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Yang S, Han X, Li J, Luan F, Zhang S, Han D, Yang M, Chen Q, Qi Z. Oceanobacillus picturae alleviates cadmium stress and promotes growth in soybean seedlings. JOURNAL OF HAZARDOUS MATERIALS 2024; 472:134568. [PMID: 38749246 DOI: 10.1016/j.jhazmat.2024.134568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Revised: 04/24/2024] [Accepted: 05/07/2024] [Indexed: 05/30/2024]
Abstract
Cadmium (Cd) is a heavy metal that significantly impacts human health and the environment. Microorganisms play a crucial role in reducing heavy metal stress in plants; however, the mechanisms by which microorganisms enhance plant tolerance to Cd stress and the interplay between plants and microorganisms under such stress remain unclear. In this study, Oceanobacillus picturae (O. picturae) was isolated for interaction with soybean seedlings under Cd stress. Results indicated that Cd treatment alone markedly inhibited soybean seedling growth. Conversely, inoculation with O. picturae significantly improved growth indices such as plant height, root length, and fresh weight, while also promoting recovery in soil physiological indicators and pH. Metabolomic and transcriptomic analyses identified 157 genes related to aspartic acid, cysteine, and flavonoid biosynthesis pathways. Sixty-three microbial species were significantly associated with metabolites in these pathways, including pathogenic, adversity-resistant, and bioconductive bacteria. This research experimentally demonstrates, for the first time, the growth-promoting effect of the O. picturae strain on soybean seedlings under non-stress conditions. It also highlights its role in enhancing root growth and reducing Cd accumulation in the roots under Cd stress. Additionally, through the utilization of untargeted metabolomics, metagenomics, and transcriptomics for a multi-omics analysis, we investigated the impact of O. picturae on the soil microbiome and its correlation with differential gene expression in plants. This innovative approach unveils the molecular mechanisms underlying O. picturae's promotion of root growth and adaptation to Cd stress.
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Affiliation(s)
- Shangjun Yang
- National Research Center of Soybean Engineering and Technology, Northeast Agricultural University, Harbin, Heilongjiang 150030, China
| | - Xue Han
- National Research Center of Soybean Engineering and Technology, Northeast Agricultural University, Harbin, Heilongjiang 150030, China
| | - Jun Li
- National Research Center of Soybean Engineering and Technology, Northeast Agricultural University, Harbin, Heilongjiang 150030, China
| | - Feng Luan
- College of Engineering, Heilongjiang Bayi Agricultural University, Daqing, Heilongjiang 163000, China
| | - Shuli Zhang
- Wuchang Branch of Heilongjiang Academy of Agricultural Sciences, Wuchang, Heilongjiang 150229, People's Republic of China
| | - Dezhi Han
- Heihe Branch of Heilongjiang Academy of Agricultural Sciences, Heihe, China
| | - Mingliang Yang
- National Research Center of Soybean Engineering and Technology, Northeast Agricultural University, Harbin, Heilongjiang 150030, China
| | - Qingshan Chen
- National Research Center of Soybean Engineering and Technology, Northeast Agricultural University, Harbin, Heilongjiang 150030, China.
| | - Zhaoming Qi
- National Research Center of Soybean Engineering and Technology, Northeast Agricultural University, Harbin, Heilongjiang 150030, China.
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Shuang M, Sun J, Teng W. Identification and growth-promoting effect of endophytic bacteria in potato. ANN MICROBIOL 2022. [DOI: 10.1186/s13213-022-01697-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
AbstractIn agriculture, Bacillus
species are efficient and ecologically tool for promote the growth of the
plant.Purpose: This study obtains the plant growth-promoting (PGP) ability of
endophytic bacteria isolated from the potato tubers.Methods: Using endophytic
bacteria to promote potato growth, achieve the purpose of increasing production.
In this experiment, the growth- promoting ability of the strain was verified by
laboratory identification and field test validation.Result: The isolates
were identified as Bacillus species based on a 16S rRNA gene sequence
and gyrB gene sequence analysis. DNA hybridization finally identified it as Bacillus
velezensis. Among the PGP attributes, the strain K-9 was found to be positive
for indole acetic acid (IAA) production, phosphate solubilization, siderophore
production, and nitrogen fixation. The isolate was found negative for potassium
solubilization. The quantitative estimation of IAA product to 9.09 μg/ml. The
isolate also had the ability to produce lytic enzymes such as amylase and
protease. The quantitative estimation of protease activity is 89.16 μg/ml. The inoculation strain K-9 improved bioaccumulation of roots
and buds and yield in the potato compared to uninoculated control plants.Conclusion: These findings give an insight into the ways to use PGP bacteria to increase
potato production.
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Bacillus fonticola sp. nov., isolated from deep sea cold seep sediment. Arch Microbiol 2021; 203:4127-4132. [PMID: 34057547 DOI: 10.1007/s00203-021-02401-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 05/20/2021] [Accepted: 05/21/2021] [Indexed: 10/21/2022]
Abstract
In this study, we report a novel Gram-positive bacterium, designated as strain CS13T, isolated from deep-sea sediment collected in the cold seep area of the South China Sea. Growth of strain CS13T occurred at 16-37 °C (optimum 25-28 °C), pH 7.0-9.0 (optimum, 7.0), and 0-8% (w/v) NaCl (optimum, 2-3%). Phylogenetic analysis based on 16S rRNA gene sequence indicated that strain CS13T belonged to the genus Bacillus. The closest phylogenetic neighbors of strain CS13T are Bacillus carboniphilus JCM 9731T (96.0%), Bacillus pakistanensis NCCP-168T (95.7%) and Bacillus acidicola 105-2T (95.6%). The genomic DNA G + C content of strain CS13T is 43.7 mol%. The principal respiratory quinone was menaquinone 7 (MK-7). The polar lipids of CS13T contained diphosphatidylglycerol, phosphatidylglycerol, phospholipid, and glycolipid. The major fatty acids of CS13T contained anteiso-C15:0, anteiso-C17:0, C16:0 and C18:0. Strain CS13T harboured meso-diaminopimelic acid as the diagnostic diamino acid. Phylogenetic, physiological, biochemical, and morphological analyses suggested that strain CS13T represents a novel species of genus Bacillus, and the name Bacillus fonticola sp. nov. is proposed for the type species CS13T (= CCTCC AB 2019194T = JCM 33663T).
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Shylla L, Barik SK, Behera MD, Singh H, Adhikari D, Upadhyay A, Thapa N, Sarma K, Joshi SR. Impact of heavy metals on water quality and indigenous Bacillus spp. prevalent in rat-hole coal mines. 3 Biotech 2021; 11:253. [PMID: 33968596 DOI: 10.1007/s13205-021-02808-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 04/22/2021] [Indexed: 11/29/2022] Open
Abstract
The present study reports pollution evaluation indices employed to assess the intensity of metal pollution in water systems affected by acid mine drainage from rat-hole coal mines prevalent in North-east India. The concentration of seven eco-toxic metals was evaluated from coal mine waters which showed concentration order of Iron (Fe) > Manganese (Mn) > Zinc (Zn) > Chromium (Cr) > Lead (Pb) > Copper (Cu) > Cadmium (Cd). The water samples were acidic with mean pH 2.67 and burdened with dissolved solids (924.8 mg/L). The heavy metal pollution index (HPI) and heavy metal evaluation index (HEI) displayed high and medium range of pollution level in majority of the water samples. Statistical correlation suggested strong positive correlation between metals such as Cr with Mn (r = 0.780), Mn with Fe (r = 0.576), Cr with Fe (r = 0.680), Pb with Mn (r = 0.579) and Cr with Pb (r = 0.606), indicating Mn, Pb, Fe and Cr to be major metal contaminants; an unequivocal affirmation of degradation in water quality. The sampled waters had lower heavy metal concentration during monsoon and post-monsoon seasons. The commonly occurring bacterial species Bacillus pseudomycoides and Bacillus siamensis were chosen to understand their behavioral responses toward metal contamination. Findings demonstrated that Bacillus spp. from control environment had low tolerance to metals stress as evident from their MTC, MIC and growth curve studies. The survival of the native isolates across varying pH, salinity and temperature in the coal mine areas suggest these isolates as promising candidates for reclamation of rat-hole coal mining sites.
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Affiliation(s)
- Lily Shylla
- Department of Biotechnology and Bioinformatics, North Eastern Hill University, Shillong, 793022 India
| | - Saroj Kanta Barik
- CSIR-National Botanical Research Institute, Lucknow, Uttar Pradesh 226001 India
| | - Mukunda Dev Behera
- Centre for Oceans, Rivers, Atmosphere and Land Sciences (CORAL) and School of Water Resources, Indian Institute of Technology Kharagpur, Kharagpur, 721302 India
| | - Harsh Singh
- Department of Botany, North Eastern Hill University, Shillong, 793022 India
| | - Dibyendu Adhikari
- Department of Botany, North Eastern Hill University, Shillong, 793022 India
| | - Anamika Upadhyay
- Department of Botany, North Eastern Hill University, Shillong, 793022 India
| | - Namita Thapa
- Department of Botany, North Eastern Hill University, Shillong, 793022 India
| | - Kiranmay Sarma
- University School of Environment Management, GGS Indraprastha University, New Delhi, Delhi 110078 India
| | - Santa Ram Joshi
- Department of Biotechnology and Bioinformatics, North Eastern Hill University, Shillong, 793022 India
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Shylla L, Barik SK, Joshi SR. Characterization and bioremediation potential of native heavy-metal tolerant bacteria isolated from rat-hole coal mine environment. Arch Microbiol 2021; 203:2379-2392. [PMID: 33665708 DOI: 10.1007/s00203-021-02218-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2020] [Revised: 01/29/2021] [Accepted: 02/09/2021] [Indexed: 10/22/2022]
Abstract
Identification and characterization of endogenous and stress adapted bacterial species, from rat-hole coal mines in Meghalaya, amplify the ambit of bioremediation for eco-restoration. 52 native bacterial isolates, drawn from soil and water samples of these mines, were analysed for bioremediation potential, based on growth and metal tolerance parameters. 12 of these isolates were metal tolerant with Bacillus spp. being the most promising taxon. Three isolates, namely, Serratia marcescens KH-CC, Bacillus altitudinis KH-16F and Bacillus siamensis KH-12A, exhibited high Maximum Tolerable Concentration (MTC) against Fe (500 ppm), Mn (830 ppm) and Pb (1400 ppm). B. siamensis showed highest Fe remediation with 48.34% removal capacity, while maximum removal for Mn and Pb was exhibited by Serratia marcescens at 72.5 and 83%, respectively. The growth profile of the isolates indicated their ability to survive under pH, temperature and salt stress conditions. In vitro growth kinetics studies of the isolates revealed their ability to decrease the acidity of growth media and improve alkalinity from an initial of pH 4.8-5.2 to an alkaline level of pH 8.5-9. These native bacteria, extracted from the stressed coal mine habitat, are potential germane applicants for rehabilitation and eco-restoration of ecologically degraded mine sites.
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Affiliation(s)
- L Shylla
- Department of Biotechnology and Bioinformatics, North Eastern Hill University, Shillong, 793022, India
| | - S K Barik
- CSIR-National Botanical Research Institute, Lucknow, Uttar Pradesh, 226001, India
| | - S R Joshi
- Department of Biotechnology and Bioinformatics, North Eastern Hill University, Shillong, 793022, India.
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Daroonpunt R, Yiamsombut S, Sitdhipol J, Tanasupawat S. Bacillus salacetis sp. nov., a slightly halophilic bacterium from Thai shrimp paste (Ka-pi). Int J Syst Evol Microbiol 2019; 69:1162-1168. [PMID: 30767851 DOI: 10.1099/ijsem.0.003286] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-positive, slightly halophilic, endospore-forming, strictly aerobic, rod-shaped bacterium, designated SKP7-4T, was isolated from shrimp paste collected from Samut Sakhon province, Thailand. Strain SKP7-4T grew at pH 6.0-9.0 (optimum, 7.5), at 20-40 °C (37 °C) and in 0-15 % (w/v) NaCl (1-3 %). The diamino acid found in the cell-wall peptidoglycan was meso-diaminopimelic acid. Menaquinone with seven isoprene units was the major isoprenoid quinone. Diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and three unidentified phospholipids were detected as polar lipids. It contained iso-C15 : 0 and anteiso-C15 : 0 as major cellular fatty acids. On the basis of 16S rRNA gene sequence analysis, strain SKP7-4T belonged to the genus Bacillus and was closely related to Bacillus vietnamensis JCM 11124T, Bacillus marisflavi JCM 11544T, Bacillus aquimaris JCM 11545T and Bacillusoryzaecorticis JCM 19602T, with 98.7, 97.9, 97.8 and 97.8 % similarity, respectively. The draft genome of SKP7-4T was 4.68 Mb with 5208 coding sequences with an average G+C content of 43.2 mol%. The ANIb and ANIm values of strain SKP7-4T were 70.0 and 84.3 %, respectively, and the digital DNA-DNA hybridization value was 20 % in comparison with the draft genome of B. vietnamensis JCM 11124T. On the basis of the results of phenotypic, chemotaxonomic and phylogenetic analyses, the strain should represent a novel species of the genus Bacillus and the name Bacillus salacetis sp. nov. is proposed. The type strain is SKP7-4T (=JCM 33205T=KCTC 43014T=TISTR 2596T).
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Affiliation(s)
- Rungsima Daroonpunt
- Department of Biochemistry and Microbiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok 10330, Thailand.,Nutritional Therapy and Dietetics Division, Faculty of Allied Health Sciences, Burapha University, Chonburi 20131, Thailand
| | - Supalurk Yiamsombut
- Department of Biochemistry and Microbiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok 10330, Thailand
| | - Jaruwan Sitdhipol
- Bioscience Department, Thailand Institute of Scientific and Technological Research (TISTR), Pathumthani 12120, Thailand
| | - Somboon Tanasupawat
- Department of Biochemistry and Microbiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok 10330, Thailand
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Halophiles: biology, adaptation, and their role in decontamination of hypersaline environments. World J Microbiol Biotechnol 2016; 32:135. [PMID: 27344438 DOI: 10.1007/s11274-016-2081-9] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Accepted: 05/07/2016] [Indexed: 10/21/2022]
Abstract
The unique cellular enzymatic machinery of halophilic microbes allows them to thrive in extreme saline environments. That these microorganisms can prosper in hypersaline environments has been correlated with the elevated acidic amino acid content in their proteins, which increase the negative protein surface potential. Because these microorganisms effectively use hydrocarbons as their sole carbon and energy sources, they may prove to be valuable bioremediation agents for the treatment of saline effluents and hypersaline waters contaminated with toxic compounds that are resistant to degradation. This review highlights the various strategies adopted by halophiles to compensate for their saline surroundings and includes descriptions of recent studies that have used these microorganisms for bioremediation of environments contaminated by petroleum hydrocarbons. The known halotolerant dehalogenase-producing microbes, their dehalogenation mechanisms, and how their proteins are stabilized is also reviewed. In view of their robustness in saline environments, efforts to document their full potential regarding remediation of contaminated hypersaline ecosystems merits further exploration.
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Daroonpunt R, Itoh T, Kudo T, Ohkuma M, Tanasupawat S. Bacillus piscicola sp. nov., isolated from Thai fish sauce (Nam-pla). Int J Syst Evol Microbiol 2016; 66:1151-1155. [DOI: 10.1099/ijsem.0.000851] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Rungsima Daroonpunt
- Department of Biochemistry and Microbiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok 10330, Thailand
| | - Takashi Itoh
- Japan Collection of Microorganisms, RIKEN BioResource Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Takuji Kudo
- Japan Collection of Microorganisms, RIKEN BioResource Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Moriya Ohkuma
- Japan Collection of Microorganisms, RIKEN BioResource Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Somboon Tanasupawat
- Department of Biochemistry and Microbiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok 10330, Thailand
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Jamal Q, Ahmed I, Rehman SU, Abbas S, Kim KY, Anees M. Isolation and Characterization of Bacteria from Coal Mines of Dara Adam Khel, Pakistan. GEOMICROBIOLOGY JOURNAL 2016; 33:1-9. [DOI: 10.1080/01490451.2014.964886] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2024]
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Abbas S, Ahmed I, Kudo T, Iqbal M, Lee YJ, Fujiwara T, Ohkuma M. A heavy metal tolerant novel bacterium, Bacillus malikii sp. nov., isolated from tannery effluent wastewater. Antonie van Leeuwenhoek 2015; 108:1319-1330. [PMID: 26362330 DOI: 10.1007/s10482-015-0584-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2015] [Accepted: 09/04/2015] [Indexed: 11/29/2022]
Abstract
The taxonomic position of a Gram-stain positive and heavy metal tolerant bacterium, designated strain NCCP-662(T), was investigated by polyphasic characterisation. Cells of strain NCCP-662(T) were observed to be rod to filamentous shaped, motile and strictly aerobic, and to grow at 10-50 °C (optimum 30-37 °C) and at pH range of 6-10 (optimum pH 7-8). The strain was found to be able to tolerate 0-12 % NaCl (w/v) and heavy metals (Cr 1200 ppm, Pb 1800 ppm and Cu 1200 ppm) in tryptic soya agar medium. The phylogenetic analysis based on the 16S rRNA gene sequence of strain NCCP-662(T) showed that it belongs to the genus Bacillus and showed high sequence similarity (98.2 and 98.0 %, respectively) with the type strains of Bacillus niabensis 4T19(T) and Bacillus halosaccharovorans E33(T). The chemotaxonomic data showed that the major quinone is MK-7; the predominant cellular fatty acids are anteiso-C15 :0, iso-C14:0, iso-C16:0 and C16:0 and iso-C15:0; the major polar lipids are diphosphatidylglycerol, phosphatidylglycerol along with several unidentified glycolipids, phospholipids and polar lipids. The DNA G+C content was determined to be 36.9 mol%. These data also support the affiliation of strain NCCP-662(T) with the genus Bacillus. The level of DNA-DNA relatedness between strain NCCP-662(T) and B. niabensis JCM 16399(T) was 20.5 ± 0.5 %. On the basis of physiological and biochemical characteristics, phylogenetic analyses and DNA-DNA hybridization data, strain NCCP-662(T) can be clearly differentiated from the validly named Bacillus species and thus represents a new species, for which the name Bacillus malikii sp. nov. is proposed with the type strain NCCP-662(T) (= LMG 28369(T) = DSM 29005(T) = JCM 30192(T)).
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Affiliation(s)
- Saira Abbas
- National Culture Collection of Pakistan (NCCP), National Institute for Genomics and Advanced Biotechnology (NIGAB), National Agricultural Research Centre (NARC), Park Road, Islamabad, 45500, Pakistan.,Department of Plant Genomics and Biotechnology (PGB), PARC Institute of Advanced Studies in Agriculture (PIASA), National Agricultural Research Centre (NARC), Park Road, Islamabad, 45500, Pakistan.,Japan Collection of Microorganisms, RIKEN BioResource Center, 3-1-1 Koyadai, Tsukuba, Ibaraki, 305-0074, Japan.,Laboratory of Plant Nutrition and Fertilizers, Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Iftikhar Ahmed
- National Culture Collection of Pakistan (NCCP), National Institute for Genomics and Advanced Biotechnology (NIGAB), National Agricultural Research Centre (NARC), Park Road, Islamabad, 45500, Pakistan. .,Department of Plant Genomics and Biotechnology (PGB), PARC Institute of Advanced Studies in Agriculture (PIASA), National Agricultural Research Centre (NARC), Park Road, Islamabad, 45500, Pakistan. .,Japan Collection of Microorganisms, RIKEN BioResource Center, 3-1-1 Koyadai, Tsukuba, Ibaraki, 305-0074, Japan. .,Laboratory of Plant Nutrition and Fertilizers, Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan.
| | - Takuji Kudo
- Japan Collection of Microorganisms, RIKEN BioResource Center, 3-1-1 Koyadai, Tsukuba, Ibaraki, 305-0074, Japan
| | - Muhammad Iqbal
- Department of Plant Genomics and Biotechnology (PGB), PARC Institute of Advanced Studies in Agriculture (PIASA), National Agricultural Research Centre (NARC), Park Road, Islamabad, 45500, Pakistan
| | - Yong-Jae Lee
- Korean Collection for Type Cultures, Biological Resources Centre, KRIBB, 125 Gwahak-ro, Yuseong-gu, Daejeon, 305-806, Republic of Korea
| | - Toru Fujiwara
- Laboratory of Plant Nutrition and Fertilizers, Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Moriya Ohkuma
- Japan Collection of Microorganisms, RIKEN BioResource Center, 3-1-1 Koyadai, Tsukuba, Ibaraki, 305-0074, Japan
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Bangash A, Ahmed I, Abbas S, Kudo T, Shahzad A, Fujiwara T, Ohkuma M. Kushneria pakistanensis sp. nov., a novel moderately halophilic bacterium isolated from rhizosphere of a plant (Saccharum spontaneum) growing in salt mines of the Karak area in Pakistan. Antonie van Leeuwenhoek 2015; 107:991-1000. [PMID: 25631404 DOI: 10.1007/s10482-015-0391-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2014] [Accepted: 01/17/2015] [Indexed: 10/24/2022]
Abstract
The taxonomic position of a Gram-stain negative, moderately halophilic bacterium, designated NCCP-934(T), was investigated using polyphasic taxonomic approach. The strain NCCP-934(T) was isolated from rhizosphere of a plant (Saccharum spontaneum, family Poaceae) growing in salt mines area in the Karak district of Khyber Pakhtunkhwa Province, Pakistan. Cells of strain NCCP-934(T) are rod shaped and motile. The bacterium is strictly aerobic, can grow at a temperature range of 10-40 °C (optimum at 30-33 °C) and in a pH range of 6.0-10.5 (optimum pH 7.0-9.0). The strain can tolerate 1-30 % (w/v) NaCl (optimal growth occurs in the presence of approximately 3-9 % NaCl). The phylogenetic analysis based on the 16S rRNA gene sequence, showed that strain NCCP-934(T) belongs to the genus Kushneria with the highest sequence similarity to K. marisflavi SW32(T) (98.9 %), K. indalinina CG2.1(T) (98.7 %), K. avicenniae MW2a(T) (98.4 %) and less than 97 % similarity with other related species (94.7 % with the type species of the genus, K. aurantia A10(T)). DNA-DNA relatedness between strain NCCP-934(T) and the type strains of the closely related species was lower than 18 %. The chemotaxonomic data (major respiratory quinone, Q9; predominant fatty acids, C18:1 ω7c and C16:0 followed by C12:0 3-OH and Summed features 3 (C16:1 ω7c/iso-C15:0 2-OH); major polar lipids, diphosphatidylglycerol, phosphatidylglycerol, phosphatidylmonomethylethanol, phosphatidylserine, phosphatidylinositol and three polar lipid of unknown structure) supported the affiliation of strain NCCP-934(T) within the genus Kushneria. The DNA G+C content of strain NCCP-934(T) was 59.2 mol%. On the basis of phenotypic, chemotaxonomic and phylogenetic data, strain NCCP-934(T) can be distinguished from the closely related taxa and thus represents a novel species in the genus Kushneria, for which the name Kushneria pakistanensis sp. nov. is proposed, with the type strain NCCP-934(T) (=LMG 28525(T) = KCTC 42082(T) = JCM 18802(T)).
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Affiliation(s)
- Asia Bangash
- National Culture Collection of Pakistan, National Institute for Genomics and Advanced Biotechnology (NIGAB), National Agricultural Research Centre (NARC), Park Road, Islamabad, 45500, Pakistan
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Ahmed I, Abbas S, Kudo T, Iqbal M, Fujiwara T, Ohkuma M. Deinococcus citri sp. nov., isolated from citrus leaf canker lesions. Int J Syst Evol Microbiol 2014; 64:4134-4140. [PMID: 25256704 DOI: 10.1099/ijs.0.066555-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2024] Open
Abstract
A Gram-stain-positive, strictly aerobic, non-motile, coccoid bacterium, designated NCCP-154(T), was isolated from citrus leaf canker lesions and was subjected to a polyphasic taxonomic study. Strain NCCP-154(T) grew at 10-37 °C (optimum 30 °C) and at pH 7.0-8.0 (optimum pH 7.0). The novel strain exhibited tolerance of UV irradiation (>1000 J m(-2)). Based on 16S rRNA gene sequence analysis, strain NCCP-154(T) showed the highest similarity to Deinococcus gobiensis CGMCC 1.7299(T) (98.8 %), and less than 94 % similarity to other closely related taxa. The chemotaxonomic data [major menaquinone, MK-8; cell-wall peptidoglycan type, A3β (Orn-Gly2); major fatty acids, summed feature 3 (C16 : 1ω7c/iso-C15 : 0 2-OH; 35.3 %) followed by C16 : 0 (12.7 %), iso-C17 : 1ω9c (9.2 %), C17 : 1ω8c (7.4 %) and iso-C17 : 0 (6.9 %); major polar lipids made up of several unidentified phosphoglycolipids and glycolipids and an aminophospholipid, and mannose as the predominant whole-cell sugar] also supported the affiliation of strain NCCP-154(T) to the genus Deinococcus. The level of DNA-DNA relatedness between strain NCCP-154(T) and D. gobiensis JCM 16679(T) was 63.3±3.7 %. The DNA G+C content of strain NCCP-154(T) was 70.0 mol%. Based on the phylogenetic analyses, DNA-DNA hybridization and physiological and biochemical characteristics, strain NCCP-154(T) can be differentiated from species with validly published names. Therefore, it represents a novel species of the genus Deinococcus. The name Deinococcus citri sp. nov. is proposed, with the type strain NCCP-154(T) ( = JCM 19024(T) = DSM 24791(T) = KCTC 13793(T)).
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Affiliation(s)
- Iftikhar Ahmed
- Laboratory of Plant Nutrition and Fertilizers, Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
- Japan Collection of Microorganisms, RIKEN BioResource Center, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan
- National Culture Collection of Pakistan, National Institute for Genomics and Advanced Biotechnology (NIGAB), National Agricultural Research Centre (NARC), Park Road, Islamabad 45500, Pakistan
| | - Saira Abbas
- Laboratory of Plant Nutrition and Fertilizers, Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
- Japan Collection of Microorganisms, RIKEN BioResource Center, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan
- National Culture Collection of Pakistan, National Institute for Genomics and Advanced Biotechnology (NIGAB), National Agricultural Research Centre (NARC), Park Road, Islamabad 45500, Pakistan
| | - Takuji Kudo
- Japan Collection of Microorganisms, RIKEN BioResource Center, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan
| | - Muhammad Iqbal
- National Culture Collection of Pakistan, National Institute for Genomics and Advanced Biotechnology (NIGAB), National Agricultural Research Centre (NARC), Park Road, Islamabad 45500, Pakistan
| | - Toru Fujiwara
- Laboratory of Plant Nutrition and Fertilizers, Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Moriya Ohkuma
- Japan Collection of Microorganisms, RIKEN BioResource Center, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan
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Oren A, Garrity GM. List of new names and new combinations previously effectively, but not validly, published. Int J Syst Evol Microbiol 2014. [DOI: 10.1099/ijs.0.068759-0] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The purpose of this announcement is to effect the valid publication of the following effectively published new names and new combinations under the procedure described in the Bacteriological Code (1990 Revision). Authors and other individuals wishing to have new names and/or combinations included in future lists should send three copies of the pertinent reprint or photocopies thereof, or an electronic copy of the published paper to the IJSEM Editorial Office for confirmation that all of the other requirements for valid publication have been met. It is also a requirement of IJSEM and the ICSP that authors of new species, new subspecies and new combinations provide evidence that types are deposited in two recognized culture collections in two different countries. It should be noted that the date of valid publication of these new names and combinations is the date of publication of this list, not the date of the original publication of the names and combinations. The authors of the new names and combinations are as given below. Inclusion of a name on these lists validates the publication of the name and thereby makes it available in the nomenclature of prokaryotes. The inclusion of a name on this list is not to be construed as taxonomic acceptance of the taxon to which the name is applied. Indeed, some of these names may, in time, be shown to be synonyms, or the organisms may be transferred to another genus, thus necessitating the creation of a new combination.
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Affiliation(s)
- Aharon Oren
- The Institute of Life Sciences, The Hebrew University of Jerusalem, The Edmond J. Safra Campus, Givat Ram, 91904 Jerusalem, Israel
| | - George M. Garrity
- Department of Microbiology & Molecular Genetics, Biomedical Physical Sciences, Michigan State University, East Lansing, MI 48824-4320, USA
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