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Pseudomonas is a ubiquitous and ambiguous opportunistic pathogen, and plays an important ecological role in the ocean. Here, a new species, Pseudomonas phage vB_PaeM_M1, is described, which was isolated from the surface coastal waters of Qingdao, China. vB_PaeM_M1 contains a linear, double-stranded 89,387-bp genome with a GC content of 41.04% and encoding 184 putative open reading frames (ORFs). There were 50 conservative domains were predicted with BLASTp, including two auxiliary metabolic genes (Phosphate-inducible gene phoH and signal peptide peptidase A, sppA ). Phylogenetic analysis of whole genome amino acid sequence and comparative genomic analysis showed that vB_PaeM_M1 has a distant evolutionary relationship with previously isolated viruses and can be grouped into a family-level novel viral cluster (VC_61) with eleven uncultured, assembled viral genomes, named as Psaeviridae. Psaeviridae contains two ORFs (ORFs 117 and 127), which were not detected in the genomes of other viral families, confirming the proposal for a new family. Combined with its ability to infect Pseudomonas and its representation of an unstudied viral family, vB_PaeM_M1 may be an important and novel model system for the study of interactions between viruses and host cells in marine ecosystems.

ABSTRACT Methanotrophs are an important group of microorganisms that counteract methane emissions to the atmosphere. Methane-oxidising bacteria of the Alpha- and Gammaproteobacteria have been studied for over a century, while methanotrophs of the phylum Verrucomicrobia are a more recent discovery. Verrucomicrobial methanotrophs are extremophiles that live in very acidic geothermal ecosystems. Currently, more than a dozen strains have been isolated, belonging to the genera Methylacidiphilum and Methylacidimicrobium. Initially, these methanotrophs were thought to be metabolically confined. However, genomic analyses and physiological and biochemical experiments over the past years revealed that verrucomicrobial methanotrophs, as well as proteobacterial methanotrophs, are much more metabolically versatile than previously assumed. Several inorganic gases and other molecules present in acidic geothermal ecosystems can be utilised, such as methane, hydrogen gas, carbon dioxide, ammonium, nitrogen gas and perhaps also hydrogen sulfide. Verrucomicrobial methanotrophs could therefore represent key players in multiple volcanic nutrient cycles and in the mitigation of greenhouse gas emissions from geothermal ecosystems. Here, we summarise the current knowledge on verrucomicrobial methanotrophs with respect to their metabolic versatility and discuss the factors that determine their diversity in their natural environment. In addition, key metabolic, morphological and ecological characteristics of verrucomicrobial and proteobacterial methanotrophs are reviewed. This review discusses the metabolic versatility of verrucomicrobial methanotrophs regarding the acidic volcanic ecosystems they thrive in and a comparison is made with the canonical proteobacterial methanotrophs.

Background Listeria monocytogenes consists of four lineages that occupy a wide variety of ecological niches. Sequence type (ST) 87 (serotype 1/2b), belonging to lineage I, is one of the most common STs isolated from food products, food associated environments and sporadic listeriosis in China. Here, we performed a comparative genomic analysis of the L. monocytogenes ST87 clone by sequencing 71 strains representing a diverse range of sources, different geographical locations and isolation years. Results The core genome and pan genome of ST87 contained 2667 genes and 3687 genes respectively. Phylogenetic analysis based on core genome SNPs divided the 71 strains into 10 clades. The clinical strains were distributed among multiple clades. Four clades contained strains from multiple geographic regions and showed high genetic diversity. The major gene content variation of ST87 genomes was due to putative prophages, with eleven hotspots of the genome that harbor prophages. All strains carry an intact CRISRP/Cas system. Two major CRISPR spacer profiles were found which were not clustered phylogenetically. A large plasmid of about 90 Kb, which carried heavy metal resistance genes, was found in 32.4% (23/71) of the strains. All ST87 strains harbored the Listeria pathogenicity island (LIPI)-4 and a unique 10-open read frame (ORF) genomic island containing a novel restriction-modification system. Conclusion Whole genome sequence analysis of L. monocytogenes ST87 enabled a clearer understanding of the population structure and the evolutionary history of ST87 L. monocytogenes in China. The novel genetic elements identified may contribute to its virulence and adaptation to different environmental niches. Our findings will be useful for the development of effective strategies for the prevention and treatment of listeriosis caused by this prevalent clone.

Background Ctenopharyngodon idella (grass carp), Mylopharyngodon piceus (black carp), Hypophthalmichthys nobilis (bighead carp), and Hypophthalmichthys molitrix (silver carp), collectively known as the four major domesticated Asian carp, are freshwater fish species from the family Cyprinidae and are widely consumed in China. Current studies on these species primarily focus on immune system regulation and the growth and development of individual species. However, in-depth genomic investigations and comprehensive comparative analysis remained limited. Methods The complete genomes of Ctenopharyngodon idella , Mylopharyngodon piceus and Hypophthalmichthys nobilis were assembled using a hybrid approach that integrated both next- and third-generation sequencing reads, followed by annotation using the MAKER2 pipeline. Based on the high-quality genomes of Ctenopharyngodon idella , Mylopharyngodon piceus Hypophthalmichthys nobilis , and Hypophthalmichthys molitrix , a comparative genomic analysis was conducted using bioinformatic tools to investigate gene family evolution in these four domesticated Asian carp species. Results High-quality genomes of Ctenopharyngodon idella, Mylopharyngodon piceus , and Hypophthalmichthys nobilis were assembled, achieving over 90% completeness. Immune-related gene families, including MHC class I and NLRC3-like genes, have undergone rapid evolution, with Ctenopharyngodon idella exhibiting significant expansion of NLRC3-like genes. Massive tandem duplication events were identified in trace amine-associated receptors (TAARs), and rapid expansion was observed in TAAR16 and TAAR29. Additionally, a novel TAAR gene cluster was identified in all four Asian carp species. Comparative genomic analysis revealed the expansion of type 1 taste receptor genes, particularly in Ctenopharyngodon idella and Mylopharyngodon piceus . Conclusion This study has successfully constructed the high-quality genomes of Ctenopharyngodon idella , Mylopharyngodon piceus , and Hypophthalmichthys nobilis . The comparative genomic analysis revealed the evolution of immune-related genes and chemosensory receptors in the four major domesticated Asian carp species. These findings suggested the enhanced immunity and sensory perception in these species, providing valuable insights into their adaptation, survival and reproduction.

Recent advances in molecular and metagenomic analyses have enhanced the ability to precisely determine the microbiota of hypersaline environments of marine origin, such as solar salterns, saline lakes, and hypersaline soils, uncovering numerous yet-to-be-isolated prokaryotic groups. Our research focused on the hypersaline ecosystems within the Odiel Saltmarshes, a natural tidal wetland situated at the confluence of the Odiel and Tinto rivers in Huelva province, Southwestern Spain. Employing culture-dependent techniques, we aimed to isolate and characterize novel halophilic prokaryotes from this area. Two haloarchaeal strains, designated S1BR25-6 T and S3BR25-2 T were classified within the genus Halogeometricum based on Overall Genome Related Indexes (OGRIs) such as Orthologous Average Nucleotide Identity, digital DNA-DNA hybridization, and Average Amino Acid Identity as standard criteria for species delineation. Moreover, this study embarks on an exhaustive genome-based comparative analysis of the haloarchaeal genus Halogeometricum , delineating the metabolic capacities, osmoregulatory adaptations, and resistance to certain heavy metals of its species. The dual osmoregulatory mechanism observed by in-silico analysis of the Halogeometricum species combines “salt-in” and “salt-out” strategies which highlights the adaptive flexibility of these haloarchaea. In addition, capability for de novo thiamine biosynthesis of strain S1BR25-6 T along with other Halogeometricum species underscores their metabolic complexity and resilience, offering insights into their role in ecosystem dynamics and potential biotechnological applications. Wet lab experimental analysis of strains S1BR25-6 T and S3BR25-2 T confirmed their resistance to heavy metals, particularly to arsenic, zinc, and cadmium, emphasizing their potential for bioremediation applications. Furthermore, conducting fragment recruitment analysis across different metagenomic datasets revealed a predominant recruitment of species from the genus Halogeometricum in hypersaline soils of Odiel Saltmarshes (especially the two novel strains), and in the brines of marine saltern ponds with high salt concentrations. These results contribute to a reinforced understanding of the extremely halophilic characteristics inherent to the genus Halogeometricum . Finally, taxogenomic analysis has substantiated that strains S1BR25-6 T (= CCM 9250 T = CECT 30624 T ), and S3BR25-2 T (= CCM 9253 T = CECT 30622 T ) denote two previously unidentified species within the genus Halogeometricum , for which we propose the names Halogeometricum salsisoli sp. nov., and Halogeometricum luteum sp. nov., respectively.

Background Although animal mitochondrial DNA sequences are known to evolve rapidly, their gene arrangements often remain unchanged over long periods of evolutionary time. Therefore, comparisons of mitochondrial genomes may result in significant insights into the evolution both of organisms and of genomes. Mammalian mitochondrial genomes recently published in the GenBank database of NCBI show numerous rearrangements in various regions of the genome, from which it may be inferred that the mammalian mitochondrial genome is more dynamic than expected. However, it is alternatively possible that these are errors of annotation and, if so, are misleading our interpretations. In order to verify these possible errors of annotation, we performed a comparative genomic analysis of mammalian mitochondrial genomes available in the NCBI database. Results Using a combination of bioinformatics methods to carefully examine the mitochondrial gene arrangements in 304 mammalian species, we determined that there are only two sets of gene arrangements, one that is shared by all of the marsupials and another that is shared by all of the monotremes and eutherians, with these two arrangements differing only by the positions of tRNA genes in the region commonly designated as “WANCY” for the genes it comprises. All of the 68 other cases of reported gene rearrangements are errors. We note that there are also numerous errors of impossibly short, incorrect gene annotations, cases where genomes that are reported as complete are actually missing portions of the sequence, and genes that are clearly present but were not annotated in these records. Conclusions We judge that the application of simple bioinformatic tools in the verification of gene annotation, particularly for organelle genomes, would be a very useful enhancement for the curation of genome sequences submitted to GenBank.

Background Pectobacterium carotovorum subsp. brasiliense is a broad host range bacterial pathogen, which causes blackleg of potatoes and bacterial soft rot of vegetables worldwide. Production of plant cell wall degrading enzymes is usually critical for Pectobacterium infection. However, other virulence factors and the mechanisms of genetic adaptation still need to be studied in detail. Results In this study, the complete genome of P. carotovorum subsp. brasiliense strain SX309 isolated from cucumber was compared with eight other pathogenic bacteria belonging to the Pectobacterium genus, which were isolated from various host plants. Genome comparison revealed that most virulence genes are highly conserved in the Pectobacterium strains, especially for the key virulence determinants involved in the biosynthesis of extracellular enzymes and others including the type II and III secretion systems, quorum sensing system, flagellar and chemotactic genes. Nevertheless, some variable regions of the T6SS and the CRISP-Cas immune system are unique for P. carotovorum subsp. brasiliense . Conclusions The extensive comparative genomics analysis revealed highly conserved virulence genes in the Pectobacterium strains. However, several variable regions of type VI secretion system and two subtype Cas mechanism-Cas immune systems possibly contribute to the process of Pectobacterium infection and adaptive immunity.

Background The genus Ehrlichia consists of tick-borne obligatory intracellular bacteria that can cause deadly diseases of medical and agricultural importance. Ehrlichia sp. HF, isolated from Ixodes ovatus ticks in Japan [also referred to as I. ovatus Ehrlichia (IOE) agent], causes acute fatal infection in laboratory mice that resembles acute fatal human monocytic ehrlichiosis caused by Ehrlichia chaffeensis . As there is no small laboratory animal model to study fatal human ehrlichiosis, Ehrlichia sp. HF provides a needed disease model. However, the inability to culture Ehrlichia sp. HF and the lack of genomic information have been a barrier to advance this animal model. In addition, Ehrlichia sp. HF has several designations in the literature as it lacks a taxonomically recognized name. Results We stably cultured Ehrlichia sp. HF in canine histiocytic leukemia DH82 cells from the HF strain-infected mice, and determined its complete genome sequence. Ehrlichia sp. HF has a single double-stranded circular chromosome of 1,148,904 bp, which encodes 866 proteins with a similar metabolic potential as E. chaffeensis . Ehrlichia sp. HF encodes homologs of all virulence factors identified in E. chaffeensis , including 23 paralogs of P28/OMP-1 family outer membrane proteins, type IV secretion system apparatus and effector proteins, two-component systems, ankyrin-repeat proteins, and tandem repeat proteins. Ehrlichia sp. HF is a novel species in the genus Ehrlichia , as demonstrated through whole genome comparisons with six representative Ehrlichia species, subspecies, and strains, using average nucleotide identity, digital DNA-DNA hybridization, and core genome alignment sequence identity. Conclusions The genome of Ehrlichia sp. HF encodes all known virulence factors found in E. chaffeensis , substantiating it as a model Ehrlichia species to study fatal human ehrlichiosis. Comparisons between Ehrlichia sp. HF and E. chaffeensis will enable identification of in vivo virulence factors that are related to host specificity, disease severity, and host inflammatory responses. We propose to name Ehrlichia sp. HF as Ehrlichia japonica sp. nov. (type strain HF), to denote the geographic region where this bacterium was initially isolated.

Background Chlamydia abortus and Chlamydia psittaci are important pathogens of livestock and avian species, respectively. While C. abortus is recognized as descended from C. psittaci species, there is emerging evidence of strains that are intermediary between the two species, suggesting they are recent evolutionary ancestors of C. abortus . Such strains include C. psittaci strain 84/2334 that was isolated from a parrot. Our aim was to classify this strain by sequencing its genome and explore its evolutionary relationship to both C. abortus and C. psittaci . Results In this study, methods based on multi-locus sequence typing (MLST) of seven housekeeping genes and on typing of five species discriminant proteins showed that strain 84/2334 clustered with C. abortus species. Furthermore, whole genome de novo sequencing of the strain revealed greater similarity to C. abortus in terms of GC content, while 16S rRNA and whole genome phylogenetic analysis, as well as network and recombination analysis showed that the strain clusters more closely with C. abortus strains. The analysis also suggested a closer evolutionary relationship between this strain and the major C. abortus clade, than to two other intermediary avian C. abortus strains or C. psittaci strains. Molecular analyses of genes (polymorphic membrane protein and transmembrane head protein genes) and loci (plasticity zone), found in key virulence-associated regions that exhibit greatest diversity within and between chlamydial species, reveal greater diversity than present in sequenced C. abortus genomes as well as similar features to both C. abortus and C. psittaci species. The strain also possesses an extrachromosomal plasmid, as found in most C. psittaci species but absent from all sequenced classical C. abortus strains. Conclusion Overall, the results show that C. psittaci strain 84/2334 clusters very closely with C. abortus strains, and are consistent with the strain being a recent C. abortus ancestral species. This suggests that the strain should be reclassified as C. abortus . Furthermore, the identification of a C. abortus strain bearing an extra-chromosomal plasmid has implications for plasmid-based transformation studies to investigate gene function as well as providing a potential route for the development of a next generation vaccine to protect livestock from C. abortus infection.