- Korea, Republic of
Md. Amdadul Huq
Kyung Hee University, Biotechnology, Graduate Student
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A Gram-stain-negative, aerobic, rod-shaped and non-motile novel bacterial strain, designated MAHUQ-58T, was isolated from soil sample of a rice field. The colonies were observed to be light pink-coloured, smooth, spherical and 0.6–1.0 mm... more
A Gram-stain-negative, aerobic, rod-shaped and non-motile novel bacterial strain, designated MAHUQ-58T, was isolated from soil sample of a rice field. The colonies were observed to be light pink-coloured, smooth, spherical and 0.6–1.0 mm in diameter when grown on nutrient agar (NA) medium for 2 days. Strain MAHUQ-58T was found to be able to grow at 15–40 °C, at pH 5.5–10.0 and with 0–1.0 % NaCl (w/v). Cell growth occurred on tryptone soya agar, Luria–Bertani agar, NA, MacConkey agar and Reasoner's 2A agar. The strain was found to be positive for both oxidase and catalase tests. The strain was positive for hydrolysis of Tween 20 and l-tyrosine. According to the 16S rRNA gene sequence comparisons, the isolate was identified as a member of the genus Pseudomonas and to be closely related to Pseudomonas oryzae WM-3T (98.9 % similarity), Pseudomonas linyingensis LYBRD3-7T (97.7 %), Pseudomonas sagittaria JCM 18195 T (97.6 %) and Pseudomonas guangdongensis SgZ-6T (97.2 %). The novel strain MAHUQ-58T has a draft genome size of 4 536 129 bp (46 contigs), annotated with 4064 protein-coding genes, 60 tRNA genes and four rRNA genes. The average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) values between strain MAHUQ-58T and four closely related type strains were in the range of 85.5–89.5 % and 29.5–38.0 %, respectively. The genomic DNA G+C content was determined to be 67.0 mol%. The predominant isoprenoid quinone was ubiquinone 9. The major fatty acids were identified as C16:0, summed feature 3 (C16 : 1 ω6c and/or C16 : 1 ω7c) and summed feature 8 (C18 : 1 ω6c and/or C18 : 1 ω7c). On the basis of dDDH and ANI values, genotypic results, and chemotaxonomic and physiological data, strain MAHUQ-58T represents a novel species within the genus Pseudomonas , for which the name Pseudomonas oryzagri sp. nov. is proposed, with MAHUQ-58T (=KACC 22005T=CGMCC 1.18518T) as the type strain.
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A Gram-staining-positive, catalase-positive, oxidase-negative, non-motile, non-flagellate and rod-shaped bacterium, was designated as DCY81(T), and isolated from soil of a ginseng field in Pocheon province, Republic of Korea. The 16S rRNA... more
A Gram-staining-positive, catalase-positive, oxidase-negative, non-motile, non-flagellate and rod-shaped bacterium, was designated as DCY81(T), and isolated from soil of a ginseng field in Pocheon province, Republic of Korea. The 16S rRNA gene sequence analysis revealed that strain DCY81(T) belonged to the genus Arthrobacter. Major fatty acid was anteiso-C15:0, while major polar lipids were diphosphatidyglycerol, phatidyglycerol, phosphatidylinositol, monogalactosyldiacylglycerol (GL1), and dimannosyldiacylglycerol (GL2). The dominant quinone was MK-9(H2). The peptidoglycan type was A3α with an L-Lys-L-Ala-L-Thr-L-Ala interpeptide bridge. The DNA-DNA hybridization relatedness between strain DCY81(T) and Arthrobacter siccitolerans LMG 27359(T) (98.2 %), Arthrobacter sulfonivorans JCM 13520(T) (97.81 %), Arthrobacter scleromae DSM 17756(T) (97.59 %), Arthrobacter oxydans KCTC 3383(T) (97.3 %) was 39.1 ± 0.2, 62.2 ± 1.6, 36.8 ± 1.1 and 48.3 ± 1.6 %, respectively which show that the genotypic separation of strain DCY81(T) from the closest reference strain of the genus Arthrobacter. The DNA G+C content was 65.2 mol%. The genotypic analysis, physiological, and chemotaxonomic results indicate that strain DCY81(T) represents a novel species of the genus Arthrobacter. Therefore, Arthrobacter ginsengisoli sp. nov., is proposed as the type strain (=KCTC 29225(T) = JCM 19357(T)).
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Minituber production in aeroponics is a growing trend in the potato seed industry for ensuring high-quality disease-free seed, as it requires vigorous, healthy plantlets to survive under stressful conditions. Fungi can assist plantlets... more
Minituber production in aeroponics is a growing trend in the potato seed industry for ensuring high-quality disease-free seed, as it requires vigorous, healthy plantlets to survive under stressful conditions. Fungi can assist plantlets endure stress, and there is a pressing need to explore various native fungi from an environmentally beneficial standpoint. In this study, three strains of Trichoderma harzianum were tested for their ability to protect the early roots of tissue culture-raised potato plantlets during hardening and to reduce transplantation stress in an aeroponic system. In the bioactivity results, strain TI21 isolated from decayed wood significantly improved root length by 42.7%, shoot length by 25.9% and biomass weight by 29.9% of tomato seedlings compared to control and demonstrated strong biocontrol activity (percentage) against four phytopathogens, including Sclerotium delphinii SCR5 (75.97 ± 8.06), Fusarium equiseti PTR3 (67.27 ± 5.11), Curvularia spicifera BLR4 (61.66 ± 2.98) and Alternaria alternata ALT10 (61.90 ± 4.58). Strains TI26 and TI27, isolated from rice rhizospheric soil, yielded no significant results. In potato-plantlet-hardening experiments, TI21 increased plantlet survival by 22.46%, 25.75% and 24.12%, compared to TI26, TI27, and control, respectively, by reducing root-rot caused by Sclerotium sp. and Fusarium sp. After 7 days of transplantation Abuhena, Golam Kabir and Faisal Azim contributed equally to this work.
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Vermicompost is a substantial source of nutrients, promotes soil fertility, and maintains or increases soil organic matter levels. Potentially toxic elements (PTEs) in vermicompost impact on nitrification activity. However, it is yet... more
Vermicompost is a substantial source of nutrients, promotes soil fertility, and maintains or increases soil organic matter levels. Potentially toxic elements (PTEs) in vermicompost impact on nitrification activity. However, it is yet unknown how vermicompost affects nitrifying bacteria and archaea, comammox Nitrospira inopinata (complete ammonia oxidizers), net nitrification rates (NNRs), and PTEs. The effects of vermicompost application on NNRs, potential nitrification rates (NPs), PTEs, and the abundances of comammox N. inopinata bacteria, nitrite-oxidizing bacteria (NOB) and ammonia-oxidizing bacteria (AOB)/archaea (AOA) were studied. NNRs and NPs were significantly higher (p<0.05) in fresh cow-dung vermicompost (stored for 40 days) as compared with other organic manure. The level of PTEs (Cu2+, Fe2+, Pb2+, Cd2+, and Zn2+) was significantly lower (p<0.05)) in vermicompost as compared with compost of waste material with Trichoderma and cow-dung. Comammox N. inopinata, NOB, A...
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A Gram-stain-negative, aerobic, short rod-shaped and motile novel bacterial strain, designated MAHUQ-52T, was isolated from the rhizospheric soil of a banana plant. Colonies grew at 10–35 °C (optimum, 28 °C), pH 6.0–9.5 (optimum, pH... more
A Gram-stain-negative, aerobic, short rod-shaped and motile novel bacterial strain, designated MAHUQ-52T, was isolated from the rhizospheric soil of a banana plant. Colonies grew at 10–35 °C (optimum, 28 °C), pH 6.0–9.5 (optimum, pH 7.0–7.5), and in the presence of 0–1.0 % NaCl (optimum 0 %). The strain was positive for catalase and oxidase tests, as well as hydrolysis of gelatin, casein, starch and Tween 20. Based on the results of phylogenetic analysis using 16S rRNA gene and genome sequences, strain MAHUQ-52T clustered together within the genus Massilia . Strain MAHUQ-52T was closely related to Massilia soli R798T (98.6 %) and Massilia polaris RP-1-19T (98.3 %). The novel strain MAHUQ-52T has a draft genome size of 4 677 454 bp (25 contigs), annotated with 4193 protein-coding genes, 64 tRNA and 19 rRNA genes. The genomic DNA G+C content was 63.0 %. The average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) values between strain MAHUQ-52T and closely related ty...
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A stressing method was adopted to produce Trichoderma harzianum TI21 spores in a dual-layer with an outerlayer spore free of media-residue by reconditioning the starch-based rice agar medium. The essential parameters were explored and... more
A stressing method was adopted to produce Trichoderma harzianum TI21 spores in a dual-layer with an outerlayer spore free of media-residue by reconditioning the starch-based rice agar medium. The essential parameters were explored and optimized using statistical methods. The single factorial test&#39;s findings demonstrated that lower-pH and starch-based media encouraged sporulation while suppressing the growth of contaminants. The Box-Behnken design identified the ideal levels as pH 4, 30 • C, and 75 %. In the reconditioning approach, the first harvest produced 4.91 (3.64 × 10 11 CFU/g) of spores (g/L) after 5 days of cultivation, while the second and third harvests produced 4.19 and 3.48 (respectively) after 4 days of cultivation, leaving 755 (g/L) (2.25 × 10 10 CFU/g) media-mixed spores. As compared to media-mixed spores, media residue-free spores had significantly longer viability (18 months) with no clogging hazards. According to the findings, the method can be used industrially to produce stable, high-density spores for widespread agricultural applications.
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Mastitis, inflammation of the mammary gland, is the most prevalent disease in dairy cattle that has a potential impact on profitability and animal welfare. Specifically designed multi-omics studies can be used to prioritize candidate... more
Mastitis, inflammation of the mammary gland, is the most prevalent disease in dairy cattle that has a potential impact on profitability and animal welfare. Specifically designed multi-omics studies can be used to prioritize candidate genes and identify biomarkers and the molecular mechanisms underlying mastitis in dairy cattle. Hence, the present study aimed to explore the genetic basis of bovine mastitis by integrating microarray and RNA-Seq data containing healthy and mastitic samples in comparative transcriptome analysis with the results of published genome-wide association studies (GWAS) using a literature mining approach. The integration of different information sources resulted in the identification of 33 common and relevant genes associated with bovine mastitis. Among these, seven genes—CXCR1, HCK, IL1RN, MMP9, S100A9, GRO1, and SOCS3—were identified as the hub genes (highly connected genes) for mastitis susceptibility and resistance, and were subjected to protein-protein int...
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A commercial plant probiotic product was developed employing Bacillus subtilis CW-S in submerged fermentation. The effects of molasses and urea on cell growth were investigated with the goal of low-cost manufacturing. Plackett–Burman and... more
A commercial plant probiotic product was developed employing Bacillus subtilis CW-S in submerged fermentation. The effects of molasses and urea on cell growth were investigated with the goal of low-cost manufacturing. Plackett–Burman and Central-Composite Design (CCD) were utilized to optimize production parameters to maximize productivity. The stability of the formulated product and its efficacy in cultivating minituber in aeroponics and industrial-grade potatoes in the field were assessed. The results showed that the medium BS10 (molasses and urea) produced satisfactory cell density (7.19 × 108 CFU/mL) as compared to the control (1.51 × 107 CFU/mL) and BS1-BS9 (expensive) media (1.84 × 107–1.37 × 109 CFU/mL). According to validated CCD results, optimized parameters fitted well in pilot (300 L; 2.05 × 109 CFU/mL) and industrial (3000 L; 2.01 × 109 CFU/mL) bioreactors, resulting in a two-fold increase in cell concentration over laboratory (9.84 × 108 CFU/mL) bioreactors. In aeroponi...
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A Gram-stain negative, aerobic, rod-shaped and creamy pink-coloured bacterium, designated MAHUQ-68T, was isolated from rhizospheric soil of a jujube tree. Colonies grew at 10–40 °C (optimum, 28 °C), pH 6.0–9.0 (optimum pH, 7.0) and in the... more
A Gram-stain negative, aerobic, rod-shaped and creamy pink-coloured bacterium, designated MAHUQ-68T, was isolated from rhizospheric soil of a jujube tree. Colonies grew at 10–40 °C (optimum, 28 °C), pH 6.0–9.0 (optimum pH, 7.0) and in the presence of 0–1.5 % NaCl (optimum 0–0.5 %). Positive for both catalase and oxidase activity. Strain MAHUQ-68T hydrolysed casein, starch, aesculin and l-tyrosine. Based on the results of phylogenetic analysis using 16S rRNA gene and genome sequences, strain MAHUQ-68T clustered together within the genus Solitalea . The closest members were Solitalea longa HR-AVT (98.8 % sequence similarity), Solitalea canadensis DSM 3403T (96.9 %) and Solitalea koreensis R2A36-4T (94.0 %). The genome of strain MAHUQ-68 T was 4 250 173 bp long with 68 scaffolds and 3 570 protein-coding genes. The genomic DNA G+C content of the type strain was 38.0 mol%. The average nucleotide identity and in silico DNA–DNA hybridization values between strain MAHUQ-68T and its closest ...
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Biosynthesized metal nanoparticles, especially silver and gold nanoparticles, and their conjugates with biopolymers have immense potential in various fields of science due to their enormous applications, including biomedical applications.... more
Biosynthesized metal nanoparticles, especially silver and gold nanoparticles, and their conjugates with biopolymers have immense potential in various fields of science due to their enormous applications, including biomedical applications. Polymeric nanoparticles are particles of small sizes from 1 nm to 1000 nm. Among different polymeric nanoparticles, chitosan-coated silver and gold nanoparticles have gained significant interest from researchers due to their various biomedical applications, such as anti-cancer, antibacterial, antiviral, antifungal, anti-inflammatory technologies, as well as targeted drug delivery, etc. Multidrug-resistant pathogenic bacteria have become a serious threat to public health day by day. Novel, effective, and safe antibacterial agents are required to control these multidrug-resistant pathogenic microorganisms. Chitosan-coated silver and gold nanoparticles could be effective and safe agents for controlling these pathogens. It is proven that both chitosan ...
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Anaerobic digestion of agricultural waste helps to decarbonize the energy sector while also increasing the use of stabilized residues in agriculture. Although digestate (Dg) contains amino acids, vitamins, humic acids, and micronutrients,... more
Anaerobic digestion of agricultural waste helps to decarbonize the energy sector while also increasing the use of stabilized residues in agriculture. Although digestate (Dg) contains amino acids, vitamins, humic acids, and micronutrients, using it directly poses an unknown risk to crops due to the presence of pathogens, heavy metals, and excessive ammonia, necessitating processing for agricultural application as fertilizer. The study aimed to minimize the undesired effects of Dg by optimizing fermentation with Bacillus subtilis CW-S and using it as a potential inoculant for endophytic-assisted hardening of micropropagated potato plantlets. The single factor test results revealed that Dg concentrations of 70%, 80%, and 90% had a greater positive impact on cell concentration than concentrations of 50%, 60%, and 100%. According to the Box-Behnken design, diluted (80%) Dg produced a higher cell concentration (4.36 × 10 8 CFU/mL) than undiluted (100%) (1.18 × 10 8 CFU/mL). In hardening experiments, Bacillus subtilis CW-S fermented digestate (FDg) had a significantly higher plantlet survival rate of 90.25% and a root length of 5.22 (cm) with greater Serendipita indica infection, whereas Dg (unprocessed) had a lower survival rate of 67.88% and a root length of 3.13 (cm) with less Serendipita indica infection. According to the findings, FDg could be employed as a non-threat bioinoculant for widespread agricultural application.
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Sweet proteins are the natural alternative to the artificial sweeteners as well as flavor enhancers. Among other sweet protein, thaumatin protein was isolated from Thaumatococcus daniellii Benth plant fruit. In this study, pinII Ti... more
Sweet proteins are the natural alternative to the artificial sweeteners as well as flavor enhancers. Among other sweet protein, thaumatin protein was isolated from Thaumatococcus daniellii Benth plant fruit. In this study, pinII Ti plasmid vector was constructed with thaumatin gene, where thaumatin was placed under the control of the duel cauliflower mosaic virus 35S promoter into rice (Oryza sativa L. var. japonica cv. ‘Dongjinbyeo’) by Agrobacterium-mediated transformation to generate transgenic plants. Thirteen plant lines were regenerated and the transgenic rice lines were confirmed by different molecular analysis. The genomic PCR result revealed that all of the plant lines were transgenic. The single copy and intergenic plant lines were selected by Taqman PCR analysis and FST analysis, respectively. Expression of thaumatin gene in transgenic rice resulted in the accumulation of thaumatin protein in the leave. Thaumatin protein was also accumulated in leave of T1 generation. S...
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The present study aimed to suggest a simple and environmentally friendly biosynthesis method of silver nanoparticles (AgNPs) using the strain Bacillus sonorensis MAHUQ-74 isolated from kimchi. Antibacterial activity and mechanisms of... more
The present study aimed to suggest a simple and environmentally friendly biosynthesis method of silver nanoparticles (AgNPs) using the strain Bacillus sonorensis MAHUQ-74 isolated from kimchi. Antibacterial activity and mechanisms of AgNPs against antibiotic-resistant pathogenic strains of Escherichia coli O157:H7 were investigated. The strain MAHUQ-74 had 99.93% relatedness to the B. sonorensis NBRC 101234T strain. The biosynthesized AgNPs had a strong surface plasmon resonance (SPR) peak at 430 nm. The transmission electron microscope (TEM) image shows the spherical shape and size of the synthesized AgNPs is 13 to 50 nm. XRD analysis and SAED pattern revealed the crystal structure of biosynthesized AgNPs. Fourier transform infrared spectroscopy (FTIR) data showed various functional groups associated with the reduction of silver ions to AgNPs. The resultant AgNPs showed strong antibacterial activity against nine E. coli O157:H7 pathogens. Minimum inhibitory concentration (MIC) valu...
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of magnolia flower tree. The isolate can grow on R2A agar/ broth at 10~37°C with optimum growth at 28~30°C and pH 7.0 without NaCl supplement. The MAH-34T was responsible for the silver nanoparticle (AgNP) production via hydrolysis of... more
of magnolia flower tree. The isolate can grow on R2A agar/ broth at 10~37°C with optimum growth at 28~30°C and pH 7.0 without NaCl supplement. The MAH-34T was responsible for the silver nanoparticle (AgNP) production via hydrolysis of AgNO3. Thus, to know about the nitrate reductase genes, the genome analysis of Paenibacillus anseongense MAH-34T was carried out. The assembled genome of MAH-34T consists of 42 scaffolds with a total of 8,647,101 bp with N50 and N75 values of 553,491 and 230,930, respectively. The DAN G + C content was 46.0 mol%. Additionally, the genome annotation also shows the nitrate and/or nitrite reductase genes using the Rapid Annotation using Subsystem Technology (RAST), which may be responsible for the production of silver nanoparticle (AgNP) through the hydrolysis of AgNO3.
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Strain DCY85(T) and DCY85-1(T), isolated from rhizosphere of ginseng, were rod-shaped, Gram-reaction-negative, strictly aerobic, catalase positive and oxidase negative. 16S rRNA gene sequence analysis revealed that strain DCY85(T) as well... more
Strain DCY85(T) and DCY85-1(T), isolated from rhizosphere of ginseng, were rod-shaped, Gram-reaction-negative, strictly aerobic, catalase positive and oxidase negative. 16S rRNA gene sequence analysis revealed that strain DCY85(T) as well as DCY85-1(T) belonged to the genus Burkholderia and were closely related to Burkholderia fungorum KACC 12023(T) (98.1 and 98.0 % similarity, respectively). The major polar lipids of strain DCY85(T) and DCY85-1(T) were phosphatidylethanolamine, one unidentified aminolipid and two unidentified phospholipids. The major fatty acids of both strains are C16:0, C18:1 ω7c and summed feature 3 (C16:1 ω6c and/or C16:1 ω7c). The predominant isoprenoid quinone of each strain DCY85(T) and DCY85-1(T) was ubiquinone (Q-8) and the G+C content of their genomic DNA was 66.0 and 59.4 mol%, respectively, which fulfill the characteristic range of the genus Burkholderia. The polyamine content of both DCY85(T) and DCY85-1(T) was putrescine. Although both DCY85(T) and DC...
Research Interests: Microbiology, Medical Microbiology, Taxonomy, Biology, Phospholipids, and 15 moreMedicine, Phylogeny, Fatty acids, Soil Microbiology, Panax, Republic of Korea, Anti-Bacterial Agents, Burkholderia, Isolation of Bacteria, Species Specificity, Ginseng, Root Rot Disease, Novel Species, Molecular Sequence Data, and Antibiosis
The establishment of a micro-propagation protocol for banana (Musa sp.) cv. Sabri, was carried out using meristematic stem cuttings explant. MS medium supplemented with BAP singly or in combination with auxin, IAA and coconut water was... more
The establishment of a micro-propagation protocol for banana (Musa sp.) cv. Sabri, was carried out using meristematic stem cuttings explant. MS medium supplemented with BAP singly or in combination with auxin, IAA and coconut water was used for this purpose. Highest percentage of shoot regeneration (90%) and maximum number of shoots (10) per explant were observed when cultured on MS + 4.0 mg/1 BAP + 2.0 mg/1 IAA + 13% (v/v) coconut water. Best response towards root induction was achieved on half MS medium supplemented with 0.5 mg/1 IBA. The regenerated healthy rooted plantlets were transferred to small plastic pot containing garden soil and compost in a ratio of 2:1. Through this method, complete micro-propagated plantlets were obtained within three months. DOI: http://dx.doi.org/10.3329/bjsir.v47i2.11444 Bangladesh J. Sci. Ind. Res. 47(2), 143-146, 2012
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An efficient protocol was developed for plant regeneration, multiplication and rooting under in vitro condition in pointed gourd. Highest percent of shoot regeneration was 91.66%, when nodal explants were cultured on MS+1.0 mg/1 BAP. The... more
An efficient protocol was developed for plant regeneration, multiplication and rooting under in vitro condition in pointed gourd. Highest percent of shoot regeneration was 91.66%, when nodal explants were cultured on MS+1.0 mg/1 BAP. The maximum number of shoots (4.8) per explant was observed in MS + 1.0 mg/1 BAP + 0.2 mg/1 NAA from nodal segment. Among the two explants, nodal segment was found better for shoot regeneration and multiplication. The best response towards root induction was achieved on half MS medium supplemented with 0.4 mg/1 NAA. The regenerated healthy rooted plantlets were transferred to small plastic pot containing garden soil and compost in a ratio of 2:1. Immediately after transplantation the plantlets were covered with polythene bag to prevent desiccation. After acclimatization the plantlets were successfully transferred to the garden soil and the percentage of survivability in such condition was 90%.
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A Gram-stain-negative, aerobic and rod-shaped novel bacterial strain, designated MAH-26T, was isolated from rhizospheric soil of a pine tree. The colonies were orange coloured, smooth, spherical and 0.7–1.8 mm in diameter when grown on... more
A Gram-stain-negative, aerobic and rod-shaped novel bacterial strain, designated MAH-26T, was isolated from rhizospheric soil of a pine tree. The colonies were orange coloured, smooth, spherical and 0.7–1.8 mm in diameter when grown on Reasoner's 2A (R2A) agar for 2 days. Strain MAH-26T was able to grow at 10–40 °C, at pH 6.0–9.0 and with 0–1.0 % NaCl. Cell growth occurred on nutrient agar, R2A agar, tryptone soya agar and Luria–Bertani agar. The strain gave positive results in oxidase and catalase tests. Strain MAH-26T was closely related to Flavihumibacter sediminis CJ663T and Parasegetibacter terrae SGM2-10T with a low 16S rRNA gene sequence similarity (92.8 and 92.9 %, respectively) and phylogenetic analysis indicated that the strain formed a distinct phylogenetic lineage from the members of the closely related genera of the family Chitinophagaceae . Strain MAH-26T has a draft genome size of 6 857 405 bp, annotated with 5173 protein-coding genes, 50 tRNA and two rRNA genes. ...
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A Gram-stain-negative, aerobic, rod-shaped and non-motile novel bacterial strain, designated MAH-13T, was isolated from a soil sample. The colonies were observed to be yellow-coloured, smooth, spherical and 1.8–3.0 mm in diameter when... more
A Gram-stain-negative, aerobic, rod-shaped and non-motile novel bacterial strain, designated MAH-13T, was isolated from a soil sample. The colonies were observed to be yellow-coloured, smooth, spherical and 1.8–3.0 mm in diameter when grown on nutrient agar medium for 2 days. Strain MAH-13T was found to be able to grow at 20–40 °C, at pH 5.0–10.0 and with 0–1.0% NaCl (w/v). Cell growth occurred on tryptone soya agar, Luria–Bertani agar, nutrient agar and Reasoner's 2A agar. The strain was found to be positive for both oxidase and catalase tests. The strain was positive for hydrolysis of casein, starch, DNA and l-tyrosine. According to 16S rRNA gene sequence comparisons, the isolate was identified as a member of the genus Frateuria and to be closely related to Frateuria terrea DSM 26515T (98.2% similarity), Dyella thiooxydans ATSB10T (98.2 %), Frateuria defendens HyOGT (97.9 %), Rhodanobacter glycinis MO64T (97.8 %) and Frateuria aurantia DSM 6220T (97.8 %). The novel strain MAH-...
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A novel, pink-pigmented, Gram-stain-positive, aerobic, motile, rod-shaped and ginsenoside-converting bacterium, designated strain MAHUQ-46T, was isolated from soil of a forest. Strain MAHUQ-46T grew in the pH range 6.0-9.0 (optimum, 7.5),... more
A novel, pink-pigmented, Gram-stain-positive, aerobic, motile, rod-shaped and ginsenoside-converting bacterium, designated strain MAHUQ-46T, was isolated from soil of a forest. Strain MAHUQ-46T grew in the pH range 6.0-9.0 (optimum, 7.5), at temperatures between 10 and 37 °C (optimum, 30 °C) and at 0-3% (w/v) NaCl (optimum, 0.5%). 16S rRNA gene sequence analysis showed that strain MAHUQ-46T was closely related to Paenibacillus pinihumi S23T (97.3% similarity), followed by Paenibacillus elymi KUDC6143T (96.7%). The draft genome of strain MAHUQ-46T had a total length of 5,367,904 base pairs. A total of 4,857 genes were identified, in which 4,629 were protein-coding genes and 137 were RNA genes. The genome annotation of MAHUQ-46T showed 172 carbohydrate genes, some of them may be responsible for the biosynthesis of ginsenoside Rd from major ginsenoside Rb1. The DNA G + C content was 48.4 mol% and the major quinone was MK-7. Main fatty acids of strain MAHUQ-46T were C15: 0 anteiso, C16:...
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The present study highlights the biosynthesis of silver nanoparticles (AgNPs) using culture supernatant of Massilia sp. MAHUQ-52 as well as the antimicrobial application of synthesized AgNPs against multi-drug resistant pathogenic... more
The present study highlights the biosynthesis of silver nanoparticles (AgNPs) using culture supernatant of Massilia sp. MAHUQ-52 as well as the antimicrobial application of synthesized AgNPs against multi-drug resistant pathogenic Klebsiella pneumoniae and Salmonella Enteritidis. Well-defined AgNPs formation occurred from the reaction mixture of cell-free supernatant and silver nitrate (AgNO3) solution within 48 h of incubation. UV-visible spectroscopy analysis showed a strong peak at 435 nm, which corresponds to the surface plasmon resonance of AgNPs. The synthesized AgNPs were characterized by FE-TEM, EDX, XRD, DLS and FT-IR. From FE-TEM analysis, it was found that most of the particles were spherical shape, and the size of synthesized nanoparticles (NPs) was 15–55 nm. EDX spectrum revealed a strong silver signal at 3 keV. XRD analysis determined the crystalline, pure, face-centered cubic AgNPs. FT-IR analysis identified various functional molecules that may be involved with the s...
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In the present study, the major ginsenoside Rb1 was transformed into the more pharmacologically active minor ginsenoside compound K (C-K) via the enzymatic activity of food grade Weissella hellenica DC06 isolated from kimchi, a... more
In the present study, the major ginsenoside Rb1 was transformed into the more pharmacologically active minor ginsenoside compound K (C-K) via the enzymatic activity of food grade Weissella hellenica DC06 isolated from kimchi, a traditional Korean fermented food. The transformation products were analyzed by TLC, HPLC, and LC/MS. Within 4 d of incubation, 100% of Rb1 was decomposed and converted into F2 and C-K. The crude enzyme of W. hellenica DC06 hydrolyzed the two glucose moieties attached to the C-3 position and the outer glucose moiety attached to the C-20 position of the ginsenoside Rb1. Strain DC06 hydrolyzed ginsenoside Rb1 along the following pathway: Rb1→Rd→F2→CK. The optimum temperature and pH of the enzyme activity was 37°C and 7.0, respectively. DC06 was identified as a W. hellenica species based on its 16S rRNA gene sequences through the construction of a phylogenetic tree and homology analysis. This is the first report of the bioconversion of ginsenoside Rb1 to ginseno...
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Sweet tasting and taste modifying proteins are the natural alternative to flavor enhancers and artificial sweeteners. Curculin is a unique protein, which has both sweet tasting and taste modifying properties. In this study, pinII Ti... more
Sweet tasting and taste modifying proteins are the natural alternative to flavor enhancers and artificial sweeteners. Curculin is a unique protein, which has both sweet tasting and taste modifying properties. In this study, pinII Ti plasmid vector was constructed with curculin gene, where the gene encoding curculin protein was placed under the control of the duel cauliflower mosaic virus 35S (2× CaMV 35S) promoter into rice ( Oryza sativa L. var. Japonica cv. Dongjinbyeo) by Agrobacterium -mediated transformation to generate transgenic plants. Here, twenty-six plant lines were regenerated and the transgenic rice plant lines were confirmed by different molecular analysis. The genomic PCR result revealed that all of the plant lines were transgenic. The single copied and intergenic plant lines were selected by Taqman PCR analysis and FST analysis, respectively. Expression of curculin gene in transgenic rice resulted in the accumulation of curculin protein in the leave. The transgenic l...
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It is essential to develop and discover alternative eco-friendly antibacterial agents due to the emergence of multi-drug-resistant microorganisms. In this study, we isolated and characterized a novel bacterium named Terrabacter humi... more
It is essential to develop and discover alternative eco-friendly antibacterial agents due to the emergence of multi-drug-resistant microorganisms. In this study, we isolated and characterized a novel bacterium named Terrabacter humi MAHUQ-38T, utilized for the eco-friendly synthesis of silver nanoparticles (AgNPs) and the synthesized AgNPs were used to control multi-drug-resistant microorganisms. The novel strain was Gram stain positive, strictly aerobic, milky white colored, rod shaped and non-motile. The optimal growth temperature, pH and NaCl concentration were 30 °C, 6.5 and 0%, respectively. Based on 16S rRNA gene sequence, strain MAHUQ-38T belongs to the genus Terrabacter and is most closely related to several Terrabacter type strains (98.2%–98.8%). Terrabacter humi MAHUQ-38T had a genome of 5,156,829 bp long (19 contigs) with 4555 protein-coding genes, 48 tRNA and 5 rRNA genes. The culture supernatant of strain MAHUQ-38T was used for the eco-friendly and facile synthesis of A...
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A novel yellow-pigmented bacterial strain (designated BR5-29T), was isolated and its taxonomy was studied. Phylogenetic study based on the 16S rRNA and draft genome sequence placed the strain BR5-29T in a distinct lineage within the... more
A novel yellow-pigmented bacterial strain (designated BR5-29T), was isolated and its taxonomy was studied. Phylogenetic study based on the 16S rRNA and draft genome sequence placed the strain BR5-29T in a distinct lineage within the family Chitinophagaceae, sharing ≤ 93.4% sequence similarity with members of the closely related genera Ferruginibacter, Flavisolibacter, Flavitalea and Niastella. The novel isolate showed the highest sequence similarity to the genus Ferruginibacter. The draft genome of strain BR5-29T had a total length of 5,505,520 base pairs. A total of 4585 genes were identified, in which 4537 were CDS and 48 RNA genes were assigned a putative function. The genome annotation of BR5-29T showed 225 carbohydrate genes which may be responsible for the conversion of major ginsenosides to minor ginsenosides. Strain BR5-29T contained MK-7 as a predominant quinone, and iso-C15:0, iso-C15:0 G, iso-C17:0 3-OH, and C16:1 ω7c and/or C16:1 ω6c (summed feature 3) as major fatty aci...
Nitrification increases soil fertility and a higher rate of grain production in cereal and leguminous crops. However, differential response of the nitrifying microbes and net nitrification rates (NNRs) of chemical fertilizers in cereals... more
Nitrification increases soil fertility and a higher rate of grain production in cereal and leguminous crops. However, differential response of the nitrifying microbes and net nitrification rates (NNRs) of chemical fertilizers in cereals and leguminous crop soils of Bangladesh are unknown. Hence, the current research was undertaken to find out the differential response of the nitrifying microbes and NNRs of chemical fertilizers in some cereals (Triticum aestivum and Zea mays) and leguminous crops (Lins esculenta, Pisum sativum, and Cicer arietinum) soils. The NNRs and occurrence of ammonia-oxidizing archaea (AOA)/ammonia-oxidizing bacteria (AOB), and nitrite-oxidizing bacteria (NOB) were enumerated by mass spectrophotometer and q-PCR, respectively. The ranges of NNRs were 2.84±0.41 to 12.86±1.09 mg kg−1 h−1 and significantly higher (p<0.05) in cereal and leguminous crop soils as compared with control soils. Linear mixed model analysis revealed that the NNRs were significantly affected (p<0.05) by NO3--N, NH4+-N, total N, pH, and soil organic carbon (SOC). NNRs and abundance of AOA, AOB, and NOB were significantly higher (p<0.05) in leguminous crop soils as compared with both cereal crop soils and control soils. 16S rRNA gene, AOA, AOB, and NOB were positive and significantly correlated (p<0.001) with the NNRs. Overall results revealed that the higher absolute abundance (copies per gram dry weight soil) of nitrifying microbes in leguminous crop soils than in cereal crop soils may reflect the potential role of leguminous crops in minimizing inorganic N fertilizer application.
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A Gram-stain-negative, strictly aerobic, cream yellow colored, non-motile, rod-shaped bacterial strain, designated MAH-1 T was isolated from rhizospheric soil of Coriandrum sativum . A polyphasic taxonomic study was performed on the... more
A Gram-stain-negative, strictly aerobic, cream yellow colored, non-motile, rod-shaped bacterial strain, designated MAH-1 T was isolated from rhizospheric soil of Coriandrum sativum . A polyphasic taxonomic study was performed on the isolated strain. Optimal growth occurred at 28–30 °C, pH 6.5 and 0% NaCl. The strain showed activity for both catalase and oxidase tests. Cell growth occurs on R2A agar, nutrient agar and Luria–Bertani agar. Cells were able to hydrolyze starch, aesculin, gelatin, and Tween 20. Alignment of 16S rRNA gene sequences indicated that strain MAH-1 T was associated with the genus Flavobacterium and was most closely related to Flavobacterium longum YIT 12745 T (94.5% sequence similarity) and Flavobacterium caeni LM5 T (93.0%). Strain MAH-1 T had a genome size of 3,975,600 bp. Genome contained 67 contigs encoded by 3,522 protein-coding genes with 38 tRNA and 6 rRNA genes. The genomic DNA G + C contents of strain MAH-1 T was 47.1 mol %. The genomic ANI and dDDH values between strain MAH-1 T and one of the close relatives F. caeni LM5 T were 72.2 and 18.8%, respectively. The major fatty acids were C 15:0 iso , C 16:0 iso and C 15:0 anteiso . The predominant respiratory quinone was menaquinone 6 (MK-6). Based on physiological, biochemical and phylogenetic data for this isolate, it was confirmed that strain MAH-1 T was affiliated to the genus Flavobacterium and represented a novel species, for which the name Flavobacterium agri sp. nov. is proposed. The type strain is MAH-1 T (= KACC 19300 T = CGMCC 1.16617 T ).
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A ginsenoside Rg2-producing, Gram stain-negative, aerobic, catalase and oxidase-positive, rod-shaped, non-motile and orange pigmented novel bacterium designated strain MAH-28 T was isolated from soil sample of a grape garden. Strain... more
A ginsenoside Rg2-producing, Gram stain-negative, aerobic, catalase and oxidase-positive, rod-shaped, non-motile and orange pigmented novel bacterium designated strain MAH-28 T was isolated from soil sample of a grape garden. Strain MAH-28 T hydrolyzed aesculin, casein and DNA. Flexirubin-type pigments are present. Phylogenetic analysis based on 16S rRNA gene sequence showed that strain MAH-28 T formed a cluster within the genus Chitinophaga and the most close relatives were Chitinophaga alhagiae T22T (98.9% 16S rRNA gene sequence similarity), Chitinophaga humicola Ktm-2 T (98.8%), Chitinophaga barathri YLT18T (98.3%) and Chitinophaga lutea ZY74T (97.4%). The novel strain MAH-28 T has a draft genome size of 6,043,180 bp (14 contigs), annotated with 4,863 protein-coding genes, 53 tRNA and 6 rRNA genes. The ANI and dDDH values between strain MAH-28 T and the closely related type strains were in the range of 76.0-83.4% and 20.3-26.7%, respectively. The novel strain MAH-28 T was able to synthesize ginsenoside Rg2 from major ginsenoside Re. The genome annotation revealed 152 carbohydrate genes which may involve with the synthesis of ginsenoside Rg2. The respiratory quinone of strain MAH-28 T was MK-7 and the dominant cellular fatty acids were C15:0 iso, C16:1 ω5c and C17:0 iso 3-OH. The DNA G + C content of strain MAH-28 T was 53.3 mol%. Based on the phenotypic, chemotaxonomic and phylogenetic studies, strain MAH-28 T represents a new member of genus Chitinophaga for which the name Chitinophaga chungangae sp. nov. is proposed with type strain MAH-28 T (= KACC 19968 T = CGMCC 1.16605 T).
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It is essential to develop and discover alternative eco-friendly antibacterial agents due to the emergence of multi-drug-resistant microorganisms. In this study, we isolated and characterized a novel bacterium named Terrabacter humi... more
It is essential to develop and discover alternative eco-friendly antibacterial agents due to the emergence of multi-drug-resistant microorganisms. In this study, we isolated and characterized a novel bacterium named Terrabacter humi MAHUQ-38T, utilized for the eco-friendly synthesis of silver nanoparticles (AgNPs) and the synthesized AgNPs were used to control multi-drug-resistant microorganisms. The novel strain was Gram stain positive, strictly aerobic, milky white colored, rod shaped and non-motile. The optimal growth temperature, pH and NaCl concentration were 30 °C, 6.5 and 0%, respectively. Based on 16S rRNA gene sequence, strain MAHUQ-38T belongs to the genus Terrabacter and is most closely related to several Terrabacter type strains (98.2%–98.8%). Terrabacter humi MAHUQ-38T had a genome of 5,156,829 bp long (19 contigs) with 4555 protein-coding genes, 48 tRNA and 5 rRNA genes. The culture supernatant of strain MAHUQ-38T was used for the eco-friendly and facile synthesis of A...
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A Gram-stain-negative, aerobic, motile and rod-shaped novel bacterial strain, designated MAH-29T, was isolated from rhizospheric soil of a persimmon tree. The colonies were light pink coloured, smooth, spherical and 0.1–0.8 mm in diameter... more
A Gram-stain-negative, aerobic, motile and rod-shaped novel bacterial strain, designated MAH-29T, was isolated from rhizospheric soil of a persimmon tree. The colonies were light pink coloured, smooth, spherical and 0.1–0.8 mm in diameter when grown on Reasoner's 2A (R2A) agar for 2 days. Strain MAH-29T was able to grow at 20–37 °C, at pH 5.0–8.5 and at 0–2.0 % NaCl. Cell growth occurred on nutrient agar and R2A agar. The strain was positive in both oxidase and catalase tests. According to the 16S rRNA gene sequence comparisons, the isolate was identified as a member of the genus Niastella and was closely related to Niastella vici DJ57T (97.7 % similarity), Niastella koreensis GR20-10T (97.1 %) and Niastella yeongjuensis GR20-13T (97.0 %). Strain MAH-29T has a draft genome size of 8 876 333 bp (31 contigs), annotated with 6920 protein-coding genes, 61 tRNA and four rRNA genes. The average nucleotide identity and digital DNA–DNA hybridization values between strain MAH-29T and thr...
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A novel bacterial strain, designated MAH-6T, was isolated from a garden soil sample. Cells were Gram-stain-negative, aerobic, non-motile and rod-shaped. The colonies were light yellow, smooth, circular and 0.6–1.2 mm in diameter when... more
A novel bacterial strain, designated MAH-6T, was isolated from a garden soil sample. Cells were Gram-stain-negative, aerobic, non-motile and rod-shaped. The colonies were light yellow, smooth, circular and 0.6–1.2 mm in diameter when grown on nutrient agar for 3 days. Strain MAH-6T grew at 15–35 °C, at pH 5.0–7.0 and with 0–0.5 % NaCl. Cell growth occurred on nutrient agar and Reasoner's 2A (R2A) agar. The strain was positive for both catalase and oxidase tests. Cells were able to hydrolyse starch, aesculin, Tween 20 and Tween 80. According to 16S rRNA gene sequence comparisons, the isolate was identified as a member of the genus Sphingomonas and was most closely related to Sphingomonas polyaromaticivorans B2-7T (98.2 % sequence similarity), Sphingomonas oligoaromativorans SY-6T (96.9 %) and Sphingomonas morindae NBD5T (96.6 %). The novel strain MAH-6T has a draft genome size of 4 370 740 bp (28 contigs), annotated with 4199 protein-coding genes, 46 tRNA and three rRNA genes. Th...
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This paper offers a critical analysis of the arsenic-accumulating, transforming bacteria and their potential use and effect in remediating agricultural soil. Given the worldwide presence, sources, types, and pathways of arsenic,... more
This paper offers a critical analysis of the arsenic-accumulating, transforming bacteria and their potential use and effect in remediating agricultural soil. Given the worldwide presence, sources, types, and pathways of arsenic, accumulating, and transforming bacteria, and the effect of arsenic contamination on plant and agricultural soil were studied. Diverse published studies have emphasized arsenic characteristics and effects on soil. In this study, we emphasized the biochemical process and the bioremediation mechanism of arsenic contamination. The method used to isolate and identify arsenic-resistant bacteria was also described. This paper provided an overview of the information about the contamination of arsenic, the effect of its accumulation in agricultural fields, and which bacteria are used to metabolize arsenic in soil. Various types of microbes, including Exiguobacterium, Aeromonas, Bacillus, Pseudomonas, Escherichia, and Acinetobacter, metabolize the activity of inorganic arsenic to generate their energy. The bacterial ars operon consists of three to five genes that are located in plasmids. These genes are involved in oxidation, reduction, methylation, or demethylation in the arsenic transformation process in bioremediation. For example, in arsenic (V) reduction, two microbial pathways known are the detoxification pathway arsC genes negotiate and the respiratory pathway arsA genes negotiate. Further, this paper demonstrates briefly the sources of arsenic contamination and its effect on plants and soils. It has been found that certain microbes’ genes facilitate the reduction and oxidization in arsenic toxicity and have some bioremediation capacity to reduce and immobilize the arsenic contamination in agricultural soil.
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The present study highlights a simple and eco-friendly method for the biosynthesis of silver nanoparticles (AgNPs) using Lysinibacillus xylanilyticus strain MAHUQ-40. Also, the synthesized AgNPs were used to investigate their... more
The present study highlights a simple and eco-friendly method for the biosynthesis of silver nanoparticles (AgNPs) using Lysinibacillus xylanilyticus strain MAHUQ-40. Also, the synthesized AgNPs were used to investigate their antibacterial activity and mechanisms against antibiotic-resistant pathogens. Biosynthesis of AgNPs was confirmed by ultraviolet–visible spectroscopy, and then, they were characterized by field emission-transmission electron microscopy (FE-TEM), X-ray diffraction (XRD), dynamic light scattering (DLS), and fourier transform-infrared (FTIR). The toxicity of AgNPs against two pathogenic bacteria was evaluated. The UV–vis spectral scanning showed the peak for synthesized AgNPs at 438 nm. Under FE-TEM, the synthesized AgNPs were spherical with diameter ranges from 8 to 30 nm. The XRD analysis revealed the crystallinity of synthesized AgNPs. FTIR data showed various biomolecules including proteins and polysaccharides that may be involved in the synthesis and stabiliz...
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A novel bacterial strain, designated MAH-20T, was isolated from a soil sample of a tomato garden. Cells of strain MAH-20T were Gram-stain negative, aerobic, motile, and rod-shaped. The colonies were light brown colored, smooth, spherical,... more
A novel bacterial strain, designated MAH-20T, was isolated from a soil sample of a tomato garden. Cells of strain MAH-20T were Gram-stain negative, aerobic, motile, and rod-shaped. The colonies were light brown colored, smooth, spherical, and 0.2-0.7 mm in diameter when grown on Luria-Bertani agar for 2 days. Strain MAH-20T grows at 15-40 °C (optimum growth temperature 30-32 °C), at pH 5.0-10.0 (optimum growth pH 7.0) and at 0-2.0% NaCl. The strain showed positive activity for both oxidase and catalase tests. Cells were able to hydrolyze starch, DNA, urea, gelatin, L-arginine, and Tween 20. According to the 16S rRNA gene sequence similarity, the strain MAH-20T was identified as a new member of the genus Sphingomonas and had the close sequence similarity with Sphingomonas changbaiensis V2M44T (98.9%) and Sphingomonas tabacisoli X1-8T (98.1%). The genomic ANI value between strain MAH-20T and S. changbaiensis NBRC 104936T was 84.4%. The novel strain MAH-20T has a draft genome size of 3,350,026 bp (25 contigs), annotated with 3210 protein-coding genes, 46 tRNA, and 3 rRNA genes. The genomic DNA G + C content of isolate was 67.3 mol%, the predominant quinone was ubiquinone 10 and the major fatty acids were C16:0, C17:1 ω6c and summed feature 8 (comprising C18:1 ω7c and/or C18:1 ω6c). On the basis of DNA-DNA hybridization results, phenotypic, genotypic, and chemotaxonomic data, the isolated strain MAH-20T represents a novel species, for which the name Sphingomonas horti sp. nov. is proposed, with MAH-20T as the type strain (= KACC 19746T = CGMCC1.13658T).