Evaluation of the infB and rpsB gene fragments as genetic markers intended for identification and phylogenetic analysis of particular representatives of the order Lactobacillales

Development of Multiplex RT qPCR Assays for Simultaneous Detection and Quantification of Faecal Indicator Bacteria in Bathing Recreational Waters

In this study, we designed and validated in silico and experimentally a rapid, sensitive, and specific multiplex RT qPCR for the detection and quantification of faecal indicator bacteria (FIB) used as microbiological references in marine bathing water regulations (Escherichia coli and intestinal enterococci). The 16S rRNA gene was used to quantify group-specific enterococci and Escherichia/Shigella and species-specific such as Enterococcus faecalis and E. faecium. Additionally, a ybbW gene encoding allantoin transporter protein was used to detect E. coli. An assessment of marine coastal systems (i.e., marine water and sediment) revealed that intestinal enterococci were the predominant group compared to Escherichia/Shigella. The low contribution of E. faecalis to the intestinal enterococci group was reported. As E. faecalis and E. faecium were reported at low concentrations, it is assumed that other enterococci of faecal origin are contributing to the high gene copy number of this group-specific enterococci. Moreover, low 16S rRNA gene copy numbers with respect to E. faecalis and E. faecium were reported in seawater compared to marine sediment. We conclude that marine sediments can affect the quantification of FIBs included in bathing water regulations. Valuing the quality of the marine coastal system through sediment monitoring is recommended.

tilS and rpoB: New Molecular Markers for Phylogenetic and Biodiversity Studies of the Genus Thiothrix

Currently, the phylogeny of the genus Thiothrix is based on comparative whole genome analysis because of the high homology of the 16S ribosomal RNA gene sequences within the genus. We analyzed the possibility of using various conservative genes as phylogenetic markers for the genus Thiothrix. We found that the levels of similarity of the nucleotide sequences of the tRNA(Ile)-lysidine synthase (tilS) and the β subunit of RNA polymerase (rpoB) genes are in good agreement with the average nucleotide identity (ANI) values between the genomes of various representatives of the genus Thiothrix. The genomes of Thiothrix strains MK1, WS, DNT52, DNT53, and H33 were sequenced. Taxonomic analysis using both whole genomes and the tilS gene consistently showed that MK1 and WS belong to Thiothrix lacustris, while DNT52, DNT53, and H33 belong to Thiothrix subterranea. The tilS gene fragments were subjected to high-throughput sequencing to profile the Thiothrix mat of a sulfidic spring, which revealed the presence of known species of Thiothrix and new species-level phylotypes. Thus, the use of tilS and rpoB as phylogenetic markers will allow for rapid analyses of pure cultures and natural communities for the purpose of phylogenetic identification of representatives of the genus Thiothrix.

Rhizosphere bacteria associated with Chenopodium quinoa promote resistance to Alternaria alternata in tomato

Microorganisms can interact with plants to promote plant growth and act as biocontrol agents. Associations with plant growth-promoting rhizobacteria (PGPR) enhance agricultural productivity by improving plant nutrition and enhancing protection from pathogens. Microbial applications can be an ideal substitute for pesticides or fungicides, which can pollute the environment and reduce biological diversity. In this study, we isolated 68 bacterial strains from the root-adhering soil of quinoa (Chenopodium quinoa) seedlings. Bacterial strains exhibited several PGPR activities in vitro, including nutrient solubilization, production of lytic enzymes (cellulase, pectinase and amylase) and siderophore synthesis. These bacteria were further found to suppress the mycelial growth of the fungal pathogen Alternaria alternata. Nine bacterial strains were selected with substantial antagonistic activity and plant growth-promotion potential. These strains were identified based on their 16S rRNA gene sequences and selected for in planta experiments with tomato (Solanum lycopersicum) to estimate their growth-promotion and disease-suppression activity. Among the selected strains, B. licheniformis and B. pumilus most effectively promoted tomato plant growth, decreased disease severity caused by A. alternata infection by enhancing the activities of antioxidant defense enzymes and contributed to induced systemic resistance. This investigation provides evidence for the effectiveness and viability of PGPR application, particularly of B. licheniformis and B. pumilus in tomato, to promote plant growth and induce systemic resistance, making these bacteria promising candidates for biofertilizers and biocontrol agents.

Multitrait Pseudomonas spp. Isolated from Monocropped Wheat (Triticum aestivum) Suppress Fusarium Root and Crown Rot

Fusarium root and crown rot is the most common disease of wheat, especially wheat grown in arid zones where drought is a common issue. The development of environmentally safe approaches to manage diseases of food crops is important for humans. The monocropping system recruits beneficial bacteria that promote plant growth through nutrient solubilization and pathogen suppression. In this study, a field where wheat was monocropped for 5 successive years under rainfed conditions was identified. A total of 29 bacterial isolates were obtained from the rhizosphere, endosphere, and phyllosphere of wheat at its harvesting stage. The Gram-negative bacteria were less prevalent (41%) but the majority (75%) exhibited plant growth-promoting traits. The ability of strains to solubilize nutrients (solubilization index = 2.3 to 4), inhibit pathogenic fungi (25 to 56%), and produce antifungal compounds was highly variable. The rhizobacteria significantly promoted the growth and disease resistance of wheat varieties such as Pirsbak-2015 and Galaxy-2013 by inducing antioxidant enzyme activity (0.2- to 2.1-fold). The bacterial strains were identified as Ochrobactrum spp., Acinetobacter spp., and Pseudomonas mediterranea by 16S rRNA and rpoD sequence analysis. The endophytic bacterium P. mediterranea HU-9 exhibited maximum biocontrol efficacy against wheat root and crown rot diseases with a disease score/disease index from 1.8 to 3.1. The monocropping systems of rainfed agriculture are an ideal source of beneficial bacteria to use as bioinoculants for different crops.

Study of helveticin gene in Lactobacillus crispatus strains and evaluation of its use as a phylogenetic marker

Lactobacilli are a part of the human microbiome in healthy humans. Studies of their physiological and genetic characteristics are the basis for their use in probiotic preparations. This report is a brief description of the helveticin gene found in two Lactobacillus crispatus strains, which are a part of the human microbiome. Our analysis showed that the two variants of the gene are not solely characteristic of strains isolated from humans. In the phylogenetic analysis, we found that the studied sequence (this gene) showed a significant difference between the species of the genus Lactobacillus and could be used as a phylogenetic marker.

Genetic marker-based multi-locus sequence analysis for classification, genotyping, and phylogenetics of the family Bifidobacteriaceae as an alternative approach to phylogenomics

Bifidobacteria are widely known for their probiotic potential; however, little is known regarding the ecological significance and potential probiotic effects of the phylogenetically related 'scardovial' genera (Aeriscardovia, Alloscardovia, Bombiscardovia, Galliscardovia, Neoscardovia, Parascardovia, Pseudoscardovia and Scardovia) and Gardnerella classified with bifidobacteria within the Bifidobacteriaceae family. Accurate classification and genotyping of bacteria using certain housekeeping genes is possible, whilst current phylogenomic analyses allow for extremely precise classification. Studies of applicable genetic markers may provide results comparable to those obtained from phylogenomic analyses of the family Bifidobacteriaceae. Segments of the glyS (624 nucleotides), pheS (555 nucleotides), rpsA (630 nucleotides), and rpsB (432 nucleotides) genes and their concatenated sequence were explored. The mean glyS, pheS, rpsB and rpsA gene sequence similarities calculated for Bifidobacterium taxa were 84.8, 85.2, 90.2 and 86.8%, respectively. Interestingly, the average value of the Average Nucleotide Identity among 67 type strains of the family Bifidobacteriaceae (84.70%) calculated based on values published recently was in agreement with the average pairwise similarity (84.6%) among 75 type strains of Bifidobacteriaceae family computed in this study using the concatenated sequences of four gene fragments. Similar to phylogenomic analyses, several gene sequence and phylogenetic analyses revealed that concatenated gene regions allow for classification of Bifidobacteriaceae strains into particular phylogenetic clusters and groups. Phylogeny reconstructed from the concatenated sequences assisted in defining two novel phylogenetic groups, the Bifidobacterium psychraerophilum group consisting of B. psychraerophilum, Bifidobacterium crudilactis and Bifidobacterium aquikefiri species and the Bifidobacterium bombi group consisting of B. bombi, Bifidobacterium bohemicum and Bifidobacterium commune.