scholarly journals Isolation, Characterization, and Molecular Identification of Phosphate Solubilizing Bacteria from Several Tropical Soils

2013 ◽  
Vol 18 (1) ◽  
pp. 67
Author(s):  
Fahrizal Hazra ◽  
Etty Pratiwi
Keyword(s):  
Acetic Acid ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Indole Acetic Acid ◽  
Tropical Soils ◽  
Rrna Gene ◽  
Gram Negative Bacteria ◽  
Phosphate Solubilizing Bacteria ◽  
Gram Negative ◽  
Phosphate Solubilizing

The objectives of the research were: (i)  to isolate and characterize of phosphate solubilizing bacteria (PSB) and (ii) to identify PSB based on molecular amplification of 16S rRNA gene.  Soil samples were collected from rhizosphere in Bogor, West Nusa Tenggara, and East Nusa Tenggara.  Several stages in this research were: (i) isolation PSB in Pikovskaya agar, (ii) morphological and biochemical characterization of PSB, (iii) measurement of  phosphatase enzymes, and (iv) measurement of secreting indole acetic acid phytohormone.   As many as 29 isolates of PSB have been collected and three isolates of them, namely: P 3.5 (East Nusa Tenggara), P 6.2 (West Nusa Tenggara), and P 10.1 (Citeureup, West Java) were chosen for further study.  There were many characteristics of isolate P 10.1: (i) it had capable to solubilize P with the value of highest solubilization index (1.80), (ii) it had the highest phosphatase enzyme (120.40 mg kg-1), and (iii) it had the highest pH decrease at each observation for six days.  Isolates P 3.5 and P 10.1 were the Gram-negative bacteria with coccus shapes and isolate P 6.2 was a Gram-negative bacteria with bacillus shape.  Deoxiribonucleat Acid (DNA) amplification of these bacteria employing 16S rRNA primers generated the 1,300bp-PCR product.  The results of the analysis of 16S rRNA gene sequences showed that isolates P 3.5 and P 10.1 has 98% similarity with Gluconacetobacter sp. strains Rg1-MS-CO and isolate P 6.2 has 97% similarity with Enterobacter sp. pp9c strains.Keywords: 16S rRNA, indole acetic acid, isolation, phosphatase enzymes, phosphate solubilizing bacteria[How to Cite : Hazra F and E Pratiwi. 2013. Isolation, Characterization, and Molecular Identification of Phosphate Solubilizing Bacteria from Several Tropical Soils. J Trop Soils, 18 (1): 67-74. doi: 10.5400/jts.2013.18.1.67][Permalink/DOI: www.dx.doi.org/10.5400/jts.2013.18.1.67]

scholarly journals In silico analysis of 16S rRNA gene sequencing based methods for identification of medically important aerobic Gram-negative bacteria

2011 ◽  
Vol 60 (9) ◽  
pp. 1281-1286 ◽  
Author(s):  
Jade L. L. Teng ◽  
Ming-Yiu Yeung ◽  
Geoffrey Yue ◽  
Rex K. H. Au-Yeung ◽  
Eugene Y. H. Yeung ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequencing ◽  
In Silico Analysis ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Gram Negative Bacteria ◽  
Gram Negative ◽  
Rrna Gene Sequencing ◽  
Silico Analysis

Sphingosinicella flava sp. nov., indole acetic acid producing bacteria isolated from maize field soil

2021 ◽  
Vol 71 (10) ◽  
Author(s):  
Geeta Chhetri ◽  
Minchung Kang ◽  
Jiyoun Kim ◽  
Inhyup Kim ◽  
Yoonseop So ◽  
...  
Keyword(s):  
Acetic Acid ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Indole Acetic Acid ◽  
Rrna Gene ◽  
Field Soil ◽  
Content Type ◽  
Link Type ◽  
Maize Field

A novel isolated yellow-pigmented bacterial designated strain UDD2T was isolated from a maize field soil sample collected in Ilsan, Republic of Korea. Cells of strain UDD2T were Gram-stain-negative, non-sporulating, long rod-shaped and exhibited flagellar motility. Cells could grow at 15–42 °C and pH 5.5–11.0. Strain UDD2T was sensitive to NaCl and barely tolerated up to 1 % NaCl (w/v). Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain UDD2T formed a separate clade with the members of genus Sphingosinicella within the family Sphingomonadaceae . Strain UDD2T showed the highest 16S rRNA gene sequence similarity to Sphingosinicella vermicomposti KCTC 224446T (98.5 %) and Sphingosinicella humi KCTC 62519T (96.7 %), followed by members of the genus Sphingomonas (96.4–94.5 %) and Sphingobium (96.1–94.9 %), but they were located in other phylogenetic clusters. Average nucleotide identity and digital DNA–DNA hybridization values between strain UDD2T and S. vermicomposti KCTC 224446T and S. humi KCTC 62519T were 80.2/24.2 and 75.6/20.4 %, respectively. The total size of the genome was 2 421 697 bp and composed of one circular chromosome, with a G+C content of 63.7 mol%. Strain UDD2T produced indole acetic acid (IAA) in the presence of l-tryptophan. Bacterial IAA is a crucial phytohormone in plant growth and development. Gene clusters for indole-3-glycerol phosphate synthase and tryptophan synthase were found in the genome of strain UDD2T. To the best of our knowledge, no member of the genus Sphingosinicella has been reported to produce IAA to date. The major cellular fatty acids (>10 %) were found to be C16 : 0, C14 : 0 2OH and summed feature 3 (comprising C16  : 1 ω7c and/or iso-C15  :  0 2-OH). Strain UDD2T had ubiquinone Q-10 as the major respiratory quinone and homospermidine as the major polyamine. The polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, sphingoglycolipid, phosphatidylglycerol, phosphatidylcholine, three unidentified phosphoglycolipids, one unidentified phospholipid, one unidentified aminoglycophospholipid, one unidentified glycolipid and one unidentified polar lipid. Based on the phylogenetic, phenotypic, chemotaxonomic and genotypic data, strain UDD2T represents a novel species of the genus Sphingosinicella , for which the name Sphingosinicella flava is proposed. The type strain is UDD2T (=KCTC 82357T=NBRC 114507T).

Gracilibacillus suaedae sp. nov., an indole acetic acid-producing endophyte isolated from a root of Suaeda salsa

2021 ◽  
Vol 71 (12) ◽  
Author(s):  
Xiao-Xian Huang ◽  
Lian Xu ◽  
Ji-Quan Sun
Keyword(s):  
Acetic Acid ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Indole Acetic Acid ◽  
Suaeda Salsa ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Gene Similarity

A Gram-stain-positive, facultatively anaerobic, spore-forming, motile with unipolar biflagella, rod-shaped, indole acetic acid-producing bacterium, named LD4P30T, was isolated from a root of Suaeda salsa collected in Inner Mongolia, northern China. Strain LD4P30T grew at pH 6.0–11.0 (optimum, pH 7.0), 10–40 °C (35 °C) and in the presence of 1–15% (w/v) NaCl (5%). The strain was positive for oxidase and negative for catalase. The major cellular fatty acids of strain LD4P30T were iso-C15:0, C15:1 ω5c and anteiso-C15:0; the major polar lipids were diphosphatidylglycerol and phosphatidylglycerol; and menaquinone-7 was the only respiratory quinone. The genomic DNA G+C content was 36.7 mol%. A phylogenetic tree based on 16S rRNA gene sequences showed that strain LD4P30T clustered with Gracilibacillus thailandensis TP2-8T, Gracilibacillus saliphilus YIM 91119T and Gracilibacillus lacisalsi BH312T, and showed 99.0, 98.9, 98.0 and <97.7% 16S rRNA gene similarity to G. thailandensis TP2-8T, G. saliphilus YIM 91119T, G. lacisalsi BH312T and all other current type strains, respectively. The digital DNA–DNA hybridization and average nucleotide identity based on blast values between strain LD4P30T and G. saliphilus YIM 91119T, G. thailandensis TP2-8T and G. lacisalsi BH312T were 44.9, 44.7 and 44.4%, and 91.1, 91.0 and 90.8%, respectively. Based on its phenotypic, physiological and phylogenetic characteristics, strain LD4P30T represents a novel species, for which the name Gracilibacillus suaedae is proposed. The type strain is LD4P30T (=CGMCC 1.17697T=KCTC 82375T).

scholarly journals Gottfriedia Endophyticus sp. nov., a Novel Indole-Acetic Acid Producing Bacterium Isolated From The Roots of Rice Plant

2022 ◽  
Author(s):  
Geeta Chhetri ◽  
Inhyup Kim ◽  
Taegun Seo
Keyword(s):  
Acetic Acid ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Rice Plant ◽  
Indole Acetic Acid ◽  
Bacterial Species ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences

Abstract A Gram-stain-positive, aerobic, motile and rod-shaped bacterium, designated RG28T, was isolated from the roots of rice plant collected from paddy fields in Goyang, South Korea. Cells of the strain were oxidase-negative but catalase-positive. Strain RG28T was found to grow at 10–50°C (optimum, 25–30°C), pH 5.0–10.0 (optimum, pH 7.0) and in 1.0–5.0 % (w/v) NaCl (optimum, 0%). The cell-wall peptidoglycan contained meso-diaminopimelic acid and the predominant menaquinones were MK-7 and MK-6.The predominant cellular fatty acids were C16:0, iso-C15:0 and anteiso-C15:0. The major polar lipids included phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, four unidentified aminophosphoglycolipids, four unidentified aminophospholipids, two unidentified glycolipids, one unidentified aminoglycolipid and four unidentified lipids. The genomic DNA G+C content was 33.5 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that the strain was closely related to Gottfriedia acidiceleris CBD 119T (98.6%), Gottfriedia solisilvae LMG 18422T (98.5 %) and Gottfriedia luciferensis LMG 18422T (98.4 %). The average nucleotide identity (ANI) and in silico DNA–DNA hybridization (isDDH) values between strain RG28T and type strains of Gottfriedia species were lower than the cut-offs (≥95–96 % for ANI and ≥70 % for isDDH) required to define a bacterial species. Meanwhile, the strain has the ability to produce indole-acetic acid (40.5 µg/mL). Phylogenetic, physiological and chemotaxonomic data suggested that strain RG28T represented a novel species of the genus Gottfriedia, for which the name Gottfriedia endophyticus sp. nov. is proposed, with the type strain RG28T (=KCTC 43327T=TBRC 15151T).Repositories: The draft genome and 16S rRNA gene sequences of strain RG28T have been deposited in GenBank/EMBL/DDBJ under accession numbers JAGIYQ000000000 and MW386408 respectively.

scholarly journals USE OF 16S rRNA GENE FOR CHARACTERIZATION OF PHOSPHATE-SOLUBILIZING BACTERIA ASSOCIATED WITH CORN

2009 ◽  
Vol 32 (1) ◽  
pp. 31-37
Author(s):  
David Espinosa-Victoria ◽  
Lucía López-Reyes ◽  
Aldo De La Cruz-Benítez
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Rrna Gene ◽  
Phosphate Solubilizing Bacteria ◽  
Accession Number ◽  
Ncbi Accession ◽  
Buffering Agent ◽  
Phosphate Solubilizing ◽  
Solubilizing Activity ◽  
Ncbi Accession Number

Thirty-six strains of phosphate-solubilizing bacteria (PSB) isolated from the rhizosphere and rhizoplane of corn (Zea mays L.) crops in different states of México were subjected to phenotypic and genotypic characterization. The phosphate-solubilizing activity of each strain was first evaluated using tricalcium phosphate as the phosphorus source in the NBRIP-BPB culture medium. Phosphatesolubilizing capacity was also evaluated by adding the pH buffering agent MES (2-[Morpholine] ethanosulfonic acid) to the growth medium. Amplified ribosomal RNA restriction pattern analysis (ARDRA) was used to evaluate the genetic diversity. From the data matrix obtained, a dendrogram was built using the UPGMA method. The 16S rRNA gene of the BUAP29, BUAP36 and CP08 strains was amplified, cloned and sequenced for taxonomic identification. The 36 bacterial strains exhibited different levels of tricalcium phosphate solubilizing activity. Only BUAP33, BUAP17 and BUAP21 strains did not show the typical solubilization halo when the MES buffering agent was added to the growth medium. The analysis of ARDRA patterns as well as the dendrogram exhibited a large genetic diversity among the 36 PSB analyzed, with BUAP36 and BUAP15 strains showing 100 % similarity. The 16S rRNA gene sequence alignment of CP08, BUAP29 and BUAP36 strains showed 99 % identity with the sequences of Advenella incenata strain R-16599 (NCBI accession number AY569458.1), Burkholderia sp (NCBI accession number AY353696) and Burkholderia gladioli strain 223-1 (NCBI accession number DQ355168.1), respectively. In this study the A. incenata strain is reported as a PSB for the first time.

scholarly journals Phylogenetic relationship of Gram Negative Bacteria of Enterobacteriaceae Family in the Positive Widal Blood Cultures based on 16S rRNA Gene Sequences

2015 ◽  
Vol 19 (1) ◽  
pp. 64
Author(s):  
Sri Darmawati ◽  
Langkah Sembiring ◽  
Widya Asmara ◽  
Wayan T. Artama ◽  
Masashi Kawaichi
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Enterobacter Cloacae ◽  
Salmonella Typhi ◽  
Blood Cultures ◽  
Rrna Gene ◽  
Gram Negative Bacteria ◽  
16S Rrna Gene Sequences ◽  
Gram Negative ◽  
Relationship Of

The purpose of this study was to analyze the phylogenetic relationship of Gram negative bacteria (3strains of Salmonella typhi, 1 strain of Escherichia coli, 1 strain of Serratia marcescens, and 3 strains of Enterobactercloacae) of Enterobacteriaceae family in positive Widal blood cultures based on 16S rRNA gene sequences. Theresults respectively showed that each two 16S rRNA gene clones of Serratia marcescens KD 08.4 had a closerelationship with 16S rRNA gene of Serrratia marcescens ATCC 13880 (similarity: 99.53-99.8%), Eschericia coliBA 30.1 with Eschericia coli ATCC 11775T (similarity: 99.38-99.67%), Salmonella typhi BA 07.4, Salmonella typhiKD 30.4, and Salmonella typhi SA 02.2 with Salmonella typhi ATCC 19430T (similarity: 99.4-100%) as well as theisolates of Enterobacter cloacae SA 02.1, Enterobacter cloacae BA 45.4.1, one 16S rRNA gene clone of Enterobactercloacae TG 03.5 with Enterobacter cloacae ATCC 23373 (similarity: 99.0-99.87%).

Aquibacillus kalidii sp. nov., an indole acetic acid-producing endophyte from a shoot of Kalidium cuspidatum, and reclassification of Virgibacillus campisalis Lee et al. 2012 as a later heterotypic synonym of Virgibacillus alimentarius Kim et al. 2011

2021 ◽  
Vol 71 (10) ◽  
Author(s):  
Hai-Tao Wang ◽  
Lian Xu ◽  
Ji-Quan Sun
Keyword(s):  
Acetic Acid ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Type Species ◽  
Indole Acetic Acid ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
Content Type ◽  
Link Type

A Gram-stain-positive, strictly aerobic, motile, endospore-forming, milk-white, indole acetic acid-producing, rod-shaped bacterial strain, designated as HU2P27T, was isolated from a shoot of Kalidium cuspidatum collected in Tumd Right Banner, Inner Mongolia, PR China. Strain grew at 10–40 °C (optimum, 30 °C), at pH 6.0–9.0 (optimum, pH 7.0) and with 0–14.0 % NaCl (optimum, 5.0–8.0 %). The strain tested positive for oxidase, catalase and nitrate reductase. The phylogenetic trees based on the 16S rRNA gene sequence and the core genome both showed that strain HU2P27T clustered with Aquibacillus koreensis BH30097T, sharing 97.7 % and <97.0 % of 16S rRNA gene similarity with A. koreensis BH30097T and any other type strain. Strain HU2P27T contained MK-7 as the major respiratory quinone. Its major fatty acids were anteiso-C15 : 0 and iso-C15 : 0, and the major polar lipids were phosphatidylglycerol, diphosphatidylglycerol and four unidentified phospholipids. The genomic DNA G+C content was 36.0 mol%. The average nucleotide identity, amino acid identity and digital DNA–DNA hybridization values of strain HU2P27T with A. koreensis BH30097T were 71.7, 69.2 and 19.4%, respectively. The phylogenetic, physiological and phenotypic results allowed the discrimination of strain HU2P27T from its phylogenetic relatives. The name Aquibacillus kalidii sp. nov. is therefore proposed. The type strain is strain HU2P27T (=CGMCC 1.18646T=KCTC 43248T). Based on the results of 16S rRNA gene and genome analyses, we propose the reclassification of Virgibacillus campisalis Lee et al. 2012 as a later heterotypic synonym of Virgibacillus alimentarius Kim et al. 2011.

scholarly journals Inorganic Phosphate Solubilization by a Novel Isolated Bacterial Strain Enterobacter sp. ITCB-09 and Its Application Potential as Biofertilizer

Agriculture ◽  
2020 ◽  
Vol 10 (9) ◽  
pp. 383 ◽  
Author(s):  
Gustavo Enrique Mendoza-Arroyo ◽  
Manuel Jesús Chan-Bacab ◽  
Ruth Noemi Aguila-Ramírez ◽  
Benjamín Otto Ortega-Morales ◽  
René Efraín Canché Solís ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Inorganic Phosphate ◽  
Extracellular Polymeric Substances ◽  
Phosphate Solubilization ◽  
Rrna Gene ◽  
Bacterial Strains ◽  
Habanero Pepper ◽  
Phosphate Solubilizing

The excessive use of fertilizers in agriculture is mainly due to the recognized plant requirements for soluble phosphorus. This problem has limited the implementation of sustainable agriculture. A viable alternative is to use phosphate solubilizing soil microorganisms. This work aimed to isolate inorganic phosphorus-solubilizing bacteria from the soils of agroecosystems, to select and identify, based on sequencing and phylogenetic analysis of the 16S rRNA gene, the bacterium with the highest capacity for in vitro solubilization of inorganic phosphate. Additionally, we aimed to determine its primary phosphate solubilizing mechanisms and to evaluate its effect on Habanero pepper seedlings growth. A total of 21 bacterial strains were isolated by their activity on Pikovskaya agar. Of these, strain ITCB-09 exhibited the highest ability to solubilize inorganic phosphate (865.98 µg/mL) through the production of organic acids. This strain produced extracellular polymeric substances and siderophores that have ecological implications for phosphate solubilization. 16S rRNA gene sequence analysis revealed that strain ITCB-09 belongs to the genus Enterobacter. Enterobacter sp. ITCB-09, especially when immobilized in beads, had a positive effect on Capsicum chinense Jacq. seedling growth, indicating its potential as a biofertilizer.

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