged to Trichoderma spp. and among these, 06 isolates namely PBTMSR4, 5, 6, 8, 9 and 10 were found most promising in their antagonistic potential against the test pathogen under in vitro conditions and were selected and evaluated under both artificial and natural epiphytotic field conditions for the management of Sclerotinia stem rot of mustard. Among Trichoderma isolate PBTMSR4 showed maximum reduction in Sclerotinia rot incidence (70.0% and 50.73%) with followed by PBTMSR8 (60.0% & 42.15%) under artificial and natural field conditions, respectively. The highest yield was with PBTMSR4 (23.70 q/ha) followed by PBTMSR8 (23.11 q/ha) as compared to check (21.48 q/ha) under natural field conditions. These two Trichoderma isolates namely, PBTMSR4 (OR351298) and PBTMSR8 (OR355825) were identified as Trichoderma afroharzianum and Trichoderma lixii respectively. The findings have practical implications for agriculture, suggesting a sustainable biocontrol strategy that can enhance crop resilience and can also contribute to integrated pest management practices.

Microscopic and Molecular Identification of Eimeria Species in Domestic Rabbits (Oryctolagus cuniculus) in Romania

Coccidiosis caused by Eimeria spp. is a parasitic disease with high morbidity that affects various animal species, including rabbits. In rabbits, eleven Eimeria species have been primarily identified through microscopic examination of oocysts; however, this technique has certain limitations that make it challenging to differentiate between Eimeria species. The main objective of this study was to morphologically identify Eimeria species infecting rabbits in Romania, as well as to confirm these identifications using molecular biology techniques, specifically through the ITS-1 rRNA gene. A total of 236 samples were collected from different regions of Romania, of which 77.56% (183/236) tested positive for at least one Eimeria species. The samples were collected from rabbits raised in individual household settings, under various management systems-both in individual cages and in common ground-based enclosures. The areas of origin were chosen randomly, without applying restrictive criteria, specifically to ensure broad representativeness of the farming conditions encountered in practice, regardless of the production system or geographic specificity. The microscopic examination of morphological characteristics identified ten Eimeria species, whereas PCR results confirmed the presence of four species. It was not always possible to identify all the species present in a given sample, likely due to the predominant parasitic load and the DNA quantity of each species. The results of this study confirm that ITS-1 is a useful molecular marker for identifying Eimeria species in domestic rabbits.

Closed genome sequence of Fretibacterium fastidiosum, a potential contributor to periodontal disease

Human oral microbiome consists of diverse bacteria. Not all oral bacteria are well characterized due to challenges in cultivation in vitro. In this study, we report the closed genome sequence of one of the recently identified oral bacteria, Fretibacterium fastidiosum.

Draft genome sequence of Solimonas sp. strain SE-A11 isolated from the rhizosphere of feral Brassica napus in South Korea

The draft genome of Solimonas sp. strain SE-A11 bacterium isolated from the rhizosphere of feral Brassica napus in South Korea, represents the first isolate of the genus Solimonas obtained from a plant rhizosphere. The strain has a genome size of 4,937,440  bp, a G + C content of 66.5%, and 281 predicted subsystems.

Four new species of Beltraniella (Amphisphaeriales, Beltraniaceae) revealed by morphology and phylogenetic analyses from China

Beltraniella is a widely-distributed genus on Earth, although its abundance is relatively limited in relation to other dematiaceous hyphomycetes. In the present study, diseased leaves of Myristicafragrans and decaying leaves were collected from Hainan and Sichuan Province. Fungal DNA was amplified and sequenced using two barcodes, the internal transcribed spacer (ITS) and large subunit of ribosomal RNA (LSU), and phylogenetic analyses were conducted through maximum likelihood (ML) and Bayesian inference (BI) algorithms. Four new species of Beltraniella, B.dujiangyanensis, B.jianfengensis, B.myristicae, and B.xinglongensis are identified through phylogenetic analyses and morphological comparison during a survey of fungal diversity in Hainan and Sichuan Provinces, China. Detailed descriptions of the morphological characteristics of these four new species are provided and illustrated with figures.

Improving ectomycorrhizal colonization and morpho-physiological traits of Pinus cooperi seedlings through organic nitrogen fertilization

Mycorrhizal associations play a crucial role in afforestation efforts, as they enhance the acquisition of nutrients and water, thereby supporting seedling establishment. However, the influence of nitrogen (N) forms in the soil, particularly the organic N, on the formation of mycorrhizal associations and their subsequent effects on seedling morpho-physiology remains poorly understood. In this study, we examine the mycorrhizal colonization, along with morpho-physiological and functional traits, in Pinus cooperi seedlings following fertilization with organic N in controlled nursery conditions. A factorial experiment was performed with Pinus cooperi C. E. Blanco seedlings using two N sources: organic N (amino acids) and inorganic N (NH4NO3) and two N doses: low and high (60 vs 200 mg N seedling-1). Seedlings were inoculated with a mixture of native fungi, but the phylogenetic analysis showed that Suillus placidus (Bonord.) Singer was the only species colonizing roots. Organic N promoted similar morphology and nutritional status as inorganic N, though at a low N rate, it improved root growth and mycorrhizal colonization. High N fertilization improved seedling growth and nutritional status but reduced mycorrhizal colonization. Mycorrhizal colonization improved needle P concentration, delayed plant desiccation, and reduced root cellular damage when seedlings were subjected to desiccation, though it decreased plant growth and needle N concentration. We conclude that organic N fertilization improves mycorrhization of P. cooperi with S. placidus, but the fertilization dose should be adjusted to meet species-specific requirements in order to optimize plant quality and promote afforestation success.

Morphological and molecular description of a novel species of Eimeria (Apicomplexa) that infects extraintestinal tissues of kiwi (Aves: Apteryx spp.)

Coccidia (Apiconmplexa) are naturally occurring and occasionally detrimental parasites of kiwi (Apteryx spp.), a unique, flightless bird species dependent upon conservation efforts for survival. Using morphological and molecular data, a new coccidia species, Eimeria koka n. sp., isolated from two closely related but geographically isolated kiwi host species, Apteryx rowi Tennyson et al. (rowi) and Apteryx mantelli Bartlett (North Island brown kiwi), is described. Oocysts are oval (20.8 × 15.9 μm) with a mean L/W ratio of 1.3, and a distinctive rough, crenellated brown oocyst wall (mean 1.2 μm), an oocyst residuum, 1-2 polar granules, and no micropyle. Sporocysts are ellipsoidal (11.6 × 6.3 μm) with a Stieda body and sporocyst residuum. Phylogenetic analysis of the cytochrome C oxidase subunit 1 (CO1) placed E. koka n. sp. in a separate clade to other Eimeria species previously identified from kiwi (Coker et al., Syst Parasitol 100(3):269-281, 2023). Comparison of DNA from oocysts with infected tissues from a single juvenile North Island brown kiwi confirmed parasitism of the kidney and lung tissues. This is the first Eimeria species identified from extraintestinal tissues in kiwi. Further molecular studies are recommended to determine the tissue distribution of E. koka n. sp. and other Eimeria species in kiwi.

Functional genomic analysis of Bacillus cereus BC4 strain for chromium remediation in contaminated soil

Soil provides a habitat for microorganisms that can mitigate metal contamination. This study presents Bacillus cereus BC4 strain, which shows significant potential for metal pollution remediation. This bacterium achieved a 98.6 % reduction in Chromium (VI) concentrations from 300 mg/L to negligible levels under specific conditions (pH 8, 37 °C, and 120 rpm agitation) in LB medium. The complete genome of Bacillus cereus BC4 was sequenced using Oxford Nanopore Technology, revealing a circular chromosome and a plasmid with a total of 5537,675 base pairs and a G + C content of 35.44 %. Fourteen genes critical for Cr metabolism were identified. qRT-PCR demonstrated that under low Cr(VI) stress, two genes, chrA and nitR1, were up-regulated, indicating their role in Cr resistance. The genome revealed gene clusters essential for resilience against various metals, including chromium, arsenic, copper, manganese, and cadmium, as well as for synthesizing secondary metabolites crucial for survival and adaptation. Additionally, genes associated with biopolymer synthesis were identified, emphasizing the organism's diverse genetic capabilities. This genomic study led to the submission of the complete genome to GenBank (CP101135), enhancing the understanding and potential of Bacillus cereus BC4 in chromium remediation and environmental restoration.

Self-documenting plasmids

Plasmids are the workhorse of biotechnology. These small DNA molecules are used to produce recombinant proteins and to engineer living organisms. They can be regarded as the blueprints of many biotechnology products. Therefore, it is critical to ensure that the sequences of these DNA molecules match their intended designs. Yet, plasmid verification remains challenging. To secure the exchange of plasmids in research and development workflows, we have developed self-documenting plasmids that encode information about themselves in their own DNA molecules. Users of self-documenting plasmids can retrieve critical information about the plasmid without prior knowledge of the plasmid identity. The insertion of documentation in the plasmid sequence does not preclude their propagation in bacteria or functional fluorescent protein expression in mammalian cells. This technology simplifies plasmid verification, hardens supply chains, and has the potential to transform the protection of intellectual property (IP) in the life sciences.

Transposition of transposable element IS1 in Edwardsiella piscicida mutant generated by CRISPR/Cas9 along with λ-Red recombineering system

This study aimed to investigate unintended mutations introduced by the CRISPR/Cas9 genome editing system in Edwardsiella piscicida. Whole-genome sequencing was conducted on the wild-type E. piscicida NH1 and its alanine racemase knockout mutants (E. piscicida Δalr325 NH1 and E. piscicida Δalr50 NH1) generated using CRISPR/Cas9 with a λ-Red recombineering system. Comparative genomic analyses revealed that the insertion sequence 1 (IS1) transpositions occurred in the CRISPR/Cas9-edited mutants, disrupting the type I restriction-modification system subunit M gene, in addition to the targeted gene deletion. Interestingly, no IS1 transpositions were detected in mutants produced via conventional plasmid-based allelic exchange, indicating the potential link between CRISPR/Cas9-mediated editing and transposition events. These results suggest that genome editing via CRISPR/Cas9 could trigger IS1 transposition, potentially due to double-stranded DNA breaks. The lack of sequence similarity between the single guide RNA (sgRNA) and the transposed regions suggests that transpositions are not CRISPR/Cas9 off-target effects. This study provides evidence of interactions between mobile genetic elements and genome editing systems, requiring further investigation into their underlying mechanisms.

Unequally Abundant Chromosomes and Unusual Collections of Transferred Sequences Characterize Mitochondrial Genomes of Gastrodia (Orchidaceae), One of the Largest Mycoheterotrophic Plant Genera

The mystery of genomic alternations in heterotrophic plants is among the most intriguing in evolutionary biology. Compared to plastid genomes (plastomes) with parallel size reduction and gene loss, mitochondrial genome (mitogenome) variation in heterotrophic plants remains underexplored in many aspects. To further unravel the evolutionary outcomes of heterotrophy, we present a comparative mitogenomic study with 13 de novo assemblies of Gastrodia (Orchidaceae), one of the largest fully mycoheterotrophic plant genera, and its relatives. Analyzed Gastrodia mitogenomes range from 0.56 to 2.1 Mb, each consisting of numerous, unequally abundant chromosomes or contigs. Size variation might have evolved through chromosome rearrangements followed by stochastic loss of "dispensable" chromosomes, with deletion-biased mutations. The discovery of a hyper-abundant (∼15 times intragenomic average) chromosome in two assemblies represents the hitherto most extreme copy number variation in any mitogenomes, with similar architectures discovered in two metazoan lineages. Transferred sequence contents highlight asymmetric evolutionary consequences of heterotrophy: despite drastically reduced intracellular plastome transfers convergent across heterotrophic plants, their rarity of horizontally acquired sequences sharply contrasts parasitic plants, where massive transfers from their hosts prevail. Rates of sequence evolution are markedly elevated but not explained by copy number variation, extending prior findings of accelerated molecular evolution from parasitic to heterotrophic plants. Putative evolutionary scenarios for these mitogenomic convergence and divergence fit well with the common (e.g. plastome contraction) and specific (e.g. host identity) aspects of the two heterotrophic types. These idiosyncratic mycoheterotrophs expand known architectural variability of plant mitogenomes and provide mechanistic insights into their content and size variation.

Origin and stepwise evolution of vertebrate lungs

Lungs are essential respiratory organs in terrestrial vertebrates, present in most bony fishes but absent in cartilaginous fishes, making them an ideal model for studying organ evolution. Here we analysed single-cell RNA sequencing data from adult and developing lungs across vertebrate species, revealing significant similarities in cell composition, developmental trajectories and gene expression patterns. Surprisingly, a large proportion of lung-related genes, coexpression patterns and many lung enhancers are present in cartilaginous fishes despite their lack of lungs, suggesting that a substantial genetic foundation for lung development existed in the last common ancestor of jawed vertebrates. In addition, the 1,040 enhancers that emerged since the last common ancestor of bony fishes probably contain lung-specific elements that led to the development of lungs. We further identified alveolar type 1 cells as a mammal-specific alveolar cell type, along with several mammal-specific genes, including ager and sfta2, that are highly expressed in lungs. Functional validation showed that deletion of sfta2 in mice leads to severe respiratory defects, highlighting its critical role in mammalian lung features. Our study provides comprehensive insights into the evolution of vertebrate lungs, demonstrating how both regulatory network modifications and the emergence of new genes have shaped lung development and specialization across species.

Comparative genomics of Mycobacterium avium subsp. hominissuis strains within a group of captive lowland tapirs

Within a group of three captive lowland tapirs (Tapirus terrestris) suffering from clinically apparent mycobacteriosis, non-tuberculous Mycobacterium avium subsp. hominissuis (MAH) strains were isolated from the animals and the tapir's enclosure. Based on MIRU-VNTR findings, which identified two closely related INMV profiles (124 and 246), a micro-evolutionary event was assumed, and four available MAH strains were submitted to whole genome sequencing (short- and long-read technologies). Surprisingly, the differences based on single nucleotide polymorphisms (SNPs) were exceptionally high between the four strains, i.e., between 841 and 11,166 bases, due to a strong impact of homologous recombination. Thus, an ad hoc core genome multilocus sequence typing (cgMLST) scheme was created and pangenome analysis was conducted for determining the genomic similarity between the strains. The INMV246 isolate obtained from sputum on the enclosure floor and one INMV124 isolate of tapir #2 showed the highest congruence, suggesting that both originated from a shared source. The other two INMV124 isolates were genomically distinct from these strains. Nevertheless, in all four strains two plasmids were detected, which were highly conserved between the strains. The study showed that the genomic variability between MAH strains isolated from the same site within a short period of time can be exceptionally high and the influence of homologous recombination needs to be considered when determining MAH strain relationships, particularly via SNP analyses.

Carbapenem-resistant Morganella morganii carrying blaKPC-2 or blaNDM-1 in the clinic: one-decade genomic epidemiology analysis

Carbapenem-resistant Morganella morganii (CRMM) isolates, particularly those producing Klebsiella pneumoniae carbapenemase-2 (KPC-2) or New Delhi metallo-β-lactamase-1 (NDM-1), are increasingly being recognized as causative agents of nosocomial infections. However, systematic phylogeography and genetic characterization of these isolates worldwide are still lacking. Here, through seven years of surveillance of CRMM in a tertiary hospital, we analyzed the genomic characteristics of blaKPC-2- or blaNDM-1-positive CRMM isolates. Furthermore, we conducted a global genomic epidemiological study of Morganella spp. harboring blaKPC or blaNDM using the NCBI database over the past decade. By combining the timeline of isolate collection with the structural analysis of the plasmids, we traced the evolution of the IncL/M plasmid, which acquired the blaKPC-2 gene. Our findings indicate that horizontal transfer of Tn6296 based on IS26 is crucial for the transmission of blaKPC in CRMM isolates. Additionally, the Tn125 transposon appears to have played an important role in early plasmid-mediated dissemination of blaNDM; however, it has been surpassed in recent years by other elements, including IS26 and ISCR. In summary, through phylogeographic analysis of Morganella spp. globally, we elucidated their spatial-temporal distribution and revealed the evolutionary characteristics of KPC- or NDM-producing CRMM isolates as the predominant "epidemic" clone.

IMPORTANCE

Currently, infections attributable to carbapenem-resistant Morganella morganii (CRMM) isolates harboring blaKPC or blaNDM are on the rise, highlighting the increasing severity of acquired antimicrobial resistance. However, systematic phylogeographic and genetic characterization of these isolates worldwide is still lacking. In this study, we elucidated the spatial-temporal distribution and evolutionary trajectory of blaKPC and blaNDM genes within their core genetic environments. We emphasize the necessity of strengthening surveillance and controlling these organisms in clinical settings to prevent the generation of so-called "superbug" isolates.

Diverse Acinetobacter species and Plasmid-Driven spread of carbapenem resistance in pharmaceutical settings in China

Acinetobacter species have emerged as a significant public health concern due to their remarkable capacity to acquire antimicrobial resistance. Environmental reservoirs play a crucial role in spreading antimicrobial resistance genes and potentially pathogenic bacteria to clinical settings. However, most studies on nonhuman isolates have focused on a limited sample size. Comprehensive population sampling on One Health principles is essential to monitor the antibiotic resistome and virulome in Acinetobacter spp. Here, we identified three carbapenems-resistant Acinetobacter spp. isolates harboring blaNDM-1 and discovered two novel Acinetobacter species in pharmaceutical production environments. A total of 94 Acinetobacter spp. strains were isolated from pharmaceutical production environments across 17 cities in China, forming 17 distinct Acinetobacter clusters comprising two novel species and 15 previously known species. Phylogenetic analysis indicated that Acinetobacter spp. isolated from pharmaceutical settings are predominantly confined to these settings. Genomic analysis revealed 10 specific families of blaCHDL genes in 51 isolates and blaNDM-1 in three isolates. The overall rates of phenotypic resistance to antimicrobials were low among Acinetobacter spp. isolates, with less than 10 % resistance observed for all tested drugs, and only three isolates carrying blaNDM-1 were resistant to carbapenems. The blaNDM-1 gene was located in approximately 49 kb PTU-Pse8 conjugative plasmids with conserved backbones, although plasmid pXH1688-NDM displayed enhanced growth and stability. Two novel Acinetobacter species, A. yuyunsongii sp. nov. and A. chenhuanii sp. nov., were characterized using phenotypic and genomic analyses. Particularly, A. yuyunsongii sp. nov. XH1639 harbors a blaOXA-58-carrying conjugative plasmid and exhibits multidrug-resistant phenotype. Our study advances Acinetobacter taxonomy and underscores the urgency of monitoring the dynamics of Acinetobacter species in environmental sources to implement effective measures to mitigate transmission risks to healthcare facilities.

Chromatin accessibility landscape of mouse early embryos revealed by single-cell NanoATAC-seq2

In mammals, fertilized eggs undergo genome-wide epigenetic reprogramming to generate the organism. However, our understanding of epigenetic dynamics during preimplantation development at single-cell resolution remains incomplete. Here, we developed scNanoATAC-seq2, a single-cell assay for transposase-accessible chromatin using long-read sequencing for scarce samples. We present a detailed chromatin accessibility landscape of mouse preimplantation development, revealing distinct chromatin signatures in the epiblast, primitive endoderm, and trophectoderm during lineage segregation. Differences between zygotes and two-cell embryos highlight reprogramming in chromatin accessibility during the maternal-to-zygotic transition. Single-cell long-read sequencing enables in-depth analysis of chromatin accessibility in noncanonical imprinting, imprinted X chromosome inactivation, and low-mappability genomic regions, such as repetitive elements and paralogs. Our data provide insights into chromatin dynamics during mammalian preimplantation development and lineage differentiation.

A review of the taxonomy and phylogenetics of the curvicauda species group within the genus Anastrepha in Mexico including descriptions of new taxa

We present a taxonomic study of Mexican fruit fly populations previously identified as Anastrepha curvicauda (Gerstaecker), describing two new taxa from Mexico, A. magnifica, new species, and A. curvicauda flavigaster, new subspecies. In addition, the phylogenetic relationships between the population samples are analysed using mitochondrial sequences of the COI gene. The results provide new insights into the geographical distribution and natural history of the Mexican species.

Characterization and Assembly Dynamics of the Microbiome Associated with Swine Anaerobic Lagoon Manure Treated with Biochar

Biochar has significant potential for livestock microbiomes and crop agriculture regarding greenhouse gas emissions reduction. Therefore, a pilot study was designed to investigate the effect of biochar application on the surface of swine manure from an open lagoon and the associated microbial communities. Samples were collected from four different treatment groups: control (n = 4), coarse biochar (n = 4), fine biochar (n = 4), and ultra-fine biochar (n = 4). Additionally, aged manure in bulk was collected (n = 4) to assess alterations from the control group. The method of 16S rRNA amplicon sequencing along with microbial analyses was performed. Diversity was significantly different between aged manure in bulk samples and all treatment groups (Kruskal-Wallis; p < 0.05). Additionally, distinct community compositions were seen using both weighted and unweighted UniFrac distance matrices (PERMANOVA; p < 0.01). Differential abundance analysis revealed four distinct features within all treatment groups that were enriched (q < 0.001): Idiomarina spp., Geovibrio thiophilus, Parapusillimonas granuli, and an uncultured Gammaproteobacteria species. Similarly, Comamonas spp. and Brumimicrobium aurantiacum (q-value < 0.001) were significantly depleted by all the treatments. Stochastic and functional analyses revealed that biochar treatments were not deterministically altering assembly patterns, and functional redundancy was evident regardless of compositional shifts.

DNA Barcode, chemical analysis, and antioxidant activity of Psidium guineense from Ecuador

This study investigates the phytochemical, genetic, and antioxidant properties of Psidium guineense, a species native to the tropical dry forests of Ecuador. Leaves were collected, preserved in recognized herbaria, and subjected to Soxhlet extraction using polar and non-polar solvents. Phytochemical screening revealed the presence of secondary metabolites, while GC-MS analysis detected chemical compounds in the extracts. Antioxidant assays demonstrated high phenolic (54.34 ± 0.49 mg GAE/g) and flavonoid (6.43 ± 0.38 mg QE/g) content, with significant antioxidant activity in DPPH (0.57 ± 0.04 mg TE/g), FRAP (105.52 ± 6.85), and ABTS (1.25 ± 0.01 mg TE/g) assays. DNA barcoding of nine loci, (seven from the chloroplast genome and two nuclear genome) using a CTAB extraction protocol and PCR, provides the first genetic characterization of this species, contributing to genetic diversity assessments and phylogenetic studies. These findings underscore the importance of P. guineense as a source of potent bioactive compounds with significant antioxidant potential, highlighting its applicability in nutritional and pharmaceutical industries. Additionally, the genetic insights gained support efforts to expand DNA barcoding databases for tropical biodiversity conservation.

Phylogeny of the European Collema species (Peltigerales, Lecanoromycetes)

The phylogenetic relationships and morphological diversity within European Collema s. str. species were investigated. A total of 104 new sequences (four molecular markers; mtSSU, b-tub, MCM7, and RPB2 genes) from 28 specimens were generated, and analysed and used for multi-locus phylogenetic analyses. Our results suggest that Collema is only monophyletic if Collemaglebulentum is considered part of Leptogium s. str. where it originally was described. This is supported by its paraplectenchymatous thallus. Degelius´ informal Collema "Flaccidum"- and "Nigrescens"-groups are not natural, as the "Flaccidum"-group is nested within the "Nigrescens"-group. Based on our findings, seven currently accepted Collema occur in Europe: C.flaccidum, C.subflaccidum, C.curtisporum, C.furfuraceum, C.nigrescens, C.ryssoleum, and C.subnigrescens. Collemafurfuraceum is further non-monophyletic, suggesting a need for taxonomic revision.

Intercontinental movement of exotic fungi on decorative wood used in aquatic and terrestrial aquariums

The intercontinental movement of fungi or fungus-like organisms brings nonnative species into areas where they may become invasive pathogens of trees and other plants. In the past century, many examples such as Dutch elm disease, sudden oak death, laurel wilt, and others have resulted in large economic losses and ecological disasters. Although various safeguards to prevent the transport of potential pathogens have been in effect, new avenues of introduction have occurred causing new disease outbreaks. This study examined fungi in wood shipped from Asia that is used for decorative purposes in aquatic and terrestrial aquariums. From 44 imported wood samples, 202 cultures representing 123 different fungal taxa were obtained and identified using molecular methods. These included 31 species not previously reported in the United States, 21 potential plant pathogens, 37 species of wood decay fungi and 24 taxa with a 97% sequence match or less to known isolates suggesting these are unknown species. The results demonstrate that wood used for decorative purposes in aquariums harbor large numbers of diverse fungi that remain viable during shipping and storage. These fungi are currently being imported into areas where they are not native, and they may pose serious biosecurity threats to the United States and other countries around the world.

Soil Microbial Recovery to the Rubber Tree Replanting Process in Ivory Coast

The resistance and resilience of soil microbial communities to an environmental disturbance are poorly documented, due to the lack on onfield diachronic experiments, limiting our ability to design adapted agroecological practices. This is especially true in rubber plantations, one of the most planted tree in tropical areas. We aimed to understand (1) how soil disturbances occurring during the rubber replanting phase affect the soil microbiome, (2) how agricultural practices combining legumes cover crops and tree logging residues shape community resilience and (3) how microbial responses vary across different edaphic contexts. In two plantations with distinct soil properties in Ivory Coast, soil microbial communities were surveyed every 6 months for 24 months after soil perturbation. Community structure, functioning and networks were described based on a 16S/18S rRNA gene investigation. Prokaryotes were generally more resistant to soil perturbation than microeukaryote communities. Prokaryotic resilience dynamics were faster than those of microeukaryotes, the latter being deeply modulated by cover treatments. These specific dynamics were exacerbated in the sandy site. Co-occurrence network modelling provided useful insights into microbial resilience trajectories. We argue that this tool should be more widely used to describe microbial community dynamics. Practices involving a combination of logging residues and legume cover crops have shown beneficial effects on the community resilience in the sandy site and appears as promising agroecological practices. However, the major influence of soil texture warns of the need to consider pedological context when designing pertinent agroecological practices.