Comparison of gyrB gene sequences, 16S rRNA gene sequences and DNA-DNA hybridization in the Bacillus subtilis group

Development of a novel PCR assay based on the gyrase B gene for species identification of Bacillus licheniformis

Bacillus licheniformis is closely related to the Bacillus subtilis group, and could not be clearly identified using phenotypic and genotypic (16S rDNA sequence analysis) techniques alone. Some strains of this species are considered to be probiotic and are widely applied in the food and feed industry. The objective of this study was to develop species-specific PCR based on the gyrB gene sequence for direct species identification of the B. licheniformis within the B. subtilis group. A pair of species-specific primer was designed and used to specifically detect B. licheniformis, but none of the other B. subtilis group strains. Our data indicate that the novel species-specific primer could be used to rapidly and accurately identify the species of B. licheniformis from B. subtilis group by a PCR based assay.

Phosphate-containing cell wall polymers of bacilli

Anionic phosphate-containing cell wall polymers of bacilli are represented by teichoic acids and poly(glycosyl 1-phosphates). Different locations of phosphodiester bonds in the main chain of teichoic acids as well as the nature and combination of the constituent structural elements underlie their structural diversity. Currently, the structures of teichoic acids of bacilli can be classified into three types, viz. poly(polyol phosphates) with glycerol or ribitol as the polyol; poly(glycosylpolyol phosphates), mainly glycerol-containing polymers; and poly(acylglycosylglycerol phosphate), in which the components are covalently linked through glycosidic, phosphodiester, and amide bonds. In addition to teichoic acids, poly(glycosyl 1-phosphates) with mono- and disaccharide residues in the repeating units have been detected in cell walls of several Bacillus subtilis and Bacillus pumilus strains. The known structures of teichoic acids and poly(glycosyl 1-phosphates) of B. subtilis, B. atrophaeus, B. licheniformis, B. pumilus, B. stearothermophilus, B. coagulans, B. cereus as well as oligomers that link the polymers to peptidoglycan are surveyed. The reported data on the structures of phosphate-containing polymers of different strains of B. subtilis suggest heterogeneity of the species and may be of interest for the taxonomy of bacilli to allow differentiation of closely related organisms according to the "structures and composition of cell wall polymers" criterion.

Reassessment of the status of Streptomyces setonii and reclassification of Streptomyces fimicarius as a later synonym of Streptomyces setonii and Streptomyces albovinaceus as a later synonym of Streptomyces globisporus based on combined 16S rRNA/gyrB gene sequence analysis

The 16S rRNA and gyrB genes of 22 Streptomyces strains belonging to the Streptomyces griseus cluster were sequenced, and their taxonomic positions were re-evaluated. For correct analysis, all of the publicly available sequences of the species were collected and compared with those obtained in this study. Species for which no consensus sequence could be identified were excluded from the phylogenetic analysis. The levels of 16S rRNA gene sequence similarity within the cluster ranged from 98.6 to 100% with a mean value of 99.6 ± 0.3%, and those of the gyrB gene ranged from 93.6 to 99.9% with a mean value of 96.3 ± 1.5%. The observed average nucleotide substitution rate of the gyrB gene was ten times higher than that of the 16S rRNA gene, showing a far higher degree of variation. Strains sharing 99.3% or more gyrB sequence similarity (corresponding to an evolutionary distance of 0.0073) always formed monophyletic groups in both trees. Through the combined analysis of the two genes, clear cases of synonymy could be identified and, according to the priority rule, the assertion of the status of Streptomyces setonii as a distinct species and the reclassification of Streptomyces fimicarius as a later synonym of S. setonii and Streptomyces albovinaceus as a later synonym of Streptomyces globisporus are proposed. Emended descriptions of S. setonii and S. globisporus are provided.

Does the applicability of Bacillus strains in probiotics rely upon their taxonomy?

The taxonomic position and biological activities of two Bacillus strains used in veterinary probiotics were studied in this work. These microorganisms inhibit growth of a broad spectrum of pathogenic cultures. They synthesize proteolytic enzymes and other biologically active metabolites, and to some extent, supplement each other with probiotic activities. It is not clear whether these versatile activities are properties of individual strains or bacterial taxa as whole. 16S rRNA comparisons were conducted and illustrated the relatedness of these strains to Bacillus amyloliquefaciens . Their cell wall fatty acid contents were consequently analysed and specified a relation to the " Bacillus velezensis " ecomorph. On account of the previous observations, a simple method of 16S rRNA profiling by polymorphic nucleotides was proposed to determine a group of organisms closely related to "B. velezensis" and B. amyloliquefaciens subsp. plantarum, for they are biologically active strains suitable for use in biotechnology. The extreme genetic plasticity of these bacteria endowed each strain with a unique spectrum of antagonistic activity.

Stenotrophomonas interspecies differentiation and identification by gyrB sequence analysis

Stenotrophomonas species are found commonly in environmental and clinical samples; Stenotrophomonas maltophilia is an important opportunistic pathogen of humans. Traditional phenotyping protocols, as well as genotyping by 16S rRNA gene sequence analysis, do not reliably distinguish the species of Stenotrophomonas. Sequence analyses of two targeted PCR-amplified regions of the gyrB gene, which encodes the β-subunit of DNA gyrase, enabled resolution and identification of these species. Most type strains of the different species of Stenotrophomonas exhibited more than 7% dissimilarity in the gyrB gene sequences. Among these, strains identified as the same species exhibited sequence dissimilarities up to 4.6% and 5.9% for the two regions, respectively. Strains identified as S. maltophilia, with 16S rRNA gene sequence similarities > 99.0%, were grouped within a 'S. maltophilia complex'; these organisms exhibited gyrB similarities as low as 93%. Many of these strains possessed genomic DNA similarities with the type strain of S. maltophilia CCUG 5866(T) below 70%. These data, including gyrB sequence comparisons, indicate that strains identified as S. maltophilia may comprise distinct, new species.

Rapid species identification of seafood spoilage and pathogenic Gram-positive bacteria by MALDI-TOF mass fingerprinting

The rapid identification of food pathogenic and spoilage bacteria is important to ensure food quality and safety. Seafood contaminated with pathogenic bacteria is one of the major causes of food intoxications, and the rapid spoilage of seafood products results in high economic losses. In this study, a collection of the main seafood pathogenic and spoilage Gram-positive bacteria was compiled, including Bacillus spp., Listeria spp., Clostridium spp., Staphylococcus spp. and Carnobacterium spp. The strains, belonging to 20 different species, were obtained from the culture collections and studied by matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS). A reference library was created, including the spectral fingerprints of 32 reference strains and the extracted peak lists with 10-30 peak masses. Genus-specific as well as species-specific peak masses were assigned and could serve as biomarkers for the rapid bacterial identification. Furthermore, the peak mass lists were clustered with the web-application SPECLUST to show the phyloproteomic relationships among the studied strains. Afterwards, the method was successfully applied to identify six strains isolated from seafood by comparison with the reference library. Additionally, phylogenetic analysis based on the 16S rRNA gene was carried out and contrasted with the proteomic approach. This is the first time MALDI-TOF MS fingerprinting is applied to Gram-positive bacterial identification in seafood, being a fast and accurate technique to ensure seafood quality and safety.

A 'universal' type II chaperonin PCR detection system for the investigation of Archaea in complex microbial communities

Bacteria and Archaea are evolutionarily and biochemically distinct domains found together in many environments. Robust 'universal' PCR primer sets targeting both the bacterial 16S rRNA gene and the type I chaperonin gene have been established. However, 'universal' PCR primers for Archaea are currently limited to the 16S rRNA gene. We investigated the type II chaperonin (known as the thermosome, TF55, CCT or TCP-1) as a potential universal target (UT) for Archaea. Reproducible amplification of thermosome gene sequences from all major phyla tested was achieved through the application of a mixture or 'cocktail' of two forward and two reverse primers. Phylogenies based on the ∼750-bp thermosome UT were congruent with 16S rRNA gene phylogenies while exhibiting longer branch lengths, improving resolution of closely related taxa. 'Universal' thermosome primers were applied to profiling the archaeal community of dairy cow rumen and results compared with profiles based on the 16S rRNA gene and methyl co-enzyme M reductase (methanogen-specific) gene. Clone libraries generated from each target gene, as well as a pyrosequencing profile of one thermosome rumen library, revealed that all three targets consistently detected Methanobrevibacter smithii, Methanobrevibacter ruminantium and Methanosphaera stadtmanae as the dominant constituents; however, thermosome gene sequences were more diverse than either of the other targets providing a higher resolution description of the archaeal community. These findings demonstrate that a 'universal' thermosome PCR protocol is a powerful metagenomic tool for detecting and characterizing Archaea and archaeal communities.

RAPD-based screening for spore-forming bacterial populations in Uruguayan commercial powdered milk

The occurrence of spore-forming bacteria in powdered milk is of concern to the dairy industry due to potential deleterious effects including those resulting from proteolytic and lipolytic activities. Twenty-two powdered milk samples representative of spring and summer production obtained from Uruguayan retail stores were analyzed for type and number of thermophilic and spore-forming bacterial species. Bacillus licheniformis isolates were found to be the most prominent milk powder contaminant followed by Anoxybacillus flavithermus representing 71.5 to 84% of the total microflora. Geobacillus stearothermophilus, however, was not found. B. licheniformis strains F and G were both found in this study but strain F was the prevalent isolate representing 98.9% of the total isolates of this species. A. flavithermus isolates corresponded to strain C in accordance with 16S rRNA gene sequence analysis, however, in contrast with other reports, the RAPD profiles showed three characteristic bands at approximately 650, 1000 and 1650 bp, but lacking a band at 1250 bp. A third group of isolates was identified corresponding to members of a Bacillus subtilis group and Bacillus megaterium. Isolates designated B. licheniformis, A. flavithermus, B. megaterium and the B. subtilis group represented 89.1 to 93.6% of those analyzed, and depended on previous heat treatment and incubation temperatures of the plates. The remaining isolates were Bacillus pumilus and unidentified spore-formers.

Predicting relatedness of bacterial genomes using the chaperonin-60 universal target (cpn60 UT): application to Thermoanaerobacter species

D.R. Zeigler determined that the sequence identity of bacterial genomes can be predicted accurately using the sequence identities of a corresponding set of genes that meet certain criteria [32]. This three-gene model for comparing bacterial genome pairs requires the determination of the sequence identities for recN, thdF, and rpoA. This involves the generation of approximately 4.2kb of genomic DNA sequence from each organism to be compared, and also normally requires that oligonucleotide primers be designed for amplification and sequencing based on the sequences of closely related organisms. However, we have developed an analogous mathematical model for predicting the sequence identity of whole genomes based on the sequence identity of the 542-567 base pair chaperonin-60 universal target (cpn60 UT). The cpn60 UT is accessible in nearly all bacterial genomes with a single set of universal primers, and its length is such that it can be completely sequenced in one pair of overlapping sequencing reads via di-deoxy sequencing. These mathematical models were applied to a set of Thermoanaerobacter isolates from a wood chip compost pile and it was shown that both the one-gene cpn60 UT-based model and the three-gene model based on recN, rpoA, and thdF predicted that these isolates could be classified as Thermoanaerobacter thermohydrosulfuricus. Furthermore, it was found that the genomic prediction model using cpn60 UT gave similar results to whole-genome sequence alignments over a broad range of taxa, suggesting that this method may have general utility for screening isolates and predicting their taxonomic affiliations.

Characterization of Bacillus isolates of potato rhizosphere from andean soils of Peru and their potential PGPR characteristics

Bacillus spp. are well known rhizosphere residents of many crops and usually show plant growth promoting (PGP) activities that include biocontrol capacity against some phytopatogenic fungi. Potato crops in the Andean Highlands of Peru face many nutritional and phytophatogenic problems that have a significant impact on production. In this context is important to investigate the natural presence of these microorganisms in the potato rhizosphere and propose a selective screening to find promising PGP strains. In this study, sixty three Bacillus strains isolated from the rhizosphere of native potato varieties growing in the Andean highlands of Peru were screened for in vitro antagonism against Rhizoctonia solani and Fusarium solani. A high prevalence (68%) of antagonists against R. solani was found. Ninety one percent of those strains also inhibited the growth of F. solani. The antagonistic strains were also tested for other plant growth promotion activities. Eighty one percent produced some level of the auxin indole-3-acetic acid, and 58% solubilized tricalcium phosphate. Phylogenetic analysis revealed that the majority of the strains belonged to the B. amyloliquefaciens species, while strains Bac17M11, Bac20M1 and Bac20M2 may correspond to a putative new Bacillus species. The results suggested that the rhizosphere of native potatoes growing in their natural habitat in the Andes is a rich source of Bacillus fungal antagonists, which have a potential to be used in the future as PGP inoculants to improve potato crop.

Pseudomonas taiwanensis sp. nov., isolated from soil

A novel Gram-negative, rod-shaped, motile, non-spore-forming bacterial strain, CMST, isolated from soil was characterized using phenotypic and molecular taxonomic methods. 16S rRNA gene sequence analysis revealed that the organism belongs phylogenetically to the genus Pseudomonas. Pseudomonas monteilii, P. plecoglossicida and P. mosselii were the most closely related species, with 16S rRNA gene sequence similarities to the respective type strains of 99.79, 99.73 and 99.59 %. Relatively low gyrB gene sequence similarities (<90 %) and DNA–DNA reassociation values (<51 %) were obtained between the strain and its phylogenetically closest neighbours. The G+C content of strain CMST was 62.7 mol%. The major cellular fatty acids were C18 : 1 ω7c, summed feature 3 (C16 : 1 ω7c and/or iso-C15 : 0 2-OH), C16 : 0 and C10 : 0 3-OH. Based on the phenotypic and genetic evidence, the strain is suggested to represent a novel species, for which the name Pseudomonas taiwanensis sp. nov. is proposed. The type strain is CMST (=BCRC 17751T =DSM 21245T).

GeoChip 3.0 as a high-throughput tool for analyzing microbial community composition, structure and functional activity

A new generation of functional gene arrays (FGAs; GeoChip 3.0) has been developed, with approximately 28 000 probes covering approximately 57 000 gene variants from 292 functional gene families involved in carbon, nitrogen, phosphorus and sulfur cycles, energy metabolism, antibiotic resistance, metal resistance and organic contaminant degradation. GeoChip 3.0 also has several other distinct features, such as a common oligo reference standard (CORS) for data normalization and comparison, a software package for data management and future updating and the gyrB gene for phylogenetic analysis. Computational evaluation of probe specificity indicated that all designed probes would have a high specificity to their corresponding targets. Experimental analysis with synthesized oligonucleotides and genomic DNAs showed that only 0.0036-0.025% false-positive rates were observed, suggesting that the designed probes are highly specific under the experimental conditions examined. In addition, GeoChip 3.0 was applied to analyze soil microbial communities in a multifactor grassland ecosystem in Minnesota, USA, which showed that the structure, composition and potential activity of soil microbial communities significantly changed with the plant species diversity. As expected, GeoChip 3.0 is a high-throughput powerful tool for studying microbial community functional structure, and linking microbial communities to ecosystem processes and functioning.

Pseudomonas cannabina pv. cannabina pv. nov., and Pseudomonas cannabina pv. alisalensis (Cintas Koike and Bull, 2000) comb. nov., are members of the emended species Pseudomonas cannabina (ex Sutic & Dowson 1959) Gardan, Shafik, Belouin, Brosch, Grimont & Grimont 1999

Sequence similarity in the 16S rDNA gene confirmed that crucifer pathogen Pseudomonas syringae pv. alisalensis belongs to P. syringae sensu lato. In reciprocal DNA/DNA hybridization experiments, DNA relatedness was high (69-100%) between P. syringae pv. alisalensis strains and the type strain of P. cannabina (genomospecies 9). In contrast, DNA relatedness was low (below 48%) between P. syringae pv. alisalensis and reference strains from the remaining genomospecies of P. syringae including the type strain of P. syringae and reference strain of genomospecies 3 (P. syringae pv. tomato) although the well-known crucifer pathogen, P. syringae pv. maculicola, also belongs to genomospecies 3. Additional evidence that P. syringae pv. alisalensis belongs to P. cannabina was sequence similarity in five gene fragments used in multilocus sequence typing, as well as similar rep-PCR patterns when using the BOX-A1R primers. The description of P. cannabina has been emended to include P. syringae pv. alisalensis. Host range testing demonstrated that P. syringae pv. alisalensis strains, originally isolated from broccoli, broccoli raab or arugula, were not pathogenic on Cannabis sativa (family Cannabinaceae). Additionally, P. cannabina strains, originally isolated from the C. sativa were not pathogenic on broccoli raab or oat while P. syringae pv. alisalensis strains were pathogenic on these hosts. Distinct host ranges for these two groups indicate that P. cannabina emend. consists of at least two distinct pathovars, P. cannabina pv. cannabina pv. nov., and P. cannabina pv. alisalensis comb. nov. Pseudomonas syringae pv. maculicola strain CFBP 1637 is a member of P. cannabina.

A gyrB-targeted PCR for rapid identification of Paenibacillus mucilaginosus

Paenibacillus mucilaginosus, one of the typical silicate bacteria, has long been used as a biofertilizer in agriculture and has recently shown potential in bioleaching and wastewater engineering. There has been considerable research involving the isolation of P. mucilaginosus for various utilizations; therefore, rapid identification of this species is of great interest. Herein, we describe a specific polymerase chain reaction (PCR) method developed for a rapid identification of P. mucilaginosus, which might provide potential utilization in the investigation of populations, detection of biofertilizers, and identification of novel isolates on a large scale. A gyrB-targeted species-specific primer pair, F2 (5'-ACG GAT ATC TCC CAG ACG TTC AT-3') and R5 (5'-ACG GGC ACG CTG CGC CTG TAC G-3'), was successfully designed to selectively amplify a 519-bp amplicon from P. mucilaginosus. Good specificity was demonstrated by both reference strains and total soil deoxyribonucleic acid, from which only the gyrB gene of P. mucilaginosus was amplified. The detection limit was 4-10 cells per assay. Using the culture-PCR method, 20 of 26 soil isolates on a nitrogen-free medium were rapidly identified as P. mucilaginosus, which was confirmed by sequencing of the gyrB gene.

Phylogeny of Photorhabdus and Xenorhabdus based on universally conserved protein-coding sequences and implications for the taxonomy of these two genera. Proposal of new taxa: X. vietnamensis sp. nov., P. luminescens subsp. caribbeanensis subsp. nov., P. luminescens subsp. hainanensis subsp. nov., P. temperata subsp. khanii subsp. nov., P. temperata subsp. tasmaniensis subsp. nov., and the reclassification of P. luminescens subsp. thracensis as P. temperata subsp. thracensis comb. nov

We used the information from a set of concatenated sequences from four genes (recA, gyrB, dnaN and gltX) to investigate the phylogeny of the genera Photorhabdus and Xenorhabdus (entomopathogenic bacteria associated with nematodes of the genera Heterorhabditis and Steinernema, respectively). The robustness of the phylogenetic tree obtained by this multigene approach was significantly better than that of the tree obtained by a single gene approach. The comparison of the topologies of single gene phylogenetic trees highlighted discrepancies which have implications for the classification of strains and new isolates; in particular, we propose the transfer of Photorhabdus luminescens subsp. thracensis to Photorhabdus temperata subsp. thracensis comb. nov. (type strain CIP 108426T =DSM 15199T). We found that, within the genus Xenorhabdus, strains or isolates that shared less than 97 % nucleotide identity (NI), calculated on the concatenated sequences of the four gene fragments (recA, gyrB, dnaN and gltX) encompassing 3395 nucleotides, did not belong to the same species. Thus, at the 97% NI cutoff, we confirm the current 20 species of the genus Xenorhabdus and propose the description of a novel species, Xenorhabdus vietnamensis sp. nov. (type strain VN01T =CIP 109945T =DSM 22392T). Within each of the three current species of the genus Photorhabdus, P. asymbiotica, P. luminescens and P. temperata, strains or isolates which shared less than 97% NI did not belong to the same subspecies. Comparisons of the four gene fragments plus the rplB gene fragment analysed separately led us to propose four novel subspecies: Photorhabdus luminescens subsp. caribbeanensis subsp. nov. (type strain HG29T =CIP 109949T =DSM 22391T), P. luminescens subsp. hainanensis subsp. nov. (type strain C8404T = CIP 109946T =DSM 22397T), P. temperata subsp. khanii subsp. nov. (type strain C1T =NC19(T) =CIP 109947T =DSM 3369T), and P. temperata subsp. tasmaniensis subsp. nov. (type strain T327T =CIP 109948T =DSM 22387T).

Species-level identification of Bacillus strains isolates from marine sediments by conventional biochemical, 16S rRNA gene sequencing and inter-tRNA gene sequence lengths analysis

The aim of this study was to compare the ability of commonly used conventional biochemical tests, sequencing analysis of 16S rRNA genes and tDNA-intergenic spacer length polymorphism (tDNA-PCR) to identify species of the genus Bacillus recovered from marine sediments. While biochemical tests were not sufficiently sensitive to distinguish between the 23 marine strains analyzed, partial 16S rRNA gene sequences allowed a correct identification, clustering them into four species belonging to Bacillus licheniformis (n = 6), Bacillus cereus (n = 9), Bacillus subtilis (n = 7) and Bacillus pumilus (n = 1). The identification results obtained with 16S rRNA sequencing were validated by tDNA-PCR analysis of 23 marine isolates that were identified by the similarities of their fingerprints to those of reference strains. tDNA-PCR fingerprinting was as discriminatory as 16S rRNA sequencing analysis. Although it was not able to distinguish among the species of the B. cereus and B. subtilis groups, it should be considered a rapid and easy approach for the reliable identification of unknown Bacillus isolates or at least for the primary differentiation of Bacillus groups.