Bacillus terrae sp. nov. isolated from Cistus ladanifer rhizosphere soil

Taxonogenomics description of Bacillus marasmi sp. nov., a new species isolated from the stool sample

Using the culturomics method, two strains were isolated, identified, and characterised following the taxonogenomics concept. Bacillus marasmi sp. nov. strain Marseille-P3556 (= CSURP3556) is isolated from a 13-month-old girl living in Niger. The phylogenetic tree, phenotypic criteria, and genomic analysis described here clearly show that this bacterium is different from previously known bacterial species withstanding in nomenclature and new members of Bacillus genus.

Visualizing and Isolating Iron-Reducing Microorganisms at the Single-Cell Level

Iron-reducing microorganisms (FeRM) play key roles in many natural and engineering processes. Visualizing and isolating FeRM from multispecies samples are essential to understand the in situ location and geochemical role of FeRM. Here, we visualized FeRM by a "turn-on" Fe2+-specific fluorescent chemodosimeter (FSFC) with high sensitivity, selectivity, and stability. This FSFC could selectively identify and locate active FeRM from either pure culture, coculture of different bacteria, or sediment-containing samples. Fluorescent intensity of the FSFC could be used as an indicator of Fe2+ concentration in bacterial cultures. By combining the use of the FSFC with that of a single-cell sorter, we obtained three FSFC-labeled cells from an enriched consortium, and all of them were subsequently shown to be capable of iron reduction; two unlabeled cells were shown to have no iron-reducing capability, further confirming the feasibility of the FSFC.IMPORTANCE Visualization and isolation of FeRM from samples containing multiple species are commonly needed by researchers from different disciplines, such as environmental microbiology, environmental sciences, and geochemistry. However, no available method has been reported. In this study, we provide a method to visualize FeRM and evaluate their activity even at the single-cell level. When this approach is combined with use of a single-cell sorter, FeRM can also be isolated from samples containing multiple species. This method can be used as a powerful tool to uncover the in situ or ex situ role of FeRM and their interactions with ambient microbes or chemicals.

Robust demarcation of 17 distinct Bacillus species clades, proposed as novel Bacillaceae genera, by phylogenomics and comparative genomic analyses: description of Robertmurraya kyonggiensis sp. nov. and proposal for an emended genus Bacillus limiting it only to the members of the Subtilis and Cereus clades of species

To clarify the evolutionary relationships and classification of Bacillus species, comprehensive phylogenomic and comparative analyses were performed on >300 Bacillus/Bacillaceae genomes. Multiple genomic-scale phylogenetic trees were initially reconstructed to identify different monophyletic clades of Bacillus species. In parallel, detailed analyses were performed on protein sequences of genomes to identify conserved signature indels (CSIs) that are specific for each of the identified clades. We show that in different reconstructed trees, most of the Bacillus species, in addition to the Subtilis and Cereus clades, consistently formed 17 novel distinct clades. Additionally, some Bacillus species reliably grouped with the genera Alkalicoccus, Caldalkalibacillus, Caldibacillus, Salibacterium and Salisediminibacterium. The distinctness of identified Bacillus species clades is independently strongly supported by 128 identified CSIs which are unique characteristics of these clades, providing reliable means for their demarcation. Based on the strong phylogenetic and molecular evidence, we are proposing that these 17 Bacillus species clades should be recognized as novel genera, with the names Alteribacter gen. nov., Ectobacillus gen. nov., Evansella gen. nov., Ferdinandcohnia gen. nov., Gottfriedia gen. nov., Heyndrickxia gen. nov., Lederbergia gen. nov., Litchfieldia gen. nov., Margalitia gen. nov., Niallia gen. nov., Priestia gen. nov., Robertmurraya gen. nov., Rossellomorea gen. nov., Schinkia gen. nov., Siminovitchia gen. nov., Sutcliffiella gen. nov. and Weizmannia gen. nov. We also propose to transfer 'Bacillus kyonggiensis' to Robertmurraya kyonggiensis sp. nov. (type strain: NB22=JCM 17569^T=DSM 26768). Additionally, we report 31 CSIs that are unique characteristics of either the members of the Subtilis clade (containing the type species B. subtilis) or the Cereus clade (containing B. anthracis and B. cereus). As most Bacillus species which are not part of these two clades can now be assigned to other genera, we are proposing an emended description of the genus Bacillus to restrict it to only the members of the Subtilis and Cereus clades.

Bacillus miscanthi sp. nov., a alkaliphilic bacterium from the rhizosphere of Miscanthus sacchariflorus

A novel bacterial strain, designated AK13^T (=KACC 21401^T=DSM 109981^T), was isolated from the rhizosphere of Miscanthus sacchariflorus. Strain AK13^T was found to be an aerobic, Gram-stain-positive, endospore-forming and rod-shaped bacterium. It formed yellow circular colonies with smooth convex surfaces. The genomic DNA G+C content of strain AK13^T was estimated to be 40 mol%. Phylogenetic analysis based on 16S rRNA gene sequence similarity showed that this strain was most closely related to Bacillus lehensis MLB2^T (99.4 %), Bacillus oshimensis K11^T (98.8 %) and Bacillus patagoniensis PAT 05^T (96.6 %). The average nucleotide identity values between strain AK13^T and B. lehensis MLB2^T, B. oshimensis K11^T and B. patagoniensis PAT 05^T were 90.93, 91.05 and 71.87 %, respectively, with the digital DNA-DNA hybridization values of 42.7, 42.6 and 18.8 %, respectively. Cells grew at 5-40 °C (optimum, 28-35 °C), pH 6.5-13 (optimum, pH 8-9) and in the presence of 0-13.0 % (w/v) NaCl (optimum, 1 %). The cell wall of strain AK13^T contained meso-diaminopimelic acid, and the major isoprenoid quinone was MK-7. Results of fatty acid methyl ester analysis revealed that iso-C_{15 : 0} was the predominant cellular fatty acid. Two-dimensional thin-layer chromatography analysis indicated that the major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and glycolipid. The genotypic and phenotypic characteristics suggested that strain AK13^T represented a novel species of the genus Bacillus, and thus the name Bacillus miscanthi sp. nov. is proposed.

Bacillus acidinfaciens sp. nov., isolated from farmland soil

A Gram-stain-positive, rod-shaped, motile bacterial strain, designated 3-2-2T, was isolated from field topsoil collected from a western suburb of Nanyang city, Henan province, China. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain 3-2-2T was a member of the genus Bacillus and most closely related to Bacillus fortis R-6514T (98.9 % similarity), Bacillus terrae RA9T (98.0 %) and Bacillus fordii R-7190T (97.7 %). A draft genome sequence determined for strain 3-2-2T revealed a DNA G+C content of 42.2 mol%. The average nucleotide identity and digital DNA–DNA hybridization values between 3-2-2T and the closely related Bacillus species ranged 79.4–84.2 % and 23.4–24.6 %. The major fatty acids of strain 3-2-2T were iso-C15 : 0, anteiso-C15 : 0, iso-C14 : 0 and iso-C16 : 0. The major isoprenoid quinone was MK-7. meso-Diaminopimelic acid was detected in the peptidoglycan. The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, an unidentified phospholipid and an unidentified lipid. The results of phylogenetic analyses, in silico genomic comparisons, and chemotaxonomic and phenotypic analyses clearly indicated that strain 3-2-2T represents a novel species within the genus Bacillus , for which the name Bacillus acidinfaciens sp. nov. is proposed. The type strain is 3-2-2T (=CGMCC 1.13685T=LMG 30839T).

Bacillus spongiae sp. nov., isolated from sponge of Jeju Island

A Gram-reaction-positive, strictly aerobic, motile, endospore- forming, and rod-shaped bacterial strain designated 135PIL107-10^T was isolated from a sponge on Jeju Island, and its taxonomic position was investigated using a polyphasic approach. Strain 135PIL107-10^T grew at 20-37°C (optimum temperature, 25°C) and pH 6.0-10.0 (optimum pH, 6.0) on marine and R2A agars. Based on 16S rRNA gene phylogeny analysis, the novel strain formed a new branch within the genus Bacillus of the family Bacillaceae, and formed clusters with Bacillus thaohiensis NHI-38^T (96.8%), Bacillus fengqiuensis NPK15^T (96.7%), and Bacillus songklensis CAU 1033^T (96.7%). Lower sequence similarities (97.0%) were found with the type strains of all other recognized members of the genus Bacillus (95.6-96.8% similarity). The G + C content of the genomic DNA was 43.6 mol%. The predominant respiratory quinone was menaquinone-7 and the major fatty acids were iso-C_15:0 and iso-C_17:1ω10c. The overall polar lipid patterns were diphosphatidylglycerol, phosphatidylglycerol, and phosphatidylethanolamine. The diagnostic diamino acid in the cell-wall peptidoglycan was meso-diaminopimelic acid. The isolate therefore represents a novel species, for which the name Bacillus spongiae sp. nov. is proposed, with the type strain 135PIL107-10^T (= KACC 19275^T = LMG 30080^T).

Cistus ladanifer (Cistaceae): a natural resource in Mediterranean-type ecosystems

Cistus ladanifer has a well-defined taxonomic identity. 2,2,6-trimethylcyclohexanone may be an authenticity and taxonomic marker. Its traits and applications make it a possible economic resource fitted for Mediterranean areas. Cistus ladanifer is a dominant shrub species endemic to the western Mediterranean region. Due to its dominant nature and its potential ecological, aromatic or pharmacological applications, C. ladanifer has been the object of numerous studies. In this review current knowledge on different aspects of this species is summarized, from its taxonomy to its chemical characterisation or its competitive traits. There are no doubts about the taxonomic entity of C. ladanifer, although the recognition of infraspecific taxa deserves more attention. Given that the fragrant exudate of C. ladanifer holds a very specific composition, one species specific carotenoid, 2,2,6-trimethylcyclohexanone, derivative is proposed as an authenticity marker for uses of C. ladanifer in pharmacological or aromatic industries. Evidence is also gathered on the extreme adaptation of C. ladanifer to stressful conditions in the Mediterranean region, such as the ability to survive in low hydric and high solar exposition conditions, presistence in poor and contaminated soils, and growth inhibition of several other plants through the release of allelochemicals. Thus, the finding of potential applications for this plant may contribute to enhance the economic dimension of derelict lands, such as mine tailings or poor agricultural Mediterranean areas.