The COG database: an updated version includes eukaryotes

In-depth comparative pathogenome, virulome, and resistome analysis of an extensive drug resistant Ralstonia mannitolilytica strain isolated from blood

INTRODUCTION

Ralstonia mannitolilytica is an global opportunistic pathogen responsible for various diseases. In this study, we reported the genome of a R. mannitolilytica isolate responsible for bacteremia in an acute exacerbation of chronic obstructive pulmonary disease (AECOPD).

METHODS

Bacterial identification was performed with a Vitek2™ Automated System and 16S rRNA sequencing with BLASTn against the Non-Redundant Protein Sequence (Nr) database. Genome sequencing and analysis were performed using PacBio RS II sequencer, Hierarchical Genome Assembly Process assembly, as well as multiple annotation databases to better understand the innate features. Antibiotic resistance genes and virulence factors were specifically identified through Antibiotic Resistance Genes database and Virulence Factors of Pathogenic Bacteria databases.

RESULTS

The complete genome sequence was assembled into two chromosomes with 3,495,817 bp and 1,342,871 bp in length and GC% of 65.37 % and 66.43 %, respectively. The two chromosomes were fully annotated. In chromosome 1 and 2, 19 and 14 antibiotic resistant genes and 48 and 55 virulence factors were predicted, respectively. Specifically, beta-lactam resistance genes blaOXA-443, blaOXA-444 were acquired.

CONCLUSIONS

This study aids in the understanding of the innate features of R. mannitolilytica in AECOPD.

Accumulation and ecological risk assessment of diazinon in surface sediments of Baiyangdian lake and its potential impact on probiotics and pathogens

Diazinon is an organophosphorus pesticide widely used in agriculture and household pest control, and its use also poses several environmental and health hazards. In this study, we investigated the spatial and temporal distribution of diazinon in Baiyangdian, evaluated its potential ecological risk and toxicity to aquatic organisms based on RQ (Risk quotient) and TU (Toxic unit) analysis, and assessed the potential effects of diazinon accumulation on probiotics and pathogens based on statistical analysis of high-throughput sequencing data. The results showed that diazinon in Baiyangdian posed a low to moderate chronic risk to sediment-dwelling organisms and a low toxicity effect on aquatic invertebrates, which was mainly concentrated in October and human-intensive areas. Meanwhile, increases in sediment electrical conductivity (EC), amorphous iron oxides content and phenol oxidase activity favored diazinon accumulation in sediments, whereas the opposite was the case for sediment organic carbon, β-1,4-glucosidase, phosphatase, catalase and pH, suggesting that environmental indicators play a key role in the behavior and distribution of diazinon. In addition, diazinon in heavily contaminated areas seem to inhibit the rare probiotics (Bifidobacterium adolescentis and Serratia sp.), while promoted dominant pathogens (e.g., Burkholderia cenocepacia), which can lead to increased disease risk to humans and ecosystems, disruption of ecological balance and potential health problems. However, probiotic Streptomyces xiamenensis resist to diazinon would be a potential degrader for diazinon remove. In conclusion, this study unveiled the effects of diazinon pollution on wetland ecosystems, emphasizing ecological impacts and potential health concerns. In addition, the discovery of diazinon resistant probiotics provided new insights into wetland ecological restoration.

Isolation, genomic analysis and functional characterization of Enterococcus rotai CMTB-CA6, a putative probiotic strain isolated from a medicinal plant Centella asiatica

Probiotics and their derivatives offer significant health benefits by supporting digestive health, boosting the immune system, and regulating the microbiomes not only of the internal gastrointestinal track but also of the skin. To be effective, probiotics and their derivatives must exhibit robust antimicrobial activity, resilience to adverse conditions, and colonization capabilities in host tissues. As an alternative to animal-derived probiotics, plant-derived lactic acid bacteria (LAB) present promising advantages, including enhanced diversity and tolerance to challenging environments. Our study focuses on exploring the potential of plant-derived LAB, particularly from the medicinal plant Centella asiatica, in improving skin conditions. Through a bacterial isolation procedure from C. asiatica leaves, Enterococcus rotai CMTB-CA6 was identified via 16S rRNA sequencing, whole genome sequencing, and bioinformatic analyses. Based on genomic analysis, antimicrobial-resistance and virulence genes were not detected. Additionally, the potential functions of E. rotai CMTB-CA6 were characterized by its lysates' ability to regulate skin microbes, such as stimulating the growth of Staphylococcus epidermidis while inhibiting that of Cutibacterium acnes, to restore the viability of human dermal fibroblasts under inflammatory conditions, and to demonstrate effective antioxidant activities both in a cell-free system and in human dermal fibroblasts. Our investigation revealed the efficacy of E. rotai CMTB-CA6 lysates in improving skin conditions, suggesting its potential use as a probiotic-derived agent for skin care products. Considering the ecological relationship between plant-inhabited bacteria and their host plants, we suggest that the utilization of E. rotai CMTB-CA6 strain for fermenting its host plant, C. asiatica, could be a novel approach to efficiently enriching bioactive molecules for human health benefits.

Complete genome sequence analysis of Pestalotiopsis microspora, a fungal pathogen causing kiwifruit postharvest rots

BACKGROUND

The postharvest rot of kiwifruit is one of the most devastating diseases affecting kiwifruit quality worldwide. However, the genomic basis and pathogenicity mechanisms of kiwifruit rot pathogens are lacking. Here we report the first whole genome sequence of Pestalotiopsis microspora, one of the main pathogens causing postharvest kiwifruit rot in China. The genome of strain KFRD-2 was sequenced, de novo assembled, and analyzed.

RESULTS

The genome of KFRD-2 was estimated to be approximately 50.31 Mb in size, with an overall GC content of 50.25%. Among 14,711 predicted genes, 14,423 (98.04%) exhibited significant matches to genes in the NCBI nr database. A phylogenetic analysis of 26 known pathogenic fungi, including P. microspora KFRD-2, based on conserved orthologous genes, revealed that KFRD-2's closest evolutionary relationships were to Neopestalotiopsis spp. Among KFRD-2's coding genes, 870 putative CAZy genes spanned six classes of CAZys, which play roles in degrading plant cell walls. Out of the 25 other plant pathogenic fungi, P. microspora possessed a greater number of CAZy genes than 22 and was especially enriched in GH and AA genes. A total of 845 transcription factors and 86 secondary metabolism gene clusters were predicted, representing various types. Furthermore, 28 effectors and 109 virulence-enhanced factors were identified using the PHI (pathogen host-interacting) database.

CONCLUSION

This complete genome sequence analysis of the kiwifruit postharvest rot pathogen P. microspora enriches our understanding its disease pathogenesis and virulence. This study establishes a theoretical foundation for future investigations into the pathogenic mechanisms of P. microspora and the development of enhanced strategies for the efficient management of kiwifruit postharvest rots.

RhizoBindingSites v2.0 Is a Bioinformatic Database of DNA Motifs Potentially Involved in Transcriptional Regulation Deduced From Their Genomic Sites

RhizoBindingSites is a de novo depurified database of conserved DNA motifs potentially involved in the transcriptional regulation of the Rhizobium, Sinorhizobium, Bradyrhizobium, Azorhizobium, and Mesorhizobium genera covering 9 representative symbiotic species, deduced from the upstream regulatory sequences of orthologous genes (O-matrices) from the Rhizobiales taxon. The sites collected with O-matrices per gene per genome from RhizoBindingSites were used to deduce matrices using the dyad-Regulatory Sequence Analysis Tool (RSAT) method, giving rise to novel S-matrices for the construction of the RizoBindingSites v2.0 database. A comparison of the S-matrix logos showed a greater frequency and/or re-definition of specific-position nucleotides found in the O-matrices. Moreover, S-matrices were better at detecting genes in the genome, and there was a more significant number of transcription factors (TFs) in the vicinity than O-matrices, corresponding to a more significant genomic coverage for S-matrices. O-matrices of 3187 TFs and S-matrices of 2754 TFs from 9 species were deposited in RhizoBindingSites and RhizoBindingSites v2.0, respectively. The homology between the matrices of TFs from a genome showed inter-regulation between the clustered TFs. In addition, matrices of AraC, ArsR, GntR, and LysR ortholog TFs showed different motifs, suggesting distinct regulation. Benchmarking showed 72%, 68%, and 81% of common genes per regulon for O-matrices and approximately 14% less common genes with S-matrices of Rhizobium etli CFN42, Rhizobium leguminosarum bv. viciae 3841, and Sinorhizobium meliloti 1021. These data were deposited in RhizoBindingSites and the RhizoBindingSites v2.0 database (http://rhizobindingsites.ccg.unam.mx/).

The nature of the last universal common ancestor and its impact on the early Earth system

The nature of the last universal common ancestor (LUCA), its age and its impact on the Earth system have been the subject of vigorous debate across diverse disciplines, often based on disparate data and methods. Age estimates for LUCA are usually based on the fossil record, varying with every reinterpretation. The nature of LUCA's metabolism has proven equally contentious, with some attributing all core metabolisms to LUCA, whereas others reconstruct a simpler life form dependent on geochemistry. Here we infer that LUCA lived ~4.2 Ga (4.09-4.33 Ga) through divergence time analysis of pre-LUCA gene duplicates, calibrated using microbial fossils and isotope records under a new cross-bracing implementation. Phylogenetic reconciliation suggests that LUCA had a genome of at least 2.5 Mb (2.49-2.99 Mb), encoding around 2,600 proteins, comparable to modern prokaryotes. Our results suggest LUCA was a prokaryote-grade anaerobic acetogen that possessed an early immune system. Although LUCA is sometimes perceived as living in isolation, we infer LUCA to have been part of an established ecological system. The metabolism of LUCA would have provided a niche for other microbial community members and hydrogen recycling by atmospheric photochemistry could have supported a modestly productive early ecosystem.

Spatially structured exchange of metabolites enhances bacterial survival and resilience in biofilms

Biofilm formation enhances bacterial survival and antibiotic tolerance, but the underlying mechanisms are incompletely understood. Here, we show that biofilm growth is accompanied by a reduction in bacterial energy metabolism and membrane potential, together with metabolic exchanges between the inner and outer regions in biofilms. More specifically, nutrient-starved cells in the interior supply amino acids to cells in the periphery, while peripheral cells experience a decrease in membrane potential and provide fatty acids to interior cells. Fatty acids facilitate the repair of starvation-induced membrane damage in inner cells and enhance their survival in the presence of antibiotics. Thus, metabolic exchanges between inner and outer cells contribute to survival of the nutrient-starved inner cells and contribute to antibiotic tolerance within the biofilm.

High-Throughput Transcriptomic Analysis of Circadian Rhythm of Chlorophyll Metabolism under Different Photoperiods in Tea Plants

Tea plants are a perennial crop with significant economic value. Chlorophyll, a key factor in tea leaf color and photosynthetic efficiency, is affected by the photoperiod and usually exhibits diurnal and seasonal variations. In this study, high-throughput transcriptomic analysis was used to study the chlorophyll metabolism, under different photoperiods, of tea plants. We conducted a time-series sampling under a skeleton photoperiod (6L6D) and continuous light conditions (24 L), measuring the chlorophyll and carotenoid content at a photoperiod interval of 3 h (24 h). Transcriptome sequencing was performed at six time points across two light cycles, followed by bioinformatics analysis to identify and annotate the differentially expressed genes (DEGs) involved in chlorophyll metabolism. The results revealed distinct expression patterns of key genes in the chlorophyll biosynthetic pathway. The expression levels of CHLE (magnesium-protoporphyrin IX monomethyl ester cyclase gene), CHLP (geranylgeranyl reductase gene), CLH (chlorophyllase gene), and POR (cytochrome P450 oxidoreductase gene), encoding enzymes in chlorophyll synthesis, were increased under continuous light conditions (24 L). At 6L6D, the expression levels of CHLP1.1, POR1.1, and POR1.2 showed an oscillating trend. The expression levels of CHLP1.2 and CLH1.1 showed the same trend, they both decreased under light treatment and increased under dark treatment. Our findings provide potential insights into the molecular basis of how photoperiods regulate chlorophyll metabolism in tea plants.

Transcriptome Analysis Identifies Key Genes Involved in Response and Recovery to High Heat Stress Induced by Fire in Schima superba

Fire-resistant tree species play a crucial role in forest fire prevention, utilizing several physiological and molecular mechanisms to respond to extreme heat stress. Many transcription factors (TFs) and genes are known to be involved in the regulatory network of heat stress response in plants. However, their roles in response to high temperatures induced by fire remain less understood. In this study, we investigated Schima superba, a fire-resistant tree, to elucidate these mechanisms. Leaves of S. superba seedlings were exposed to fire stimulation for 10 s, 30 s, and 1 min, followed by a 24-h recovery period. Fifteen transcriptomes were assembled to identify key molecular and biological pathways affected by high temperatures. Differentially expressed genes (DEGs) analysis revealed essential candidate genes and TFs involved in the heat stress response, including members of the ethylene-responsive factors, WRKY, MYB, bHLH, and Nin-like families. Genes related to heat shock proteins/factors, lipid metabolism, antioxidant enzymes, dehydration responses, and hormone signal transduction were differentially expressed after heat stress and recovery, underscoring their roles in cellular process and recovery after heat stress. This study advances our understanding of plant response and defense strategies against extreme abiotic stresses.

Draft genome sequence and annotation of the polyextremotolerant polyol lipid-producing fungus aureobasidium pullulans NRRL 62042

OBJECTIVES

The ascomycotic yeast-like fungus Aureobasidium exhibits the natural ability to synthesize several secondary metabolites, like polymalic acid, pullulan, or polyol lipids, with potential biotechnological applications. Combined with its polyextremotolerance, these properties make Aureobasidium a promising production host candidate. Hence, plenty of genomes of Aureobasidia have been sequenced recently. Here, we provide the annotated draft genome sequence of the polyol lipid-producing strain A. pullulans NRRL 62042.

DATA DESCRIPTION

The genome of A. pullulans NRRL 62042 was sequenced using Illumina NovaSeq 6000. Genome assembly revealed a genome size of 24.2 Mb divided into 39 scaffolds with a GC content of 50.1%. Genome annotation using Genemark v4.68 and GenDBE yielded 9,596 genes.

Datasets of fungal diversity and pseudo-chromosomal genomes of mangrove rhizosphere soil in China

With climate change and anthropic influence on the coastal ecosystems, mangrove ecosystems are disappearing at an alarming rate. Accordingly, it becomes important to track, study, record and store the mangrove microbial community considering their ecological importance and potential for biotechnological applications. Here, we provide information on mangrove fungal community composition and diversity in mangrove ecosystems with different plant species and from various locations differing in relation to anthropic influences. We describe twelve newly assembled genomes, including four chromosomal-level genomes of fungal isolates from the mangrove ecosystems coupled with functional annotations. We envisage that these data will be of value for future studies including comparative genome analysis and large-scale temporal and/or spatial research to elucidate the potential mechanisms by which mangrove fungal communities assemble and evolve. We further anticipate that the genomes represent valuable resources for bioprospecting related to industrial or clinical uses.

Functional genomics identifies a small secreted protein that plays a role during the biotrophic to necrotrophic shift in the root rot pathogen Phytophthora medicaginis

Introduction

Hemibiotrophic Phytophthora are a group of agriculturally and ecologically important pathogenic oomycetes causing severe decline in plant growth and fitness. The lifestyle of these pathogens consists of an initial biotrophic phase followed by a switch to a necrotrophic phase in the latter stages of infection. Between these two phases is the biotrophic to necrotrophic switch (BNS) phase, the timing and controls of which are not well understood particularly in Phytophthora spp. where host resistance has a purely quantitative genetic basis.

Methods

To investigate this we sequenced and annotated the genome of Phytophthora medicaginis, causal agent of root rot and substantial yield losses to Fabaceae hosts. We analyzed the transcriptome of P. medicaginis across three phases of colonization of a susceptible chickpea host (Cicer arietinum) and performed co-regulatory analysis to identify putative small secreted protein (SSP) effectors that influence timing of the BNS in a quantitative pathosystem.

Results

The genome of P. medicaginis is ~78 Mb, comparable to P. fragariae and P. rubi which also cause root rot. Despite this, it encodes the second smallest number of RxLR (arginine-any amino acid-leucine-arginine) containing proteins of currently sequenced Phytophthora species. Only quantitative resistance is known in chickpea to P. medicaginis, however, we found that many RxLR, Crinkler (CRN), and Nep1-like protein (NLP) proteins and carbohydrate active enzymes (CAZymes) were regulated during infection. Characterization of one of these, Phytmed_10271, which encodes an RxLR effector demonstrates that it plays a role in the timing of the BNS phase and root cell death.

Discussion

These findings provide an important framework and resource for understanding the role of pathogenicity factors in purely quantitative Phytophthora pathosystems and their implications to the timing of the BNS phase.

Persistent glucose consumption under antibiotic treatment protects bacterial community

Antibiotics typically induce major physiological changes in bacteria. However, their effect on nutrient consumption remains unclear. Here we found that Escherichia coli communities can sustain normal levels of glucose consumption under a broad range of antibiotics. The community-living resulted in a low membrane potential in the bacteria, allowing slow antibiotic accumulation on treatment and better adaptation. Through multi-omics analysis, we identified a prevalent adaptive response characterized by the upregulation of lipid synthesis, which substantially contributes to sustained glucose consumption. The consumption was maintained by the periphery region of the community, thereby restricting glucose penetration into the community interior. The resulting spatial heterogeneity in glucose availability protected the interior from antibiotic accumulation in a membrane potential-dependent manner, ensuring rapid recovery of the community postantibiotic treatment. Our findings unveiled a community-level antibiotic response through spatial regulation of metabolism and suggested new strategies for antibiotic therapies.

Transcriptome analysis unravels key pathways and hub genes related to immature fruit abscission in Camellia oleifera

Immature fruit abscission of Camellia oleifera (C. oleifera) is a common problem limiting yield increases. However, the regulatory mechanisms underlying immature fruit abscission in C. oleifera are unclear. In this study, we systematically investigated changes in the morphological, physiological, and gene expression of fruit abscission zones (FAZs) of soon-to-abscise fruits (M2). We found that fruit abscission before ripening mainly occurs during the August abscission stage of 'Huashuo'. At the beginning of this stage, the FAZs of M2 have a marked dent, and the separation layer structures are preliminarily formed. Phytohormone analysis showed that the contents of indole-3-acetic acid (IAA) and jasmonic acid (JA) in the FAZs of M2 were significantly decreased compared with the non-abscised fruits, while the content of trans-zeatin (TZR) was increased. Transcriptome analysis identified differentially expressed genes (DEGs) mainly involved in phytohormone metabolism, including ethylene, auxin, JA, and the cis-zeatin signal transduction pathway. There were also many DEGs involved in cell wall catabolism. Weighted gene co-expression network analysis (WGCNA) further suggested that the transcription factors NAC100 and ERF114 participate in the immature fruit abscission of C. oleifera. This study provides insights into the fruit abscission mechanism of C. oleifera.

Characterization and genomic analysis of Bacillus megaterium with the ability to degrade aflatoxin B1

Coix seed is a good product for both medicinal and food use, which is highly susceptible to aflatoxin B1 (AFB1) contamination during field transport, storage, and processing. The aim of this study is to find microbial strains that can solve the problem of contamination of coix seed. In this study, the AFB1-degrading microorganism SX1-1 was isolated and identified as a Bacillus megaterium based on morphology, microscopy, and 16S rDNA sequencing. The optimum culture conditions for SX1-1 to degrade AFB1 were determined to be 12 h. The optimum degradation conditions were 72 h, 57°C, and an initial pH of 8.0. The highest degradation of AFB1 was observed in the fermentation supernatant of the SX1-1 strain, with a degradation rate of 97.45%. In addition, whole-genome sequencing analysis of this strain revealed the presence of a number of enzymes that could potentially degrade AFB1. Importantly, SX1-1 was able to degrade AFB1-contaminated coix seed in situ by 50.06% after co-culture. In conclusion, this strain had a high AFB1 degradation ability, and has great potential and great application as a biocontrol agent for AFB1 degradation of coix seed.

Insights into the molecular basis of reduced vancomycin susceptibility among three prominent Staphylococcus aureus clonal complexes

Staphylococcus aureus is a leading cause of healthcare-associated infections globally. Vancomycin-resistant S. aureus (VRSA), those with high-level resistance [minimum inhibitory concentration (MIC) of 16-32 µg/mL vancomycin], are uncommon, whereas vancomycin-intermediate S. aureus (VISA; MIC of 4-8 µg/mL), are isolated more frequently and develop during long-term and/or repeated use of the antibiotic. VISA can be difficult to eradicate and infections may persist. Our knowledge of mechanisms that underlie the development of VISA is incomplete. We used a genomics approach to investigate the VISA phenotype in three prominent S. aureus lineages. All VISA clinical isolates tested had increased cell wall thickness compared with vancomycin-susceptible S. aureus strains. Growth rates of clonal complex (CC) 5, CC8, and CC45 clinical isolates were reduced in 2 µg/mL vancomycin compared to media alone. Culture in 2 and 4 µg/mL vancomycin sequentially for two weeks reduced susceptibility to daptomycin, televancin, tigecycline, and vancomycin in a majority of CC5, CC8, and CC45 isolates tested. We identified alleles reported previously to contribute to the VISA phenotype, but unexpectedly, these alleles were unique to each CC. A subtherapeutic concentration of vancomycin elicited changes in the VISA transcriptome-common and unique-among the three CCs tested. Multiple genes, including those encoding a glycerate kinase, an M50 family metallopeptidase, and an uncharacterized membrane protein, were upregulated among all three lineages and not reported previously as associated with VISA. Although there are lineage-specific changes in DNA sequence, our findings suggest changes in the VISA transcriptome constitute a general response to stress that confers reduced susceptibility to multiple antibiotics.

IMPORTANCE

Our understanding of the mechanisms that underlie the development of vancomycin-intermediate Staphylococcus aureus (VISA) is incomplete. To provide a more comprehensive view of this process, we compared genome sequences of clonal complex (CC) 5, CC8, and CC45 VISA clinical isolates and measured changes in the transcriptomes of these isolates during culture with a subtherapeutic concentration of vancomycin. Notably, we identified differentially expressed genes that were lineage-specific or common to the lineages tested, including genes that have not been previously reported to contribute to a VISA phenotype. Changes in gene expression were accompanied by reduced growth rate, increased cell wall thickness, and reduced susceptibility to daptomycin, televancin, tigecycline, and vancomycin. Our results provide support to the idea that changes in gene expression contribute to the development of VISA among three CCs that are a prominent cause of human infections.

Identification of the effects of alkalinity exposure on the gills of oriental river prawns, Macrobrachium nipponense

Macrobrachium nipponense is an important commercial freshwater species in China. However, the ability of alkali tolerance of M. nipponense is insufficient to culture in the major saline-alkali water source in China. Thus, it is urgently needed to perform the genetic improvement of alkali tolerance in this species. In the present study, we aimed to analyse the effects of alkali treatment on gills in this species after 96 h alkalinity exposure under the alkali concentrations of 0 mmol/L, 4 mmol/L, 8 mmol/L, and 12 mmol/L through performing the histological observations, measurement of antioxidant enzymes, metabolic profiling analysis, and transcriptome profiling analysis. The results of the present study revealed that alkali treatment stimulated the contents of malondialdehyde, glutathione, glutathione peroxidase in gills, indicating these antioxidant enzymes plays essential roles in the protection of body from the damage, caused by the alkali treatment. In addition, high concentration of alkali treatment (> 8 mmol/L) resulted in the damage of gill membrane and haemolymph vessel, affecting the normal respiratory function of gill. Metabolic profiling analysis revealed that Metabolic pathways, Biosynthesis of secondary metabolites, Biosynthesis of plant secondary metabolites, Microbial metabolism in diverse environments, Biosynthesis of amino acids were identified as the main enriched metabolic pathways of differentially expressed metabolites, which are consistent with the previous publications, treated by the various environmental factors. Transcriptome profiling analyses revealed that the alkali concentration of 12 mmol/L has more regulatory effects on the changes of gene expression than the other alkali concentrations. KEGG analysis revealed that Phagosome, Lysosome, Glycolysis/Gluconeogenesis, Purine Metabolism, Amino sugar and nucleotide sugar metabolism, and Endocytosis were identified as the main enriched metabolic pathways in the present study, predicting these metabolic pathways may be involved in the adaption of alkali treatment in M. nipponense. Phagosome, Lysosome, Purine Metabolism, and Endocytosis are immune-related metabolic pathways, while Glycolysis/Gluconeogenesis, and Amino sugar and nucleotide sugar metabolism are energy metabolism-related metabolic pathways. Quantitative PCR analyses of differentially expressed genes (DEGs) verified the accuracy of the RNA-Seq. Alkali treatment significantly stimulated the expressions of DEGs from the metabolic pathways of Phagosome and Lysosome, suggesting Phagosome and Lysosome play essential roles in the regulation of alkali tolerance in this species, as well as the genes from these metabolic pathways. The present study identified the effects of alkali treatment on gills, providing valuable evidences for the genetic improvement of alkali tolerance in M. nipponense.

Organellar Genomes of Sargassum hemiphyllum var. chinense Provide Insight into the Characteristics of Phaeophyceae

Sargassum hemiphyllum var. chinense, a prevalent seaweed along the Chinese coast, has economic and ecological significance. However, systematic positions within Sargassum and among the three orders of Phaeophyceae, Fucales, Ectocarpales, and Laminariales are in debate. Here, we reported the organellar genomes of S. hemiphyllum var. chinense (34,686-bp mitogenome with 65 genes and 124,323 bp plastome with 173 genes) and the investigation of comparative genomics and systematics of 37 mitogenomes and 22 plastomes of Fucales (including S. hemiphyllum var. chinense), Ectocarpales, and Laminariales in Phaeophyceae. Whole genome collinearity analysis showed gene number, type, and arrangement were consistent in organellar genomes of Sargassum with 360 SNP loci identified as S. hemiphyllum var. chinense and two genes (rps7 and cox2) identified as intrageneric classifications of Sargassum. Comparative genomics of the three orders of Phaeophyceae exhibited the same content and different types (petL was only found in plastomes of the order Fucales and Ectocarpales) and arrangements (most plastomes were rearranged, but trnA and trnD in the mitogenome represented different orders) in genes. We quantified the frequency of RNA-editing (canonical C-to-U) in both organellar genomes; the proportion of edited sites corresponded to 0.02% of the plastome and 0.23% of the mitogenome (in reference to the total genome) of S. hemiphyllum var. chinense. The repetition ratio of Fucales was relatively low, with scattered and tandem repeats (nine tandem repeats of 14-24 bp) dominating, while most protein-coding genes underwent negative selection (Ka/Ks < 1). Collectively, these findings provide valuable insights to guide future species identification and evolutionary status of three important Phaeophyceae order species.

Phenotypic, genotypic and proteomic variations between poor and robust colonizing Campylobacter jejuni strains

Campylobacter jejuni is one of the major causes of bacterial gastrointestinal disease in humans worldwide. This foodborne pathogen colonizes the intestinal tracts of chickens, and consumption of chicken and poultry products is identified as a common route of transmission. We analyzed two C. jejuni strains after oral challenge with 105 CFU/ml of C. jejuni per chick; one strain was a robust colonizer (A74/C) and the other a poor colonizer (A74/O). We also found extensive phenotypic differences in growth rate, biofilm production, and in vitro adherence, invasion, intracellular survival, and transcytosis. Strains A74/C and A74/O were genotypically similar with respect to their whole genome alignment, core genome, and ribosomal MLST, MLST, flaA, porA, and PFGE typing. The global proteomes of the two congenic strains were quantitatively analyzed by ultra-high performance liquid chromatography-tandem mass spectrometry (UHPLC-MS/MS) and 618 and 453 proteins were identified from A74/C and A74/O isolates, respectively. Cluster of Orthologous Groups (COG) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses showed that carbon metabolism and motility proteins were distinctively overexpressed in strain A74/C. The robust colonizer also exhibited a unique proteome profile characterized by significantly increased expression of proteins linked to adhesion, invasion, chemotaxis, energy, protein synthesis, heat shock proteins, iron regulation, two-component regulatory systems, and multidrug efflux pump. Our study underlines phenotypic, genotypic, and proteomic variations of the poor and robust colonizing C. jejuni strains, suggesting that several factors may contribute to mediating the different colonization potentials of the isogenic isolates.

Distinct microbial nitrogen cycling processes in the deepest part of the ocean

The Mariana Trench (MT) is the deepest part of the ocean on Earth. Previous studies have described the microbial community structures and functional potential in the seawater and surface sediment of MT. Still, the metabolic features and adaptation strategies of the microorganisms involved in nitrogen cycling processes are poorly understood. In this study, comparative metagenomic approaches were used to study microbial nitrogen cycling in three MT habitats, including hadal seawater [9,600-10,500 m below sea level (mbsl)], surface sediments [0-46 cm below seafloor (cmbsf) at a water depth between 7,143 and 8,638 mbsl], and deep sediments (200-306 cmbsf at a water depth of 8,300 mbsl). We identified five new nitrite-oxidizing bacteria (NOB) lineages that had adapted to the oligotrophic MT slope sediment, via their CO2 fixation capability through the reductive tricarboxylic acid (rTCA) or Calvin-Benson-Bassham (CBB) cycle; an anammox bacterium might perform aerobic respiration and utilize sedimentary carbohydrates for energy generation because it contains genes encoding type A cytochrome c oxidase and complete glycolysis pathway. In seawater, abundant alkane-oxidizing Ketobacter species can fix inert N2 released from other denitrifying and/or anammox bacteria. This study further expands our understanding of microbial life in the largely unexplored deepest part of the ocean.

IMPORTANCE

The metabolic features and adaptation strategies of the nitrogen cycling microorganisms in the deepest part of the ocean are largely unknown. This study revealed that anammox bacteria might perform aerobic respiration in response to nutrient limitation or O2 fluctuations in the Mariana Trench sediments. Meanwhile, an abundant alkane-oxidizing Ketobacter species could fix N2 in hadal seawater. This study provides new insights into the roles of hadal microorganisms in global nitrogen biogeochemical cycles. It substantially expands our understanding of the microbial life in the largely unexplored deepest part of the ocean.

A cross-sectional comparison of gut metagenomes between dairy workers and community controls

BACKGROUND

As a nexus of routine antibiotic use and zoonotic pathogen presence, the livestock farming environment is a potential hotspot for the emergence of zoonotic diseases and antibiotic resistant bacteria. Livestock can further facilitate disease transmission by serving as intermediary hosts for pathogens before a spillover event. In light of this, we aimed to characterize the microbiomes and resistomes of dairy workers, whose exposure to the livestock farming environment places them at risk for facilitating community transmission of antibiotic resistant genes and emerging zoonotic diseases.

RESULTS

Using shotgun sequencing, we investigated differences in the taxonomy, diversity and gene presence of 10 dairy farm workers and 6 community controls' gut metagenomes, contextualizing these samples with additional publicly available gut metagenomes. We found no significant differences in the prevalence of resistance genes, virulence factors, or taxonomic composition between the two groups. The lack of statistical significance may be attributed, in part, to the limited sample size of our study or the potential similarities in exposures between the dairy workers and community controls. We did, however, observe patterns warranting further investigation including greater abundance of tetracycline resistance genes and prevalence of cephamycin resistance genes as well as lower average gene diversity (even after accounting for differential sequencing depth) in dairy workers' metagenomes. We also found evidence of commensal organism association with tetracycline resistance genes in both groups (including Faecalibacterium prausnitzii, Ligilactobacillus animalis, and Simiaoa sunii).

CONCLUSIONS

This study highlights the utility of shotgun metagenomics in examining the microbiomes and resistomes of livestock workers, focusing on a cohort of dairy workers in the United States. While our study revealed no statistically significant differences between groups in taxonomy, diversity and gene presence, we observed patterns in antibiotic resistance gene abundance and prevalence that align with findings from previous studies of livestock workers in China and Europe. Our results lay the groundwork for future research involving larger cohorts of dairy and non-dairy workers to better understand the impact of occupational exposure to livestock farming on the microbiomes and resistomes of workers.

Microbial Sulfur and Arsenic Oxidation Facilitate the Establishment of Biocrusts during Reclamation of Degraded Mine Tailings

Degraded tailings generated by the mining of metal ores are major environmental threats to the surrounding ecosystems. Tailing reclamation, however, is often impeded due to adverse environmental conditions, with depleted key nutrients (i.e., nitrogen (N) and phosphorus (P)) and elevated sulfur and metal(loid) concentrations. Formation of biocrusts may significantly accelerate nutrient accumulation and is therefore an essential stage for tailing reclamation. Although suggested to play an important role, the microbial community composition and key metabolisms in biocrusts remain largely unknown and are therefore investigated in the current study. The results suggested that sulfur and arsenic oxidation are potential energy sources utilized by members of predominant biocrust bacterial families, including Beijerinckiaceae, Burkholderiaceae, Hyphomicrobiaceae, and Rhizobiaceae. Accordingly, the S and As oxidation potentials are elevated in biocrusts compared to those in their adjacent tailings. Biocrust growth, as proxied by chlorophyll concentrations, is enhanced in treatments supplemented with S and As. The elevated biocrust growth might benefit from nutrient acquisition services (i.e., nitrogen fixation and phosphorus solubilization) fueled by microbial sulfur and arsenic oxidation. The current study suggests that sulfur- and arsenic-oxidizing microorganisms may play important ecological roles in promoting biocrust formation and facilitating tailing reclamation.

The Development of a Fluorescent Microsatellite Marker Assay for the Pitaya Canker Pathogen (Neoscytalidium dimidiatum)

Pitaya canker, caused by Neoscytalidium dimidiatum, is a destructive disease that significantly threatens the safety of the pitaya industry. The authors of previous studies have mainly focused on its biological characteristics and chemical control. However, there are no molecular markers available thus far that can be used for the population genetics study of this pathogen. In the present study, a draft genome of N. dimidiatum with a total length of 41.46 MB was assembled in which 9863 coding genes were predicted and annotated. In particular, the microsatellite sequences in the draft genome were investigated. To improve the successful screening rate of potentially polymorphic microsatellite makers, another five N. dimidiatum isolates were resequenced and assembled. A total of eight pairs of polymorphic microsatellite primers were screened out based on the polymorphic microsatellite loci after investigating the sequencing and resequencing assemblies of the six isolates. A total of thirteen representative isolates sampled from different pitaya plantations were genotyped in order to validate the polymorphism of the resulting eight markers. The results indicated that these markers were able to distinguish the isolates well. Lastly, a neighbor-joining tree of 35 isolates, sampled from different pitaya plantations located in different regions, was constructed according to the genotypes of the eight molecular markers. The developed tree indicated that these molecular markers had sufficient genotyping capabilities for our test panel of isolates. In summary, we developed a set of polymorphic microsatellite markers in the following study that can effectively genotype and distinguish N. dimidiatum isolates and be utilized in the population genetics study of N. dimidiatum.

Single-cell transcriptomics across 2,534 microbial species reveals functional heterogeneity in the rumen microbiome

Deciphering the activity of individual microbes within complex communities and environments remains a challenge. Here we describe the development of microbiome single-cell transcriptomics using droplet-based single-cell RNA sequencing and pangenome-based computational analysis to characterize the functional heterogeneity of the rumen microbiome. We generated a microbial genome database (the Bovine Gastro Microbial Genome Map) as a functional reference map for the construction of a single-cell transcriptomic atlas of the rumen microbiome. The atlas includes 174,531 microbial cells and 2,534 species, of which 172 are core active species grouped into 12 functional clusters. We detected single-cell-level functional roles, including a key role for Basfia succiniciproducens in the carbohydrate metabolic niche of the rumen microbiome. Furthermore, we explored functional heterogeneity and reveal metabolic niche trajectories driven by biofilm formation pathway genes within B. succiniciproducens. Our results provide a resource for studying the rumen microbiome and illustrate the diverse functions of individual microbial cells that drive their ecological niche stability or adaptation within the ecosystem.

Comparative genomic analysis of Bacillus atrophaeus HAB-5 reveals genes associated with antimicrobial and plant growth-promoting activities

Bacillus atrophaeus HAB-5 is a plant growth-promoting rhizobacterium (PGPR) that exhibits several biotechnological traits, such as enhancing plant growth, colonizing the rhizosphere, and engaging in biocontrol activities. In this study, we conducted whole-genome sequencing of B. atrophaeus HAB-5 using the single-molecule real-time (SMRT) sequencing platform by Pacific Biosciences (PacBio; United States), which has a circular chromosome with a total length of 4,083,597 bp and a G + C content of 44.21%. The comparative genomic analysis of B. atrophaeus HAB-5 with other strains, Bacillus amyloliquefaciens DSM7, B. atrophaeus SRCM101359, Bacillus velezensis FZB42, B. velezensis HAB-2, and Bacillus subtilis 168, revealed that these strains share 2,465 CDSs, while 599 CDSs are exclusive to the B. atrophaeus HAB-5 strain. Many gene clusters in the B. atrophaeus HAB-5 genome are associated with the production of antimicrobial lipopeptides and polypeptides. These gene clusters comprise distinct enzymes that encode three NRPs, two Transat-Pks, one terpene, one lanthipeptide, one T3PKS, one Ripp, and one thiopeptide. In addition to the likely IAA-producing genes (trpA, trpB, trpC, trpD, trpE, trpS, ywkB, miaA, and nadE), there are probable genes that produce volatile chemicals (acoA, acoB, acoR, acuB, and acuC). Moreover, HAB-5 contained genes linked to iron transportation (fbpA, fetB, feuC, feuB, feuA, and fecD), sulfur metabolism (cysC, sat, cysK, cysS, and sulP), phosphorus solubilization (ispH, pstA, pstC, pstS, pstB, gltP, and phoH), and nitrogen fixation (nif3-like, gltP, gltX, glnR, glnA, nadR, nirB, nirD, nasD, narl, narH, narJ, and nark). In conclusion, this study provides a comprehensive genomic analysis of B. atrophaeus HAB-5, pinpointing the genes and genomic regions linked to the antimicrobial properties of the strain. These findings advance our knowledge of the genetic basis of the antimicrobial properties of B. atrophaeus and imply that HAB-5 may employ a variety of commercial biopesticides and biofertilizers as a substitute strategy to increase agricultural output and manage a variety of plant diseases.

Fusion/fission protein family identification in Archaea

The majority of newly discovered archaeal lineages remain without a cultivated representative, but scarce experimental data from the cultivated organisms show that they harbor distinct functional repertoires. To unveil the ecological as well as evolutionary impact of Archaea from metagenomics, new computational methods need to be developed, followed by in-depth analysis. Among them is the genome-wide protein fusion screening performed here. Natural fusions and fissions of genes not only contribute to microbial evolution but also complicate the correct identification and functional annotation of sequences. The products of these processes can be defined as fusion (or composite) proteins, the ones consisting of two or more domains originally encoded by different genes and split proteins, and the ones originating from the separation of a gene in two (fission). Fusion identifications are required for proper phylogenetic reconstructions and metabolic pathway completeness assessments, while mappings between fused and unfused proteins can fill some of the existing gaps in metabolic models. In the archaeal genome-wide screening, more than 1,900 fusion/fission protein clusters were identified, belonging to both newly sequenced and well-studied lineages. These protein families are mainly associated with different types of metabolism, genetic, and cellular processes. Moreover, 162 of the identified fusion/fission protein families are archaeal specific, having no identified fused homolog within the bacterial domain. Our approach was validated by the identification of experimentally characterized fusion/fission cases. However, around 25% of the identified fusion/fission families lack functional annotations for both composite and split states, showing the need for experimental characterization in Archaea.IMPORTANCEGenome-wide fusion screening has never been performed in Archaea on a broad taxonomic scale. The overlay of multiple computational techniques allows the detection of a fine-grained set of predicted fusion/fission families, instead of rough estimations based on conserved domain annotations only. The exhaustive mapping of fused proteins to bacterial organisms allows us to capture fusion/fission families that are specific to archaeal biology, as well as to identify links between bacterial and archaeal lineages based on cooccurrence of taxonomically restricted proteins and their sequence features. Furthermore, the identification of poorly characterized lineage-specific fusion proteins opens up possibilities for future experimental and computational investigations. This approach enhances our understanding of Archaea in general and provides potential candidates for in-depth studies in the future.

Chicken Juice Enhances C. jejuni NCTC 11168 Biofilm Formation with Distinct Morphological Features and Altered Protein Expression

Campylobacter jejuni is the foodborne pathogen causing most gastrointestinal infections. Understanding its ability to form biofilms is crucial for devising effective control strategies in food processing environments. In this study, we investigated the growth dynamics and biofilm formation of C. jejuni NCTC 11168 in various culture media, including chicken juice (CJ), brain heart infusion (BHI), and Mueller Hinton (MH) broth. Our results demonstrated that C. jejuni exhibited a higher growth rate and enhanced biofilm formation in CJ and in 1:1 mixtures of CJ with BHI or MH broth compared to these measures in BHI or MH broth alone. Electron microscopy unveiled distinct morphological attributes of late-stage biofilm cells in CJ, including the presence of elongated spiral-shaped cells, thinner stretched structures compared to regular cells, and extended thread-like structures within the biofilms. Proteomic analysis identified significant alterations in protein expression profiles in C. jejuni biofilms, with a predominance of downregulated proteins associated with vital functions like metabolism, energy production, and amino acid and protein biosynthesis. Additionally, a significant proportion of proteins linked to biofilm formation, virulence, and iron uptake were suppressed. This shift toward a predominantly coccoid morphology echoed the reduced energy demands of these biofilm communities. Our study unlocks valuable insights into C. jejuni's biofilm in CJ, demonstrating its adaptation and survival.

Structural variant landscapes reveal convergent signatures of evolution in sheep and goats

BACKGROUND

Sheep and goats have undergone domestication and improvement to produce similar phenotypes, which have been greatly impacted by structural variants (SVs). Here, we report a high-quality chromosome-level reference genome of Asiatic mouflon, and implement a comprehensive analysis of SVs in 897 genomes of worldwide wild and domestic populations of sheep and goats to reveal genetic signatures underlying convergent evolution.

RESULTS

We characterize the SV landscapes in terms of genetic diversity, chromosomal distribution and their links with genes, QTLs and transposable elements, and examine their impacts on regulatory elements. We identify several novel SVs and annotate corresponding genes (e.g., BMPR1B, BMPR2, RALYL, COL21A1, and LRP1B) associated with important production traits such as fertility, meat and milk production, and wool/hair fineness. We detect signatures of selection involving the parallel evolution of orthologous SV-associated genes during domestication, local environmental adaptation, and improvement. In particular, we find that fecundity traits experienced convergent selection targeting the gene BMPR1B, with the DEL00067921 deletion explaining ~10.4% of the phenotypic variation observed in goats.

CONCLUSIONS

Our results provide new insights into the convergent evolution of SVs and serve as a rich resource for the future improvement of sheep, goats, and related livestock.

Toxin production and transcriptomic response to nitrate concentrations in the toxic dinoflagellate Alexandrium tamarense

The bloom-forming dinoflagellate Alexandrium tamarense is one of the most important producers of paralytic shellfish poisoning toxins. Annually recurrent blooms of this dinoflagellate species is associated with the incremental nitrogen influx, especially excessive nitrate input. However, limited studies have been conducted on the toxin production and underlying molecular regulation mechanisms of A. tamarense under various nitrate (N) conditions. Therefore, toxin production and transcriptomic responses of this species were investigated. The toxin profile of A. tamarense was consistently dominated by the C2-toxins, and the cellular toxicity increased with N concentrations peaking at 9.23 ± 0.03 fmol/cell in the 883 μM N-added group. Under lower N conditions, expressions of two STX-core genes, sxtA and sxtG, were significantly down-regulated, suggesting that N regulated sxt expression and triggered responses related to toxin biosynthesis. Results of this study provided valuable insights into the ecophysiology of A. tamarense, enhancing our understanding of the occurrence of toxification events in natural environments.

Complete characterization of the yak testicular development using accurate full-length transcriptome sequencing

Alternative splicing is a prevalent phenomenon in testicular tissues. Due to the low assembly accuracy of short-read RNA sequencing technology in analyzing post-transcriptional regulatory events, full-length (FL) transcript sequencing is highly demanded to accurately determine FL splicing variants. In this study, we performed FL transcriptome sequencing of testicular tissues from 0.5, 1.5, 2.5, and 4-year-old yaks and 4-year-old cattle-yaks using Oxford Nanopore Technologies. The obtained sequencing data were predicted to have 47,185 open reading frames (ORFs), including 26,630 complete ORFs, detected 7645 fusion transcripts, 15,355 alternative splicing events, 25,798 simple sequence repeats, 7628 transcription factors, and 35,503 long non-coding RNAs. A total of 40,038 novel transcripts were obtained from the sequencing data, and the proportion was almost close to the number of known transcripts identified. Structural analysis and functional annotation of these novel transcripts resulted in the successful annotation of 9568 transcripts, with the highest and lowest annotation numbers in the Nr and KOG databases, respectively. Weighted gene co-expression network analysis revealed the key regulatory pathways and hub genes at various stages of yak testicular development. Our findings enhance our comprehension of transcriptome complexity, contribute to genome annotation refinement, and provide foundational data for further investigations into male sterility in cattle-yaks.

Triglyceride-Catabolizing Lactiplantibacillus plantarum GBCC_F0227 Shows an Anti-Obesity Effect in a High-Fat-Diet-Induced C57BL/6 Mouse Obesity Model

Given the recognized involvement of the gut microbiome in the development of obesity, considerable efforts are being made to discover probiotics capable of preventing and managing obesity. In this study, we report the discovery of Lactiplantibacillus plantarum GBCC_F0227, isolated from fermented food, which exhibited superior triglyceride catabolism efficacy compared to L. plantarum WCSF1. Molecular analysis showed elevated expression levels of α/β hydrolases with lipase activity (abH04, abH08_1, abH08_2, abH11_1, and abH11_2) in L. plantarum GBCC_F0227 compared to L. plantarum WCFS1, demonstrating its enhanced lipolytic activity. In a high-fat-diet (HFD)-induced mouse obesity model, the administration of L. plantarum GBCC_F0227 mitigated weight gain, reduced blood triglycerides, and diminished fat mass. Furthermore, L. plantarum GBCC_F0227 upregulated adiponectin gene expression in adipose tissue, indicative of favorable metabolic modulation, and showed robust growth and low cytotoxicity, underscoring its industrial viability. Therefore, our findings encourage the further investigation of L. plantarum GBCC_F0227's therapeutic applications for the prevention and treatment of obesity and associated metabolic diseases.

A high-quality chromosome-level genome assembly of Ficus hirta

Ficus species (Moraceae) play pivotal roles in tropical and subtropical ecosystems. Thriving across diverse habitats, from rainforests to deserts, they harbor a multitude of mutualistic and antagonistic interactions with insects, nematodes, and pathogens. Despite their ecological significance, knowledge about the genomic background of Ficus remains limited. In this study, we report a chromosome-level reference genome of F. hirta, with a total size of 297.27 Mb, containing 28,625 protein-coding genes and 44.67% repeat sequences. These findings illuminate the genetic basis of Ficus responses to environmental challenges, offering valuable genomic resources for understanding genome size, adaptive evolution, and co-evolution with natural enemies and mutualists within the genus.

The first chromosomal-level genome assembly and annotation of white suckerfish Remora albescens

Remora albescens, also known as white suckerfish, recognized for its distinctive suction-cup attachment behavior and medicinal significance. In this study, we produced a high-quality chromosome-level genome assembly of R. albescens through the integration of 23.87 Gb PacBio long reads, 64.54 Gb T7 short reads, and 88.63 Gb Hi-C data. Initially, we constructed a contig-level genome assembly totaling 605.30 Mb with a contig N50 of 23.12 Mb. Subsequently, employing Hi-C technology, approximately 99.68% (603.38 Mb) of the contig-level genome was successfully assigned to 23 pseudo-chromosomes. Through the integration of homologous-based predictions, ab initio predictions, and RNA-sequencing methods, we successfully identified a comprehensive set of 22,445 protein-coding genes. Notably, 96.36% (21,629 genes) of these were effectively annotated with functional information. The genome assembly achieved an estimated completeness of 98.1% according to BUSCO analysis. This work promotes the applicability of the R. albescens genome, laying a solid foundation for future investigations into genomics, biology, and medicinal importance within this species.

Genome-wide identification analysis in wild-type Solanum pinnatisectum reveals some genes defending against Phytophthora infestans

Solanum pinnatisectum exhibits strong resistance to late blight caused by Phytophthora infestans but only an incomplete genome assembly based on short Illumina reads has been published. In this study, we generated the first chromosome-level draft genome for the wild-type potato species S. pinnatisectum in China using Oxford Nanopore technology sequencing and Hi-C technology. The high-quality assembled genome size is 664 Mb with a scaffold N50 value of 49.17 Mb, of which 65.87% was occupied by repetitive sequences, and predominant long terminal repeats (42.51% of the entire genome). The genome of S. pinnatisectum was predicted to contain 34,245 genes, of which 99.34% were functionally annotated. Moreover, 303 NBS-coding disease resistance (R) genes were predicted in the S. pinnatisectum genome to investigate the potential mechanisms of resistance to late blight disease. The high-quality chromosome-level reference genome of S. pinnatisectum is expected to provide potential valuable resources for intensively and effectively investigating molecular breeding and genetic research in the future.

Genome Characteristics of the Endophytic Fungus Talaromyces sp. DC2 Isolated from Catharanthus roseus (L.) G. Don

Talaromyces sp. DC2 is an endophytic fungus that was isolated from the stem of Catharanthus roseus (L.) G. Don in Hanoi, Vietnam and is capable of producing vinca alkaloids. This study utilizes the PacBio Sequel technology to completely sequence the whole genome of Talaromyces sp. DC2The genome study revealed that DC2 contains a total of 34.58 Mb spanned by 156 contigs, with a GC content of 46.5%. The identification and prediction of functional protein-coding genes, tRNA, and rRNA were comprehensively predicted and highly annotated using various BLAST databases, including non-redundant (Nr) protein sequence, Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), Clusters of Orthologous Groups (COG), and Carbohydrate-Active Enzymes (CAZy) databases. The genome of DC2 has a total of 149, 227, 65, 153, 53, and 6 genes responsible for cellulose, hemicellulose, lignin, pectin, chitin, starch, and inulin degradation, respectively. The Antibiotics and Secondary Metabolites Analysis Shell (AntiSMASH) analyses revealed that strain DC2 possesses 20 biosynthetic gene clusters responsible for producing secondary metabolites. The strain DC2 has also been found to harbor the DDC gene encoding aromatic L-amino acid decarboxylase enzyme. Conclusively, this study has provided a comprehensive understanding of the processes involved in secondary metabolites and the ability of the Talaromyces sp. DC2 strain to degrade plant cell walls.

Whole-genome sequencing of Ganoderma boninense, the causal agent of basal stem rot disease in oil palm, via combined short- and long-read sequencing

The hemibiotrophic Basidiomycete pathogen Ganoderma boninense (Gb) is the dominant causal agent of oil palm basal stem rot disease. Here, we report a complete chromosomal genome map of Gb using a combination of short-read Illumina and long-read Pacific Biosciences (PacBio) sequencing platforms combined with chromatin conformation capture data from the Chicago and Hi-C platforms. The genome was 55.87 Mb in length and assembled to a high contiguity (N50: 304.34 kb) of 12 chromosomes built from 112 scaffolds, with a total of only 4.34 Mb (~ 7.77%) remaining unplaced. The final assemblies were evaluated for completeness of the genome by using Benchmarking Universal Single Copy Orthologs (BUSCO) v4.1.4, and based on 4464 total BUSCO polyporales group searches, the assemblies yielded 4264 (95.52%) of the conserved orthologs as complete and only a few fragmented BUSCO of 42 (0.94%) as well as a missing BUSCO of 158 (3.53%). Genome annotation predicted a total of 21,074 coding genes, with a GC content ratio of 59.2%. The genome features were analyzed with different databases, which revealed 2471 Gene Ontology/GO (11.72%), 5418 KEGG (Kyoto Encyclopedia of Genes and Genomes) Orthologous/KO (25.71%), 13,913 Cluster of Orthologous Groups of proteins/COG (66.02%), 60 ABC transporter (0.28%), 1049 Carbohydrate-Active Enzymes/CAZy (4.98%), 4005 pathogen-host interactions/PHI (19%), and 515 fungal transcription factor/FTFD (2.44%) genes. The results obtained in this study provide deep insight for further studies in the future.

Comprehensive analysis of genomic variation, pan-genome and biosynthetic potential of Corynebacterium glutamicum strains

Corynebacterium glutamicum is a non-pathogenic species of the Corynebacteriaceae family. It has been broadly used in industrial biotechnology for the production of valuable products. Though it is widely accepted at the industrial level, knowledge about the genomic diversity of the strains is limited. Here, we investigated the comparative genomic features of the strains and pan-genomic characteristics. We also observed phylogenetic relationships among the strains based on average nucleotide identity (ANI). We found diversity between strains at the genomic and pan-genomic levels. Less than one-third of the C. glutamicum pan-genome consists of core genes and soft-core genes. Whereas, a large number of strain-specific genes covered about half of the total pan-genome. Besides, C. glutamicum pan-genome is open and expanding, which indicates the possible addition of new gene families to the pan-genome. We also investigated the distribution of biosynthetic gene clusters (BGCs) among the strains. We discovered slight variations of BGCs at the strain level. Several BGCs with the potential to express novel bioactive secondary metabolites have been identified. Therefore, by utilizing the characteristic advantages of C. glutamicum, different strains can be potential applicants for natural drug discovery.

An improved chromosome-level genome assembly and annotation of Echeneis naucrates

Echeneis naucrates, as known as live sharksucker, is famous for the behavior of attaching to hosts using a highly modified dorsal fin with oval-shaped sucking disc. Here, we generated an improved high-quality chromosome-level genome assembly of E. naucrates using Illumina short reads, PacBio long reads and Hi-C data. Our assembled genome spans 572.85 Mb with a contig N50 of 23.19 Mb and is positioned to 24 pseudo-chromosomes. Additionally, at least one telomere was identified for 23 out of 24 chromosomes. Furthermore, we identified a total of 22,161 protein-coding genes, of which 21,402 genes (96.9%) were annotated successfully with functions. The combination of ab initio predictions and Repbase-based searches revealed that 15.57% of the assembled E. naucrates genome was identified as repetitive sequences. The completeness of the genome assembly and the gene annotation were estimated to be 97.5% and 95.4% with BUSCO analyses. This work enhances the utility of the live sharksucker genome and provides a valuable groundwork for the future study of genomics, biology and adaptive evolution in this species.

Chromosome-level genome assembly of the bethylid ectoparasitoid wasp Sclerodermus sp. 'alternatusi'

The Bethylidae are the most diverse of Hymenoptera chrysidoid families. As external parasitoids, the bethylids have been widely adopted as biocontrol agents to control insect pests worldwide. Thus far, the genomic information of the family Bethylidae has not been reported yet. In this study, we crystallized into a high-quality chromosome-level genome of ant-like bethylid wasps Sclerodermus sp. 'alternatusi' (Hymenoptera: Bethylidae) using PacBio sequencing as well as Hi-C technology. The assembled S. alternatusi genome was 162.30 Mb in size with a contig N50 size of 3.83 Mb and scaffold N50 size of 11.10 Mb. Totally, 92.85% assembled sequences anchored to 15 pseudo-chromosomes. A total of 10,204 protein-coding genes were annotated, and 23.01 Mb repetitive sequences occupying 14.17% of genome were pinpointed. The BUSCO results showed that 97.9% of the complete core Insecta genes were identified in the genome, while 97.1% in the gene sets. The high-quality genome of S. alternatusi will not only provide valuable genomic information, but also show insights into parasitoid wasp evolution and bio-control application in future studies.

Multi-omics analyses provide insights into the evolutionary history and the synthesis of medicinal components of the Chinese wingnut

Chinese wingnut (Pterocarya stenoptera) is a medicinally and economically important tree species within the family Juglandaceae. However, the lack of high-quality reference genome has hindered its in-depth research. In this study, we successfully assembled its chromosome-level genome and performed multi-omics analyses to address its evolutionary history and synthesis of medicinal components. A thorough examination of genomes has uncovered a significant expansion in the Lateral Organ Boundaries Domain gene family among the winged group in Juglandaceae. This notable increase may be attributed to their frequent exposure to flood-prone environments. After further differentiation between Chinese wingnut and Cyclocarya paliurus, significant positive selection occurred on the genes of NADH dehydrogenase related to mitochondrial aerobic respiration in Chinese wingnut, enhancing its ability to cope with waterlogging stress. Comparative genomic analysis revealed Chinese wingnut evolved more unique genes related to arginine synthesis, potentially endowing it with a higher capacity to purify nutrient-rich water bodies. Expansion of terpene synthase families enables the production of increased quantities of terpenoid volatiles, potentially serving as an evolved defense mechanism against herbivorous insects. Through combined transcriptomic and metabolomic analysis, we identified the candidate genes involved in the synthesis of terpenoid volatiles. Our study offers essential genetic resources for Chinese wingnut, unveiling its evolutionary history and identifying key genes linked to the production of terpenoid volatiles.

Marinicella meishanensis sp. nov., a novel Marinicella member isolated from coastal mudflat sediment of Meishan Islandin the East China Sea

A Gram-negative, rod-shaped, non-motile and strictly aerobic strain, designated NBU2979T, was isolated from a coastal mudflat located on Meishan Island in the East China Sea. Strain NBU2979T grew optimally at 32 °C, with 2.0 % NaCl (w/v) and at pH 7.0-7.5. The predominant fatty acid (>10 %) was iso-C15 : 0. The major polar lipids included phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol, phosphatidyldimethylethanolamine, phosphatidylcholine, an unidentified glycolipid, two unidentified aminophospholipids, an unidentified phospholipid and an unidentified lipid. The only respiratory quinone was ubiquinone-8. Comparative analysis of 16S rRNA gene sequences showed that strain NBU2979T exhibited highest similarity to Marinicella sediminis F2T (98.0 %), Marinicella marina S1101T (97.5 %), Marinicella litoralis KMM 3900T (96.6 %), Marinicella rhabdoformis 3539T (95.5 %), Marinicella pacifica sw153T (95.2 %) and Marinicella gelatinilytica S6413T (94.9 %). Phylogenetic analyses indicated that strain NBU2979T clustered with the genus Marinicella and was closely related to strain M. sediminis F2T. The average nucleotide identity and digital DNA-DNA hybridization values between strain NBU2979T and related species of genus Marinicella were well below the threshold limit for prokaryotic species delineation. The DNA G+C content of strain NBU2979T was 51.6 mol%. Based on its phenotypic, chemotaxonomic and genotypic data, strain NBU2979T (=KCTC 82911T=MCCC 1K06402T) is considered to be a representative of a novel species in the genus Marinicella, for which the name Marinicella meishanensis sp. nov. is proposed.

Chromosome-level genome assembly of Prunella vulgaris L. provides insights into pentacyclic triterpenoid biosynthesis

Prunella vulgaris is one of the bestselling and widely used medicinal herbs. It is recorded as an ace medicine for cleansing and protecting the liver in Chinese Pharmacopoeia and has been used as the main constitutions of many herbal tea formulas in China for centuries. It is also a traditional folk medicine in Europe and other countries of Asia. Pentacyclic triterpenoids are a major class of bioactive compounds produced in P. vulgaris. However, their biosynthetic mechanism remains to be elucidated. Here, we report a chromosome-level reference genome of P. vulgaris using an approach combining Illumina, ONT, and Hi-C technologies. It is 671.95 Mb in size with a scaffold N50 of 49.10 Mb and a complete BUSCO of 98.45%. About 98.31% of the sequence was anchored into 14 pseudochromosomes. Comparative genome analysis revealed a recent WGD in P. vulgaris. Genome-wide analysis identified 35 932 protein-coding genes (PCGs), of which 59 encode enzymes involved in 2,3-oxidosqualene biosynthesis. In addition, 10 PvOSC, 358 PvCYP, and 177 PvUGT genes were identified, of which five PvOSCs, 25 PvCYPs, and 9 PvUGTs were predicted to be involved in the biosynthesis of pentacyclic triterpenoids. Biochemical activity assay of PvOSC2, PvOSC4, and PvOSC6 recombinant proteins showed that they were mixed amyrin synthase (MAS), lupeol synthase (LUS), and β-amyrin synthase (BAS), respectively. The results provide a solid foundation for further elucidating the biosynthetic mechanism of pentacyclic triterpenoids in P. vulgaris.

Chromosome-level genome assembly and population genomic analysis reveal evolution and local adaptation in common hairfin anchovy (Setipinna tenuifilis)

Understanding the genetic structure and the factors associated with adaptive diversity has significant implications for the effective management of wild populations under threat from overfishing and climate change. The common hairfin anchovy (Setipinna tenuifilis) is an economically and ecologically important pelagic fish species, spanning a broad latitudinal gradient along marginal seas of the Northwest Pacific. In this study, we constructed the first reference genome of S. tenuifilis using PacBio long reads and high-resolution chromosome conformation capture (Hi-C) technology. The assembled genome was 798.38 Mb with a contig N50 of 1.43 Mb and a scaffold N50 of 32.42 Mb, which were anchored onto 24 pseudochromosomes. A total of 22,019 genes were functionally annotated, which accounted for 95.27% of the predicted protein-coding genes. Chromosomal collinearity analysis revealed chromosome fusion or fission events in Clupeiformes species. Three genetic groups of S. tenuifilis were revealed along the Chinese coast using restriction site-associated DNA sequencing (RADseq). We investigated the influence of four bioclimatic variables as potential drivers of adaptive divergence in S. tenuifilis, suggesting that these environmental variables, especially sea surface temperature, may play important roles as drivers of spatially varying selection for S. tenuifilis. We also identified candidate functional genes underlying adaptive mechanisms and ecological tradeoffs using redundancy analysis (RDA) and BayeScan analysis. In summary, this study sheds light on the evolution and spatial patterns of genetic variation of S. tenuifilis, providing a valuable genomic resource for further biological and genetic studies on this species and other closely related Clupeiformes.

Acidithiobacillus acidisediminis sp. nov., an acidophilic sulphur-oxidizing chemolithotroph isolated from acid mine drainage sediment

Strain S30A2T, isolated from the acid mine drainage sediment of Mengzi Copper Mine, Yunnan, is proposed to represent a novel species of the sulphur-oxidizing genus Acidithiobacillus. Cells were Gram-stain-negative, non-endospore forming, highly motile with one or two monopolar flagella and rod-shaped. The strain was mesophilic, growing at 30-50 °C (optimum, 38 °C), acidophilic, growing at pH 2.0-4.5 (optimum, pH 2.5), and tolerant of 0-4 % (w/v; 684 mol l-1) NaCl. The 16S rRNA gene-based sequence analysis showed that strain S30A2T belongs to the genus Acidithiobacillus and shows the largest similarity of 96.6 % to the type strain Acidithiobacillus caldus KUT. The genomic DNA G+C content of strain S30A2T was 59.25 mol%. The average nucleotide identity ANIb and ANIm values between strain S30A2T and A. caldus KUT were 70.95 and 89.78 %, respectively and the digital DNA-DNA hybridization value was 24.9 %. Strain S30A2T was strictly aerobic and could utilize elementary sulphur and tetrathionate to support chemolithotrophic growth. The major cellular fatty acid of S30A2T was C19 : 1ω7c. The respiratory quinones were ubiquinone-8 and ubiquinone-7. Based upon its phylogenetic, genetic, phenotypic, physiologic and chemotaxonomic characteristics, strain S30A2T is considered to represent a novel species of the genus Acidithiobacillus, for which the name Acidithiobacillus acidisediminis sp. nov. is proposed. The type strain is S30A2T (=CGMCC 1.17059T=KCTC 72580T).

De novo genome assembly and population genomics of a shrub tree Barthea barthei (Hance) krass provide insights into the adaptive color variations

Flower color is a classic example of an ecologically important trait under selection in plants. Understanding the genetic mechanisms underlying shifts in flower color can provide key insights into ecological speciation. In this study, we investigated the genetic basis of flower color divergence in Barthea barthei, a shrub tree species exhibiting natural variation in flower color. We assembled a high-quality genome assembly for B. barthei with a contig N50 of 2.39 Mb and a scaffold N50 of 16.21 Mb. The assembly was annotated with 46,430 protein-coding genes and 1,560 non-coding RNAs. Genome synteny analysis revealed two recent tetraploidization events in B. barthei, estimated to have occurred at approximately 17 and 63 million years ago. These tetraploidization events resulted in massive duplicated gene content, with over 70% of genes retained in collinear blocks. Gene family members of the core regulators of the MBW complex were significantly expanded in B. barthei compared to Arabidopsis, suggesting that these duplications may have provided raw genetic material for the evolution of novel regulatory interactions and the diversification of anthocyanin pigmentation. Transcriptome profiling of B. barthei flowers revealed differential expression of 9 transcription factors related to anthocyanin biosynthesis between the two ecotypes. Six of these differentially expressed transcription factors were identified as high-confidence candidates for adaptive evolution based on positive selection signals. This study provides insights into the genetic basis of flower color divergence and the evolutionary mechanisms underlying ecological adaptation in plants.

Degradation of edible mushroom waste by Hermetia illucens L. and consequent adaptation of its gut microbiota

The edible fungus industry is one of the pillar industries in the Yunnan-Guizhou Plateau, China. The expansion of the planting scale has led to the release of various mushroom residues, such as mushroom feet, and other wastes, which are not treated adequately, resulting in environmental pollution. This study investigated the ability of black soldier fly (Hermetia illucens L.) larvae (BSFL) to degrade mushroom waste. Moreover, this study analyzed changes in the intestinal bacterial community and gene expression of BSFL after feeding on mushroom waste. Under identical feeding conditions, the remaining amount of mushroom waste in Pleurotus ostreatus treatment group was reduced by 18.66%, whereas that in Flammulina velutipes treatment group was increased by 31.08%. Regarding gut microbial diversity, compared with wheat bran-treated control group, Dysgonomonas, Providencia, Enterococcus, Pseudochrobactrum, Actinomyces, Morganella, Ochrobactrum, Raoultella, and Ignatzschineria were the most abundant bacteria in the midgut of BSFL in F. velutipes treatment group. Furthermore, Dysgonomonas, Campylobacter, Providencia, Ignatzschineria, Actinomyces, Enterococcus, Morganella, Raoultella, and Pseudochrobactrum were the most abundant bacteria in the midgut of BSFL in P. ostreatus treatment group. Compared with wheat bran-treated control group, 501 upregulated and 285 downregulated genes were identified in F. velutipes treatment group, whereas 211 upregulated and 43 downregulated genes were identified in P. ostreatus treatment group. Using Kyoto Encyclopedia of Genes and Genomes and Gene Ontology enrichment analyses, we identified 14 differentially expressed genes (DEGs) related to amino sugar and nucleotide sugar metabolism in F. velutipes treatment group, followed by 12 DEGs related to protein digestion and absorption. Moreover, in P. ostreatus treatment group, two DEGs were detected for fructose and mannose metabolism, and two were noted for fatty acid metabolism. These results indicate that feeding on edible mushroom waste can alter the intestinal microbial community structure of BSFL; moreover, the larval intestine can generate a corresponding feedback. These changes contribute to the degradation of edible mushroom waste by BSFL and provide a reference for treating edible mushroom waste using BSFL.

Unraveling the molecular dynamics of Pseudomonas aeruginosa biofilms at the air-liquid interface

Aim: The aim of this study was to probe the dynamics of Pseudomonas aeruginosa PA14 air-liquid interface (ALI) biofilms over time through global proteomic analysis. Materials & methods: P. aeruginosa PA14 ALI biofilm samples, collected over 48-144 h, underwent differential expression analysis to identify varying proteins at each time point. Results: A consistent set of 778 proteins was identified, with variable expression over time. Upregulated proteins were mainly linked to 'amino acid transport and metabolism'. Biofilm-related pathways, including cAMP/Vfr and QS, underwent significant changes. Flagella were more influential than pili, especially in early biofilm development. Proteins associated with virulence, transporters and iron showed differential expression throughout. Conclusion: The findings enhance our understanding of ALI biofilm development.

Chromosome-level genome assembly of the diploid oat species Avena longiglumis

Diploid wild oat Avena longiglumis has nutritional and adaptive traits which are valuable for common oat (A. sativa) breeding. The combination of Illumina, Nanopore and Hi-C data allowed us to assemble a high-quality chromosome-level genome of A. longiglumis (ALO), evidenced by contig N50 of 12.68 Mb with 99% BUSCO completeness for the assembly size of 3,960.97 Mb. A total of 40,845 protein-coding genes were annotated. The assembled genome was composed of 87.04% repetitive DNA sequences. Dotplots of the genome assembly (PI657387) with two published ALO genomes were compared to indicate the conservation of gene order and equal expansion of all syntenic blocks among three genome assemblies. Two recent whole-genome duplication events were characterized in genomes of diploid Avena species. These findings provide new knowledge for the genomic features of A. longiglumis, give information about the species diversity, and will accelerate the functional genomics and breeding studies in oat and related cereal crops.

Isolation, characterisation and description of the roseoflavin producer Streptomyces berlinensis sp. nov

The Gram-positive bacteria Streptomyces davaonensis and Streptomyces cinnabarinus have been the only organisms known to produce roseoflavin, a riboflavin (vitamin B2) derived red antibiotic. Using a selective growth medium and a phenotypic screening, we were able to isolate a novel roseoflavin producer from a German soil sample. The isolation procedure was repeated twice, that is, the same strain could be isolated from the same location in Berlin 6 months and 12 months after its first isolation. Whole genome sequencing of the novel roseoflavin producer revealed an unusual chromosomal arrangement and the deposited genome sequence of the new isolate (G + C content of 71.47%) contains 897 genes per inverted terminal repeat, 6190 genes in the core and 107 genes located on an illegitimate terminal end. We identified the roseoflavin biosynthetic genes rosA, rosB and rosC and an unusually high number of riboflavin biosynthetic genes. Overexpression of rosA, rosB and rosC in Escherichia coli and enzyme assays confirmed their predicted functions in roseoflavin biosynthesis. A full taxonomic analysis revealed that the isolate represents a previously unknown Streptomyces species and we propose the name Streptomyces berlinensis sp. nov. for this roseoflavin producer.

Chromosome-level genome assembly of the aster leafhopper (Macrosteles quadrilineatus) reveals the role of environment and microbial symbiosis in shaping pest insect genome evolution

Leafhoppers comprise over 20,000 plant-sap feeding species, many of which are important agricultural pests. Most species rely on two ancestral bacterial symbionts, Sulcia and Nasuia, for essential nutrition lacking in their phloem and xylem plant sap diets. To understand how pest leafhopper genomes evolve and are shaped by microbial symbioses, we completed a chromosomal-level assembly of the aster leafhopper's genome (ALF; Macrosteles quadrilineatus). We compared ALF's genome to three other pest leafhoppers, Nephotettix cincticeps, Homalodisca vitripennis, and Empoasca onukii, which have distinct ecologies and symbiotic relationships. Despite diverging ~155 million years ago, leafhoppers have high levels of chromosomal synteny and gene family conservation. Conserved genes include those involved in plant chemical detoxification, resistance to various insecticides, and defence against environmental stress. Positive selection acting upon these genes further points to ongoing adaptive evolution in response to agricultural environments. In relation to leafhoppers' general dependence on symbionts, species that retain the ancestral symbiont, Sulcia, displayed gene enrichment of metabolic processes in their genomes. Leafhoppers with both Sulcia and its ancient partner, Nasuia, showed genomic enrichment in genes related to microbial population regulation and immune responses. Finally, horizontally transferred genes (HTGs) associated with symbiont support of Sulcia and Nasuia are only observed in leafhoppers that maintain symbionts. In contrast, HTGs involved in non-symbiotic functions are conserved across all species. The high-quality ALF genome provides deep insights into how host ecology and symbioses shape genome evolution and a wealth of genetic resources for pest control targets.