Planomicrobium koreense gen. nov., sp. nov., a bacterium isolated from the Korean traditional fermented seafood jeotgal, and transfer of Planococcus okeanokoites (Nakagawa et al. 1996) and Planococcus mcmeekinii (Junge et al. 1998) to the genus Planomicrobium

Planococcus shenhongbingii sp. nov., Planococcus shixiaomingii sp. nov. and Planococcus liqunii sp. nov., isolated from soil of the Qinghai-Tibet Plateau

Six novel bacterial strains, designated N016T, N017, N022T, N028, N056T, and N064, were isolated from soil sampled on the Qinghai-Tibet Plateau. Cells were aerobic, orange or yellow, globular or rod-shaped, non-motile, non-spore-forming, Gram-stain-positive, catalase-positive and oxidase-negative. All the isolates were salt-tolerant and could grow in the range of 4-42 °C. Results of phylogenomic analyses based on 16S rRNA gene sequences and core genomic genes showed that the three pairs of strains (N016T/N017, N022T/N028, and N056T/N064) were closely related to the members of the genus Planococcus, and clustered with Planococcus ruber, Planococcus glaciei, and Planococcus chinensis. The digital DNA-DNA hybridization and average nucleotide identity values of the six novel strains with other members of the genus Planococcus were within the ranges of 18.7-53 % and 70.58-93.49 %, respectively, all below the respective recommended thresholds of 70.0 % and 95-96 %. The genomic DNA G+C content of the six strains ranged from 43.5 to 46.0 mol%. The major fatty acids of the six strains were anteiso-C15 : 0, iso-C14 : 0, and C16 : 1  ω7c alcohol. The predominant polar lipids of strains N016T, N022T, and N056T were diphosphatidylglycerol, phosphatidylglycerol, and phosphatidylethanolamine. Menaquinones 7 and 8 were the respiratory quinones. The results of the above analyses indicated that the six strains represent three novel species of the genus Planococcus, for which the names Planococcus shenhongbingii sp. nov. (type strain N016T=GDMCC 1.4062T=JCM 36224T), Planococcus shixiaomingii sp. nov. (type strain N022T=GDMCC 1.4063T=JCM 36225T), and Planococcus liqunii sp. nov. (type strain N056T=GDMCC 1.4064T=JCM 36226T) are proposed.

Planococcus notacanthi sp. nov., isolated from the skin of a deep-sea snub-nosed spiny eel

A novel bacterial strain, APC 4016T, was previously isolated from the skin of a snub-nosed spiny eel, Notacanthus chemnitzii, from a depth of 1000 m in the northern Atlantic Ocean. Cells were aerobic, cocci, motile, Gram-positive to Gram-variable staining, and gave rise to orange-pigmented colonies. Growth occurred at 4-40 °C (optimum, 25-28 °C), pH 5.5-12 (optimum, pH 7-7.5), and 0-12 % (w/v) NaCl (optimum, 1 %). 16S rRNA gene phylogenetic analysis confirmed that strain APC 4016T belonged to the genus Planococcus and was most closely related to Planococcus okeanokoites IFO 12536T (98.98 % 16S similarity). However, digital DNA-DNA hybridization and average nucleotide identity values between these two strains were low, at 20.1 and 83.8 %, respectively. Major (>10 %) cellular fatty acids of strain APC 4016T were iso-C14 : 0, anteiso-C15 : 0 and C16 : 1-ω-Alc. The predominant respiratory quinones were menaquinones 5, 6, 7 and 8. The major cellular polar lipids were phosphatidylglycerol, diphosphatidylglycerol and phosphatidylethanolamine, and three unknown lipids were also present. The draft genome sequence is 3.6 Mb with a G+C content of 45.25 mol%. This strain was previously shown to have antimicrobial activity and to encode bacteriocin and secondary metabolite biosynthetic gene clusters. Based on the phylogenetic analysis and its distinct phenotypic characteristics, strain APC 4016T is deemed to represent a novel species of the genus Planococcus, and for which the name Planococcus notacanthi sp. nov. is proposed. The type strain of this species is APC 4016T (=DSM 115753T=NCIMB 15463T).

Two novel Planococcus species isolated from baijiu pit mud with potential application in brewing

Two novel Gram-positive bacteria, designated strains REN8^T and REN14^T, were isolated from baijiu pit mud in Sichuan Province, China. REN8^T achieved the best growth at 37°C, a pH of 8.0, and a NaCl concentration of 2%, while REN14^T displayed optimal growth at 37°C, a pH of 6.0, and a NaCl concentration of 1%. 16S rRNA and genomic phylogenetic analysis showed that REN8^T and REN14^T were clustered with the genus Planococcus. The genomic DNA G + C contents of REN8^T and REN14^T were 46.7 and 45.1 mol%, respectively. The dDDH and ANI values were 24.5 and 80.43% between REN8^T and P. salinarum (the most closely related type strain) and 25.1 and 82.42% between REN14^T and P. soli (the most closely related type strain). Genomic analysis showed that several carbohydrate-active enzymes and secondary metabolite gene clusters existed in REN8^T and REN14^T. Chemotaxonomic characteristics of REN8^T and REN14^T included major fatty acids, predominant menaquinones, and polar lipids, all of which were consistent with the genus Planococcus. Based on the polyphasic taxonomic method, these two strains represent two novel species of the genus Planococcus; the name Planococcus beigongshangi sp. nov. is proposed for the type strain REN8^T (=JCM 33964^T = GDMCC 1.2213^T), and the name Planococcus beijingensis sp. nov. is proposed for the type strain REN14^T (=JCM 34410^T = GDMCC 1.2209^T). The addition of REN8^T and REN14^T might improve the quality of huangjiu by considerably increasing the amino acid nitrogen content and acidity and decreasing the bioamine content, with no significant change in alcohol content.

First report of Planomicrobium okeanokoites associated with Himantothallus grandifolius (Desmarestiales, Phaeophyta) from Southern Hemisphere

Gram-positive, aerobic, motile, rod-shaped, mesophilic epiphytic bacterium Planomicrobium okeanokoites was isolated from the surface of endemic species Himantothallus grandifolius in Larsemann Hills, Eastern Antarctica. The diversity of epiphytic bacterial communities living on marine algae remains primarily unexplored; virtually no reports from Antarctic seaweeds. The present study used morpho-molecular approaches for the macroalgae and epiphytic bacterium characterization. Phylogenetic analysis was performed using mitochondrial genome encoded COX1 gene; chloroplast genome encodes rbcL; nuclear genome encoded large subunit ribosomal RNA gene (LSU rRNA) for Himantothallus grandifolius and ribosomal encoded 16S rRNA for Planomicrobium okeanokoites. Morphological and molecular data revealed that the isolate is identified as Himantothallus grandifolius, which belongs to Family Desmarestiaceae of Order Desmarestiales in Class Phaeophyceae showing 99.8% similarity to the sequences of Himantothallus grandifolius, from King George Island, Antarctica (HE866853). The isolated bacterial strain was identified on the basis of chemotaxonomic, morpho-phylogenetic, and biochemical assays. A phylogenetic study based on 16S rRNA gene sequences revealed that the epiphytic bacterial strain SLA-357 was closest related to the Planomicrobium okeanokoites showing 98.7% sequence similarity. The study revealed the first report of this species from the Southern Hemisphere to date. Also, there has been no report regarding the association between the Planomicrobium okeanokoites and Himantothallus grandifolius; however, there are some reports on this bacterium isolated from sediments, soils, and lakes from Northern Hemisphere. This study may open a gateway for further research to know about the mode of interactions and how they affect the physiology and metabolism of each other.

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.

Transcriptional and biochemical analyses of Planomicrobium strain AX6 from Qinghai-Tibetan Plateau, China, reveal hydrogen peroxide scavenging potential

Background

The bacterial mechanisms responsible for hydrogen peroxide (H₂O₂) scavenging have been well-reported, yet little is known about how bacteria isolated from cold-environments respond to H₂O₂ stress. Therefore, we investigated the transcriptional profiling of the Planomicrobium strain AX6 strain isolated from the cold-desert ecosystem in the Qaidam Basin, Qinghai-Tibet Plateau, China, in response to H₂O₂ stress aiming to uncover the molecular mechanisms associated with H₂O₂ scavenging potential.

Methods

We investigated the H₂O₂-scavenging potential of the bacterial Planomicrobium strain AX6 isolated from the cold-desert ecosystem in the Qaidam Basin, Qinghai-Tibet Plateau, China. Furthermore, we used high-throughput RNA-sequencing to unravel the molecular aspects associated with the H₂O₂ scavenging potential of the Planomicrobium strain AX6 isolate.

Results

In total, 3,427 differentially expressed genes (DEGs) were identified in Planomicrobium strain AX6 isolate in response to 4 h of H₂O₂ (1.5 mM) exposure. Besides, Kyoto Encyclopedia of Genes and Genomes pathway and Gene Ontology analyses revealed the down- and/or up-regulated pathways following H₂O₂ treatment. Our study not only identified the H₂O₂ scavenging capability of the strain nevertheless also a range of mechanisms to cope with the toxic effect of H₂O₂ through genes involved in oxidative stress response. Compared to control, several genes coding for antioxidant proteins, including glutathione peroxidase (GSH-Px), Coproporphyrinogen III oxidase, and superoxide dismutase (SOD), were relatively up-regulated in Planomicrobium strain AX6, when exposed to H₂O₂.

Conclusions

Overall, the results suggest that the up-regulated genes responsible for antioxidant defense pathways serve as essential regulatory mechanisms for removing H₂O₂ in Planomicrobium strain AX6. The DEGs identified here could provide a competitive advantage for the existence of Planomicrobium strain AX6 in H₂O₂-polluted environments.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12866-022-02677-w.

The first case of Planococcus glaciei found in blood, a report from the Czech Republic

The isolation of Planococcus glaciei (designed strain CNCTC 7660) from blood of a patient with appendicitis is reported. Species P. glaciei (type strain CGMCC 1.6846 ^T) was for the first time identified as an environmental bacterium acquired from a glacier in China in 2009. To reveal the identity of the isolate CNCTC 7660, the 16S rDNA sequencing and the whole genome sequencing (Illumina MiSeq, Oxford Nanopore) were performed. The level of 16S rDNA gene sequencing similarity between CNCTC 7660 and CGMCC 1.6846 ^T was 99.55%. Phylogenetic analysis and average nucleotide analysis (ANI) based on the whole genome sequencing confirmed that the isolate CNCTC 7660 and CGMCC1.6846 ^T had ANI value above the taxonomic threshold for belonging to the same species (95%). The G + C content of CNCTC 7660 DNA was 46.8% (mol/mol). Except for the growth temperature, strains CGMCC1.6846 ^T and CNCTC 7660 were distinguished also biochemically. Due to the lack of information about the pathogenicity of P. glaciei, the possibility that it exerts pathogenicity in persons is suggested. But for understanding the nature of this species, further cases are needed.

Planococcus soli sp. nov., isolated from antarctic soil

A novel bacterial strain, designated C23^T, was isolated from a soil sample obtained from King George Island, Antarctica. Phenotypic, phylogenetic, chemotaxonomic and molecular analyses were performed on the new isolate. Strain C23^T formed orange colonies on agar plates and was Gram-stain-positive. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain C23^T was a member of the genus Planococcus and was closely related to Planococcus salinarum DSM 23802^T (98.5% sequence similarity), Planococcus halotolerans SCU63^T (98.3%), Planomicrobium okeanokoites IFO 12526^T (98.3%), Planococcus donghaensis DSM 22276^T (98.3%) and Planococcus maitriensisi S1^T (98.2%). This organism grew at 2-38 °C (optimum, 25-30 °C), pH 6.0-12.0 (optimum, pH 7.5) and 0-14% (w/v) NaCl (optimum, 2%). The predominant menaquinone was MK-8. The major cellular fatty acids were anteiso-C_15:0, iso-C_14:0 and C_16:1 ω7c alcohol. The whole genome DNA of C23^T was deposited in the GenBank database under accession number WXYN00000000. According to the whole genome, the DNA G + C content of strain C23^T was determined to be 46.8 mol%; the average nucleotide identity (ANI) of strain C23^T and P. salinarum DSM 23802^T, P. halotolerans SCU63^T, P. okeanokoites IFO 12526^T, P. donghaensis DSM 22276^T and P. maitriensis S1^T were 74.1%, 74.3%, 74.1%, 78.8 and 73.6%; the digital DNA-DNA hybridization (dDDH) values between strain C23^T and the five closely related species were 19.7%, 19.6%, 19.5%, 22.4 and 18.6%; the average amino acid identity (AAI) values between strain C23^T and the five closely related species were 73.9%, 74.5%, 74.4%, 84.6 and 74.5%. All data were below the threshold range for species determination. Based on the polyphasic taxonomic study, we considered that strain C23^T represented a novel species of the genus Planococcus for which the name Planococcus soli sp. nov. is proposed. The type strain is C23^T (= KCTC 33644^T = CGMCC 1.15115^T).

Characteristics of Planococcus antioxidans sp. nov., an antioxidant-producing strain isolated from the desert soil in the Qinghai-Tibetan Plateau

Strain Y74^T was an isolate from the sandy soil in the town of Huatugou, Qinghai-Tibet Plateau, China. An analysis of this strain's phenotypic, chemotaxonomic, and genomic characteristics established the relationship of the isolate with the genus Planococcus. Strain Y74^T was able to grow between 4 and 42°C (with an optimum temperature of 28°C) at pH values of 6-8.5 and in 0%-7% (w/v) NaCl. The dominant quinones were MK-8 and MK-7. The polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, and an unknown phospholipid. The majority of the fatty acid content was anteiso-C_15:0 (28.8%) followed by C_16:1 ω7c alcohol (20.9%) and iso-C_14:0 (13.4%). The 16S rRNA gene sequence similarity analysis demonstrated a stable branch formed by strain Y74^T and Planococcus halotolerans SCU63^T (99.66%). The digital DNA-DNA hybridization between these two strains was 57.2%. The G + C content in the DNA of Y74^T was 44.5 mol%. In addition, the morphological, physiological, and chemotaxonomic pattern clearly differentiated the isolates from their known relatives. In conclusion, the strain Y74^T (=JCM 32826^T  = CICC24461^T ) represents a novel member of the genus Planococcus, for which the name Planococcus antioxidans sp. nov. is proposed. Strain Y74^T was found to have potent antioxidant activity via its hydrogen peroxide tolerance and its 1,1-diphenyl-2-picrylhydrazyl (DPPH) radical-scavenging activity. The DPPH radical-scavenging activity was determined to be 40.2 ± 0.7%. The genomic analysis indicated that six peroxidases genes, one superoxide dismutase gene, and one dprA (DNA-protecting protein) are present in the genome of Y74^T .

Planococcus lenghuensis sp. nov., an oil-degrading bacterium isolated from petroleum-contaminated soil

A Gram-staining-positive and aerobic coccus with the ability to degrade petroleum bacterium, designated Y42^T, was isolated from the Lenghu oil field located in the northern margin of the Qaidam Basin. Phylogenetic and signature nucleotides analyses revealed that strain Y42^T belongs to the genus Planococcus. The multiple sequence alignments of 16S rRNA and housekeeping genes showed that strain Y42^T formed a distinct lineage with the other Planococcus clade. The average nucleotide identity (ANI) and DNA-DNA hybridization values (DDH) between strain Y42^T and the reference strains were 69.5-70.1 and 19.4-21.7%, respectively, which values were below the threshold for species delineation. The major fatty acids of strain Y42^T were anteiso-C_15:0. The respiratory quinone was MK-7 (71.8%) as the predominant menaquinone followed the MK-6 (28.2%) and the cell-wall hydrolysates contained LL-diaminopimelic acid. The polar lipid was composed of diphosphatidyl glycerol, phosphatidyl glycerol, phosphoglycolipid, aminophospholipid and four unidentified lipids. The peptidoglycan type was A4α (L-Lys-D-Glu). The strain Y42^T possessed larger genome (approximately 4 MB) and revealed obvious differences for the abundance of the COG categories compared with the other Planococcus bacteria. Also, the strain Y42^T also possessed more unique orthologous proteins. The structural characteristics of the strain Y42^T genome provided a competitive advantage for better survival in petroleum-polluted environments. Combined with the 16S rRNA gene and genome sequence, phenotypic as well as chemotaxonomic characterisations, strain Y42^T is considered to represent a novel species of the genus Planococcus, for which the name Planococcus lenghuensis sp. nov. be proposed. The type strain is Y42^T (= CGMCC 1.15921^T = JCM 32719^T).

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.

Indiicoccus explosivorum gen. nov., sp. nov., isolated from an explosives waste contaminated site

A pink-pigmented, Gram-stain-positive, aerobic, coccoid-shaped bacterial strain, designated as S5-TSA-19^T, was isolated from an explosives contaminated site in Panchkula, Haryana, India. The 16S rRNA gene sequencing blast analysis indicated that the strain is a member of the family Planococcaceae with the highest sequence similarity to Planomicrobium soli XN13^T (96.1 %), followed by Planococcus maitriensis S1^T (95.6 %), Planococcus plakortidis DSM 23997^T (95.6 %), Planomicrobium flavidum ISL-41^T (95.6 %), Planococcus rifietoensis M8^T (95.5 %), Planococcus salinus LCB217^T (95.5 %) and Planococcus maritimus DSM 17275^T (95.5 %). Phylogenetic analysis based on 16S rRNA gene and whole-genome sequences (based on a conserved set of 400 proteins) retrieved the strain in a distinct branch indicating a separate lineage within the family Planococcaceae. Strain S5-TSA-19^T had a distinctive chemotaxonomic pattern comprising A4α type peptidoglycan based on l-Lys-d-Asp, iso-C15 : 0 as the major fatty acid, absence of phosphatidylethanolamine as a major lipid and MK-7 and MK-6 as the major menaquinones, differentiating it from the genera Planococcus and Planomicrobium, thus supporting the findings of molecular phylogeny. Further, strain S5-TSA-19^T was able to biotransform hexahydro-1,3,5,-trinitro-1,2,5-triazine (RDX) into nitrite derivatives under aerobic conditions in 2-4 days, whereas the closest reference strains did not possess this property. On the basis of polyphasic taxonomic characterization and a phylogenomics approach, strain S5-TSA-19^T is proposed as the type strain of a novel species in a novel genus for which the name Indiicoccus explosivorum gen. nov., sp. nov. is proposed (=JCM 31737^T=KCTC 33871^T=MTCC 12608^T).

Planomicrobium iranicum sp. nov., a novel slightly halophilic bacterium isolated from a hypersaline wetland

A novel strain, designated as MX6^T was isolated from Meighan wetland, in the centre of Iran. The cells were Gram-stain-positive, motile, coccoid to rod-shaped, oxidase- and catalase-positive. The strain grew optimally at 35 °C, 3 % (w/v) NaCl and pH 7-7.5. A polyphasic taxonomic study was undertaken in order to characterize the strain in detail. The results of phylogenetic analysis based on 16S rRNA gene sequences indicated that MX6^T represented a member of the phylum Firmicutes, family Planococcaceae, genus Planomicrobium, and showed the highest similarity with Planomicrobium flavidum ISL-41^T (98.2 %) and Planomicrobium psychrophilum CMC 53or^T (98.0 %). The main polar lipids of MX6^T consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and seven unidentified phospholipids and its DNA G+C content was 45.5 mol%. Major cellular fatty acids were anteiso-C15 : 0, C16 : 1ω7c alcohol, iso-C14 : 0, iso-C15 : 0 and iso-C16 : 0 and the predominant respiratory quinone was Q-8 (62 %). Experimental DNA-DNA hybridization between MX6^T and Planomicrobium flavidum IBRC-M 11047^T was 20 %, supporting the differential taxonomic status of MX6^T as representing a different taxon. All these data indicate that MX6^T represents a novel species of the genus Planomicrobium, for which the name Planomicrobium iranicum sp. nov. is proposed. The type strain is MX6^T (=IBRC M 10928^T=LMG 28548^T).

Aerobic biodegradation of HMX by Planomicrobium flavidum

In this report, aerobic biodegradation of octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine or high melting explosive (HMX), a highly explosive chemical by Planomicrobium flavidum strain S5-TSA-19, an isolate from an explosive-contaminated soil, was investigated. The isolate S5-TSA-19 degraded 70% of HMX in 20 days during which time nitrite ion was produced with the subsequent formation of metabolites, viz. methylenedintramine and N-methyl-N,N'-dinitromethanediamine with molecular weights 136 Da and 149 Da, respectively. The degradation mechanism was found to follow first-order kinetics with a half-life of 11.55 days and formation of above intermediates indicate single nitrite elimination pathway. The proliferation of isolate S5-TSA-19 in the absence of nitramines indicates the cometabolic degradation of HMX. Isolate S5-TSA-19 can thus be used as futuristic microbe for degradation of HMX at explosive-contaminated site.

Planococcus halotolerans sp. nov., isolated from a saline soil sample in China

A novel Gram-stain-positive, coccoid or short rod-shaped, moderate-orange-pigmented, halotolerant and psychrotolerant bacterium, designated strain SCU63^T, was isolated from a saline soil sample in China, and characterized by a polyphasic taxonomic approach. 16S rRNA gene sequence similarity of strain SCU63^T to species in the genera Planococcus and Planomicrobium ranged from 96.5 to 98.6 %. Phylogenetic trees as well as diagnostic signature nucleotides in the 16S rRNA gene sequence supported the view that this strain should be assigned to the genus Planococcus. Further, average nucleotide identity and digital DNA-DNA hybridization analyses confirmed the separate species status of strain SCU63^T relative to the closely related taxa. The isolate grew at 0-40 °C (optimum, 30-35 °C), at pH 6.5-9.0 (pH 7.0-7.5) and in the presence of 0-15 % (w/v) NaCl (3 %). The principal fatty acids were anteiso-C15 : 0, C16 : 1ω7c alcohol, iso-C16 : 0 and iso-C14 : 0, and the dominant isoprenoid quinones were MK-8 and MK-7. The peptidoglycan type was determined to be A4α (l-Lys-d-Glu), and the polar lipids contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, one unidentified aminophospholipid and one unidentified lipid. The DNA G+C content was 44.6 mol%. Based on the genotypic, phenotypic and chemotaxonomic data, strain SCU63^T can be classified as a novel species in the genus Planococcus, for which the name Planococcushalotolerans sp. nov. is proposed. The type strain is SCU63^T (=CGMCC 1.13628^T=KCTC 43001^T).

Taxonomic hierarchy of the phylum Firmicutes and novel Firmicutes species originated from various environments in Korea

This study assessed the taxonomic hierarchy of the phylum Firmicutes as well as elucidated the isolation and classification states of novel Firmicutes species isolated from Korean territory. The hierarchical classification system of the phylum Firmicutes has been developed since 1872 when the genus Bacillus was first reported and has been generally adopted since 2001. However, this taxonomic hierarchy is still being modified. Until Feb. 2017, the phylum Firmicutes consisted of seven classes (Bacilli, Clostridia, Erysipelotrichia, Limnochordia, Negativicutes, Thermolithobacteria, and Tissierellia), 13 orders, 45 families, and 421 genera. Firmicutes species isolated from various environments in Korea have been reported from 2000, and 187 species have been approved as of Feb. 2017. All Firmicutes species were affiliated with three classes (Bacilli, Clostridia, and Erysipelotrichia), four orders (Bacillales, Lactobacillales, Clostridiales, and Erysipelotrichales), 17 families, and 54 genera. A total of 173 species belong to the class Bacilli, of which 151 species were affiliated with the order Bacillales and the remaining 22 species with the order Lactobacillales. Twelve species belonging to the class Clostridia were affiliated within only one order, Clostridiales. The most abundant family was Bacillaceae (67 species), followed by the family Paenibacillaceae (56 species). Thirteen novel genera were created using isolates from the Korean environment. A number of Firmicutes species were isolated from natural environments in Korean territory. In addition, a considerable number of species were isolated from artificial resources such as fermented foods. Most Firmicutes species, belonging to the families Bacillaceae, Planococcaceae, and Staphylococcaceae, isolated from Korean fermented foods and solar salterns were halophilic or halotolerant. Firmicutes species were isolated from the whole territory of Korea, especially large numbers from Provinces Gyeonggi, Chungnam, and Daejeon.

Emended description of the family Chromatiaceae, phylogenetic analyses of the genera Alishewanella, Rheinheimera and Arsukibacterium, transfer of Rheinheimera longhuensis LH2-2T to the genus Alishewanella and description of Alishewanella alkalitolerans sp. nov. from Lonar Lake, India

Phylogenetic analyses were performed for members of the family Chromatiaceae, signature nucleotides deduced and the genus Alishewanella transferred to Chromatiaceae. Phylogenetic analyses were executed for the genera Alishewanella, Arsukibacterium and Rheinheimera and the genus Rheinheimera is proposed to be split, with the creation of the Pararheinheimera gen. nov. Furthermore, the species Rheinheimera longhuensis, is transferred to the genus Alishewanella as Alishewanella longhuensis comb. nov. Besides, the genera Alishewanella and Rheinheimera are also emended. Strain LNK-7.1^T was isolated from a water sample from the Lonar Lake, India. Cells were Gram-negative, motile rods, positive for catalase, oxidase, phosphatase, contained C_16:0, C_17:1ω8c, summed feature3 (C_16:1ω6c and/or C_16:1ω7c) and summed feature 8 (C_18:1ω7c) as major fatty acids, PE and PG as the major lipids and Q-8 as the sole respiratory quinone. Phylogenetic analyses using NJ, ME, ML and Maximum parsimony, based on 16S rRNA gene sequences, identified Alishewanella tabrizica RCRI4^T as the closely related species of strain LNK-7.1^T with a 16S rRNA gene sequence similarity of 98.13%. The DNA-DNA similarity between LNK-7.1^T and the closely related species (A. tabrizica) was only 12.0% and, therefore, strain LNK-7.1^T was identified as a novel species of the genus Alishewanella with the proposed name Alishewanella alkalitolerans sp. nov. In addition phenotypic characteristics confirmed the species status to strain LNK-7.1^T. The type strain of A. alkalitolerans is LNK-7.1^T (LMG 29592^T = KCTC 52279^T), isolated from a water sample collected from the Lonar lake, India.

Molecular diversity and multifarious plant growth promoting attributes of Bacilli associated with wheat (Triticum aestivum L.) rhizosphere from six diverse agro-ecological zones of India

The diversity of culturable Bacilli was investigated in six wheat cultivating agro-ecological zones of India viz: northern hills, north western plains, north eastern plains, central, peninsular, and southern hills. These agro-ecological regions are based on the climatic conditions such as pH, salinity, drought, and temperature. A total of 395 Bacilli were isolated by heat enrichment and different growth media. Amplified ribosomal DNA restriction analysis using three restriction enzymes AluI, MspI, and HaeIII led to the clustering of these isolates into 19-27 clusters in the different zones at >70% similarity index, adding up to 137 groups. Phylogenetic analysis based on 16S rRNA gene sequencing led to the identification of 55 distinct Bacilli that could be grouped in five families, Bacillaceae (68%), Paenibacillaceae (15%), Planococcaceae (8%), Staphylococcaceae (7%), and Bacillales incertae sedis (2%), which included eight genera namely Bacillus, Exiguobacterium, Lysinibacillus, Paenibacillus, Planococcus, Planomicrobium, Sporosarcina, and Staphylococcus. All 395 isolated Bacilli were screened for their plant growth promoting attributes, which included direct-plant growth promoting (solubilization of phosphorus, potassium, and zinc; production of phytohormones; 1-aminocyclopropane-1-carboxylate deaminase activity and nitrogen fixation), and indirect-plant growth promotion (antagonistic, production of lytic enzymes, siderophore, hydrogen cyanide, and ammonia). To our knowledge, this is the first report for the presence of Bacillus endophyticus, Paenibacillus xylanexedens, Planococcus citreus, Planomicrobium okeanokoites, Sporosarcina sp., and Staphylococcus succinus in wheat rhizosphere and exhibit multifunctional PGP attributes. These niche-specific and multifarious PGP Bacilli may serve as inoculants for crops growing in respective climatic conditions.

Aureibacillus halotolerans gen. nov., sp. nov., isolated from marine sediment

A Gram-staining-positive, strictly aerobic, spore-forming and rod-shaped motile bacterium with peritrichous flagellae, designated strain S1203T, was isolated from the sediment of the northern Okinawa Trough. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain S1203T formed a lineage within the family Bacillaceae that was distinct from the most closely related genera Bacillus, Bhargavaea, Planomicrobium and Virgibacillus with gene sequence similarities ranging from 86.2 to 93.76 %. Optimal growth occurred in the presence of 4-8 % (w/v) NaCl, at pH 7.0-8.0 and 25-32 °C. The cell-wall peptidoglycan was based on meso-diaminopimelic acid and unsaturated menaquinone with seven isoprene units (MK-7) as the predominant respiratory quinone. The major fatty acids (>10 % of total fatty acids) were anteiso-C15 : 0, iso-C15 : 0 and C16 : 0.The major polar lipids were phosphatidylglycerol, diphosphatidylglycerol, an unidentified glycolipid and an unidentified phospholipid. The DNA G+C content of strain S1203T was 47.7 mol%. On the basis of polyphasic analysis, strainS1203T was considered to represent a novel species in a new genus of the family Bacillaceae, for which the name Aureibacillus halotolerans gen. nov., sp. nov. is proposed; the type strain of Aureibacillus halotolerans is S1203T ( = DSM 28697T = JCM 30067T = MCCC 1K00259T).

Draft Genome Sequence of Planomicrobium glaciei UCD-HAM (Phylum Firmicutes)

Here, we present the draft genome of Planomicrobium glaciei, a member of the phylum Firmicutes, found at the University of California Davis. Paired-end, 300-bp reads were generated on an Illumina MiSeq. The assembly consists of 3,925,122 bp, contained in 109 contigs, with a G+C content of 46.7%.

Planococcus faecalis sp. nov., a carotenoid-producing species isolated from stools of Antarctic penguins

Taxonomic studies were performed on a novel carotenoid-producing strain, designated AJ003T, isolated from faeces of Antarctic penguins. Cells of strain AJ003T were aerobic, Gram-stain-positive, cocci-shaped and orange. Strain AJ003T was capable of growing in a broad temperature range, including sub-zero growth (below − 20 to 30 °C). 16S rRNA gene sequence analysis revealed that strain AJ003T was closely related to Planococcus halocryophilus Or1T (97.4 % similarity), Planococcus antarcticus DSM 14505T (97.3 %), Planococcus kocurii NCIMB 629T (97.3 %), and Planococcus donghaensis JH1T (97.1 %). The predominant cellular fatty acids were anteiso-C15 : 0, and iso-C16 : 0.MK-7 and MK-8 were the quinones identified, and the major pigment was glycosyl-4,4′-diaponeurosporen-4′-ol-4-oic acid. The major polar lipid was phosphatidylglycerol. DNA–DNA relatedness of strain AJ003T with respect to its closest phylogenetic neighbours was 38.2 ± 0.5 % for Planococcus halocryophilus DSM 24743T, 32.2 ± 0.2 % for Planococcus antarcticus DSM 14505T, 21.0 ± 0.3 % for Planococcus kocurii DSM 20747T and 18.6 ± 1.4 % for Planococcus donghaensis KCTC 13050T. The DNA G+C content of strain AJ003T was 40.0 ± 0.6 mol%. Based on the phenotypic, chemotaxonomic and phylogenetic data, strain AJ003T is concluded to represent a novel species of the genus Planococcus, for which the name Planococcus faecalis sp. nov. is proposed. The type strain is AJ003T ( = KCTC 33580T = CECT 8759T).

Planomicrobium soli sp. nov., isolated from soil

A Gram-staining-positive bacterium, designated strain XN13T, was isolated from a soil sample collected from ALaShan National Geological Park in Inner Mongolia Autonomous Region, China and subjected to a taxonomic study using a polyphasic approach. Strain XN13T was found to have a range of chemical and morphological properties consistent with its classification in the genus Planomicrobium . Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain XN13T was related to members of the genus Planomicrobium . The closest phylogenetic relatives were Planomicrobium okeanokoites NBRC 12536T, Planomicrobium koreense JG07T, Planomicrobium mcmeekinii S23F2T and Planomicrobium flavidum ISL-41T with 98.2 %, 97.8 %, 97.8 % and 97.7 % 16S rRNA gene sequence similarity, respectively. The major cellular fatty acids were anteiso-C15 : 0, C16 : 1ω7c alcohol, iso-C14 : 0 and C16 : 1ω11c. The predominant menaquinones were MK-8 and MK-7. The DNA G+C content was 40.3 mol%. The DNA–DNA relatedness values between strain XN13T and Planomicrobium okeanokoites KCTC 3672T, Planomicrobium koreense KCTC 3684T, P. mcmeekinii CGMCC 1.2724T, Planomicrobium flavidum KCTC 13261T, Planomicrobium chinense CGMCC 1.3454T and Planomicrobium glaciei CGMCC 1.6846T were 36 %, 30 %, 34 %, 29 %, 30 % and 31 %, respectively. The organism is different from recognized species of the genus Planomicrobium in several phenotypic characteristics. On the basis of phenotypic and genotypic properties, strain XN13T represents a novel species of the genus Planomicrobium , for which the name Planomicrobium soli sp. nov. is proposed. The type strain is XN13T ( = CGMCC 1.12259T = KCTC 33047T).

A primary assessment of the endophytic bacterial community in a xerophilous moss (Grimmia montana) using molecular method and cultivated isolates

Investigating the endophytic bacterial community in special moss species is fundamental to understanding the microbial-plant interactions and discovering the bacteria with stresses tolerance. Thus, the community structure of endophytic bacteria in the xerophilous moss Grimmia montana were estimated using a 16S rDNA library and traditional cultivation methods. In total, 212 sequences derived from the 16S rDNA library were used to assess the bacterial diversity. Sequence alignment showed that the endophytes were assigned to 54 genera in 4 phyla (Proteobacteria, Firmicutes, Actinobacteria and Cytophaga/Flexibacter/Bacteroids). Of them, the dominant phyla were Proteobacteria (45.9%) and Firmicutes (27.6%), the most abundant genera included Acinetobacter, Aeromonas, Enterobacter, Leclercia, Microvirga, Pseudomonas, Rhizobium, Planococcus, Paenisporosarcina and Planomicrobium. In addition, a total of 14 species belonging to 8 genera in 3 phyla (Proteobacteria, Firmicutes, Actinobacteria) were isolated, Curtobacterium, Massilia, Pseudomonas and Sphingomonas were the dominant genera. Although some of the genera isolated were inconsistent with those detected by molecular method, both of two methods proved that many different endophytic bacteria coexist in G. montana. According to the potential functional analyses of these bacteria, some species are known to have possible beneficial effects on hosts, but whether this is the case in G. montana needs to be confirmed.

Purification and Characterization of a Protease Produced by a Planomicrobium sp. L-2 from Gut of Octopus vulgaris

Protease widely exists in the digestive tract of animals and humans, playing a very important role in protein digestion and absorption. In this study, a high protease-producing strain Planomicrobium sp. L-2 was isolated and identified from the digestive tract of Octopus variabilis. The strain was identified by physiological and biochemical experiments and 16S rDNA sequences analysis. A protease was obtained from the strain Planomicrobium sp. L-2 through ammonium sulfate precipitation, dialysis and enrichment, DEAE-Sephadex A50 anion-exchange chromatography, and Sephadex G-100 gel chromatography. The molecular weight and properties of the protease were characterized, including optimum temperature and pH, thermal stability, protease inhibitions and metal ions. According to our results, the protease from Planomicrobium sp. L-2 strain designated as F1-1 was obtained by three-step separation and purification from crude enzyme. The molecular weight of the protease was 61.4 kDa and its optimum temperature was 40°C. The protease F1-1 showed a broad pH profile for casein hydrolysis between 5.0~11.0. No residual activity was observed after incubation for 40 min at 60°C and 60 min at 50°C. F1-1 protease was inhibited by Mn²⁺, Hg²⁺, Pb²⁺, Zn²⁺, and Cu²⁺ ions, as well as PMSF, indicating that the protease F1-1 was a serine protease. Additionally, research basis provided by this study could be considered for industrial application of octopus intestinal proteases.

Domibacillus robiginosus gen. nov., sp. nov., isolated from a pharmaceutical clean room

A novel red-pigmented bacterial strain, designated WS 4628T, was isolated from a pharmaceutical clean room of a vaccine-producing company and was investigated in a taxonomic study using a polyphasic approach. The strain was Gram-stain-positive, strictly aerobic, motile, catalase-positive and produced spherical to slightly ellipsoidal endospores in rods. The genomic DNA G+C content was 44.1 mol%. The major fatty acids were anteiso-C15 : 0, iso-C15 : 0 and anteiso-C17 : 0 and the predominant quinone was MK-6. The polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol, an unidentified phosphoglycolipid and an unidentified phospholipid. meso-diaminopimelic acid (type A1γ) was present in the cell-wall peptidoglycan and the major whole-cell sugars were glucose and ribose. The closest phylogenetic neighbours were identified as Bacillus badius ATCC 14574T (95.8 % 16S rRNA gene sequence similarity), Bacillus indicus Sd/3T (94.8 %), Jeotgalibacillus alimentarius YKJ-13T (94.8 %) and Bacillus cibi JG-30T (94.8 %). Phylogenetic, physiological, biochemical and morphological differences between strain WS 4628T and its closest relatives in the families Bacillaceae and Planococcaceae suggest that this strain represents a novel species in a new genus in the family Bacillaceae for which the name Domibacillus robiginosus gen. nov., sp. nov. is proposed; the type strain of the type species is WS 4628T ( = DSM 25058T = LMG 26645T).

Planococcus halocryophilus sp. nov., an extreme sub-zero species from high Arctic permafrost

A novel aerobic, Gram-positive, motile, coccoid bacterial strain, designated Or1T, was isolated from permafrost active-layer soil collected from the Canadian high Arctic. Strain Or1T was capable of growth over a broad temperature range, including sub-zero growth (below −10 to 37 °C), and at high salinity (0–19 % NaCl), growing optimally at 25 °C, at pH 7.0–8.0 and in the presence of 2 % NaCl. Its taxonomic and phylogenetic position was determined by using a polyphasic approach, which indicated that strain Or1T was a member of the genus Planococcus . Phylogenetic analysis based on 16S rRNA gene sequences showed that strain Or1T belonged to the genus Planococcus , differing by 0.4–3.6 % from the type strains of all recognized Planococcus species, and was related most closely to Planococcus antarcticus CMS 26orT (98.8 % similarity) and Planococcus donghaensis JH1T (99.6 %). However, DNA–DNA hybridization experiments showed that strain Or1T had low genomic relatedness to Planococcus antarcticus CMS 26orT (18 %) and Planococcus donghaensis JH1T (46 %). The major menaquinones of strain Or1T were MK-7 (55 %), MK-8 (36 %) and MK-6 (9 %) and the major fatty acids were anteiso-C15 : 0, C16 : 1ω7c alcohol and anteiso-C17 : 0. The DNA G+C content of strain Or1T was 40.5 mol%. Differential phenotypic, phylogenetic and genomic data suggest that strain Or1T represents a novel species of the genus Planococcus , for which the name Planococcus halocryophilus sp. nov. is proposed. The type strain is Or1T ( = DSM 24743T = JCM 17719T).

Chryseomicrobium imtechense gen. nov., sp. nov., a new member of the family Planococcaceae

A Gram-stain-positive, rod-shaped, yellow, non-motile, non-spore-forming, strictly aerobic bacterial strain, designated MW 10(T), was isolated from seawater of the Bay of Bengal, India, and was subjected to a polyphasic taxonomic study. Analysis of the 16S rRNA gene sequence revealed that strain MW 10(T) showed highest similarity to the type strains of Psychrobacillus psychrodurans (96.15 %) and Psychrobacillus psychrotolerans (96.01 %) and showed less than 96 % similarity to members of the genera Paenisporosarcina, Planococcus, Sporosarcina and Planomicrobium. Phylogenetic analysis based on the 16S rRNA gene sequence showed that strain MW 10(T) formed a clade separate from members of closely related genera. The morphological, physiological and chemotaxonomic characteristics of strain MW 10(T) differed from those of members of closely related genera. The major fatty acid in strain MW 10(T) was iso-C(15 : 0) and the menaquinones were MK-7 (48.4 %), MK-8 (32.3 %), MK-7(H(2)) (13.7 %) and MK-6 (5.6 %). The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, an unknown phospholipid, an unknown lipid and an unknown glycolipid. The cell-wall peptidoglycan type was l-Lys-d-Asp. The genomic DNA G+C content (53.4 mol%) of strain MW 10(T) was significantly different from those of members of closely related genera. On the basis of its morphological, physiological and chemotaxonomic characteristics as well as our phylogenetic analysis, we conclude that strain MW 10(T) is a member of a novel genus and species, for which the name Chryseomicrobium imtechense gen. nov., sp. nov., is proposed. The type strain of Chryseomicrobium imtechense is MW 10(T) ( = MTCC 10098(T)  = JCM 16573(T)).

Phylogenetic relationships between Bacillus species and related genera inferred from 16s rDNA sequences

Neighbor-joining, maximum-parsimony, minimum-evolution, maximum-likelihood and Bayesian trees constructed based on 16S rDNA sequences of 181 type strains of Bacillus species and related taxa manifested nine phylogenetic groups. The phylogenetic analysis showed that Bacillus was not a monophyletic group. B. subtilis was in Group 1. Group 4, 6 and 8 respectively consisted of thermophiles, halophilic or halotolerant bacilli and alkaliphilic bacilli. Group 2, 4 and 8 consisting of Bacillus species and related genera demonstrated that the current taxonomic system did not agree well with the 16S rDNA evolutionary trees. The position of Caryophanaceae and Planococcaceae in Group 2 suggested that they might be transferred into Bacillaceae, and the heterogeneity of Group 2 implied that some Bacillus species in it might belong to several new genera. Group 9 was mainly comprised of the genera (excluding Bacillus) of Bacillaceae, so some Bacillus species in Group 9: B. salarius, B. qingdaonensis and B. thermcloacae might not belong to Bacillus. Four Bacillus species, B. schlegelii, B. tusciae, B. edaphicus and B. mucilaginosus were clearly placed outside the nine groups.

Planococcus salinarum sp. nov., isolated from a marine solar saltern, and emended description of the genus Planococcus

A Gram-positive, non-motile and coccoid-, short rod- or rod-shaped bacterial strain, ISL-16(T), was isolated from a marine solar saltern in Korea and its taxonomic position was investigated using a polyphasic taxonomic approach. Strain ISL-16(T) grew optimally at pH 7.0-8.0, at 30 degrees C and in the presence of 2 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain ISL-16(T) joined the cluster comprising species of the genus Planococcus. Its 16S rRNA gene sequence contained the same signature nucleotides as those defined for the genus Planococcus. Strain ISL-16(T) exhibited 16S rRNA gene sequence similarity values of 96.9-98.2 % to the type strains of species of the genus Planococcus. Strain ISL-16(T) contained MK-8 and MK-7 as the predominant menaquinones and anteiso-C(15 : 0), C(16 : 1)omega7c alcohol and anteiso-C(17 : 0) as the major fatty acids. The DNA G+C content was 48.3 mol%. DNA-DNA relatedness values between strain ISL-16(T) and the type strains of species of the genus Planococcus were 15-28 %. Differential phenotypic properties, together with its phylogenetic and genetic distinctiveness, enabled strain ISL-16(T) to be differentiated from recognized species of the genus Planococcus. On the basis of the data presented, strain ISL-16(T) is considered to represent a novel species of the genus Planococcus, for which the name Planococcus salinarum sp. nov. is proposed. The type strain is ISL-16(T) (=KCTC 13584(T)=CCUG 57753(T)). An emended description of the genus Planococcus is also given.

Bhargavaea cecembensis gen. nov., sp. nov., isolated from the Chagos-Laccadive ridge system in the Indian Ocean

A novel Gram-positive, rod-shaped, non-motile, non-spore-forming bacterium, strain DSE10(T), was isolated from a deep-sea sediment sample collected at a depth of 5904 m from the Chagos-Laccadive ridge system in the Indian Ocean. Cells of strain DSE10(T) were positive for catalase, oxidase, urease and lipase activities and contained iso-C(14 : 0), iso-C(15 : 0), iso-C(16 : 0) and anteiso-C(15 : 0) as the major fatty acids. The major respiratory quinones were MK-6 and MK-8 and the major lipids were phosphatidylglycerol and diphosphatidylglycerol. The cell-wall peptidoglycan contained diaminopimelic acid as the diagnostic diamino acid. A blast sequence similarity search based on 16S rRNA gene sequences indicated that the genera Planococcus, Planomicrobium, Bacillus and Geobacillus were the nearest phylogenetic neighbours to the novel isolate with gene sequence similarities ranging from 94.9 to 95.2 %. Phylogenetic analyses using neighbour-joining, minimum-evolution and maximum-parsimony methods indicated that strain DSE10(T) formed a deeply rooted lineage distinct from the clades represented by the genera Planococcus, Planomicrobium, Bacillus and Geobacillus. Further, strain DSE10(T) could be distinguished from the above-mentioned genera based on the presence of signature nucleotides G, A, C, T, C, A, G, C and T at positions 182, 444, 480, 492, 563, 931, 1253, 1300 and 1391, respectively, in the 16S rRNA gene sequence. Based on the phenotypic and phylogenetic characteristics determined in this study, strain DSE10(T) was assigned as the type species of a new genus, Bhargavaea gen. nov., as Bhargavaea cecembensis sp. nov. The type strain of Bhargavaea cecembensis gen. nov., sp. nov. is DSE10(T) (=LMG 24411(T)=JCM 14375(T)). The genomic DNA G+C content of strain DSE10(T) is 59.5+/-2.5 mol%.

Proposal of Viridibacillus gen. nov. and reclassification of Bacillus arvi, Bacillus arenosi and Bacillus neidei as Viridibacillus arvi gen. nov., comb. nov., Viridibacillus arenosi comb. nov. and Viridibacillus neidei comb. nov

A polyphasic study was undertaken to clarify the taxonomic position of endospore-forming strains 433-D9, 433-E17 and 121-X1. BOX-PCR-generated fingerprints indicated that they may be members of a single species. 16S rRNA gene sequence similarity demonstrated that a representative of this group, 433-D9, is affiliated closely with Bacillus arvi DSM 16317(T) (100 %), Bacillus arenosi DSM 16319(T) (99.8 %) and Bacillus neidei NRRL BD-87(T) (97.1 %). Sequence similarities revealed Bacillus pycnus NRRL NRS-1691(T) and several Kurthia species as the next nearest relatives. DNA-DNA hybridization results showed that strain 433-D9 is a member of B. arvi. Detection of l-Lys-d-Asp-based peptidoglycan in strain 433-D9, B. arvi DSM 16317(T) and B. arenosi DSM 16319(T) was in agreement with their close relationship, but differentiated these strains from B. neidei NRRL BD-87(T) and B. pycnus NRRL NRS-1691(T), for which l-Lys-d-Glu was reported. A similar quinone system was detected in strains 433-D9, 433-E17, 121-X1, B. arvi DSM 16317(T), B. arenosi DSM 16319(T) and B. neidei NRRL BD-87(T). This system, unusual for bacilli, consisted of the major compound menaquinone MK-8 (69-80 %) and moderate amounts of MK-7 (19-30 %). This observation was in contrast to the predominance of MK-7 of the closest relative B. pycnus NRRL NRS-1691(T), as also reported for representatives of the closely related non-endospore-forming genus Kurthia. Strains 433-D9, B. arvi DSM 16317(T) and B. arenosi DSM 16319(T) exhibited homogeneous and discriminative polar lipid profiles and fatty acid profiles consisting of major acids i-C(15 : 0) and ai-C(15 : 0) and moderate amounts of i-C(17 : 1)omega10c and i-C(17 : 1) I/ai-C(17 : 1) B that discriminated them from closely related strains such as B. neidei NRRL BD-87(T). On the basis of clear-cut discriminative chemotaxonomic markers, we propose strains 433-D9, 433-E17 and 121-X1, B. arvi DSM 16317(T), B. arenosi DSM 16319(T) and B. neidei NRRL BD-87(T) to be reclassified within a separate genus. For this new taxon, we propose the name Viridibacillus gen. nov., and we propose the reclassification of Bacillus arvi, Bacillus arenosi and Bacillus neidei as Viridibacillus arvi gen. nov., comb. nov. (the type species of Viridibacillus, with the type strain DSM 16317(T) =LMG 22165(T)), Viridibacillus arenosi comb. nov. (type strain DSM 16319(T) =LMG 22166(T)) and Viridibacillus neidei comb. nov. (type strain NRRL BD-87(T) =DSM 15031(T) =JCM 11077(T)).

Planococcus donghaensis sp. nov., a starch-degrading bacterium isolated from the East Sea, South Korea

A novel Gram-positive, aerobic bacterium, strain JH1T, was isolated from deep-sea sediment of the East Sea, South Korea, and identified by methods of polyphasic taxonomy. The strain was oxidase-positive, motile and coccus-shaped. The genomic DNA G+C content of strain JH1T was 47 mol%. The major fatty acid of strain JH1T was anteiso-C15:0 and the predominant menaquinones were MK-7 and MK-8. Similarity of the 16S rRNA gene sequence (1452 nt) of strain JH1T to those of species of the genera Planococcus and Planomicrobium was 96.0-98.2%. The signature nucleotides in the 16S rRNA gene sequence were compared with those of previously studied type strains of species in the genera Planococcus and Planomicrobium, and suggested that strain JH1T belongs to the genus Planococcus. In addition, phylogenetic analysis showed that strain JH1T was located within the cluster comprising Planococcus antarcticus and Planococcus kocurii. DNA-DNA hybridization showed that it had 9.3% genomic relatedness with Planococcus antarcticus DSM 14505T and 22.9% with Planococcus kocurii DSM 20747T. On the basis of the phenotypic, phylogenetic and genomic data, a novel species of the genus Planococcus, Planococcus donghaensis sp. nov., is proposed, with type strain JH1T (=KCTC 13050T=LMG 23779T).

Planococcus columbae sp. nov., isolated from pigeon faeces

An orange-pigmented, Gram-positive bacterial strain, designated PgEx11T, was isolated from pigeon faeces. Analysis of the 16S rRNA gene sequence of the isolate indicated that it had 94.2–98.2 % sequence identity with respect to those of seven recognized species of the genus Planococcus. The strain PgEx11T contained anteiso-C15 : 0 as a major cellular fatty acid and MK-7 and MK-8 as the major menaquinones. The DNA G+C content of strain PgEx11T was 50.5 mol%. Furthermore, analysis of the 16S rRNA gene sequence indicated high levels of similarity with Planococcus rifietoensis (98.2 %), Planococcus maitriensis (97.6 %), Planococcus citreus (97.5 %) and Planococcus maritimus (97.1 %). However, the mean value for DNA–DNA relatedness between PgEx11T and these four closely related species was in the range 45.4–16.8 %, respectively. Moreover, strain PgEx11T also differs from its close relatives with regard to biochemical and chemotaxonomic characteristics. On the basis of phenotypic, chemotaxonomic and genotypic differences, strain PgEx11T represents a novel species of the genus Planococcus, for which the name Planococcus columbae sp. nov. is proposed. The type strain is PgEx11T (=MTCC 7251T=DSM 17517T).

Salinicoccus jeotgali sp. nov., isolated from jeotgal, a traditional Korean fermented seafood

A novel, moderately halophilic, Gram-positive coccus, designated strain S2R53-5(T), was isolated from jeotgal, a traditional Korean fermented seafood. The organism was strictly aerobic, non-motile, non-sporulating and catalase- and oxidase-positive. Strain S2R53-5(T) grew in the presence of 0.5-15 % (w/v) NaCl and at pH 6.5-11.0, with optimum growth at 5 % (w/v) NaCl and pH 7.0. The temperature range for growth was 20.0-30.0 degrees C, with an optimum temperature of 30 degrees C. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain S2R53-5(T) belongs to the family Staphylococcaceae and was most closely related to Salinicoccus roseus DSM 5351(T) (96.8 % gene sequence similarity), Salinicoccus hispanicus DSM 5352(T) (96.1 %), Salinicoccus alkaliphilus T8(T) (95.2 %) and Jeotgalicoccus halotolerans YKJ-101(T) (95.1 %). The genomic DNA G+C content was 47.0 mol%, which is in the range of 46-51 mol% that is characteristic for the genus Salinicoccus. Levels of DNA-DNA relatedness between strain S2R53-5(T) and S. roseus DSM 5351(T), S. hispanicus DSM 5352(T) and S. alkaliphilus KCTC 13928(T) were 32.2, 15.4 and 4.6 %, respectively. Chemotaxonomic data (major menaquinone, MK-6; major fatty acids, iso-C(15 : 0) and anteiso-C(15 : 0); cell-wall murein type, Lys and Gly) and 16S rRNA gene sequence analysis supported the affiliation of strain S2R53-5(T) with the genus Salinicoccus. The combined evidence from the low DNA-DNA relatedness, physiological, biochemical and other genotypic data indicate that strain S2R53-5(T) clearly represents a novel species of the genus Salinicoccus, for which the name Salinicoccus jeotgali sp. nov. is proposed. The type strain is S2R53-5(T) (=KCTC 13030(T)=LMG 23640(T)).

Planococcus rifietensis sp. nov, Isolated from Algal Mat Collected from a Sulfurous Spring in Campania (Italy)

The taxomony of strain M8, isolated from algal mat formed at the origin of a sulfurous spring in Rifieto (Savignano Irpino, Campania, Italy), was investigated in a polyphasic approach. The morphological, physiological and genetic characteristics were compared with of Planococcus and Planomicrobium species. The isolate grew optimally at pH 9.0, 1.8 M NaCl at 37 degrees C. The cells were Gram-positive cocci that form pairs, tetrads and aggregates of several cells. The isolate was aerobic/microaerophilic and accumulated glycine-betaine, as a major osmolyte, with minor components glutamate and an unknown compound. M8 was able to hydrolyse X-Glc (5-bromo-4-chloro-3-indoyl beta-d-glucopyranoside). The polar lipid profile consisted of phosphatidylglycerol and diphosphatidylglycerol as major components, and phosphocholine as a minor compound. MK8 was the only quinone found and the fatty acid composition was dominated by branched acids, mainly aiC15:0. The G+C content of DNA was 47.9% and its phylogenetic position was established by 16S rRNA gene sequencing as a member of the genus Planococcus. The DNA/DNA similarity of M8 to the type species Planococcus citreus was less than 55%. For this reason and for physiological and chemotaxonomic features, it is proposed to create a new species Planococcus rifietensis sp. nov.

Psychrophilic Planococcus maitriensis sp.nov. from Antarctica

An orange pigmented bacterium, S1, was isolated from a cyanobacterial mat sample collected in the vicinity of Schirmacher Oasis, Maitri, the Indian station, in Antarctica. The bacterium is Gram-positive and possesses all the characteristics of the genus Planococcus. It is non-sporulating, motile and has A4alpha type peptidoglycan, MK-7 and MK-8 as the major menaquinones and anteiso-C(15:0) as the major fatty acid. Based on the phylogenetic characteristics, the bacterium S1 is identified as a close relative of Planococcus citreus with which it shares 98.12% similarity at the 16S rRNA gene level but exhibits a low similarity of 52% at the whole genome level. Apart from the above major differences, S1 also exhibits phenotypic differences with Planococcus citreus and other members of the genus Planococcus. Based on these differences, the bacterium S1 is identified as a new species of the genus Planococcus for which the name Planococcus maitriensis is proposed. The type strain of Planococcus maitriensis is S1(T) (= MTCC 4827; DSM 15305).