The Histidine Biosynthetic Genes in the Superphylum Bacteroidota-Rhodothermota-Balneolota-Chlorobiota: Insights into the Evolution of Gene Structure and Organization

One of the most studied metabolic routes is the biosynthesis of histidine, especially in enterobacteria where a single compact operon composed of eight adjacent genes encodes the complete set of biosynthetic enzymes. It is still not clear how his genes were organized in the genome of the last universal common ancestor community. The aim of this work was to analyze the structure, organization, phylogenetic distribution, and degree of horizontal gene transfer (HGT) of his genes in the Bacteroidota-Rhodothermota-Balneolota-Chlorobiota superphylum, a group of phylogenetically close bacteria with different surviving strategies. The analysis of the large variety of his gene structures and organizations revealed different scenarios with genes organized in more or less compact—heterogeneous or homogeneous—operons, in suboperons, or in regulons. The organization of his genes in the extant members of the superphylum suggests that in the common ancestor of this group, genes were scattered throughout the chromosome and that different forces have driven the assembly of his genes in compact operons. Gene fusion events and/or paralog formation, HGT of single genes or entire operons between strains of the same or different taxonomic groups, and other molecular rearrangements shaped the his gene structure in this superphylum

Biodiversity of Soil Bacterial Communities from the Sasso Fratino Integral Nature Reserve

The Sasso Fratino Integral Nature Reserve (Italy) aims to protect nature and territory. Since no anthropic activities are allowed, it represents a good model to study the bacterial community of a wild environment. The aim of this work was to characterise the cultivable and the total bacterial community of soil samples from the reserve in terms of taxonomy, composition, and structure. Seven soil samples were collected at different altitudes, and the chemical composition, the total and the cultivable microbiota, and the antibiotic resistance profiles of isolates were investigated. Total bacterial communities, studied through Next Generation Sequences analysis, included 390 genera. Samples differed in terms of microbial composition basing on the different altitude/vegetation of collection points. Random Amplified Polymorphic DNA Analysis (RAPD) allowed to identify 82 haplotypes out of 158 bacterial isolates. The taxonomic identification through 16S rDNA sequencing revealed that the strains were affiliated to 21 genera. Antibiotic resistance profiles of bacteria were also investigated, highlighting a high resistance against streptomycin and kanamycin. This work represents the first description of the soil bacterial community from the Natural Reserve of Sasso Fratino, and it is the first study considering the soil microbiota of an Italian integral nature reserve

Exploring the Bacterial Communities of Infernaccio Waterfalls: A Phenotypic and Molecular Characterization of Acinetobacter and Pseudomonas Strains Living in a Red Epilithic Biofilm

Acquarossa river (Viterbo, Italy) was the site of a prospering Etruscan civilization thanks to metallurgical activity around 625–550 B.C. This caused the spread of heavy metals throughout the area. Rocks along the river probably act as a filter for these elements and they are covered by two different biofilms (epilithons). They differ for both color and bacterial composition. One is red and is enriched with Pseudomonas strains, while the other one is black and Acinetobacter is the most represented genus. Along the river lay the Infernaccio waterfalls, whose surrounding rocks are covered only by the red epilithon. The bacterial composition of this biofilm was analyzed through high throughput sequencing and compared to those ones of red and black epilithons of Acquarossa river. Moreover, cultivable bacteria were isolated and their phenotype (i.e., resistance against antibiotics and heavy metals) was studied. As previously observed in the case of Acquarossa river, characterization of bacterial composition of the Infernaccio red epilithon revealed that the two most represented genera were Acinetobacter and Pseudomonas. Nonetheless, these strains differed from those isolated from Acquarossa, as revealed by RAPD analysis. This work, besides increasing knowledge about the ecological properties of this site, allowed to isolate new bacterial strains, which could potentially be exploited for biotechnological applications, because of their resistance against environmental pollutants

Endophytic Bacteria and Essential Oil from Origanum vulgare ssp. vulgare Share Some VOCs with an Antibacterial Activity

Medicinal aromatic plants’ essential oils (EOs) are mixtures of volatile compounds showing antimicrobial activity, which could be exploited to face the emerging problem of multi-drug resistance. Their chemical composition can depend on the interactions between the plant and its endophytic microbiota, which is known to synthesize volatile organic compounds (VOCs). However, it is still not clear whether those volatile metabolites can contribute to the composition of the aroma profile of plants’ EOs. The aims of this study were to characterize medicinal plant O. vulgare ssp. vulgare bacterial endophyte VOCs, evaluating their ability to antagonize the growth of opportunistic human pathogens belonging to the Burkholderia cepacia complex (Bcc) and compare them with O. vulgare EO composition. Many of the tested endophytic strains showed (i) a bactericidal and/or bacteriostatic activity against most of Bcc strains and (ii) the production of VOCs with widely recognized antimicrobial properties, such as dimethyl disulfide, dimethyl trisulfide, and monoterpenes. Moreover, these monoterpenes were also detected in the EOs extracted from the same O. vulgare plants from which endophytes were isolated. Obtained results suggest that endophytes could also play a role in the antibacterial properties of O. vulgare ssp. vulgare and, potentially, in determining its aromatic composition

Endophytic Bacteria and Essential Oil from Origanum vulgare ssp. vulgare Share Some VOCs with an Antibacterial Activity

Medicinal aromatic plants' essential oils (EOs) are mixtures of volatile compounds showing antimicrobial activity, which could be exploited to face the emerging problem of multi-drug resistance. Their chemical composition can depend on the interactions between the plant and its endophytic microbiota, which is known to synthesize volatile organic compounds (VOCs). However, it is still not clear whether those volatile metabolites can contribute to the composition of the aroma profile of plants' EOs. The aims of this study were to characterize medicinal plant O. vulgare ssp. vulgare bacterial endophyte VOCs, evaluating their ability to antagonize the growth of opportunistic human pathogens belonging to the Burkholderia cepacia complex (Bcc) and compare them with O. vulgare EO composition. Many of the tested endophytic strains showed (i) a bactericidal and/or bacteriostatic activity against most of Bcc strains and (ii) the production of VOCs with widely recognized antimicrobial properties, such as dimethyl disulfide, dimethyl trisulfide, and monoterpenes. Moreover, these monoterpenes were also detected in the EOs extracted from the same O. vulgare plants from which endophytes were isolated. Obtained results suggest that endophytes could also play a role in the antibacterial properties of O. vulgare ssp. vulgare and, potentially, in determining its aromatic composition