Abstract
Strain MBLB1234T was isolated from bentonite samples collected at Guryong mining area located in Pohang, Republic of Korea and was taxonomically characterized by a polyphasic approach. This strain was a Gram-stain-negative, motile, endospore-forming, facultative anaerobic, catalase-positive, oxidase-negative, and rod-shaped bacterium. Strain MBLB1234T was able to grow at 20‒45 °C (optimum, 37 °C), pH 6.0‒10.0 (optimum, 7.0–8.0), and 0‒5.0% (w/v) NaCl (optimum, 0.5%). Genome size was 6,497,679 bp with a G + C content of 46.4 mol %. The genome was predicted to contain 5233 protein-coding genes, and 135 rRNA genes consisted of 10 5S rRNAs, 10 16S rRNAs, 10 23S rRNAs, and 105 tRNAs. Phylogenetic analysis based on the 16S rRNA gene sequences revealed that strain MBLB1234T clustered with Paenibacillus motobuensis JCM 12774T and P. aceti JCM 31170T with 98.3–98.5% and 97.2–97.4% sequencing similarity, respectively. The major fatty acids of strain MBLB1234T were anteiso-C15:0 (35.7%), anteiso-C17:0 (17.8%), iso-C17:0 (14.5%), and C16:0 (11.0%). The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylmethylethanolamine, and one unidentified phospholipid, six unidentified aminophospholipids, and one unidentified lipid. The predominant isoprenoid quinone was menaquinone-7. DNA–DNA hybridization values between strain MBLB1234T and P. motobuensis JCM 12774T and P. aceti JCM 31170T were 34 and 38%, respectively. Average nucleotide identity value between strains MBLB1234T and P. aceti L14T was 82.3%. Based on characteristics of genomic, phenotypic, chemotaxonomic, and phylogenetic analyses, strain MBLB1234T represents a novel species of the genus P. , for which the name P. lutimineralis sp. nov. is proposed. The type strain is MBLB1234T (= JCM 32684T = KCTC 33978T).
Similar content being viewed by others
Avoid common mistakes on your manuscript.
Introduction
The genus Paenibacillus, belonging to the family Paenibacillaceae in phylum Firmicutes, was first proposed by Ash et al. [1] by dividing the genus Bacillus sensu lato into five distinct groups based on comparative 16S rRNA gene sequence analysis according to which the genus Paenibacillus was established as group 3 [2]. Subsequently, an emended description of the genus Paenibacillus was provided by Shida et al. [3]. At the time of writing, the genus Paenibacillus comprises 238 species and four subspecies with validly published names (http://www.bacterio.net/paenibacillus.html), among which Paenibacillus polymyxa is the type species of the genus [4]. The members of the genus Paenibacillus are widely distributed in various habitats and mostly isolated from human-enriched soils, decomposing plant materials, other soil samples [5, 6].
Bentonite is a clay mineral mostly composed of smectite, predominant composition of which is montmorillonite [7]. Bentonite containing various elements, such as potassium, sodium, aluminum, calcium, have been investigated for the adsorption of heavy metals and molecular species in a variety of environments and industries and also identified as low-cost adsorbents [8,9,10]. In addition to studies on the physicochemical properties of bentonites, some studies on the antibacterial effect of bentonite against Escherichia coli and Staphylococcus aureus have been reported [11]. Therefore, it has been applied to the development of health-related products including functional foods, cosmetics, and pharmaceuticals [8]. Although there have been several studies on the characterizations of bentonite properties themselves and its biological effects, few studies have reported the microbial diversity in bentonite [12] and the isolation of novel microorganism present in bentonite [13]. Accordingly, a large number of microbial strains were isolated during a study targeting the culture-dependent microbial diversity in bentonite collected from Guryong mining area located in Pohang, Republic of Korea. Based on 16S rRNA gene sequence similarity, one of the isolated strains designated MBLB1234T was found to be a member of the genus Paenibacillus. Further study of strain MBLB1234T based on the polyphasic analyses also determined the taxonomic position as a representative of a novel species of the genus Paenibacillus.
Materials and Methods
Isolation and Culture Conditions
Four bentonite samples were collected at Guryong mining area located in Pohang, Gyeongsangbuk-do, Republic of Korea (36°00′55.1″N 129°32′02.9″E), pooled in autoclaved bag and stored at 4 °C before the isolation of bacterial strains. The chemical compositions of bentonite samples were analyzed using energy dispersive X-ray fluorescence spectrometer (Rigaku NEX CG) [14], resulting that major chemical components of bentonite samples were SiO2 with 52.4–62.6 wt%, followed by Al2O3 with 13.4–16.4 wt%. The bentonite samples were thoroughly crushed and diluted in 0.85% (w/v) NaCl. The suspensions were spread on TSB agar (BD Difco) to isolate bacterial strains. The plates were then incubated at 30 °C for 2 weeks until colonies formed. These colonies were subsequently re-streaked at least three times on the same kind of fresh medium to obtain pure colonies. After 16S rRNA gene sequencing analysis of the isolates, one isolate designated strain MBLB1234T exhibiting less than 99.0% similarity in 16S rRNA gene sequence was finally selected as the primary candidate for novel species and then stored at ‒ 80 °C in 25% (w/v) glycerol stock solution until further analysis. Strain MBLB1234T has been deposited at the JCM (Japan Collection of Microorganisms) and the KCTC (Korean Collection for Type Cultures).
Primary Identification
To monitor the taxonomic information, a HiYield™ Genomic DNA Mini Kit (RBC, Taiwan) was used to extract the genomic DNA of the isolates. The 16S rRNA gene was amplified by PCR using universal primers 27F and 1492R [15], after which the PCR products were sequenced at Macrogen Co., Ltd. and the 16S rRNA gene sequences were assembled using the SeqMan software (DNAStar) [16]. To align the 16S rRNA gene sequence of each isolate with related species, SILVA (http://www.arb-silva.de/aligner) was used [17].
Whole Genome Sequencing, Genome Annotation and Phylogenetic Tree Construction
Whole genome of strain MBLB1234T was sequenced and assembled using the PacBio RS II sequencing system and Hierachical Genome Assembly Process (HGAP) (Pacific Biosciences). Genome annotation was performed using the Rapid Annotation using Subsystem Technology (RAST) server for gene prediction, RNAmmer 1.2 sever (http://www.cbs.dtu.dk/services/RNAmmer/) [18] for fining rRNA, tRNA scan-SE (http://lowelab.ucsc.edu/tRNAscan-SE/) [19] for scanning tRNA, eggNOG web (http://eggnogdb.embl.de/) [20] for comparing orthologous groups of proteins at different taxonomic levels and summarizing functional annotations, and the Bacterial Pan Genome Analysis pipeline (BPGA) (http://iicb.res.in/bpga/index.html) for analyzing the core, accessory, unique, and exclusively absent genes. The 16S rRNA gene sequence of strain MBLA1234T was sorted from the whole genome using the RAST and RNAmmer 1.2 servers. To construct the phylogenetic tree, the 16S rRNA gene sequences of the strains belonging to the genus Paenibacillus were subsequently obtained from the EzBioCloud server (http://www.ezbiocloud.net/) [21], after which the evolutionary distances were calculated using the Kimura two-parameter model [22]. A phylogenetic tree was built with the MEGA7 program [23] using the maximum likelihood (ML) [24], maximum parsimony (MP) [25], and neighbor-joining (NJ) [26] methods (each employed 1000 replicates).
Genomic DNA–DNA Relatedness
DNA–DNA hybridization (DDH) values of strain MBLB1234T and two reference strains were determined by using photobiotin-labeled DNA probes and microdilution wells [27]. The highest and lowest values were omitted for each sample, and the means of the remaining three values were used as the DNA–DNA relatedness values. Genomic DNA–DNA relatedness between strain MBLB1234T and closely related reference genome was computed using the Average Nucleotide Identity (ANI) calculator (ver. 0.93.1) supplied by EzBioCloud sever.
Reference Strains
Paenibacillus motobuensis JCM 12774T and Paenibacillus aceti JCM 31170T were selected as reference strains to analyze the biochemical and chemotaxonomic characteristics of strain MBLA1234T. These reference strains were purchased from JCM and routinely cultivated on TSB agar at 30 °C. We have also used the genomes of P. aceti L14 (MDDO01000000), P. glucanolyticus 5162 (CP015286), P. pini JCM 16418 (BAVZ00000000), P. solani FJAT-22460 (LIUT00000000), and P. terrae HPL-003 (CP003107) as reference strains for genomic analysis of strain MBLA1234T.
Phenotype and Biochemical Characterization and In Silico Phenotypic Analysis
The cell morphology of strain MBLB1234T was observed by light microscopy (model CX 23; Olympus) and transmission electron microscopy (JEM-101; JEOL). Gram staining was conducted using a BD Gram-stain kit according to the manufacturer’s instructions. Anaerobic growth was evaluated using a GasPak™ EZ anaerobe gas-generating pouch system with indicator (BD) on TSA at 30 °C for 4 weeks. Growth range and optimal growth were determined with modified TSA. To determine the optimal temperature, strain MBLB1234T was incubated on TSA at 4, 10, 15, 20, 25, 30, 35, 37, 40, 45, 50, and 55 °C for 4 weeks. To measure the NaCl tolerance, TSA as basal medium was modified by adjusting the NaCl in the medium to 0, 0.5% (w/v), and 1.0‒10.0% (w/v) at intervals of 1.0%. The growth range in different pH was determined by cultivating on TSA at 37 °C after adjusting the medium pH using the following buffer systems: pH 5.0 and 6.0 with 10 mM 2-(N-morpholino) ethanesulfonic acid; pH 7.0–9.0 with 10 mM Bis–Tris propane; pH 10.0 and 11.0 with 10 mM 3-(cyclohexylamino)-1-propanesulfonic acid. Catalase activity was determined by testing bubble production in 3% (w/v) hydrogen peroxide, while oxidase activity was assessed using 1% (w/v) tetramethyl-p-phenylenediamine solution. Hydrolysis of starch, casein, Tweens 20, 40, and 80, gelatin, and l-tyrosine were evaluated as described by Benson [28], while H2S production was tested according to Gerhardt et al. [29]. Utilization of various substrates as sole carbon and energy sources, and enzyme activities of strain MBLB1234T were determined using the API 20NE, API 50CH, and API ZYM (bioMérieux) strips according to the manufacturer’s instructions. Antibiotic susceptibility was tested by the disk diffusion plate method as described by Bauer et al. [30]. Disks were impregnated with the following antibiotics (µg ml−1 disk unless otherwise indicated): ampicillin (10), carbenicillin (100), cephalothin (30), ciprofloxacin (10), erythromycin (25), gentamicin (30), kanamycin (30), lincomycin (15), neomycin (30), norfloxacin (20), novobiocin (10), penicillin G (20 UI), polymyxin B (100 UI), streptomycin (50), and tetracycline (30). The strain was incubated at 30 °C for 2 weeks. In silico phenotypic traits’ analyses were performed with the predicted genes from genome annotation using the RAST, eggNOG, and BPGA.
Chemotaxonomic Characterization
Cellular fatty acid profiles of strains MBLA1234T, P. motobuensis JCM 12774T, and P. aceti JCM 31170T were analyzed according to the methods described by Miller [31] using an Agilent 6890 gas chromatography system and a crosslinked methyl siloxane column (HP-1; A30 m × 0.320 mm × 0.25 µm). Cells of strain MBLB1234T and related taxa were prepared by cultivation on TSA at 37 °C for 2 days, and cell pellets were saponified, methylated, and extracted to analyze the fatty acid profiles using the Sherlock MIS Software version 6.2 based on the TSBA6 database [32]. Polar lipids of strain MBLB1234T and the reference strain Paenibacillus motobuensis JCM 12774T were extracted according to the protocols of Minnikin et al. [33]. Two-dimensional thin-layer chromatography of polar lipids was analyzed on silica gel 60 F254 (10 × 10 cm; Merck) by spraying with proper reagents [33, 34]. To investigate the isoprenoid quinone, strain MBLB1234T and related taxa were cultivated on TSA at 37 °C for 2 days. Freeze-dried cells were used to extract the isoprenoid quinone according to the method described by Collins and Jones [35] and identified using an HPLC system (YL9100; Younglin).
Results and Discussion
Genotypic Characteristics and Phylogenetic and Genomic Analyses
From the primary identification of the 16S rRNA gene sequence, one isolate designated strain MBLB1234T was selected as the primary candidate for novel species within the genus Paenibacillus. After sequencing the whole genome of strain MBLB1234T, the genome sequence was deposited in GenBank/EMBL/DDBJ under accession number CP034346. The genome size of strain MBLB1234T was 6,497,679 bp. Base on the RAST, RNAmmer 1.2, and tRNA scan-SE sever, 135 RNAs were predicted with distribution of 10 5S rRNAs, 10 16S rRNAs, 10 23S rRNAs, and 105 tRNA. The genomic DNA G + C content was 46.4 mol % which is similar to values previously reported for the genus Paenibacillus (39–59 mol%) [6]. According to the eggNOG, 5233 protein-coding genes were predicted (Supplementary Table S1). Of them, functional unknown genes occupied the most as 24.31%. The next most predicted genes were related with carbohydrate transport metabolism (9.52%) and transcription (9.50%). From the BPGA, numbers of core, accessory, unique, and exclusively absent genes were expected to 1140, 2833, 1239, and 13, respectively (Supplementary Table S2). Length of the predicted 10 16S rRNA gene sequences was 1555 bp, and similarities of between them were in the range of 99.4 to 99.9% (Fig. 1). Strain MBLB1234T shared the highest sequence similarity with P. motobuensis JCM 12774T (98.3–98.5%), followed by P. aceti JCM 31170T (97.2–97.4%). The pairwise sequence similarities to another valid published species of the genus Paenibacillus including Paenibacillus chibensis JCM 9905T and Paenibacillus anaericanus MH21T were less than 96.1%. Strain MBLB1234T clustered with P. aceti L14T and P. motobuensis MC 10T with a high bootstrap value in the phylogenetic tree analysis using the ML, MP, and NJ algorithms, while it formed a separate lineage remote from P. polymyxa ATCC 842T as type species of the genus Paenibacillus (Fig. 1). The DDH values of strain MBLB1234T with P. motobuensis JCM 12774T and P. aceti JCM 31170T were 34% and 38%, respectively. According to current prokaryotic systematics defining DDH values of < 70% as indicative of a distinct species [36], the determined DDH values indicated that the strain MBLB1234T could be considered a new species within the genus Paenibacillus. Since the genome of P. motobuensis JCM 12774T was not available, other related genomes including P. aceti L14, P. glucanolyticus 5162, P. pini JCM 16418, P. solani FJAT-22460, and P. terrae HPL-003, were obtained from the GenBank and then employed to analyze genomic DNA–DNA relatedness. ANI value between strain MBLB1234T and P. aceti L14 was 82.29%, while ANI values with other reference strains ranged from 69.24 to 70.02% (data not shown). The ANI value was therefore far below the generally accepted rule in delineation of prokaryotic novel species [37]. Thus, strain MBLB1234T was confirmed to represent a novel species in the genus Paenibacillus.
Phenotype and Biochemical Characteristics and In Silico Phenotypic Analysis
Strain MBLB1234T optimally grew at 37 °C and pH 7.0‒8.0 and with 0.5% (w/v) NaCl, and was sensitive to ampicillin, carbenicillin, cephalothin, ciprofloxacin, gentamicin, kanamycin, lincomycin, neomycin, norfloxacin, novobiocin, polymyxin B, streptomycin, and tetracycline, but resistant to erythromycin, and penicillin G. Colonies of strain MBLB1234T were observed to be circular, flat, and opaque white on TSA plates. The cells were Gram-stain-negative, motile by flagella, facultative anaerobic, endospore-forming, and rod-shaped (0.5‒0.7 µm in width by 1.5‒2.4 µm in length). An ellipsoidal endospore in swollen sporangia formed in the terminal region of the cell (Supplementary Fig. S1). The strain MBLB1234T and reference strains were positive for H2S production, but negative for indole production. While strain MBLB1234T was found to be negative for nitrate reduction and Voges-Proskauer test, P. motobuensis JCM 12774T was positive for these tests. Starch, casein, and l-tyrosine were hydrolyzed, while Tweens 20, 40, and 80 were not hydrolyzed in all strains. Strain MBLB1234T and reference strains also shared numerous similarities including being positive for activities of esterase (C4) and esterase lipase (C8) and negative for lipase (C14) activity. However, some characteristics were found to discriminate strain MBLB1234T from the reference strains. The detailed physiological and biochemical characteristics of strain MBLB1234T are presented in Supplementary Table S3, and the species description and are compared to those of closely related Paenibacillus species in Table 1.
Through In silico phenotypic tests, glycerol dehydrogenase (EC 1.1.16), l-arabinose isomerase (EC 5.3.1.4), ribose ABC transporter system (TC 3.A.1.2.1), xylose isomerase (EC 5.3.1.5), xyloside transporter XynT, galactose/methyl galactoside ABC transporter (EC 3.6.3.17), glucose-6-phosphate 1-dehydrogenase (EC 1.1.1.49), N-acetylglucosamine-6-phosphate deacetylase (EC 3.5.1.25), cellobiose phosphotransferase system, maltose/maltodextrin ABC transporter, galactose-1-phosphate uridylyltrasnferase (EC 2.7.7.10), sucrose 6-phosphate hydrolase (EC 3.2.1.26), and trehalose phosphorylase (EC 2.4.1.64) were identified from genome of strain MBLB1234T. Glycerol, l-arabinose, d-ribose, d-xylose, methyl-β-d-xyloside, d-galactose, d-glucose, N-acetylglucosamine, d-cellobiose, d-maltose, d-lactose, sucrose, and trehalose were utilized as a sole carbon source. Although 4-diphosphocytidly-2-C-metyl-d-erythritol kinase (EC 2.7.1.48), mannose-6-phosphate isomerase (EC 5.3.1.8), α-glucoside transporter system, glycogen phosphorylase, and 6-phosphogluconate dehydrogenase were detected from the genome of strain MBLB1234T, erythritol, d-mannose, methyl-α-d-glucoside, glycogen,and gluconate were not used as a sole carbon source.
Chemotaxonomic Characteristics
The respiratory quinone detected in strain MBLB1234T was menaquinone-7 (MK-7), which was in accordance with the genus Paenibacillus [6]. The predominant fatty acids of strain MBLB1234T (> 10% of the total fatty acids) were anteiso-C15:0 (35.7%), anteiso-C17:0 (17.8%), iso-C17:0 (14.5%), and C16:0 (11.0%). The anteiso-C15:0 and anteiso-C17:0 as major polar lipids were similar with two reference strains: P. motobuensis JCM 12774T and P. aceti JCM 31170T. However, a few differences between MBLB1234T and the reference strains were shown, with more C16:0 and less iso-C15:0 in strain MBLB1234T (Table 2). The polar lipids of strain MBLB1234T were identified as diphosphatidylglycerol (DPG), phosphatidylglycerol (PG), phosphatidylethanolamine (PE), phosphatidylmethylethanolamine (PME), one unidentified phospholipid (PL), six unidentified aminophospholipids (APL1-APL6), and one unidentified lipid (L). The reference strain P. motobuensis JCM 12774T showed a similar polar lipid profile to type strain MBLB1234T, but two additional unidentified aminophospholipids were detected for the strain P. motobuensis JCM 12774T (Supplementary Fig. S2). According to the available polar lipid data, DPG, PG, and PE are known to be the major polar lipids of the genus Paenibacillus [38, 39]. In summary, strain MBLB1234T possessed chemotaxonomic characteristics typical of the genus Paenibacillus, and furthermore, some distinctions were also detected between MBLB1234T and the related type strains.
All data generated by phenotypic, phylogenetic, chemotaxonomic, and genomic analyses suggest that the strain MBLB1234T isolated from bentonite samples is considered to represent a novel species within the genus Paenibacillus for which the name P. lutimineralis sp. nov. is proposed.
Description of Paenibacillus lutimineralis sp. nov.
Paenibacillus lutimineralis (lu.ti.minera’lis. lŭtum L. n. lutum clay; minerális. L. gen. adj, mineralis of the mineral; N.L. gen. n. lutimineralis, of a clay mineral, the source from which the type strain was isolated).
Cells are Gram-stain-negative, facultative anaerobic, motile by flagella, spore-forming, and rod-shaped (0.5‒0.7 × 1.5‒2.4 µm). Colonies on TSA are nonpigmented, circular, convex, bright, and cream-colored with a diameter of 1.0‒1.5 mm. Cell growth can be observed in the presence of 0‒5.0% (w/v) NaCl (optimum, 0.5%) at 20‒45 °C (optimum, 37 °C) and pH 6.0‒10.0 (optimum, 7.0–8.0). Cells are positive for catalase test, H2S production, and methyl red test, but negative for oxidase, indole production, and Voges‒Proskauer test. Reduction of nitrate to nitrite is negative. Cells can hydrolyze casein, l-tyrosine, and starch, but not Tweens 20, 40, and 80, and gelatin does not occur. In API 20NE test, β-galactosidase utilization of glucose, mannose, mannitol, N-acetyl-glucosamine, maltose, and gluconate is positive. In API ZYM test, results show activities of alkaline phosphatase, esterase (C4), esterase lipase (C8), leucine arylamidase, naphthol-AS-BI-phosphohydrolase, α-galactosidase, β-galactosidase, α-glucosidase, and β-glucosidase. In API 50CH assays, results for glycerol, l-arabinose, d-ribose, d-xylose, methyl-β-d-xyloside, d-galactose, d-glucose, d-fructose, N-acetylglucosamine, amygdalin, arbutin, esculin, salicin, d-cellobiose, d-maltose, d-lactose, d-melibiose, sucrose, d-trehalose, d-raffinose, starch, gentiobiose, and d-turanose are positive. The predominant fatty acids are anteiso-C15:0, anteiso-C17:0, iso-C17:0, and C16:0. The major respiratory quinone is MK-7. The major polar lipids of strain MBLB1234T are diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylmethylethanolamine, one unidentified phospholipid, six unidentified aminophospholipids, and one unidentified lipid. The DNA G + C content of the type strain is 46.4 mol%.
The type strain, MBLB1234T (= JCM 32684T = KCTC 33978T), was isolated from bentonite samples collected at Guryong mining area located in Pohang, Republic of Korea.
References
Ash C, Farrow JAE, Wallbanks S, Collins MD (1991) Phylogenetic heterogeneity of the genus Bacillus revealed by comparative analysis of small-subunit-ribosomal RNA sequences. Lett Appl Microbiol 13:202–206
Ash C, Priest FG, Collins MD (1993) Molecular identification of rRNA group 3 bacilli (Ash, Farrow, Wallbanks and Collins) using a PCR probe test. Proposal for the creation of a new genus Paenibacillus. Antonie Van Leeuwenhoek 64:253–260
Shida O, Takagi H, Kadowaki K, Nakamura LK, Komagata K (1997) Transfer of Bacillus alginolyticus, Bacillus chondroitinus, Bacillus curdlanolyticus, Bacillus glucanolyticus, Bacillus kobensis, and Bacillus thiaminolyticus to the genus Paenibacillus and emended description of the genus Paenibacillus. Int J Syst Bacteriol 47:289–298
Ash C, Priest FG, Collins MD (1994) Paenibacillus gen. nov. and Paenibacillus polymyxa comb. nov. In validation of the publication of new names and new combinations previously effectively published outside the IJSB, list no. 51. Int J Syst Bacteriol 44:852
Logan NA, De Clerck E, Lebbe L, Verhelst A, Goris J, Forsynth G, Rodríguez-Díaz M, Heyndrickx M, De Vos P (2004) Paenibacillus cineris sp. nov. and Paenibacillus cookii sp. mov., from Antarctic volcanic soils and s gelatin-processing plant. Int J Syst Evol Microbiol 54:1071–1076
Yao R, Wang R, Wang D, Su J, Zheng S, Wang G (2014) Paenibacillus selenitireducens sp. nov., a selenite-reducing bacterium isolated from a selenium mineral soil. Int J Syst Evol Microbiol 64:805–811
Kaufhold S, Dohrmann R, Ufer K, Meyer FM (2002) Comparison of methods for the quantification of montmorillonite in bentonites. Appl Clay Sci 22:145–151
Allo WA, Murray HH (2004) Mineralogy, chemistry and potential applications of a white bentonite in San Juan province, Argentina. Appl Clay Sci 25:237–243
Bereket G, Aroğuz AZ, Özel MZ (1997) Removal of Pb(II), Cd(II), Cu(II), and Zn(II) from aqueous solutions by adsorption on bentonite. J Colloid Interface Sci 187:338–343
Shahwan T, Erten HN, Unugur S (2006) A characterization study of some aspects of the adsorption of aqueous Co2+ ions on a natural bentonite clay. J. Colloid Interf. Sci. 300:447–452
Oya A, Funato Y, Sugiyama K (1994) Antimicrobial and antifungal agents derived from clay minerals. J Mater Sci 29:11–14
López-Fernández M, Fernández-Sanfrancisco O, Moreno-García A, Martín-Sánchez I, Sánchez-Castro I, Merroun ML (2014) Microbial communities in bentonite formations and their interactions with uranium. Appl Geochem 49:77–86
Sánchez-Castro I, Ruiz-Fresneda MA, Bakkali M, Kämpfer P, Glaeser SP, Busse HJ, López-Fernández M, Martínez-Rodríguez P, Merroun ML (2017) Stenotrophomonas bentonitica sp. nov., isolated from bentonite formations. Int J Syst Evol Microbiol 67:2779–2786
Seo SM, Kim D, Kim D, Kim JH, Lee YJ, Roh KM, Kang IM (2018) A simple synthesis of nitrate cancrinite from natural bentonite. J Porous Mat 25:1561–1565
Lane DJ (1991) 16S/23S rRNA sequencing. In: Stackbrandt E, Goodfellow M (eds) Nucleic acid techniques in bacterial systematics. Wiley, New York, pp 115–175
Swindell SR, Plasterer TN (1997) Seqman, contig assembly. In: Swindell SR (ed) Sequence data analysis guidebook. Springer, Totowa (NJ), pp 75–89
Pruesse E, Peplies J, Glӧckner FO (2012) SINA: accurate high-throughput multiple sequence alignment of ribosomal RNA genes. Bioinformatics 28:1823–1829
Lagesen K, Hallin P, Rødland EA, Stærfeldt HH, Rognes T, Ussery DW (2007) RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res 35:3100–3108
Lowe TM, Chan PP (2016) tRNAscan-SE On-line: search and contextual analysis of transfer RNA genes. Nucl Acids Res 44:54–57
Huerta-Cepas J, Szklarczyk D, Forslund K, Cook H, Heller D, Walter MC, Rattei T, Mende DR, Sunagwa S, Kuhn M, Jensen LJ, Mering C, Bork P (2015) eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences. Nucleic Acids Res 44:286–293
Yoon SH, Ha SM, Kwon S, Lim J, Kim Y, Seo H, Chun J (2017) Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies. Int J Syst Evol Microbiol 67:1613–1617
Kimura M (1983) The neutral theory of molecular evolution. Cambridge University Press, Cambridge
Kumar S, Stecher G, Tamura K (2016) MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 33:1870–1874
Felsenstein J (1981) Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17:368–376
Kluge AG, Farris JS (1969) Quantitative phyletics and the evolution of anurans. Syst Biol 18:1–32
Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425
Ezaki T, Hashimoto Y, Yabuuchi E (1989) Fluorometric deoxyribonucleic acid-deoxyribonucleic acid hybridization in microdilution wells as an alternative to membrane filter hybridization in which radioisotopes are used to determine genetic relatedness among bacterial strains. Int J Syst Evol Microbiol 39:224–229
Benson HJ (2002) Microbiological applications. Laboratory Manual in General Microbiology. McGraw-Hill, New York
Gerhardt P, Murray RGE, Wood WA, Krieg NR (1994) Methods for general and molecular bacteriology. American Society for Microbiology, Washington, DC
Bauer AW, Kirby MM, Sherris JC, Truck M (1966) Antibiotic susceptibility testing by a standardized single disk method. Am J Clin Pathol 45:493–496
Miller LT (1982) Single derivatization method for routine analysis of bacterial whole-cell fatty acid methyl esters, including hydroxy acids. J Clin Microbiol 16:584–586
Sasser M (1990) Identification of bacteria by gas chromatography of cellular fatty acids. MIDI Inc, MIDI Technical Note 101, Newark, DE
Minnikin DE, O’Donnell AG, Goodfellow M, Alderson G, Athalye M, Schaal A, Parlett JH (1984) An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. J Microbiol Methods 2:233–241
Komagata K, Suzuki K (1987) Lipids and cell-wall analysis in bacterial systematics. Methods Microbiol 19:161–207
Collins MD, Jones D (1981) Distribution of isoprenoid quinone structural types in bacteria and their taxonomic implication. Microbiol Rev 45:316–354
Wayne LG, Brenner DJ, Colwell RR, Grimont PAD, Kandler O, Krichevsky MI, Moore LH, Moore WEC, Murray RGE, Stackebrandt E, Starr MP, Trüper HG (1987) Report of the ad hoc Committee on reconciliation of approaches to bacterial systematics. Int J Syst Bacteriol 37:463–464
Chun J, Oren A, Ventosa A, Christensen H, Arahal DR, da Costa MS, Rooney AP, Yi H, Xu XW, De Meyer S, Trujillo ME (2018) Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. Int J Syst Evol Microbiol 68:461–466
Li P, Lin W, Liu X, Li S, Luo L, Lin WT (2016) Paenibacillus aceti sp. nov., isolated from the traditional solid-state acetic acid fermentation culture of Chinese cereal vinegar. Int J Syst Evol Microbiol 66:3426–3431
Lida K, Ueda Y, Kawamura Y, Ezaki T, Takade A, Yoshida S, Amako K (2005) Paenibacillus motobuensis sp. nov., isolated from a composting machine utilizing soil from Motobu-town, Okinawa. Japan. Int J Syst Evol Microbiol 55:1811–1816
Acknowledgements
This research was supported by the Basic Research Project (18-3214) of the Korea Institute of Geoscience and Mineral Resources (KIGAM) funded by the Ministry of Science and ICT. This research was also supported by Basic Science Research Program through the National Research Foundation of Korea (NRF) funded by the Ministry of Education (NRF-2016R1D1A1B03931582), and the World Institute of Kimchi (KE1902-2) funded by the Ministry of Science, ICT & Future Planning.
Author information
Authors and Affiliations
Corresponding authors
Ethics declarations
Conflict of interest
The authors declare that there are no conflicts of interest.
Additional information
Publisher's Note
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
The GenBank/EMBL/DDBJ accession number for genome and the Digital Protologue Database Taxon Number for of strain MBLB1234T are CP034346 and TA00598, respectively.
Electronic supplementary material
Below is the link to the electronic supplementary material.
Rights and permissions
About this article
Cite this article
Cho, ES., Cha, IT., Seo, DH. et al. Paenibacillus lutimineralis sp. nov., Isolated From Bentonite. Curr Microbiol 76, 995–1002 (2019). https://doi.org/10.1007/s00284-019-01710-y
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s00284-019-01710-y