A taxonomic note on the order Caryophanales: description of 12 novel families and emended description of 21 families

The order Caryophanales, belonging to class Bacilli, is globally distributed in various ecosystems. Currently, this order comprised 12 families that show vast phenotypic, ecological and genotypic variation. The classification of Caryophanales at the family level is currently mainly based on 16S rRNA gene sequencing analysis and the presence of shared phenotypic characteristics, resulting in noticeable anomalies. Our present study revises the taxonomy of Caryophanales based on 1080 available high-quality genome sequences of type strains. The evaluated parameters included the core-genome phylogeny, pairwise average aa identity, lineage-specific core genes, physiological criteria and ecological parameters. Based on the results of this polyphasic approach, we propose that the order Caryophanales be reclassified into 41 families, which include the existing 12 families, 17 families in a recent Validation List in the IJSEM (Validation List no. 215) and 12 novel families for which we propose the names Aureibacillaceae, Cytobacillaceae, Domibacillaceae, Falsibacillaceae, Heyndrickxiaceae, Lottiidibacillaceae, Oxalophagaceae, Pradoshiaceae, Rossellomoreaceae, Schinkiaceae, Sulfoacidibacillaceae and Sutcliffiellaceae. This work represents a genomic sequence-based and systematic framework for classifying the order Caryophanales at the family level, providing new insights into its evolution.

Aquibacillus rhizosphaerae sp. nov., an Indole Acetic Acid (IAA)-producing Halotolerant Bacterium Isolated from the Rhizosphere Soil of Kalidium cuspidatum

A bacterium (named strain LR5S19T) was isolated from the rhizosphere soil of the halophyte Kalidium cuspidatum in Baotou, Inner Mongolia, China. Strain LR5S19T was Gram-stain-positive, motile with a polar flagellum, rod shaped, and spore forming at the terminal position in swollen sporangia, and it grew at 10-40 ℃ (optimum 30 ℃), pH 6.0-9.0 (optimum pH 7.0), and in the presence of 1.0-15.0% (w/v) NaCl (optimum 2.0%). The phylogenetic analysis of the 16S rRNA gene showed that strain LR5S19T shared the highest similarity (96.7%) with A. koreensis JCM 12387T, followed by A. kalidii HU2P27T (96.2%), A. sediminis BH258T (96.1%), and 'A. salsiterrae' 3ASR75-54T (96.0%). The ANIb, AAI and dDDH values between strain LR5S19T and its closely related type strains were 69.3-73.8%, 65.4-72.4% and 19.2-20.3%, respectively. The major polar lipids in strain LR5S19T consisted of diphosphatidylglycerol, phosphatidylglycerol, and three unidentified phospholipids, while MK-7 was the major respiratory quinone. The major fatty acids of the strain were anteiso-C15:0 and iso-C15:0. Based on phylogenomic and phenotypic results, strain LR5S19T should be classified as a novel species within the genus Aquibacillus, for which Aquibacillus rhizosphaerae sp. nov. is proposed. The type strain is LR5S19T (= CGMCC 1.62028T = KCTC 43434T). The comparative genomic analysis revealed that all eight members of Aquibacillus could utilize D-glucose via the glycolysis-gluconeogenesis pathway or the pentose phosphate pathway and use the tricarboxylic acid cycle as the metabolic center. The potassium ion transport proteins and compatible solute synthesis pathways in all the members likely also help them cope with hypersaline environments.

A step into the rare biosphere: genomic features of the new genus Terrihalobacillus and the new species Aquibacillus salsiterrae from hypersaline soils

Hypersaline soils are a source of prokaryotic diversity that has been overlooked until very recently. The phylum Bacillota, which includes the genus Aquibacillus, is one of the 26 phyla that inhabit the heavy metal contaminated soils of the Odiel Saltmarshers Natural Area (Southwest Spain), according to previous research. In this study, we isolated a total of 32 strains closely related to the genus Aquibacillus by the traditional dilution-plating technique. Phylogenetic studies clustered them into two groups, and comparative genomic analyses revealed that one of them represents a new species within the genus Aquibacillus, whereas the other cluster constitutes a novel genus of the family Bacillaceae. We propose the designations Aquibacillus salsiterrae sp. nov. and Terrihalobacillus insolitus gen. nov., sp. nov., respectively, for these two new taxa. Genome mining analysis revealed dissimilitude in the metabolic traits of the isolates and their closest related genera, remarkably the distinctive presence of the well-conserved pathway for the biosynthesis of molybdenum cofactor in the species of the genera Aquibacillus and Terrihalobacillus, along with genes that encode molybdoenzymes and molybdate transporters, scarcely found in metagenomic dataset from this area. In-silico studies of the osmoregulatory strategy revealed a salt-out mechanism in the new species, which harbor the genes for biosynthesis and transport of the compatible solutes ectoine and glycine betaine. Comparative genomics showed genes related to heavy metal resistance, which seem required due to the contamination in the sampling area. The low values in the genome recruitment analysis indicate that the new species of the two genera, Terrihalobacillus and Aquibacillus, belong to the rare biosphere of representative hypersaline environments.

Bacillales: From Taxonomy to Biotechnological and Industrial Perspectives

For a long time, the genus Bacillus has been known and considered among the most applicable genera in several fields. Recent taxonomical developments resulted in the identification of more species in Bacillus-related genera, particularly in the order Bacillales (earlier heterotypic synonym: Caryophanales), with potential application for biotechnological and industrial purposes such as biofuels, bioactive agents, biopolymers, and enzymes. Therefore, a thorough understanding of the taxonomy, growth requirements and physiology, genomics, and metabolic pathways in the highly diverse bacterial order, Bacillales, will facilitate a more robust designing and sustainable production of strain lines relevant to a circular economy. This paper is focused principally on less-known genera and their potential in the order Bacillales for promising applications in the industry and addresses the taxonomical complexities of this order. Moreover, it emphasizes the biotechnological usage of some engineered strains of the order Bacillales. The elucidation of novel taxa, their metabolic pathways, and growth conditions would make it possible to drive industrial processes toward an upgraded functionality based on the microbial nature.

Aquibacillus saliphilus sp. nov., a moderately halophilic bacterium isolated from a grey saltern

A novel moderately halophilic bacterium, designated strain KHM2T, was isolated from the sediment of a grey solar saltern located on Sinui Island, Shinan, Republic of Korea. Cells were rod-shaped, endospore-forming, Gram-stain-positive, motile and facultative anaerobic. Strain KHM2T performed anaerobic respiration using nitrates and did not produce glucose acids, indicating the absence of fermentation. Strain KHM2T grew at 10–45 °C (optimum, 37 °C), pH 6.0–10.0 (optimum, pH 8.0) and with 1.0–20.0 % (w/v) NaCl (optimum, 10.0%). Based on 16S rRNA gene sequence similarity and chemotaxonomic properties, strain KHM2T was assigned to the genus Aquibacillus , with high 16S rRNA gene sequence similarity to Aquibacillus halophilus B6BT (98.2%) and less than 96.8 % similarity to the other recognized members of the genus Aquibacillus . The polar lipid profile consisted of diphosphatidylglycerol (DPG), phosphatidylglycerol (PG) and one unidentified phospholipid (PL). Major fatty acids were anteiso-C15 : 0 and anteiso-C17 : 0. The average nucleotide identity and digital DNA–DNA hybridization values of strain KHM2T with A. halophilus B6BT were 77.6 and 22.0 %, respectively. Based on the results of polyphasic analysis, strain KHM2T is proposed to represent a bacterial species within the genus Aquibacillus with the name Aquibacillus saliphilus sp. nov. The type strain is KHM2T (=KACC 19068T=NBRC 112577T)

Diversity of cultivable bacteria from deep-sea sediments of the Colombian Caribbean and their potential in bioremediation

The diversity of deep-sea cultivable bacteria was studied in seven sediment samples of the Colombian Caribbean. Three hundred and fifty two marine bacteria were isolated according to its distinct morphological character on the solid media, then DNA sequences of the 16S rRNA were amplified to identify the isolated strains. The identified bacterial were arranged in three phylogenetic groups, Firmicutes, Proteobacteria, and Actinobacteria, with 34 different OTUs defined at ≥ 97% of similarity and 70 OTUs at ≥ 98.65%, being the 51% Firmicutes, 34% Proteobacteria and 15% Actinobacteria. Bacillus and Fictibacillus were the dominant genera in Firmicutes, Halomonas and Pseudomonas in Proteobacteria and Streptomyces and Micromonospora in Actinobacteria. In addition, the strains were tested for biosurfactants and lipolytic enzymes production, with 120 biosurfactant producing strains (mainly Firmicutes) and, 56 lipolytic enzymes producing strains (Proteobacteria). This report contributes to the understanding of the diversity of the marine deep-sea cultivable bacteria from the Colombian Caribbean, and their potential application as bioremediation agents.

Aquibacillus kalidii sp. nov., an indole acetic acid-producing endophyte from a shoot of Kalidium cuspidatum, and reclassification of Virgibacillus campisalis Lee et al. 2012 as a later heterotypic synonym of Virgibacillus alimentarius Kim et al. 2011

A Gram-stain-positive, strictly aerobic, motile, endospore-forming, milk-white, indole acetic acid-producing, rod-shaped bacterial strain, designated as HU2P27^T, was isolated from a shoot of Kalidium cuspidatum collected in Tumd Right Banner, Inner Mongolia, PR China. Strain grew at 10-40 °C (optimum, 30 °C), at pH 6.0-9.0 (optimum, pH 7.0) and with 0-14.0 % NaCl (optimum, 5.0-8.0 %). The strain tested positive for oxidase, catalase and nitrate reductase. The phylogenetic trees based on the 16S rRNA gene sequence and the core genome both showed that strain HU2P27^T clustered with Aquibacillus koreensis BH30097^T, sharing 97.7 % and <97.0 % of 16S rRNA gene similarity with A. koreensis BH30097^T and any other type strain. Strain HU2P27^T contained MK-7 as the major respiratory quinone. Its major fatty acids were anteiso-C_15 : 0 and iso-C_15 : 0, and the major polar lipids were phosphatidylglycerol, diphosphatidylglycerol and four unidentified phospholipids. The genomic DNA G+C content was 36.0 mol%. The average nucleotide identity, amino acid identity and digital DNA-DNA hybridization values of strain HU2P27^T with A. koreensis BH30097^T were 71.7, 69.2 and 19.4%, respectively. The phylogenetic, physiological and phenotypic results allowed the discrimination of strain HU2P27^T from its phylogenetic relatives. The name Aquibacillus kalidii sp. nov. is therefore proposed. The type strain is strain HU2P27^T (=CGMCC 1.18646^T=KCTC 43248^T). Based on the results of 16S rRNA gene and genome analyses, we propose the reclassification of Virgibacillus campisalis Lee et al. 2012 as a later heterotypic synonym of Virgibacillus alimentarius Kim et al. 2011.

Radiobacillus deserti gen. nov., sp. nov., a UV-resistant bacterium isolated from desert soil

A Gram-stain-positive, aerobic, rod-shaped, non-motile, endospore-forming and UV-resistant bacterial strain, designated strain TKL69^T, was isolated from sandy soil sampled in the Taklimakan Desert. The strain grew at 20-50 °C, pH 6-9 and with 0-12 % (w/v) NaCl. The major fatty acids were anteiso-C_15 : 0, iso-C_15 : 0 and C_16 : 0. The only respiratory quinone was MK-7. The cell-wall peptidoglycan was meso-diaminopimelic acid. Diphosphatidyl glycerol, two unidentified aminophospholipids and one unidentified phospholipid were identified as the major polar lipids. Genomic DNA analysis revealed a G+C content of 38.5 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain TKL69^T has the highest similarity to Salinibacillus xinjiangensis CGMCC 1.12331^T (96.9 %) but belongs to an independent taxon separated from other genera of the family Bacillaceae. Phylogenetic, phenotypic and chemotaxonomic analyses suggested that strain TKL69^T represents a novel species of a new genus, for which the name Radiobacillus gen. nov., sp. nov. is proposed, with the type strain being Radiobacillus deserti TKL69^T (=JCM 33497^T=CICC 24779^T).

Microbial Diversity in an Arid, Naturally Saline Environment

The Arava Valley in is a rock desert within the Great African Rift valley. Soil from this area is covered with a salt crust. Here, we report microbial diversity from arid, naturally saline samples collected near Ein Yahav from the Arava Valley by culture-independent as well as culture-dependent analysis. High-throughput sequencing of the hypervariable region V4 of the 16S rRNA gene revealed that the microbial community consists of halophiles from the domain Bacteria as well as Archaea. Bacterial diversity was mainly represented by the genus Salinimicrobium of the order Flavobacteriales within the phylum Bacteroidetes, from the gammaproteobacterial orders Alteromonadales and Oceanospirillales as well as representatives from the order Bacillales of the phylum Firmicutes. Archaeal diversity was dominated by euryarchaeal Halobacteria from the orders Halobacteriales, Haloferacales, and Natrialbales. But more than 40% of the sequences affiliated with Archaea were assigned to unknown or unclassified archaea. Even if taxonomic resolution of the 16S rRNA gene V4 region for Archaea is limited, this study indicates the need of further and more detailed studies of Archaea. By using culture-dependent analysis, bacteria of the order Bacillales as well as archaea from all three halobacterial orders Halobacteriales, Haloferacales, and Natrialbales including potentially novel species from the genera Halorubrum and Haloparvum were isolated.

Aquibacillus sediminis sp. nov., a moderately halophilic bacterium isolated from saltern soil

A Gram-stain-positive, moderately halophilic bacterium, designated strain BH258^T, was isolated from solar saltern sediment sampled at Shinan in the Republic of Korea. Cells of strain BH258^T were found to be strictly aerobic, motile, endospore-forming rods which could grow at 15-45 °C (optimum, 35 °C), at pH 5.5-9.0 (pH 7.0) and at salinities of 0.5-20 % (w/v) NaCl (7-10%). Phylogenetic analyses based on 16S rRNA gene sequences indicated that strain BH258^T belongs to the genus Aquibacillus, showing highest sequence similarity to Aquibacillus koreensis BH30097^T (96.1 %), Aquibacillus albus YIM 93624^T (95.9 %), Aquibacillus halophilus B6B^T (95.6 %) and Aquibacillus salifodinae WSY08-1^T (95.1 %). The predominant isoprenoid quinone was identified as menaquinone-7, and the cell-wall peptidoglycan was found to contain meso-diaminopimelic acid as the diagnostic diamino acid. The major fatty acids were identified as anteiso-C_15 : 0, iso-C_16 : 0, anteiso-C_17 : 0 and iso-C_15 : 0. The major polar lipids were identified as phosphatidylglycerol, diphosphatidylglycerol and three unidentified phospholipids. The DNA G+C content of this novel isolate was determined to be 37.35 mol%. On the basis of the results of phylogenetic, phenotypic and chemotaxonomic analyses in this study, strain BH258^T is considered to represent a novel species of the genus Aquibacillus, for which the name Aquibacillus sediminis sp. nov. is proposed. The type strain is BH258^T (=KACC 18680^T=NBRC 111875^T).

Insights Into the Microbiology of the Chaotropic Brines of Salar de Atacama, Chile

Microbial life inhabiting hypersaline environments belong to a limited group of extremophile or extremotolerant taxa. Natural or artificial hypersaline environments are not limited to high concentrations of NaCl, and under such conditions, specific adaptation mechanisms are necessary to permit microbial survival and growth. Argentina, Bolivia, and Chile include three large salars (salt flats) which globally, represent the largest lithium reserves, and are commonly referred to as the Lithium Triangle Zone. To date, a large amount of information has been generated regarding chemical, geological, meteorological and economical perspectives of these salars. However, there is a remarkable lack of information regarding the biology of these unique environments. Here, we report the presence of two bacterial strains (isolates LIBR002 and LIBR003) from one of the most hypersaline lithium-dominated man-made environments (total salinity 556 g/L; 11.7 M LiCl) reported to date. Both isolates were classified to the Bacillus genera, but displayed differences in 16S rRNA gene and fatty acid profiles. Our results also revealed that the isolates are lithium-tolerant and that they are phylogenetically differentiated from those Bacillus associated with high NaCl concentration environments, and form a new clade from the Lithium Triangle Zone. To determine osmoadaptation strategies in these microorganisms, both isolates were characterized using morphological, metabolic and physiological attributes. We suggest that our characterization of bacterial isolates from a highly lithium-enriched environment has revealed that even at such extreme salinities with high concentrations of chaotropic solutes, scope for microbial life exists. These conditions have previously been considered to limit the development of life, and our work extends the window of life beyond high concentrations of MgCl2, as previously reported, to LiCl. Our results can be used to further the understanding of salt tolerance, most especially for LiCl-dominated brines, and likely have value as models for the understanding of putative extra-terrestrial (e.g., Martian) life.

Description of Ornithinibacillus gellani sp. nov., a halophilic bacterium isolated from lake sediment, and emended description of the genus Ornithinibacillus

A Gram-stain-positive, strictly aerobic, motile and rod-shaped bacterium, designated strain LJ137^T, was isolated from the sediment of Taihu Lake in China. A polyphasic approach was used to investigate its taxonomic position. Strain LJ137^T grew optimally at pH 7.5, at 37 °C and with 2.5 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain LJ137^T was most closely related to the genera Ornithinibacillus and Oceanobacillus. The closest phylogenetic neighbours were Ornithinibacillus halophilus KCTC 13822^T, Ornithinibacillus salinisoli LCB256^T and Oceanobacillus limi KCTC 13823^T, with 95.2, 96.5 and 95.6 % 16S rRNA gene sequence similarity, respectively. The peptidoglycan amino acid type was A4α (l-Lys-d-Asp). The major respiratory quinone was menaquinone-7 (MK-7). The polar lipids of strain LJ137^T contained diphosphatidylglycerol, phosphatidylglycerol, three unidentified phospholipids, two aminophospholipids and one unidentified lipid. The G+C content of the genomic DNA was 40.4 mol%. The dominant cellular fatty acids were anteiso-C_15 : 0, anteiso-C_17 : 0 and iso-C_15 : 0. Based on the phenotypic, chemotaxonomic, phylogenetic and genome sequence characteristics of this strain, a novel species, Ornithinibacillus gellani sp. nov., is proposed. The type strain is LJ137^T (=CGMCC 1.13678^T=NBRC 113552^T). An emended description of the genus Ornithinibacillus is presented.

Aidingibacillus halophilus gen. nov., sp. nov., a novel member of the family Bacillaceae

A Gram-positive, non-motile, asporogenous and aerobic bacterium, designated YIM 98012^T, was isolated from a salt lake in China. Strain YIM 98012^T was found to be catalase and oxidase positive. Optimal growth of strain YIM 98012^T was observed at 37 °C and pH 7.0 and it was found to grow in the presence of 5-20% (w/v) NaCl (optimum 10% NaCl). Phylogenetic analysis based on the 16S rRNA gene sequence indicated that the novel strain is affiliated with the family Bacillaceae of the phylum Firmicutes and that it shares high (94.7%) sequence similarity with Alteribacillus persepolensis DSM 21632^T and does not show sequence similarities of more than 94.0% to known members of other related genera. The major fatty acids (> 10%) were identified as anteiso-C_15:0, anteiso-C_17:0, iso-C_16:0 and C_16:0. The genomic DNA G+C content was determined to be 41.0 mol% and the dominated respiratory quinone was identified as MK-7. The cell wall peptidoglycan of strain YIM 98012^T was found to contain meso-diaminopimelic acid, while the polar lipids profile was found to include diphosphatidylglycerol, phosphatidylglycerol and phosphatidylcholine. Based on physiological and chemotaxonomic characteristics, strain YIM 98012^T is concluded to be the type strain of the type species of a novel genus in the family Bacillaceae for which the name Aidingibacillus halophilus gen. nov., sp. nov. is proposed. The type strain is YIM 98012^T (= KCTC 33868^T = DSM 104332^T).

Ecology of Bacillaceae

Members of the family Bacillaceae are among the most robust bacteria on Earth, which is mainly due to their ability to form resistant endospores. This trait is believed to be the key factor determining the ecology of these bacteria. However, they also perform fundamental roles in soil ecology (i.e., the cycling of organic matter) and in plant health and growth stimulation (e.g., via suppression of plant pathogens and phosphate solubilization). In this review, we describe the high functional and genetic diversity that is found within the Bacillaceae (a family of low-G+C% Gram-positive spore-forming bacteria), their roles in ecology and in applied sciences related to agriculture. We then pose questions with respect to their ecological behavior, zooming in on the intricate social behavior that is becoming increasingly well characterized for some members of Bacillaceae. Such social behavior, which includes cell-to-cell signaling via quorum sensing or other mechanisms (e.g., the production of extracellular hydrolytic enzymes, toxins, antibiotics and/or surfactants) is a key determinant of their lifestyle and is also believed to drive diversification processes. It is only with a deeper understanding of cell-to-cell interactions that we will be able to understand the ecological and diversification processes of natural populations within the family Bacillaceae. Ultimately, the resulting improvements in understanding will benefit practical efforts to apply representatives of these bacteria in promoting plant growth as well as biological control of plant pathogens.