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 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 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.

ARDRA and Identification of Intestinal Aerobic Bacteria from 4th Instar Larvae of Dendrolimu. kikuchii

2012 ◽  
Vol 518-523 ◽  
pp. 5523-5527
Author(s):  
Wu Xian Zhang ◽  
Jin Hua Wang ◽  
You He Sun ◽  
Biao Li ◽  
Zhi Xiong
Keyword(s):  
Genetic Diversity ◽  
Bacillus Subtilis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
16S Rdna ◽  
Enzyme Digestion ◽  
Aerobic Bacteria ◽  
Rrna Gene ◽  
Accession Number ◽  
16S Rrna Gene Sequences

Genetic diversity of 11 intestinal aerobic bacteria isolated from Dendrolimu. kikuchii was analysed, using PCR and ARDRA which used enzyme digestion of cloned 16S rRNA gene sequences. The results showed that 11 strains could be divided into 6 groups on 84% similarity level, it indicated that the intestinal aerobic bacteria genetic diversity was abundant. Sequencing the 6 representative strains’ 16S rDNA and submitting to GenBank, the accession number being JQ308104 to JQ308109 respectively. The 6 strains belonged to Klebsiella sp., Lysinibacillus sp., Brevibacillus sp., Bacillus subtilis, Gamma Proteobacterium and Brevibacillus limnophilus.

scholarly journals Phylogenetic Relationship of Phosphate Solubilizing Bacteria according to 16S rRNA Genes

2015 ◽  
Vol 2015 ◽  
pp. 1-5 ◽  
Author(s):  
Mohammad Bagher Javadi Nobandegani ◽  
Halimi Mohd Saud ◽  
Wong Mui Yun
Keyword(s):  
16S Rrna ◽  
Oil Palm ◽  
Phosphorus Uptake ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Phosphate Solubilizing Bacteria ◽  
Bacterial Isolates ◽  
Serratia Plymuthica ◽  
Phosphate Solubilizing

Phosphate solubilizing bacteria (PSB) can convert insoluble form of phosphorous to an available form. Applications of PSB as inoculants increase the phosphorus uptake by plant in the field. In this study, isolation and precise identification of PSB were carried out in Malaysian (Serdang) oil palm field (University Putra Malaysia). Identification and phylogenetic analysis of 8 better isolates were carried out by 16S rRNA gene sequencing in which as a result five isolates belong to the Beta subdivision ofProteobacteria, one isolate was related to the Gama subdivision ofProteobacteria, and two isolates were related to theFirmicutes. Bacterial isolates of 6upmr, 2upmr, 19upmnr, 10upmr, and 24upmr were identified asAlcaligenes faecalis. Also, bacterial isolates of 20upmnr and 17upmnr were identified asBacillus cereusandVagococcus carniphilus, respectively, and bacterial isolates of 31upmr were identified asSerratia plymuthica. Molecular identification and characterization of oil palm strains as the specific phosphate solubilizer can reduce the time and cost of producing effective inoculate (biofertilizer) in an oil palm field.

scholarly journals Sporaefaciens musculi gen. nov., sp. nov., a novel bacterium isolated from the caecum of an obese mouse

2019 ◽  
Author(s):  
Torben Sølbeck Rasmussen ◽  
Theresa Streidl ◽  
Thomas C.A. Hitch ◽  
Esther Wortmann ◽  
Paulina Deptula ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Obese Mouse ◽  
Rrna Gene ◽  
Strictly Anaerobic ◽  
Accession Number ◽  
Novel Bacterium ◽  
The Family ◽  
The 16S Rrna Gene

AbstractA bacterial strain, designated WCA-9-b2, was isolated from the caecal content of an 18-week-old obese C57BL/6NTac male mouse. According to phenotypic analyses, the isolate is rod-shaped, Gram-positive, strictly anaerobic, spore-forming and non-motile under the conditions tested. Bacterial colonies were irregular and non-pigmented. Analysis of the 16S rRNA gene indicated that the isolate belonged to the family Lachnospiraceae with Clostridium scindens ATTC 35704 (94.9% sequence identity) and Dorea formicigenerans ATCC 27755 (94.8%) being the closest relatives. Whole genome sequencing showed average nucleotide identity (ANI) ranging from 69.80–74.23% and percentage of conserved proteins (POCP) values < 50% against the nine closest relatives. The genome-based G+C content of genomic DNA was 44.4%. The predominant metabolic end products of glucose fermentation were acetate and succinate. Based on these data, we propose that strain WCA-9-b2 represents a novel species within a novel genus, for which the name Sporaefaciens musculi gen. nov., sp. nov. is proposed. The type strain is WCA-9-b2T (=DSM 106039T = CCUG pending IDT).RepositoriesThe GenBank accession number for the 16S rRNA gene sequence of strain WCA-9-b2T is MN756014, and the accession number for the genome assembly is PRJNA592877. Raw sequencing Illumina NextSeq (PRJEB35655) and ONT MinION (PRJEB35656) data can be accessed at EMBL-EBI.

The tadpole of the toadlet Scaphiophryne marmorata from Madagascar

Zootaxa ◽  
2009 ◽  
Vol 1986 (1) ◽  
pp. 67-68 ◽  
Author(s):  
STÉPHANE GROSJEAN ◽  
MIGUEL VENCES
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Temporary Pond ◽  
Rrna Gene ◽  
Larval Morphology ◽  
Accession Number ◽  
Adult Specimen ◽  
Stereo Microscope ◽  
Maximum Water ◽  
The 16S Rrna Gene

The genus Scaphiophryne Boulenger comprises eight species of microhylid toadlets (Vences et al. 2003; Glos et al. 2005), all of which are endemic to Madagascar. They are characterized by a unique larval morphology, intermediate between Orton's (1953) types II and IV (Blommers-Schlösser 1975; Wassersug 1984). Recently, Grosjean et al. (2007) provided a comparative study of larval morphology of the genus, and found evidence for two morphological subgroups based on larval characters. Tadpoles remained unknown for only two species, Scaphiophryne boribory Vences, Raxworthy, Nussbaum & Glaw, and S. marmorata Boulenger. Three tadpoles of S. marmorata were collected by M. Vences, H. Kurrer and L. du Preez on 7 February 2006 close to Andasibe (18°56′S/48°25′E, 915 m a.s.l.), in a large temporary pond of about 15 m diameter and maximum water depth of 1 m, at the edge of rainforest. They were found syntopically with larvae of Paradoxophyla palmata and Boophis pauliani. Identity of one of these specimens (ZSM 554/2008) was verified by DNA barcoding; the sequence of a fragment of the 16S rRNA gene has the Genbank accession number EU717878 and was identical to a sequence of an adult specimen from the same locality (accession AY834191). Vouchers were deposited in the Zoologische Staatssammlung München, Germany (ZSM). We here provide a detailed description of these larvae, based mainly on one specimen at stage 39, ZSM 555/2008 (field number ZCMV 3602). Measurements were taken using a stereo microscope (Zeiss Stereo Discovery) using landmarks as in Grosjean et al. (2007).

scholarly journals Identification of 16SrXXX-A Phytoplasma Associated with Salt cedar (Tamarix chinensis Lour.) witches'-broom (SCWB) in Southern Xinjiang of China

Plant Disease ◽  
2021 ◽  
Author(s):  
Feng Li ◽  
Lai Gang-Gang ◽  
Zhi Hui Zhao ◽  
Jing Xia Li ◽  
Ping Zhang ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Pcr Amplification ◽  
Rrna Gene ◽  
Accession Number ◽  
Tamarix Chinensis ◽  
Salt Cedar ◽  
Blast Analysis ◽  
The 16S Rrna Gene ◽  
Southern Xinjiang

Salt cedar is an ornamental shrub/moderate tree species native to Asia and East Europe, and grows in salt-alkali soil, desert and other dry areas, which plays an important role in wind prevention and sand fixation as well as maintaining ecological balance. Salt cedar witches’-broom (SCWB), which was extremely pernicious to Salt cedar. It was first observed and reported in Xi’an, China in 2005 (Zhao et al.2005). Witches' broom symptoms were observed on 20 out of 150 (13.3%) salt plants surveyed from the Alar region and 10 out of 86 (11.6%) plants from the Akesu region in southern of Xinjiang in May 2020. The damaged plants compared with asymptomatic plants (Fig.1A), the major symptoms included branches clustered, intersegment shorten and coarsen, giving rise to the formation of clusters (Fig.1B). Total plant DNA was extracted from phloem tissues with asymptomatic symptoms and phloem tissues with witches'-broom symptoms by a CTAB-based DNA extraction method (Green et al.1999). The 16S rRNA gene and the phytoplasma universal primers P1/P7 and rpF1/rpR1 of the rp (ribosomal protein) gene were used for Polymerase chain reaction (PCR) amplification by using the extracted plant total DNA as the template. The PCR product was used as the template and the R16F2n/R16R2 prmer was used for nested PCR amplification of the 16S rRNA gene after the amplification was completed. The results show that no product was obtained in asymptomatic plants. When DNA samples from witches’-broom symptomatic plants were used as templates, fragments with lengths 1219 bp and 1174 bp, corresponding to 16S rRNA gene and rp gene, were obtained. 16S rRNA gene was sequenced and deposited in GenBank under accession number MW447513. BLAST analysis revealed that the partial 16S rRNA sequence of the phytoplasma associated with P. aphylla witches’ broom showed highest sequence identity (99.67%) to salt cedar witches’ broom phytoplasma, ‘Candidatus Phytoplasma tamaricis’ (Accession Number: FJ432664). Phylogenetic and molecular evolutionary analyses were conducted using MEGA-X (Kumar et al., 2018). Results showed taht the SCWB and 16S rXXX group’s‘Candidatus Phytoplasma tamaricis’, (GenBank accession: FJ432664) have the highest affinity (Fig.2A). A virtual restriction fragment length polymorphism(RFLP) was done to determinethe subgroup ( Zhao et al. 2009). The 16S rDNA sequence from the Tamarix chinensis plant showed 99.3% similarity with that of the “Candidatus Phytoplasma tamaricis” reference strain (GenBank accession: FJ432664), suggesting that the phytoplasma in this study belongs to “Candidatus Phytoplasma tamaricis”-related strain. Therefore, it can be stated that SCWB belongs to the 16S rXXX group. The partial rp sequences only shared 84.74% sequence similarity with that of ‘Candidatus Phytoplasma prunorum’ (MG383523) of Apple proliferation group, a known subgroup 16S rX. Blast analysis based on the partial rp sequences showed that it shares less than 90% similarity with that of any known phytoplasma (Fig 2B), we suspect that this is due to a lack of sequenced rp gene sequences for the 16S rXXX group. To our knowledge, this is the first report of Salt Cedar Witches' Broom phytoplasma in Xinjiang province, China. As a consequence, we guess the SCWB phytoplasma rp gene belongs to 16S rXXX-rp group, which is also the first report about the 16SrXXX-rp group. Because SCWB1 is the only strain in the 16S rXXX group, and it is the representative strain of the 16S rXXX-A subgroup (Zhao et al. 2009). So, the SCWB disease we found in southern Xinjiang belongs to the 16S rXXX-A subgroup.

scholarly journals First report of 'Candidatus Phytoplasma trifolii' associated with little leaf and floral virescence disease in Solanum violaceum from the North East Region of India.

Plant Disease ◽  
2021 ◽  
Author(s):  
Dibya Sree Dutta ◽  
Jutimala Phookan ◽  
Manoj Kalita ◽  
Palash Deb Nath
Keyword(s):  
16S Rrna ◽  
Medicinal Plant ◽  
16S Rrna Gene ◽  
Rrna Gene ◽  
Accession Number ◽  
Sequence Identity ◽  
North East ◽  
The North ◽  
East Region ◽  
Seca Gene

Solanum violaceum Ortega, (Indian nightshade), is a medicinal plant belonging to the family Solanaceae. It grows naturally as a weed in agricultural fields, forest edges, road sides and fallow lands throughout the North East Region of India. It is mostly consumed as a vegetable by the native people of the region because of its promising therapeutic effects (Islam and Islam 2018). In November 2019, typical phytoplasma-suspected symptoms such as little leaf, yellowing and floral virescence were observed on S. violaceum plants (Figure 1) in Kaliabor, Nagaon district of Assam, India (26.3220′N, 92.5540′E), with about 8% incidence based on visual observations. To investigate the possibility of a phytoplasma association with the symptoms, total DNA was isolated from collected leaf samples (symptomatic-6 and asymptomatic-9) by following the CTAB protocol (Kollar et al. 1990). The DNAs isolated were assayed for the presence of phytoplasma using polymerase chain reaction (PCR) assays performed with P1/P6 primer pair for 16S rRNA gene (Deng and Hiruki 1991) and SecAfor1/SecArev3 for secA gene (Hodgetts et al. 2008). The direct PCR targeting the 16S rRNA gene and secA gene amplified a product of about 1.5 kb and 840 bp, respectively, from all the symptomatic plant samples but not from any of the asymptomatic plant samples. All amplicons were double strand sequenced and corresponding high quality sequences were deposited in the GenBank with accession numbers MW261863 for 16S rRNA gene and MW885174 for secA gene with a sequence length of 1406 bp and 532 bp, respectively. Pairwise sequence comparison of 16S rRNA gene sequence of S. violaceum phytoplasma isolate revealed 100% sequence identity with strain of ‘Candidatus Phytoplasma trifolii’ (Accession number, EF186820) and secA gene showed up to 95% sequence identity with the same organism (Accession number, KX784498). Further analyses of the 16S rRNA and secA genes based phylogenetic tree (Figure 2A and B) and the iPhyClassifier-based virtual RFLP analysis of 16S rRNA gene revealed that the phytoplasma-associated with little leaf and floral virescence of S. violaceum belongs to 16SrIV-D subgroup with a similarity coefficient of 1.0. The 16S rRNA and secA gene sequences comparison confirmed the close association of phytoplasma strain associated with S. violaceum with 16SrVI-D subgroup phytoplasma. Earlier, the 16SrVI-D subgroup of phytoplasma has been reported to be associated with many horticultural and other agricultural crops in India (Rao 2021). Recently, the 16SrVI-D strain was reported in eggplant from Assam, India (Accession number, MW261866), showing up to 100% sequence identity with S. violaceum strain (Accession number, MW261863) (Dutta et al. 2020). To the best of our knowledge, this is the first report of the association of the 16SrVI-D subgroup of phytoplasma strain with S. violaceum plant, which is an important medicinal plant widely used in folk and traditional Indian systems of medicine. Since this study has confirmed S. violaceum as a new host of 16SrVI-D group of phytoplasma, further studies on the disease epidemiology and insects vectoring the phytoplasma would help formulate effective management strategies in preventing further spread to other hosts.

Differentiation Of Clarias Batrachus, C. Gariepinus And Heteropneustes Fossilis By Pcr-Sequencing Of Mitochondrial 16s Rrna Gene

2015 ◽  
Vol 41 (1) ◽  
pp. 51-58
Author(s):  
Mohammad Shamimul Alam ◽  
Hawa Jahan ◽  
Rowshan Ara Begum ◽  
Reza M Shahjahan
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Fish Larva ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Valuable Insight ◽  
Multiple Sequence ◽  
Pcr Rflp ◽  
Alternative Means

Heteropneustesfossilis, Clariasbatrachus and C. gariepinus are three major catfishes ofecological and economic importance. Identification of these fish species becomes aproblem when the usual external morphological features of the fish are lost or removed,such as in canned fish. Also, newly hatched fish larva is often difficult to identify. PCRsequencingprovides accurate alternative means of identification of individuals at specieslevel. So, 16S rRNA genes of three locally collected catfishes were sequenced after PCRamplification and compared with the same gene sequences available from othergeographical regions. Multiple sequence alignment of the 16S rRNA gene fragments ofthe catfish species has revealed polymorphic sites which can be used to differentiate thesethree species from one another and will provide valuable insight in choosing appropriaterestriction enzymes for PCR-RFLP based identification in future. Asiat. Soc. Bangladesh, Sci. 41(1): 51-58, June 2015

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