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Abstract This study explores the organization, conservation, and diversity of biosynthetic gene clusters (BGCs) among Bacillus sp. strain BH32, a plant-beneficial bacterial endophyte, and its closest nontype Bacillus cereus group strains. BGC profiles were predicted for each of the 17 selected strains using antiSMASH, resulting in the detection of a total of 198 BGCs. We quantitatively compared the BGCs and analysed their conservation, distribution, and evolutionary relationships. The study identified both conserved and singleton BGCs across the studied Bacillus strains, with minimal variation, and discovered two major BGC synteny blocks composed of homologous BGCs conserved within the B. cereus group. The identified BGC synteny blocks provide insight into the evolutionary relationships and diversity of BGCs within this complex group. Using bioinformatics, this study advances microbiology by analysing the conservation and diversity of secondary metabolite biosynthetic gene clusters in Bacillus cereus group strains.

Plant pests (including pathogens) threaten forests, reduce carbon sequestration, disrupt trade, and are costly to manage. Traditionally, forest surveys involve the visual inspection of trees for symptoms of disease; however, this process is time consuming and by the time symptoms are observed, the disease may be widespread. New methods of surveillance are needed to help plant health authorities monitor and protect forests from disease. Previous research has shown that metabarcoding of environmental DNA (eDNA) can be used to identify plant pests. This study collected rainwater samples from five forest sites across Northern Ireland every month for a year to examine whether eDNA metabarcoding could help authorities detect plant diseases in forests. Metabarcoding of the internal transcribed spacer (ITS) region was used to determine the fungal and oomycete profile of rainwater samples that passed through the canopy of spruce, pine, oak, and ash trees, along with a non-tree field trap. In total, 65 known plant fungal and oomycete pests were detected; seven were regulated pests, and two were pests that had not been previously identified in Northern Ireland. This work demonstrates that metabarcoding of eDNA from rainwater can detect plant pests and could be used in forest surveillance programmes.

The use of halotolerant beneficial plant-growth-promoting (PGP) bacteria is considered as a promising eco-friendly approach to improve the salt tolerance of cash crops. One strategy to enhance the possibility of obtaining stress-alleviating bacteria is to screen salt impacted soils. In this study, amongst the 40 endophytic bacteria isolated from the roots of Sahara-inhabiting halophytes Atriplex halimus L. and Lygeum spartum L., 8 showed interesting NaCl tolerance in vitro. Their evaluation, through different tomato plant trials, permitted the isolate IS26 to be distinguished as the most effective seed inoculum for both plant growth promotion and mitigation of salt stress. On the basis of 16S rRNA gene sequence, the isolate was closely related to Stenotrophomonas rhizophila. It was then screened in vitro for multiple PGP traits and the strain-complete genome was sequenced and analysed to further decipher the genomic basis of the putative mechanisms underlying its osmoprotective and plant growth abilities. A remarkable number of genes putatively involved in mechanisms responsible for rhizosphere colonization, plant association, strong competition for nutrients, and the production of important plant growth regulator compounds, such as AIA and spermidine, were highlighted, as were substances protecting against stress, including different osmolytes like trehalose, glucosylglycerol, proline, and glycine betaine. By having genes related to complementary mechanisms of osmosensing, osmoregulation and osmoprotection, the strain confirmed its great capacity to adapt to highly saline environments. Moreover, the presence of various genes potentially related to multiple enzymatic antioxidant processes, able to reduce salt-induced overproduction of ROS, was also detected.

The present study used genome-based approaches to investigate the taxonomic relationship between Kitasatospora cineracea DSM 44780T and Kitasatospora niigatensis DSM 44781T, two species that were previously described by Tajima et al. (Int J Syst Evol Microbiol 51:1765–1771, 2001). The digital DNA-DNA hybridization (dDDH), average amino acid identity (AAI), and average nucleotide identity (ANI) values between the genomes of the two type strains were 90.3, 98.7, and 99.1%, respectively. These values exceeded the established thresholds of 70% (dDDH) and 95–96% (ANI and AAI) for bacterial species delineation, suggesting that K. cineracea and K. niigatensis should share the same taxonomic position. Furthermore, our analysis using the ‘Bacterial Pan Genome Analysis’ (BPGA) pipeline and the Maximum Likelihood core-genes tree inferred using FastTree2 consistently demonstrated that K. cineracea DSM 44780T and K. niigatensis DSM 44781T are closely related, as indicated by the clustering of these strains in the core-genes phylogenomic tree. Based on these findings, we propose that K. niigatensis should be considered a later heterotypic synonym of K. cineracea.

This study employs genome-based methodologies to explore the taxonomic relationship between Caldicoprobacter faecalis DSM 20678T and Caldicoprobacter oshimai DSM 21659T. The genome-based similarity indices calculations consisting of digital DNA–DNA Hybridization (dDDH), Average Amino Aid Identity (AAI), and Average Nucleotide Identity (ANI) between the genomes of these two type strains yielded percentages of 91.2%, 98.9%, and 99.1%, respectively. These values were above the recommended thresholds of 70% (dDDH) and 95–96% (ANI and AAI) for bacterial species delineation, indicating a shared taxonomic position for C. faecalis and C. oshimai. Furthermore, analysis utilizing the 'Bacterial Pan Genome Analysis' (BPGA) pipeline and constructing a Maximum Likelihood core-genes tree using FastTree2 consistently demonstrated the close relationship between C. faecalis DSM 20678T and C. oshimai DSM 21659T, evident from their clustering in the core-genes phylogenomic tree. Based on these comprehensive findings, we propose the reclassification of C. faecalis as a later heterotypic synonym of C. oshimai.

Endophytic strains belonging to the Bacillus cereus group were isolated from the halophytes Atriplex halimus L. ( Amaranthaceae ) and Tamarix aphylla L. ( Tamaricaceae ) from costal and continental regions in Algeria. Based on their salt tolerance (up to 5%), the strains were tested for their ability to alleviate salt stress in tomato and wheat. Bacillus sp. strain BH32 showed the highest potential to reduce salinity stress (up to + 50% and + 58% of dry weight improvement, in tomato and wheat, respectively, compared to the control). To determine putative mechanisms involved in salt tolerance and plant growth promotion, the whole genome of Bacillus sp. BH32 was sequenced, annotated, and used for comparative genomics against the genomes of closely related strains. The pangenome of Bacillus sp. BH32 and its closest relative was further analyzed. The phylogenomic analyses confirmed its taxonomic position, a member of the Bacillus cereus group, with intergenomic distances (GBDP analysis) pinpointing to a new taxon (digital DNA-DNA hybridization, dDDH < 70%). Genome mining unveiled several genes involved in stress tolerance, production of anti-oxidants and genes involved in plant growth promotion as well as in the production of secondary metabolites. Key points • Bacillus sp. BH32 and other bacterial endophytes were isolated from halophytes, to be tested on tomato and wheat and to limit salt stress adverse effects . • The strain with the highest potential was then studied at the genomic level to highlight numerous genes linked to plant growth promotion and stress tolerance . • Pangenome approaches suggest that the strain belongs to a new taxon within the Bacillus cereus group .

The taxonomy of the Listeriaceae family has undergone substantial revisions, expanding the Listeria genus from 6 to 29 species since 2009. However, these classifications have relied on 16S rRNA gene sequences and conventional polyphasic taxonomy, with limited use of genomic approaches. This study aimed to employ genomic tools, including phylogenomics, Overall Genomic Relatedness Indices (OGRIs), and core-genome phylogenomic analyses, to reevaluate the taxonomy of the Listeriaceae family. The analyses involved the construction of phylogenetic and phylogenomic trees based on 16S rRNA gene sequences and core genomes from 34 type strain genomes belonging to Listeriaceae family. OGRIs, which encompass Average Amino acid Identity (AAI), core-proteome AAI (cAAI), and Percentage of Conserved Proteins (POCP), were calculated, and specific threshold values of 70%, 87%, and 72–73% were established, respectively, to delimitate genera in the Listeriaceae family. These newly proposed OGRI thresholds unveiled distinct evolutionary lineages. The outcomes of this taxonomic re-evaluation were: (i): the division of the Listeria genus into an emended Listeria genus regrouping only Listeria senso stricto species; (ii): the remaining Listeria senso lato species were transferred into three newly proposed genera: Murraya gen. nov., Mesolisteria gen. nov., and Paenilisteria gen. nov. within Listeriaceae ; (iii): Brochothrix was transferred to the newly proposed family Brochothricaceae fam. nov. within the Caryophanales order; (iiii): Listeria ivanovii subsp. londonensis was elevated to the species level as Listeria londonensis sp. nov.; and (iiiii): Murraya murrayi comb. nov. was reclassified as a later heterotypic synonym of Murraya grayi comb. nov. This taxonomic framework enables more precise identification of pathogenic Listeriaceae species, with significant implications for important areas such as food safety, clinical diagnostics, epidemiology, and public health.

This study explores the isolation and characterization of Streptomyces strain D15 from the Algerian steppes, with a focus on combating antibiotic-resistant microbial strains. In response to the global health threat posed by antimicrobial resistance, the research delves into the unique ecological niche of Algerian steppes. The isolated strain, identified as belonging to the genus Streptomyces , exhibits typical morphological and cultural traits, supported by chemical and genomic analyses. Phylogenetic analysis establishes the genetic closeness of D15 to Streptomyces lavendofoliae . The strain demonstrates potent antagonistic activity against various microorganisms, showcasing significant antimicrobial effects, particularly against Micrococcus luteus , Enterococcus faecalis , and Candida albicans . Genomic analysis unveils a rich repertoire of biosynthetic gene clusters, emphasizing the strain’s potential to produce diverse secondary metabolites, essential for combating antibiotic resistance. Streptomyces strain D15 emerges as a promising candidate for novel antimicrobial agents, with its broad-spectrum activity and genomic potential. The study underscores the importance of exploring untapped environments, like Algerian steppes, to discover new strains capable of addressing the challenges posed by antibiotic-resistant microbial strains. This research contributes to the ongoing global efforts to find innovative solutions and underscores the pivotal role Streptomyces plays in the search for effective antibiotics.

The Metagenomics Days event was organized to enhance understanding of metagenomics and microbiome analysis among participants new to the field. This paper presents an evaluation of the course's impact through a comprehensive survey administered before and after the event. We assessed participants' prior knowledge, experience with bioinformatics tools, and confidence levels regarding key concepts in microbiome analysis. Word clouds generated from open-ended survey responses provided additional insights into participants' interests and pre-course familiarity with metagenomic tools and concepts. Surveys results showed substantial improvements in participants' confidence, particularly in building bioinformatics pipelines (+41%), understanding diversity metrics (+44.1%), and applying microbiome analysis concepts (+34.8%). Similarly, understanding of core topics like cloud computing (+28%), bioinformatics workflows (+34%), and 16S rRNA gene variable regions (+27.5%) increased significantly. The course's impact on knowledge retention was also evaluated, with participants achieving an average of 64.87% correct responses, with 25.76% unsure answers and only 9.35% incorrect responses, highlighting the effectiveness of the course in enhancing comprehension. Overall, the survey results indicate a significant increase in participants' confidence and knowledge acquisition, particularly in the areas of cloud computing, diversity metrics, and bioinformatics pipelines. These improvements in confidence and knowledge acquisition underscore the effectiveness of the course in bridging knowledge gaps and preparing participants for future research in the complex and rapidly evolving fields of metagenomics and microbiome analysis. Keywords: Metagenomics, Microbiome analysis, environmental DNA, Bioinformatics, Training, Knowledge acquisition, Cloud computing, Participant engagement.Competing Interest StatementThe authors have declared no competing interest.

In Algeria, Culex pipiens is the most important mosquito species due to its wide geographical distribution, abundance and nuisance. This specie transmits multiple arboviruses such as the West Nile virus and encephalitis virus that have a global impact on human health. Multiple strategies are adopted for its control including elimination of mosquito breeding sites, by improving water storage and solid waste disposal, as well as treating breeding sites with biological or chemical larvicidal components. This study reports the isolation, morphological and molecular characterization as well as virulence of five entomopathogenic fungi strains, from Algerian soils, against 3 rd instar larvae of Cx . pipiens . Based on morphology and ITS sequences, all fungal strains were assigned to genus Purpureocillium including three P . lavendulum strains (RS10B, RS7 and RS5 under the GenBank accession numbers MW426500, MW426502 and MW426503, respectively) and two P. lilacinum strains (RS10A and MICH1 under the GenBank accession numbers MW426501 and OL614981, respectively). These two species were reported for the first time in Algeria and until now, no study have reported the virulence of P . lavendulum against Cx . pipiens. Furthermore, the strains were tested for their efficacy against 3 rd instar larvae of Cx. pipiens at 1 × 10 6 , 1 × 10 7 and 1 × 10 8 conidia/mL concentration under laboratory conditions. Among these strains, RS10A and RS10B were the most effective strains due to their relatively low LC 50 , LT 50 and LT 90 values. These results indicated that these two entomopathogenic fungi strains have potential as biocontrol agents of Cx . pipiens .