Genome-based reclassification of Kitasatospora niigatensis as a later heterotypic synonym of Kitasatospora cineracea Tajima et al. (2001).

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.

Determinants of COVID-19 Vaccine Engagement in Algeria: A Population-Based Study With Systematic Review of Studies From Arab Countries of the MENA Region.

Background: The Algerian COVID-19 vaccination campaign, which started at the end of January 2021, is marked by a slowly ascending curve despite the deployed resources. To tackle the issue, we assessed the levels and explored determinants of engagement toward the COVID-19 vaccine among the Algerian population. Methods: A nationwide, online-based cross-sectional study was conducted between March 27 and April 30, 2021. A two-stage stratified snowball sampling method was used to include an equivalent number of participants from the four cardinal regions of the country. A vaccine engagement scale was developed, defining vaccine engagement as a multidimensional parameter (5 items) that combined self-stated acceptance and willingness with perceived safety and efficacy of the vaccine. An Engagement score was calculated and the median was used to define engagement vs. non-engagement. Sociodemographic and clinical data, perceptions about COVID-19, and levels of adherence to preventive measures were analyzed as predictors for non-engagement. Results: We included 1,019 participants, 54% were female and 64% were aged 18-29 years. Overall, there were low rates of self-declared acceptance (26%) and willingness (21%) to take the vaccine, as well as low levels of agreement regarding vaccine safety (21%) and efficacy (30%). Thus, the vaccine engagement rate was estimated at 33.5%, and ranged between 29.6-38.5% depending on the region (p > 0.05). Non-engagement was independently associated with female gender (OR = 2.31, p < 0.001), low adherence level to preventive measures (OR = 6.93, p < 0.001), private-sector jobs (OR = 0.53, p = 0.038), perceived COVID-19 severity (OR = 0.66, p = 0.014), and fear from contracting the disease (OR = 0.56, p = 0.018). Concern about vaccine side effects (72.0%) and exigence for more efficacy and safety studies (48.3%) were the most commonly reported barrier and enabler for vaccine acceptance respectively; whereas beliefs in the conspiracy theory were reported by 23.4%. Conclusions: The very low rates of vaccine engagement among the Algerian population probably explain the slow ascension of the vaccination curve in the country. Vaccine awareness campaigns should be implemented to address the multiple misconceptions and enhance the levels of knowledge and perception both about the disease and the vaccine, by prioritizing target populations and engaging both healthcare workers and the general population.

In-depth genome analysis of Bacillus sp. BH32, a salt stress-tolerant endophyte obtained from a halophyte in a semiarid region.

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.

Performance of halotolerant bacteria associated with Sahara-inhabiting halophytes Atriplex halimus L. and Lygeum spartum L. ameliorate tomato plant growth and tolerance to saline stress: from selective isolation to genomic analysis of potential determinants.

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.