Lysinibacillus alkaliphilus sp. nov., an extremely alkaliphilic bacterium, and emended description of genus Lysinibacillus

Bacillus pinisoli sp. nov., Isolated from Soil of a Decayed Pine Tree

A Gram-stain-positive, rod-shaped, facultatively anaerobic, motile and spore-forming bacterium with multiple flagella designated GXH0341^T was isolated from the soil associated with decayed pine tree samples collected from Weizhou Island, Beihai, Guangxi, China. Growth occurred at 4-37 °C (optimum 30 °C), at pH 5.0-11.0 (optimum 8.0) and in the presence of 0-7% (w/v) NaCl (optimum 2%). Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain GXH0341^T was most closely related to Bacillus mesophilus DSM 101000 ^T (98.9%), followed by Bacillus salitolerans KC1^T (96.95%) and Margalitia shackletonii DSM 18435 ^T (96.67%). Phylogenetic analysis revealed that strain GXH0341^T represented a separate lineage within the genus Bacillus. Peroxidase is positive. The predominant quinone was MK-7 and the cell-wall diagnostic diamino acid was meso-diaminopimelic acid. The predominant polar lipids are diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, and two unidentified phospholipids. The major fatty acids are iso-C_14:0, iso-C_15:0, anteiso-C_15:0 and iso-C_16:0. The genome of GXH0341^T comprises the biosynthetic gene cluster for T3PKS, terpene, lassopeptide and RRE-containing element as secondary metabolites. The average nucleotide identity values and the digital DNA-DNA hybridization values between GXH0341^T and B. mesophilus DSM 101000 ^T were 78.22% and 21.00%, respectively, which were in the range of the recommended level for interspecies identity. The results of phenotypic, chemotaxonomic and genotypic analyses clearly indicated strain GXH0341^T represents a novel species of the genus Bacillus, for which the name Bacillus pinisoli sp. nov. is proposed. The type strain is GXH0341^T (= MCCC 1K07157^T = JCM 35212 ^T).

Biological selenite removal and recovery of selenium nanoparticles by haloalkaliphilic bacteria isolated from the Nakdong River

Microbial selenite reduction has increasingly attracted attention from the scientific community because it allows the separation of toxic Se from waste sources with the concurrent recovery of Se nanoparticles, a multifunctional material in nanotechnology industries. In this study, four selenite-reducing bacteria, isolated from a river water sample, were found to reduce selenite by > 85% within 3 d of incubation, at ambient temperature. Among them, strain NDSe-7, belonging to genus Lysinibacillus, can reduce selenite and produce Se nanospheres in alkaline conditions, up to pH 10.0, and in salinity of up to 7.0%. This strain can reduce 80 mg/L of selenite to elemental Se within 24 h at pH 6.0-8.0, at a temperature of 30-40 °C, and salinity of 0.1-3.5%. Strain NDSe-7 exhibited potential for use in Se removal and recovery from industrial saline wastewater with high alkalinity. This study indicates that extremophilic microorganisms for environmental remediation can be found in a conventional environment.

Robust Demarcation of the Family Caryophanaceae (Planococcaceae) and Its Different Genera Including Three Novel Genera Based on Phylogenomics and Highly Specific Molecular Signatures

The family Caryophanaceae/Planococcaceae is a taxonomically heterogeneous assemblage of >100 species classified within 13 genera, many of which are polyphyletic. Exhibiting considerable phylogenetic overlap with other families, primarily Bacillaceae, the evolutionary history of this family, containing the potent mosquitocidal species Lysinibacillus sphaericus, remains incoherent. To develop a reliable phylogenetic and taxonomic framework for the family Caryophanaceae/Planococcaceae and its genera, we report comprehensive phylogenetic and comparative genomic analyses on 124 genome sequences from all available Caryophanaceae/Planococcaceae and representative Bacillaceae species. Phylogenetic trees were constructed based on multiple datasets of proteins including 819 core proteins for this group and 87 conserved Firmicutes proteins. Using the core proteins, pairwise average amino acid identity was also determined. In parallel, comparative analyses on protein sequences from these species have identified 92 unique molecular markers (synapomorphies) consisting of conserved signature indels that are specifically shared by either the entire family Caryophanaceae/Planococcaceae or different monophyletic clades present within this family, enabling their reliable demarcation in molecular terms. Based on multiple lines of investigations, 18 monophyletic clades can be reliably distinguished within the family Caryophanaceae/Planococcaceae based on their phylogenetic affinities and identified molecular signatures. Some of these clades are comprised of species from several polyphyletic genera within this family as well as other families. Based on our results, we are proposing the creation of three novel genera within the family Caryophanaceae/Planococcaceae, namely Metalysinibacillus gen. nov., Metasolibacillus gen. nov., and Metaplanococcus gen. nov., as well as the transfer of 25 misclassified species from the families Caryophanaceae/Planococcaceae and Bacillaceae into these three genera and in Planococcus, Solibacillus, Sporosarcina, and Ureibacillus genera. These amendments establish a coherent taxonomy and evolutionary history for the family Caryophanaceae/Planococcaceae, and the described molecular markers provide novel means for diagnostic, genetic, and biochemical studies. Lastly, we are also proposing a consolidation of the family Planococcaceae within the emended family Caryophanaceae.

Isolation and characterization of a novel piezotolerant bacterium Lysinibacillus yapensis sp. nov., from deep-sea sediment of the Yap Trench, Pacific Ocean

A Gram-positive, aerobic, rod-shaped, spore-forming bacterium, designated YLB-03^T, with peritrichous flagella was isolated from deep-sea sediment of the Yap Trench at a depth of 4435 m. The bacterium was found to be catalase-positive but oxidase-negative. Growth of this bacterium was observed at 15-50°C (optimum 37°C), pH 5-10.5 (optimum 7), 0-5% NaCl (optimum 1%, w/v) and 0.1-50 MPa (optimum 0.1 MPa). Phylogenetic analysis based on 16S rRNA gene sequences showed that strain YLB-03^T was a member of the genus Lysinibacillus. Strain YLB-03^T was closely related to Lysinibacillus sinduriensis BLB-1^T and Lysinibacillus chungkukjangi 2RL3-2^T (98.4%), Lysinibacillus halotolerans LAM-612^T (98.0%), Lysinibacillus telephonicus KT735049^T (97.5%), Lysinibacillus endophyticus C9^T (97.5%), Lysinibacillus composti NCCP-36^T and Lysinibacillus massiliensis 4400831^T (97.3%). The ANI and the GGDC DNA-DNA hybridization estimate values between strain YLB-03^T and closely related type strains were 73.7-76.3% and 34.7-38.7%, respectively. The principal fatty acids were anteiso-C_15:0 and iso-C_15:0. The G+C content of the chromosomal DNA was 39.6 mol%. The respiratory quinone was determined to be MK-7. The diagnostic amino acids in the cell wall peptidoglycan contained Lys-Asp (type A4α) and the cell-wall sugars were glucose and xylose. The polar lipids included diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, and an unidentified phospholipid. The combined genotypic and phenotypic data showed that strain YLB-03^T represents a novel species within the genus Lysinibacillus, for which the name Lysinibacillus yapensis sp. nov. is proposed, with the type strain YLB-03^T (= MCCC 1A12698^T = JCM 32871^T).

Description of Lysinibacillus telephonicus sp. nov., isolated from the screen of a cellular phone

A novel bacterial strain, designated S5H2222T, was isolated form the screen of a cellular phone. The cells were Gram-stain-positive, rod-shaped, aerobic and motile, and endospores are formed. S5H2222T grew as pale white colonies on trypticase soy agar and the best growth was observed at 37 °C (10-55 °C) and at pH 7.0 (5.0-9.0). S5H2222T could tolerate up to 10 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences placed this strain within the genus Lysinibacillus and it exhibited high 16S rRNA gene sequence similarity to Lysinibacillus halotolerans LAM612T (97.8 %), Lysinibacillus chungkukjangi 2RL3-2T (97.4 %) and Lysinibacillus sinduriensis BLB-1T (97.2 %). The DNA-DNA relatedness of the strain with L. halotolerans JCM 19611T, L. chungkukjangi KACC 16626T and L. sinduriensis KACC 16611T was 57, 64 and 55 % respectively. The genomic DNA G+C content was 39.8 mol%. The major fatty acids of S5H2222T were iso-C15 : 0, anteiso-C15 : 0, iso-C16 : 0 and anteiso-C17 : 0. MK-7 was the only menaquinone and the main polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine, four unidentified polar lipids were also present. The diagnostic amino acids in the cell wall peptidoglycan contained Lys-Asp (type A4α). On the basis of the results of the phenotypic and genotypic characterizations, it was concluded that S5H2222T represents a novel species of the genus Lysinibacillus, for which the name Lysinibacillus telephonicus sp. nov. is proposed. The type strain is S5H2222T (=MCC 3065T=KACC 18714T=LMG 29294T).

Lysinibacillus endophyticus sp. nov., an indole-3-acetic acid producing endophytic bacterium isolated from corn root (Zea mays cv. Xinken-5)

A Gram-positive, aerobic, motile, rod-shaped bacterium, designated strain C9(T), was isolated from surface sterilised corn roots (Zea mays cv. Xinken-5) and found to be able to produce indole-3-acetic acid. A polyphasic taxonomic study was carried out to determine the status of strain C9(T). The major cellular fatty acids were found to contain iso-C15:0, anteiso-C15:0 and anteiso-C17:0, and the only menaquinone was identified as MK-7. The polar lipid profile was found to contain diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, two unidentified phospholipids and an unidentified lipid. The cell wall peptidoglycan was found to be of the A4α L-Lys-D-Asp type and the whole cell sugar was found to be glucose. Phylogenetic analysis based on the 16S rRNA gene sequence showed that strain C9(T) belongs to the genus Lysinibacillus and is closely related to Lysinibacillus chungkukjangi NBRC 108948(T) (98.1 % similarity) and Lysinibacillus sinduriensis DSM 27595(T) (98.0 %). However, the low levels of DNA-DNA relatedness and some differential phenotypic characteristics allowed the strain to be distinguished from its close relatives. Therefore, it is concluded that strain C9(T) represents a novel species of the genus Lysinibacillus, for which the name Lysinibacillus endophyticus sp. nov. is proposed. The type strain is C9(T) (=DSM 100506(T) = CGMCC 1.15291(T)).

Lysinibacillus xyleni sp. nov., isolated from a bottle of xylene

A Gram-staining-positive, solvent-tolerating (acetophenone, benzene, toluene, xylene and hexane), aerobic, non-motile, terminal endospore-forming, rod-shaped bacterium was isolated from a bottle of xylene. The strain, designated JC22(T), was found to be oxidase and catalase positive. The strain was able to tolerate solvents with different log p values like acetophenone (log P = 1.5), benzene (log P = 2.0), toluene (log P = 2.5), xylene (log P = 3.2) and hexane (log P = 3.4), though it could not use them as sole carbon sources. Based on the 16S rRNA gene sequence analysis, strain JC22(T) was identified as belonging to the genus Lysinibacillus and was most closely related to Lysinibacillus sinduriensis BLB-1(T) (98.1 %), Lysinibacillus halotolerans LAM612(T) (97.8 %), Lysinibacillus chungkukjangi 2RL3-2(T) (97.6 %) and Lysinibacillus xylanilyticus XDB9(T) (97.1 %). The DNA-DNA relatedness of strain JC22(T) with the type strains of closest species was <30 %. Strain JC22(T) grew chemoorganoheterotrophically with an optimal pH of 7-8 (range 6-10) at 35-37 °C (range 25-40 °C). The DNA G+C content was 41.2 mol%. The major cellular fatty acids were iso-C15:0, anteiso-C15:0 and iso-C16:0. Cell wall peptidoglycan type was determined to be A4α (L-Lys-D-Asp). Predominant quinone system was MK-7 with moderate amounts of MK-6, MK-6(H2) and MK-7(H2). Polar lipids of strain JC22(T) contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and an unidentified phospholipid. On the basis of morphological, physiological, genetic, phylogenetic and chemotaxonomical analyses, we conclude that strain JC22(T) be assigned the status of novel species of the genus Lysinibacillus for which the name Lysinibacillus xyleni sp. nov. is proposed. Type strain of the species is JC22(T) (= CCUG 57912(T) = KCTC 13604(T) = NBRC 105753(T) = DSM 23555(T)).